Daily Papers

Length generalization, the ability to generalize from small training context sizes to larger ones, is a critical challenge in the development of Transformer-based language models. Positional encoding (PE) has been identified as a major factor influencing length generalization, but the exact impact of different PE schemes on extrapolation in downstream tasks remains unclear. In this paper, we conduct a systematic empirical study comparing the length generalization performance of decoder-only Transformers with five different position encoding approaches including Absolute Position Embedding (APE), T5's Relative PE, ALiBi, and Rotary, in addition to Transformers without positional encoding (NoPE). Our evaluation encompasses a battery of reasoning and mathematical tasks. Our findings reveal that the most commonly used positional encoding methods, such as ALiBi, Rotary, and APE, are not well suited for length generalization in downstream tasks. More importantly, NoPE outperforms other explicit positional encoding methods while requiring no additional computation. We theoretically demonstrate that NoPE can represent both absolute and relative PEs, but when trained with SGD, it mostly resembles T5's relative PE attention patterns. Finally, we find that scratchpad is not always helpful to solve length generalization and its format highly impacts the model's performance. Overall, our work suggests that explicit position embeddings are not essential for decoder-only Transformers to generalize well to longer sequences.

Transformer has taken the field of natural language processing (NLP) by storm since its birth. Further, Large language models (LLMs) built upon it have captured worldwide attention due to its superior abilities. Nevertheless, all Transformer-based models including these powerful LLMs suffer from a preset length limit and can hardly generalize from short training sequences to longer inference ones, namely, they can not perform length extrapolation. Hence, a plethora of methods have been proposed to enhance length extrapolation of Transformer, in which the positional encoding (PE) is recognized as the major factor. In this survey, we present these advances towards length extrapolation in a unified notation from the perspective of PE. Specifically, we first introduce extrapolatable PEs, including absolute and relative PEs. Then, we dive into extrapolation methods based on them, covering position interpolation and randomized position methods. Finally, several challenges and future directions in this area are highlighted. Through this survey, We aim to enable the reader to gain a deep understanding of existing methods and provide stimuli for future research.

The development of effective explainability tools for Transformers is a crucial pursuit in deep learning research. One of the most promising approaches in this domain is Layer-wise Relevance Propagation (LRP), which propagates relevance scores backward through the network to the input space by redistributing activation values based on predefined rules. However, existing LRP-based methods for Transformer explainability entirely overlook a critical component of the Transformer architecture: its positional encoding (PE), resulting in violation of the conservation property, and the loss of an important and unique type of relevance, which is also associated with structural and positional features. To address this limitation, we reformulate the input space for Transformer explainability as a set of position-token pairs. This allows us to propose specialized theoretically-grounded LRP rules designed to propagate attributions across various positional encoding methods, including Rotary, Learnable, and Absolute PE. Extensive experiments with both fine-tuned classifiers and zero-shot foundation models, such as LLaMA 3, demonstrate that our method significantly outperforms the state-of-the-art in both vision and NLP explainability tasks. Our code is publicly available.

End-to-end region-based object detectors like Sparse R-CNN usually have multiple cascade bounding box decoding stages, which refine the current predictions according to their previous results. Model parameters within each stage are independent, evolving a huge cost. In this paper, we find the general setting of decoding stages is actually redundant. By simply sharing parameters and making a recursive decoder, the detector already obtains a significant improvement. The recursive decoder can be further enhanced by positional encoding (PE) of the proposal box, which makes it aware of the exact locations and sizes of input bounding boxes, thus becoming adaptive to proposals from different stages during the recursion. Moreover, we also design centerness-based PE to distinguish the RoI feature element and dynamic convolution kernels at different positions within the bounding box. To validate the effectiveness of the proposed method, we conduct intensive ablations and build the full model on three recent mainstream region-based detectors. The RecusiveDet is able to achieve obvious performance boosts with even fewer model parameters and slightly increased computation cost. Codes are available at https://github.com/bravezzzzzz/RecursiveDet.

In the last few years, graph neural networks (GNNs) have become the standard toolkit for analyzing and learning from data on graphs. This emerging field has witnessed an extensive growth of promising techniques that have been applied with success to computer science, mathematics, biology, physics and chemistry. But for any successful field to become mainstream and reliable, benchmarks must be developed to quantify progress. This led us in March 2020 to release a benchmark framework that i) comprises of a diverse collection of mathematical and real-world graphs, ii) enables fair model comparison with the same parameter budget to identify key architectures, iii) has an open-source, easy-to-use and reproducible code infrastructure, and iv) is flexible for researchers to experiment with new theoretical ideas. As of December 2022, the GitHub repository has reached 2,000 stars and 380 forks, which demonstrates the utility of the proposed open-source framework through the wide usage by the GNN community. In this paper, we present an updated version of our benchmark with a concise presentation of the aforementioned framework characteristics, an additional medium-sized molecular dataset AQSOL, similar to the popular ZINC, but with a real-world measured chemical target, and discuss how this framework can be leveraged to explore new GNN designs and insights. As a proof of value of our benchmark, we study the case of graph positional encoding (PE) in GNNs, which was introduced with this benchmark and has since spurred interest of exploring more powerful PE for Transformers and GNNs in a robust experimental setting.

In this work, we build a simple but strong baseline for sounding video generation. Given base diffusion models for audio and video, we integrate them with additional modules into a single model and train it to make the model jointly generate audio and video. To enhance alignment between audio-video pairs, we introduce two novel mechanisms in our model. The first one is timestep adjustment, which provides different timestep information to each base model. It is designed to align how samples are generated along with timesteps across modalities. The second one is a new design of the additional modules, termed Cross-Modal Conditioning as Positional Encoding (CMC-PE). In CMC-PE, cross-modal information is embedded as if it represents temporal position information, and the embeddings are fed into the model like positional encoding. Compared with the popular cross-attention mechanism, CMC-PE provides a better inductive bias for temporal alignment in the generated data. Experimental results validate the effectiveness of the two newly introduced mechanisms and also demonstrate that our method outperforms existing methods.

Two main families of node feature augmentation schemes have been explored for enhancing GNNs: random features and spectral positional encoding. Surprisingly, however, there is still no clear understanding of the relation between these two augmentation schemes. Here we propose a novel family of positional encoding schemes which draws a link between the above two approaches and improves over both. The new approach, named Random Feature Propagation (RFP), is inspired by the power iteration method and its generalizations. It concatenates several intermediate steps of an iterative algorithm for computing the dominant eigenvectors of a propagation matrix, starting from random node features. Notably, these propagation steps are based on graph-dependent propagation operators that can be either predefined or learned. We explore the theoretical and empirical benefits of RFP. First, we provide theoretical justifications for using random features, for incorporating early propagation steps, and for using multiple random initializations. Then, we empirically demonstrate that RFP significantly outperforms both spectral PE and random features in multiple node classification and graph classification benchmarks.

Graph Neural Networks (GNNs) have shown promising potential in graph representation learning. The majority of GNNs define a local message-passing mechanism, propagating information over the graph by stacking multiple layers. These methods, however, are known to suffer from two major limitations: over-squashing and poor capturing of long-range dependencies. Recently, Graph Transformers (GTs) emerged as a powerful alternative to Message-Passing Neural Networks (MPNNs). GTs, however, have quadratic computational cost, lack inductive biases on graph structures, and rely on complex Positional/Structural Encodings (SE/PE). In this paper, we show that while Transformers, complex message-passing, and SE/PE are sufficient for good performance in practice, neither is necessary. Motivated by the recent success of State Space Models (SSMs), such as Mamba, we present Graph Mamba Networks (GMNs), a general framework for a new class of GNNs based on selective SSMs. We discuss and categorize the new challenges when adopting SSMs to graph-structured data, and present four required and one optional steps to design GMNs, where we choose (1) Neighborhood Tokenization, (2) Token Ordering, (3) Architecture of Bidirectional Selective SSM Encoder, (4) Local Encoding, and dispensable (5) PE and SE. We further provide theoretical justification for the power of GMNs. Experiments demonstrate that despite much less computational cost, GMNs attain an outstanding performance in long-range, small-scale, large-scale, and heterophilic benchmark datasets.

Position encoding (PE), an essential part of self-attention networks (SANs), is used to preserve the word order information for natural language processing tasks, generating fixed position indices for input sequences. However, in cross-lingual scenarios, e.g. machine translation, the PEs of source and target sentences are modeled independently. Due to word order divergences in different languages, modeling the cross-lingual positional relationships might help SANs tackle this problem. In this paper, we augment SANs with cross-lingual position representations to model the bilingually aware latent structure for the input sentence. Specifically, we utilize bracketing transduction grammar (BTG)-based reordering information to encourage SANs to learn bilingual diagonal alignments. Experimental results on WMT'14 EnglishRightarrowGerman, WAT'17 JapaneseRightarrowEnglish, and WMT'17 ChineseLeftrightarrowEnglish translation tasks demonstrate that our approach significantly and consistently improves translation quality over strong baselines. Extensive analyses confirm that the performance gains come from the cross-lingual information.

The attention mechanism is a critical component of Large Language Models (LLMs) that allows tokens in a sequence to interact with each other, but is order-invariant. Incorporating position encoding (PE) makes it possible to address by position, such as attending to the i-th token. However, current PE methods use token counts to derive position, and thus cannot generalize to higher levels of abstraction, such as attending to the i-th sentence. In this paper, we propose a new position encoding method, Contextual Position Encoding (CoPE), that allows positions to be conditioned on context by incrementing position only on certain tokens determined by the model. This allows more general position addressing such as attending to the i-th particular word, noun, or sentence. We show that CoPE can solve the selective copy, counting and Flip-Flop tasks where popular position embeddings fail, and improves perplexity on language modeling and coding tasks.

Since self-attention layers in Transformers are permutation invariant by design, positional encodings must be explicitly incorporated to enable spatial understanding. However, fixed-size lookup tables used in traditional learnable position embeddings (PEs) limit extrapolation capabilities beyond pre-trained sequence lengths. Expert-designed methods such as ALiBi and RoPE, mitigate this limitation but demand extensive modifications for adapting to new modalities, underscoring fundamental challenges in adaptability and scalability. In this work, we present SeqPE, a unified and fully learnable position encoding framework that represents each n-dimensional position index as a symbolic sequence and employs a lightweight sequential position encoder to learn their embeddings in an end-to-end manner. To regularize SeqPE's embedding space, we introduce two complementary objectives: a contrastive objective that aligns embedding distances with a predefined position-distance function, and a knowledge distillation loss that anchors out-of-distribution position embeddings to in-distribution teacher representations, further enhancing extrapolation performance. Experiments across language modeling, long-context question answering, and 2D image classification demonstrate that SeqPE not only surpasses strong baselines in perplexity, exact match (EM), and accuracy--particularly under context length extrapolation--but also enables seamless generalization to multi-dimensional inputs without requiring manual architectural redesign. We release our code, data, and checkpoints at https://github.com/ghrua/seqpe.

Attentional mechanisms are order-invariant. Positional encoding is a crucial component to allow attention-based deep model architectures such as Transformer to address sequences or images where the position of information matters. In this paper, we propose a novel positional encoding method based on learnable Fourier features. Instead of hard-coding each position as a token or a vector, we represent each position, which can be multi-dimensional, as a trainable encoding based on learnable Fourier feature mapping, modulated with a multi-layer perceptron. The representation is particularly advantageous for a spatial multi-dimensional position, e.g., pixel positions on an image, where L_2 distances or more complex positional relationships need to be captured. Our experiments based on several public benchmark tasks show that our learnable Fourier feature representation for multi-dimensional positional encoding outperforms existing methods by both improving the accuracy and allowing faster convergence.

Recent studies show that paddings in convolutional neural networks encode absolute position information which can negatively affect the model performance for certain tasks. However, existing metrics for quantifying the strength of positional information remain unreliable and frequently lead to erroneous results. To address this issue, we propose novel metrics for measuring (and visualizing) the encoded positional information. We formally define the encoded information as PPP (Position-information Pattern from Padding) and conduct a series of experiments to study its properties as well as its formation. The proposed metrics measure the presence of positional information more reliably than the existing metrics based on PosENet and a test in F-Conv. We also demonstrate that for any extant (and proposed) padding schemes, PPP is primarily a learning artifact and is less dependent on the characteristics of the underlying padding schemes.

We propose a conditional positional encoding (CPE) scheme for vision Transformers. Unlike previous fixed or learnable positional encodings, which are pre-defined and independent of input tokens, CPE is dynamically generated and conditioned on the local neighborhood of the input tokens. As a result, CPE can easily generalize to the input sequences that are longer than what the model has ever seen during training. Besides, CPE can keep the desired translation-invariance in the image classification task, resulting in improved performance. We implement CPE with a simple Position Encoding Generator (PEG) to get seamlessly incorporated into the current Transformer framework. Built on PEG, we present Conditional Position encoding Vision Transformer (CPVT). We demonstrate that CPVT has visually similar attention maps compared to those with learned positional encodings and delivers outperforming results. Our code is available at https://github.com/Meituan-AutoML/CPVT .

Relative position encoding (RPE) is important for transformer to capture sequence ordering of input tokens. General efficacy has been proven in natural language processing. However, in computer vision, its efficacy is not well studied and even remains controversial, e.g., whether relative position encoding can work equally well as absolute position? In order to clarify this, we first review existing relative position encoding methods and analyze their pros and cons when applied in vision transformers. We then propose new relative position encoding methods dedicated to 2D images, called image RPE (iRPE). Our methods consider directional relative distance modeling as well as the interactions between queries and relative position embeddings in self-attention mechanism. The proposed iRPE methods are simple and lightweight. They can be easily plugged into transformer blocks. Experiments demonstrate that solely due to the proposed encoding methods, DeiT and DETR obtain up to 1.5% (top-1 Acc) and 1.3% (mAP) stable improvements over their original versions on ImageNet and COCO respectively, without tuning any extra hyperparameters such as learning rate and weight decay. Our ablation and analysis also yield interesting findings, some of which run counter to previous understanding. Code and models are open-sourced at https://github.com/microsoft/Cream/tree/main/iRPE.

Sequential recommendation (SR), which encodes user activity to predict the next action, has emerged as a widely adopted strategy in developing commercial personalized recommendation systems. A critical component of modern SR models is the attention mechanism, which synthesizes users' historical activities. This mechanism is typically order-invariant and generally relies on position encoding (PE). Conventional SR models simply assign a learnable vector to each position, resulting in only modest gains compared to traditional recommendation models. Moreover, limited research has been conducted on position encoding tailored for sequential recommendation, leaving a significant gap in addressing its unique requirements. To bridge this gap, we propose a novel Contextual-Aware Position Encoding method for sequential recommendation, abbreviated as CAPE. To the best of our knowledge, CAPE is the first PE method specifically designed for sequential recommendation. Comprehensive experiments conducted on benchmark SR datasets demonstrate that CAPE consistently enhances multiple mainstream backbone models and achieves state-of-the-art performance, across small and large scale model size. Furthermore, we deployed CAPE in an industrial setting on a real-world commercial platform, clearly showcasing the effectiveness of our approach. Our source code is available at https://github.com/yjdy/CAPE.

In this work, we leverage the intrinsic segmentation of language sequences and design a new positional encoding method called Bilevel Positional Encoding (BiPE). For each position, our BiPE blends an intra-segment encoding and an inter-segment encoding. The intra-segment encoding identifies the locations within a segment and helps the model capture the semantic information therein via absolute positional encoding. The inter-segment encoding specifies the segment index, models the relationships between segments, and aims to improve extrapolation capabilities via relative positional encoding. Theoretical analysis shows this disentanglement of positional information makes learning more effective. The empirical results also show that our BiPE has superior length extrapolation capabilities across a wide range of tasks in diverse text modalities.

Transformers rely on both content-based and position-based addressing mechanisms to make predictions, but existing positional encoding techniques often diminish the effectiveness of position-based addressing. Many current methods enforce rigid patterns in attention maps, limiting the ability to model long-range dependencies and adapt to diverse tasks. Additionally, most positional encodings are learned as general biases, lacking the specialization required for different instances within a dataset. To address this, we propose conTextualized equivariAnt Position Embedding (TAPE), a novel framework that enhances positional embeddings by incorporating sequence content across layers. TAPE introduces dynamic, context-aware positional encodings, overcoming the constraints of traditional fixed patterns. By enforcing permutation and orthogonal equivariance, TAPE ensures the stability of positional encodings during updates, improving robustness and adaptability. Our method can be easily integrated into pre-trained transformers, offering parameter-efficient fine-tuning with minimal overhead. Extensive experiments shows that TAPE achieves superior performance in language modeling, arithmetic reasoning, and long-context retrieval tasks compared to existing positional embedding techniques.

In this work, we investigate a typical scenario in code generation where a developer edits existing code in real time and requests a code assistant, e.g., a large language model, to re-predict the next token or next line on the fly. Naively, the LLM needs to re-encode the entire KV cache to provide an accurate prediction. However, this process is computationally expensive, especially when the sequence length is long. Simply encoding the edited subsequence and integrating it to the original KV cache meets the temporal confusion problem, leading to significantly worse performance. We address this efficiency and accuracy trade-off by introducing \textbf{Positional \textbf{Integrity Encoding} (PIE). Building upon the rotary positional encoding, PIE first removes the rotary matrices in the Key cache that introduce temporal confusion and then reapplies the correct rotary matrices. This process ensures that positional relationships between tokens are correct and requires only a single round of matrix multiplication. We validate the effectiveness of PIE through extensive experiments on the RepoBench-C-8k dataset, utilizing DeepSeek-Coder models with 1.3B, 6.7B, and 33B parameters. Our evaluation includes three real-world coding tasks: code insertion, code deletion, and multi-place code editing. Results demonstrate that PIE reduces computational overhead by over 85% compared to the standard full recomputation approach across all model sizes and tasks while well approximating the model performance.

Positional Encodings (PEs) are a critical component of Transformer-based Large Language Models (LLMs), providing the attention mechanism with important sequence-position information. One of the most popular types of encoding used today in LLMs are Rotary Positional Encodings (RoPE), that rotate the queries and keys based on their relative distance. A common belief is that RoPE is useful because it helps to decay token dependency as relative distance increases. In this work, we argue that this is unlikely to be the core reason. We study the internals of a trained Gemma 7B model to understand how RoPE is being used at a mechanical level. We find that Gemma learns to use RoPE to construct robust "positional" attention patterns by exploiting the highest frequencies. We also find that, in general, Gemma greatly prefers to use the lowest frequencies of RoPE, which we suspect are used to carry semantic information. We mathematically prove interesting behaviours of RoPE and conduct experiments to verify our findings, proposing a modification of RoPE that fixes some highlighted issues and improves performance. We believe that this work represents an interesting step in better understanding PEs in LLMs, which we believe holds crucial value for scaling LLMs to large sizes and context lengths.

The Position Embedding (PE) is critical for Vision Transformers (VTs) due to the permutation-invariance of self-attention operation. By analyzing the input and output of each encoder layer in VTs using reparameterization and visualization, we find that the default PE joining method (simply adding the PE and patch embedding together) operates the same affine transformation to token embedding and PE, which limits the expressiveness of PE and hence constrains the performance of VTs. To overcome this limitation, we propose a simple, effective, and robust method. Specifically, we provide two independent layer normalizations for token embeddings and PE for each layer, and add them together as the input of each layer's Muti-Head Self-Attention module. Since the method allows the model to adaptively adjust the information of PE for different layers, we name it as Layer-adaptive Position Embedding, abbreviated as LaPE. Extensive experiments demonstrate that LaPE can improve various VTs with different types of PE and make VTs robust to PE types. For example, LaPE improves 0.94% accuracy for ViT-Lite on Cifar10, 0.98% for CCT on Cifar100, and 1.72% for DeiT on ImageNet-1K, which is remarkable considering the negligible extra parameters, memory and computational cost brought by LaPE. The code is publicly available at https://github.com/Ingrid725/LaPE.

It is well noted that coordinate based MLPs benefit -- in terms of preserving high-frequency information -- through the encoding of coordinate positions as an array of Fourier features. Hitherto, the rationale for the effectiveness of these positional encodings has been solely studied through a Fourier lens. In this paper, we strive to broaden this understanding by showing that alternative non-Fourier embedding functions can indeed be used for positional encoding. Moreover, we show that their performance is entirely determined by a trade-off between the stable rank of the embedded matrix and the distance preservation between embedded coordinates. We further establish that the now ubiquitous Fourier feature mapping of position is a special case that fulfills these conditions. Consequently, we present a more general theory to analyze positional encoding in terms of shifted basis functions. To this end, we develop the necessary theoretical formulae and empirically verify that our theoretical claims hold in practice. Codes available at https://github.com/osiriszjq/Rethinking-positional-encoding.

Recent advances in Graph Neural Networks (GNNs) and Graph Transformers (GTs) have been driven by innovations in architectures and Positional Encodings (PEs), which are critical for augmenting node features and capturing graph topology. PEs are essential for GTs, where topological information would otherwise be lost without message-passing. However, PEs are often tested alongside novel architectures, making it difficult to isolate their effect on established models. To address this, we present a comprehensive benchmark of PEs in a unified framework that includes both message-passing GNNs and GTs. We also establish theoretical connections between MPNNs and GTs and introduce a sparsified GRIT attention mechanism to examine the influence of global connectivity. Our findings demonstrate that previously untested combinations of GNN architectures and PEs can outperform existing methods and offer a more comprehensive picture of the state-of-the-art. To support future research and experimentation in our framework, we make the code publicly available.

Current large vision-language models (VLMs) often encounter challenges such as insufficient capabilities of a single visual component and excessively long visual tokens. These issues can limit the model's effectiveness in accurately interpreting complex visual information and over-lengthy contextual information. Addressing these challenges is crucial for enhancing the performance and applicability of VLMs. This paper proposes the use of ensemble experts technique to synergizes the capabilities of individual visual encoders, including those skilled in image-text matching, OCR, image segmentation, etc. This technique introduces a fusion network to unify the processing of outputs from different visual experts, while bridging the gap between image encoders and pre-trained LLMs. In addition, we explore different positional encoding schemes to alleviate the waste of positional encoding caused by lengthy image feature sequences, effectively addressing the issue of position overflow and length limitations. For instance, in our implementation, this technique significantly reduces the positional occupancy in models like SAM, from a substantial 4096 to a more efficient and manageable 64 or even down to 1. Experimental results demonstrate that VLMs with multiple experts exhibit consistently superior performance over isolated visual encoders and mark a significant performance boost as more experts are integrated. We have open-sourced the training code used in this report. All of these resources can be found on our project website.

Relative Positional Encoding (RPE), which encodes the relative distance between any pair of tokens, is one of the most successful modifications to the original Transformer. As far as we know, theoretical understanding of the RPE-based Transformers is largely unexplored. In this work, we mathematically analyze the power of RPE-based Transformers regarding whether the model is capable of approximating any continuous sequence-to-sequence functions. One may naturally assume the answer is in the affirmative -- RPE-based Transformers are universal function approximators. However, we present a negative result by showing there exist continuous sequence-to-sequence functions that RPE-based Transformers cannot approximate no matter how deep and wide the neural network is. One key reason lies in that most RPEs are placed in the softmax attention that always generates a right stochastic matrix. This restricts the network from capturing positional information in the RPEs and limits its capacity. To overcome the problem and make the model more powerful, we first present sufficient conditions for RPE-based Transformers to achieve universal function approximation. With the theoretical guidance, we develop a novel attention module, called Universal RPE-based (URPE) Attention, which satisfies the conditions. Therefore, the corresponding URPE-based Transformers become universal function approximators. Extensive experiments covering typical architectures and tasks demonstrate that our model is parameter-efficient and can achieve superior performance to strong baselines in a wide range of applications. The code will be made publicly available at https://github.com/lsj2408/URPE.

Recurrent models have been dominating the field of neural machine translation (NMT) for the past few years. Transformers vaswani2017attention, have radically changed it by proposing a novel architecture that relies on a feed-forward backbone and self-attention mechanism. Although Transformers are powerful, they could fail to properly encode sequential/positional information due to their non-recurrent nature. To solve this problem, position embeddings are defined exclusively for each time step to enrich word information. However, such embeddings are fixed after training regardless of the task and the word ordering system of the source or target language. In this paper, we propose a novel architecture with new position embeddings depending on the input text to address this shortcoming by taking the order of target words into consideration. Instead of using predefined position embeddings, our solution generates new embeddings to refine each word's position information. Since we do not dictate the position of source tokens and learn them in an end-to-end fashion, we refer to our method as dynamic position encoding (DPE). We evaluated the impact of our model on multiple datasets to translate from English into German, French, and Italian and observed meaningful improvements in comparison to the original Transformer.

Transformers' ability to generalize to longer sequences than they have been trained on, known as length extrapolation, degrades as sequence length increases. Most of Relative Positional Encoding (RPE) methods address this problem by either adding constant linear biases or learning general biases, lacking the ability to specialize for different sequences. In this work, inspired by ALiBi, we propose Context-aware Biases for Length Extrapolation (Cable), that learns token-specific biases for each head in decoder-based transformers. Cable learns adaptive, context-aware biases, overcoming the limitations of fixed patterns by adding dynamic biases specific to each token in the sequence. Results show that when tested on a sequence length of 1024, a GPT-3 Medium (334M parameters) with our positional encoding, trained on a sequence length of 512, achieves better perplexity (-0.65) than a similar network with sinusoidal positional encoding trained on a sequence length of 1024. This is achieved with 48% lower memory usage, and only 3.5% higher training time. Furthermore, our method notably improves the extrapolation ability of existing RPE methods on the Edu-FineWeb10B and WikiText-103 datasets. Code is available at: https://github.com/axiomlab/Cable

The mixing of two or more languages is called Code-Mixing (CM). CM is a social norm in multilingual societies. Neural Language Models (NLMs) like transformers have been effective on many NLP tasks. However, NLM for CM is an under-explored area. Though transformers are capable and powerful, they cannot always encode positional information since they are non-recurrent. Therefore, to enrich word information and incorporate positional information, positional encoding is defined. We hypothesize that Switching Points (SPs), i.e., junctions in the text where the language switches (L1 -> L2 or L2 -> L1), pose a challenge for CM Language Models (LMs), and hence give special emphasis to SPs in the modeling process. We experiment with several positional encoding mechanisms and show that rotatory positional encodings along with switching point information yield the best results. We introduce CONFLATOR: a neural language modeling approach for code-mixed languages. CONFLATOR tries to learn to emphasize switching points using smarter positional encoding, both at unigram and bigram levels. CONFLATOR outperforms the state-of-the-art on two tasks based on code-mixed Hindi and English (Hinglish): (i) sentiment analysis and (ii) machine translation.

Vision-Language Models (VLMs) have shown promising capabilities in handling various multimodal tasks, yet they struggle in long-context scenarios, particularly in tasks involving videos, high-resolution images, or lengthy image-text documents. In our work, we first conduct an empirical analysis of the long-context capabilities of VLMs using our augmented long-context multimodal datasets. Our findings reveal that directly applying the positional encoding mechanism used for textual tokens to visual tokens is suboptimal, and VLM performance degrades sharply when the position encoding exceeds the model's context window. To address this, we propose Variable Visual Position Encoding (V2PE), a novel positional encoding approach that employs variable and smaller increments for visual tokens, enabling more efficient management of long multimodal sequences. Our experiments demonstrate the effectiveness of V2PE to enhances VLMs' ability to effectively understand and reason over long multimodal contexts. We further integrate V2PE with our augmented long-context multimodal datasets to fine-tune the open-source VLM, InternVL2. The fine-tuned model achieves strong performance on both standard and long-context multimodal tasks. Notably, when the sequence length of the training dataset is increased to 256K tokens, the model is capable of processing multimodal sequences up to 1M tokens, highlighting its potential for real-world long-context applications.

Rotary Position Embedding (RoPE) is an efficient position encoding approach and is widely utilized in numerous large language models (LLMs). Recently, a lot of methods have been put forward to further expand the context window based on RoPE. The core concept of those methods is to predefine or search for a set of factors to rescale the base frequencies of RoPE. Nevertheless, it is quite a challenge for existing methods to predefine an optimal factor due to the exponential search space. In view of this, we introduce PSC (Phase Shift Calibration), a small module for calibrating the frequencies predefined by existing methods. With the employment of PSC, we demonstrate that many existing methods can be further enhanced, like PI, YaRN, and LongRoPE. We conducted extensive experiments across multiple models and tasks. The results demonstrate that (1) when PSC is enabled, the comparative reductions in perplexity increase as the context window size is varied from 16k, to 32k, and up to 64k. (2) Our approach is broadly applicable and exhibits robustness across a variety of models and tasks. The code can be found at https://github.com/WNQzhu/PSC.

Positional embeddings (PE) play a crucial role in Vision Transformers (ViTs) by providing spatial information otherwise lost due to the permutation invariant nature of self attention. While absolute positional embeddings (APE) have shown theoretical advantages over relative positional embeddings (RPE), particularly due to the ability of sinusoidal functions to preserve spatial inductive biases like monotonicity and shift invariance, a fundamental challenge arises when mapping a 2D grid to a 1D sequence. Existing methods have mostly overlooked or never explored the impact of patch ordering in positional embeddings. To address this, we propose LOOPE, a learnable patch-ordering method that optimizes spatial representation for a given set of frequencies, providing a principled approach to patch order optimization. Empirical results show that our PE significantly improves classification accuracy across various ViT architectures. To rigorously evaluate the effectiveness of positional embeddings, we introduce the "Three Cell Experiment", a novel benchmarking framework that assesses the ability of PEs to retain relative and absolute positional information across different ViT architectures. Unlike standard evaluations, which typically report a performance gap of 4 to 6% between models with and without PE, our method reveals a striking 30 to 35% difference, offering a more sensitive diagnostic tool to measure the efficacy of PEs. Our experimental analysis confirms that the proposed LOOPE demonstrates enhanced effectiveness in retaining both relative and absolute positional information.

Autoregressive models, such as the GPT family, use a fixed order, usually left-to-right, to generate sequences. However, this is not a necessity. In this paper, we challenge this assumption and show that by simply adding a positional encoding for the output, this order can be modulated on-the-fly per-sample which offers key advantageous properties. It allows for the sampling of and conditioning on arbitrary subsets of tokens, and it also allows sampling in one shot multiple tokens dynamically according to a rejection strategy, leading to a sub-linear number of model evaluations. We evaluate our method across various domains, including language modeling, path-solving, and aircraft vertical rate prediction, decreasing the number of steps required for generation by an order of magnitude.

Tokenization methods like Byte-Pair Encoding (BPE) enhance computational efficiency in large language models (LLMs) but often obscure internal character structures within tokens. This limitation hinders LLMs' ability to predict precise character positions, which is crucial in tasks like Chinese Spelling Correction (CSC) where identifying the positions of misspelled characters accelerates correction processes. We propose Token Internal Position Awareness (TIPA), a method that significantly improves models' ability to capture character positions within tokens by training them on reverse character prediction tasks using the tokenizer's vocabulary. Experiments demonstrate that TIPA enhances position prediction accuracy in LLMs, enabling more precise identification of target characters in original text. Furthermore, when applied to downstream tasks that do not require exact position prediction, TIPA still boosts performance in tasks needing character-level information, validating its versatility and effectiveness.

Transformers have impressive generalization capabilities on tasks with a fixed context length. However, they fail to generalize to sequences of arbitrary length, even for seemingly simple tasks such as duplicating a string. Moreover, simply training on longer sequences is inefficient due to the quadratic computation complexity of the global attention mechanism. In this work, we demonstrate that this failure mode is linked to positional encodings being out-of-distribution for longer sequences (even for relative encodings) and introduce a novel family of positional encodings that can overcome this problem. Concretely, our randomized positional encoding scheme simulates the positions of longer sequences and randomly selects an ordered subset to fit the sequence's length. Our large-scale empirical evaluation of 6000 models across 15 algorithmic reasoning tasks shows that our method allows Transformers to generalize to sequences of unseen length (increasing test accuracy by 12.0% on average).

Encoder-decoder models have become an effective approach for sequence learning tasks like machine translation, image captioning and speech recognition, but have yet to show competitive results for handwritten text recognition. To this end, we propose an attention-based sequence-to-sequence model. It combines a convolutional neural network as a generic feature extractor with a recurrent neural network to encode both the visual information, as well as the temporal context between characters in the input image, and uses a separate recurrent neural network to decode the actual character sequence. We make experimental comparisons between various attention mechanisms and positional encodings, in order to find an appropriate alignment between the input and output sequence. The model can be trained end-to-end and the optional integration of a hybrid loss allows the encoder to retain an interpretable and usable output, if desired. We achieve competitive results on the IAM and ICFHR2016 READ data sets compared to the state-of-the-art without the use of a language model, and we significantly improve over any recent sequence-to-sequence approaches.

As transformers are equivariant to the permutation of input tokens, encoding the positional information of tokens is necessary for many tasks. However, since existing positional encoding schemes have been initially designed for NLP tasks, their suitability for vision tasks, which typically exhibit different structural properties in their data, is questionable. We argue that existing positional encoding schemes are suboptimal for 3D vision tasks, as they do not respect their underlying 3D geometric structure. Based on this hypothesis, we propose a geometry-aware attention mechanism that encodes the geometric structure of tokens as relative transformation determined by the geometric relationship between queries and key-value pairs. By evaluating on multiple novel view synthesis (NVS) datasets in the sparse wide-baseline multi-view setting, we show that our attention, called Geometric Transform Attention (GTA), improves learning efficiency and performance of state-of-the-art transformer-based NVS models without any additional learned parameters and only minor computational overhead.

In this paper, we aim to do code completion based on implementing a Neural Network from Li et. al.. Our contribution is that we use an encoding that is in-between character and word encoding called Byte Pair Encoding (BPE). We use this on the source code files treating them as natural text without first going through the abstract syntax tree (AST). We have implemented two models: an attention-enhanced LSTM and a pointer network, where the pointer network was originally introduced to solve out of vocabulary problems. We are interested to see if BPE can replace the need for the pointer network for code completion.

Natural reading orders of words are crucial for information extraction from form-like documents. Despite recent advances in Graph Convolutional Networks (GCNs) on modeling spatial layout patterns of documents, they have limited ability to capture reading orders of given word-level node representations in a graph. We propose Reading Order Equivariant Positional Encoding (ROPE), a new positional encoding technique designed to apprehend the sequential presentation of words in documents. ROPE generates unique reading order codes for neighboring words relative to the target word given a word-level graph connectivity. We study two fundamental document entity extraction tasks including word labeling and word grouping on the public FUNSD dataset and a large-scale payment dataset. We show that ROPE consistently improves existing GCNs with a margin up to 8.4% F1-score.

The attention mechanism is a core primitive in modern large language models (LLMs) and AI more broadly. Since attention by itself is permutation-invariant, position encoding is essential for modeling structured domains such as language. Rotary position encoding (RoPE) has emerged as the de facto standard approach for position encoding and is part of many modern LLMs. However, in RoPE the key/query transformation between two elements in a sequence is only a function of their relative position and otherwise independent of the actual input. This limits the expressivity of RoPE-based transformers. This paper describes PaTH, a flexible data-dependent position encoding scheme based on accumulated products of Householder(like) transformations, where each transformation is data-dependent, i.e., a function of the input. We derive an efficient parallel algorithm for training through exploiting a compact representation of products of Householder matrices, and implement a FlashAttention-style blockwise algorithm that minimizes I/O cost. Across both targeted synthetic benchmarks and moderate-scale real-world language modeling experiments, we find that PaTH demonstrates superior performance compared to RoPE and other recent baselines.

Length extrapolation has attracted considerable attention recently since it allows transformers to be tested on longer sequences than those used in training. Previous research has shown that this property can be attained by using carefully designed Relative Positional Encodings (RPEs). While these methods perform well on a variety of corpora, the conditions for length extrapolation have yet to be investigated. This paper attempts to determine what types of RPEs allow for length extrapolation through a thorough mathematical and empirical analysis. We discover that a transformer is certain to possess this property as long as the series that corresponds to the RPE's exponential converges. Two practices are derived from the conditions and examined in language modeling tasks on a variety of corpora. As a bonus from the conditions, we derive a new Theoretical Receptive Field (TRF) to measure the receptive field of RPEs without taking any training steps. Extensive experiments are conducted on the Wikitext-103, Books, Github, and WikiBook datasets to demonstrate the viability of our discovered conditions. We also compare TRF to Empirical Receptive Field (ERF) across different models, showing consistently matched trends on the aforementioned datasets. The code is available at https://github.com/OpenNLPLab/Rpe.

We explore deep autoregressive Transformer models in language modeling for speech recognition. We focus on two aspects. First, we revisit Transformer model configurations specifically for language modeling. We show that well configured Transformer models outperform our baseline models based on the shallow stack of LSTM recurrent neural network layers. We carry out experiments on the open-source LibriSpeech 960hr task, for both 200K vocabulary word-level and 10K byte-pair encoding subword-level language modeling. We apply our word-level models to conventional hybrid speech recognition by lattice rescoring, and the subword-level models to attention based encoder-decoder models by shallow fusion. Second, we show that deep Transformer language models do not require positional encoding. The positional encoding is an essential augmentation for the self-attention mechanism which is invariant to sequence ordering. However, in autoregressive setup, as is the case for language modeling, the amount of information increases along the position dimension, which is a positional signal by its own. The analysis of attention weights shows that deep autoregressive self-attention models can automatically make use of such positional information. We find that removing the positional encoding even slightly improves the performance of these models.

Relative positional embeddings (RPE) have received considerable attention since RPEs effectively model the relative distance among tokens and enable length extrapolation. We propose KERPLE, a framework that generalizes relative position embedding for extrapolation by kernelizing positional differences. We achieve this goal using conditionally positive definite (CPD) kernels, a class of functions known for generalizing distance metrics. To maintain the inner product interpretation of self-attention, we show that a CPD kernel can be transformed into a PD kernel by adding a constant offset. This offset is implicitly absorbed in the Softmax normalization during self-attention. The diversity of CPD kernels allows us to derive various RPEs that enable length extrapolation in a principled way. Experiments demonstrate that the logarithmic variant achieves excellent extrapolation performance on three large language modeling datasets. Our implementation and pretrained checkpoints are released at https://github.com/chijames/KERPLE.git.

Handwritten Mathematical Expression Recognition (HMER) has wide applications in human-machine interaction scenarios, such as digitized education and automated offices. Recently, sequence-based models with encoder-decoder architectures have been commonly adopted to address this task by directly predicting LaTeX sequences of expression images. However, these methods only implicitly learn the syntax rules provided by LaTeX, which may fail to describe the position and hierarchical relationship between symbols due to complex structural relations and diverse handwriting styles. To overcome this challenge, we propose a position forest transformer (PosFormer) for HMER, which jointly optimizes two tasks: expression recognition and position recognition, to explicitly enable position-aware symbol feature representation learning. Specifically, we first design a position forest that models the mathematical expression as a forest structure and parses the relative position relationships between symbols. Without requiring extra annotations, each symbol is assigned a position identifier in the forest to denote its relative spatial position. Second, we propose an implicit attention correction module to accurately capture attention for HMER in the sequence-based decoder architecture. Extensive experiments validate the superiority of PosFormer, which consistently outperforms the state-of-the-art methods 2.03%/1.22%/2.00%, 1.83%, and 4.62% gains on the single-line CROHME 2014/2016/2019, multi-line M2E, and complex MNE datasets, respectively, with no additional latency or computational cost. Code is available at https://github.com/SJTU-DeepVisionLab/PosFormer.

Transformers with causal attention can solve tasks that require positional information without using positional encodings. In this work, we propose and investigate a new hypothesis about how positional information can be stored without using explicit positional encoding. We observe that nearby embeddings are more similar to each other than faraway embeddings, allowing the transformer to potentially reconstruct the positions of tokens. We show that this pattern can occur in both the trained and the randomly initialized Transformer models with causal attention and no positional encodings over a common range of hyperparameters.

Linear attention mechanisms have gained prominence in causal language models due to their linear computational complexity and enhanced speed. However, the inherent decay mechanism in linear attention presents challenges when applied to multi-dimensional sequence modeling tasks, such as image processing and multi-modal learning. In these scenarios, the utilization of sequential scanning to establish a global receptive field necessitates multiple scans for multi-dimensional data, thereby leading to inefficiencies. This paper identifies the inefficiency caused by a multiplicative linear recurrence and proposes an efficient alternative additive linear recurrence to avoid the issue, as it can handle multi-dimensional data within a single scan. We further develop an efficient multi-dimensional sequential modeling framework called LightNet based on the new recurrence. Moreover, we present two new multi-dimensional linear relative positional encoding methods, MD-TPE and MD-LRPE to enhance the model's ability to discern positional information in multi-dimensional scenarios. Our empirical evaluations across various tasks, including image classification, image generation, bidirectional language modeling, and autoregressive language modeling, demonstrate the efficacy of LightNet, showcasing its potential as a versatile and efficient solution for multi-dimensional sequential modeling.

Preventing the performance decay of Transformers on inputs longer than those used for training has been an important challenge in extending the context length of these models. Though the Transformer architecture has fundamentally no limits on the input sequence lengths it can process, the choice of position encoding used during training can limit the performance of these models on longer inputs. We propose a novel functional relative position encoding with progressive interpolation, FIRE, to improve Transformer generalization to longer contexts. We theoretically prove that this can represent some of the popular relative position encodings, such as T5's RPE, Alibi, and Kerple. We next empirically show that FIRE models have better generalization to longer contexts on both zero-shot language modeling and long text benchmarks.

There is a growing interest in the ability of neural networks to execute algorithmic tasks (e.g., arithmetic, summary statistics, and sorting). The goal of this work is to better understand the role of attention in Transformers for algorithmic execution. Its importance for algorithmic execution has been studied theoretically and empirically using parallel computational models. Notably, many parallel algorithms communicate between processors solely using positional information. Inspired by this observation, we investigate how Transformers can execute algorithms using positional attention, where attention weights depend exclusively on positional encodings. We prove that Transformers with positional attention (positional Transformers) maintain the same expressivity of parallel computational models, incurring a logarithmic depth cost relative to the input length. We analyze their in-distribution learnability and explore how parameter norms in positional attention affect sample complexity. Our results show that positional Transformers introduce a learning trade-off: while they exhibit better theoretical dependence on parameter norms, certain tasks may require more layers, which can, in turn, increase sample complexity. Finally, we empirically explore the out-of-distribution performance of positional Transformers and find that they perform well in tasks where their underlying algorithmic solution relies on positional information.

Rotary Position Embedding (RoPE) has shown strong performance in text-based Large Language Models (LLMs), but extending it to video remains a challenge due to the intricate spatiotemporal structure of video frames. Existing adaptations, such as RoPE-3D, attempt to encode spatial and temporal dimensions separately but suffer from two major limitations: positional bias in attention distribution and disruptions in video-text transitions. To overcome these issues, we propose Video Rotary Position Embedding (VRoPE), a novel positional encoding method tailored for Video-LLMs. Our approach restructures positional indices to preserve spatial coherence and ensure a smooth transition between video and text tokens. Additionally, we introduce a more balanced encoding strategy that mitigates attention biases, ensuring a more uniform distribution of spatial focus. Extensive experiments on Vicuna and Qwen2 across different model scales demonstrate that VRoPE consistently outperforms previous RoPE variants, achieving significant improvements in video understanding, temporal reasoning, and retrieval tasks. Code will be available at https://github.com/johncaged/VRoPE

Recently, state space models have exhibited strong global modeling capabilities and linear computational complexity in contrast to transformers. This research focuses on applying such architecture to more efficiently and effectively model point cloud data globally with linear computational complexity. In particular, for the first time, we demonstrate that Mamba-based point cloud methods can outperform previous methods based on transformer or multi-layer perceptrons (MLPs). To enable Mamba to process 3-D point cloud data more effectively, we propose a novel Consistent Traverse Serialization method to convert point clouds into 1-D point sequences while ensuring that neighboring points in the sequence are also spatially adjacent. Consistent Traverse Serialization yields six variants by permuting the order of x, y, and z coordinates, and the synergistic use of these variants aids Mamba in comprehensively observing point cloud data. Furthermore, to assist Mamba in handling point sequences with different orders more effectively, we introduce point prompts to inform Mamba of the sequence's arrangement rules. Finally, we propose positional encoding based on spatial coordinate mapping to inject positional information into point cloud sequences more effectively. Point Cloud Mamba surpasses the state-of-the-art (SOTA) point-based method PointNeXt and achieves new SOTA performance on the ScanObjectNN, ModelNet40, ShapeNetPart, and S3DIS datasets. It is worth mentioning that when using a more powerful local feature extraction module, our PCM achieves 79.6 mIoU on S3DIS, significantly surpassing the previous SOTA models, DeLA and PTv3, by 5.5 mIoU and 4.9 mIoU, respectively.

DNA sequence alignment involves assigning short DNA reads to the most probable locations on an extensive reference genome. This process is crucial for various genomic analyses, including variant calling, transcriptomics, and epigenomics. Conventional methods, refined over decades, tackle this challenge in 2 steps: genome indexing followed by efficient search to locate likely positions for given reads. Building on the success of Large Language Models in encoding text into embeddings, where the distance metric captures semantic similarity, recent efforts have explored whether the same Transformer architecture can produce embeddings for DNA sequences. Such models have shown early promise in classifying short DNA sequences, such as detecting coding/non-coding regions, and enhancer, promoter sequences. However, performance at sequence classification tasks does not translate to sequence alignment, where it is necessary to search across the genome to align each read, a significantly longer-range task. We bridge this gap by framing the Sequence Alignment task for Transformer models as an "Embed-Search-Align" task. In this framework, a novel Reference-Free DNA Embedding model generates embeddings of reads and reference fragments, which are projected into a shared vector space where the read-fragment distance is used as a surrogate for alignment. Technical contributions include: (1) Contrastive loss for self-supervised training of DNA sequence representations, facilitating rich reference-free, sequence-level embeddings, and (2) a DNA vector store to enable search across fragments on a global scale. DNA-ESA is 99% accurate when aligning 250-length reads onto a human genome (3gb), rivaling conventional methods such as Bowtie and BWA-Mem. DNA-ESA exceeds the performance of 6 Transformer model baselines such as Nucleotide Transformer, Hyena-DNA, and shows task transfer across chromosomes and species.

Rotary Position Embeddings (RoPE) have been shown to effectively encode positional information in transformer-based language models. However, these models fail to generalize past the sequence length they were trained on. We present YaRN (Yet another RoPE extensioN method), a compute-efficient method to extend the context window of such models, requiring 10x less tokens and 2.5x less training steps than previous methods. Using YaRN, we show that LLaMA models can effectively utilize and extrapolate to context lengths much longer than their original pre-training would allow, while also surpassing previous the state-of-the-art at context window extension. In addition, we demonstrate that YaRN exhibits the capability to extrapolate beyond the limited context of a fine-tuning dataset. We publish the checkpoints of Llama 2 7B/13B fine-tuned using YaRN with 64k and 128k context windows at https://github.com/jquesnelle/yarn

Vision-language Models (VLMs) have shown remarkable capabilities in advancing general artificial intelligence, yet the irrational encoding of visual positions persists in inhibiting the models' comprehensive perception performance across different levels of granularity. In this work, we propose Pyramid-descent Visual Position Encoding (PyPE), a novel approach designed to enhance the perception of visual tokens within VLMs. By assigning visual position indexes from the periphery to the center and expanding the central receptive field incrementally, PyPE addresses the limitations of traditional raster-scan methods and mitigates the long-term decay effects induced by Rotary Position Embedding (RoPE). Our method reduces the relative distance between interrelated visual elements and instruction tokens, promoting a more rational allocation of attention weights and allowing for a multi-granularity perception of visual elements and countering the over-reliance on anchor tokens. Extensive experimental evaluations demonstrate that PyPE consistently improves the general capabilities of VLMs across various sizes. Code is available at https://github.com/SakuraTroyChen/PyPE.

Transformers have recently been shown to generate high quality images from text input. However, the existing method of pose conditioning using skeleton image tokens is computationally inefficient and generate low quality images. Therefore we propose a new method; Keypoint Pose Encoding (KPE); KPE is 10 times more memory efficient and over 73% faster at generating high quality images from text input conditioned on the pose. The pose constraint improves the image quality and reduces errors on body extremities such as arms and legs. The additional benefits include invariance to changes in the target image domain and image resolution, making it easily scalable to higher resolution images. We demonstrate the versatility of KPE by generating photorealistic multiperson images derived from the DeepFashion dataset. We also introduce a evaluation method People Count Error (PCE) that is effective in detecting error in generated human images.

Length extrapolation algorithms based on Rotary position embedding (RoPE) have shown promising results in extending the context length of language models. However, understanding how position embedding can capture longer-range contextual information remains elusive. Based on the intuition that different dimensions correspond to different frequency of changes in RoPE encoding, we conducted a dimension-level analysis to investigate the correlation between a hidden dimension of an attention head and its contribution to capturing long-distance dependencies. Using our correlation metric, we identified a particular type of attention heads, which we named Positional Heads, from various length-extrapolated models. These heads exhibit a strong focus on long-range information interaction and play a pivotal role in long input processing, as evidence by our ablation. We further demonstrate the correlation between the efficiency of length extrapolation and the extension of the high-dimensional attention allocation of these heads. The identification of Positional Heads provides insights for future research in long-text comprehension.

We explore different ways to utilize position-based cross-attention in seq2seq networks to enable length generalization in algorithmic tasks. We show that a simple approach of interpolating the original and reversed encoded representations combined with relative attention allows near-perfect length generalization for both forward and reverse lookup tasks or copy tasks that had been generally hard to tackle. We also devise harder diagnostic tasks where the relative distance of the ideal attention position varies with timestep. In such settings, the simple interpolation trick with relative attention is not sufficient. We introduce novel variants of location attention building on top of Dubois et al. (2020) to address the new diagnostic tasks. We also show the benefits of our approaches for length generalization in SCAN (Lake & Baroni, 2018) and CFQ (Keysers et al., 2020). Our code is available on GitHub.

Gaussian processes (GPs) are popular nonparametric statistical models for learning unknown functions and quantifying the spatiotemporal uncertainty in data. Recent works have extended GPs to model scalar and vector quantities distributed over non-Euclidean domains, including smooth manifolds appearing in numerous fields such as computer vision, dynamical systems, and neuroscience. However, these approaches assume that the manifold underlying the data is known, limiting their practical utility. We introduce RVGP, a generalisation of GPs for learning vector signals over latent Riemannian manifolds. Our method uses positional encoding with eigenfunctions of the connection Laplacian, associated with the tangent bundle, readily derived from common graph-based approximation of data. We demonstrate that RVGP possesses global regularity over the manifold, which allows it to super-resolve and inpaint vector fields while preserving singularities. Furthermore, we use RVGP to reconstruct high-density neural dynamics derived from low-density EEG recordings in healthy individuals and Alzheimer's patients. We show that vector field singularities are important disease markers and that their reconstruction leads to a comparable classification accuracy of disease states to high-density recordings. Thus, our method overcomes a significant practical limitation in experimental and clinical applications.

We address the challenge of representing long captions in vision-language models, such as CLIP. By design these models are limited by fixed, absolute positional encodings, restricting inputs to a maximum of 77 tokens and hindering performance on tasks requiring longer descriptions. Although recent work has attempted to overcome this limit, their proposed approaches struggle to model token relationships over longer distances and simply extend to a fixed new token length. Instead, we propose a generalizable method, named TULIP, able to upgrade the token length to any length for CLIP-like models. We do so by improving the architecture with relative position encodings, followed by a training procedure that (i) distills the original CLIP text encoder into an encoder with relative position encodings and (ii) enhances the model for aligning longer captions with images. By effectively encoding captions longer than the default 77 tokens, our model outperforms baselines on cross-modal tasks such as retrieval and text-to-image generation.

Semantic parsing models with applications in task oriented dialog systems require efficient sequence to sequence (seq2seq) architectures to be run on-device. To this end, we propose a projection based encoder-decoder model referred to as pQRNN-MAtt. Studies based on projection methods were restricted to encoder-only models, and we believe this is the first study extending it to seq2seq architectures. The resulting quantized models are less than 3.5MB in size and are well suited for on-device latency critical applications. We show that on MTOP, a challenging multilingual semantic parsing dataset, the average model performance surpasses LSTM based seq2seq model that uses pre-trained embeddings despite being 85x smaller. Furthermore, the model can be an effective student for distilling large pre-trained models such as T5/BERT.

Transformer-based Large Language Models (LLMs) are pioneering advances in many natural language processing tasks, however, their exceptional capabilities are restricted within the preset context window of Transformer. Position Embedding (PE) scaling methods, while effective in extending the context window to a specific length, demonstrate either notable limitations in their extrapolation abilities or sacrificing partial performance within the context window. Length extrapolation methods, although theoretically capable of extending the context window beyond the training sequence length, often underperform in practical long-context applications. To address these challenges, we propose Continuous Length EXtrapolation (CLEX) for LLMs. We generalise the PE scaling approaches to model the continuous dynamics by ordinary differential equations over the length scaling factor, thereby overcoming the constraints of current PE scaling methods designed for specific lengths. Moreover, by extending the dynamics to desired context lengths beyond the training sequence length, CLEX facilitates the length extrapolation with impressive performance in practical tasks. We demonstrate that CLEX can be seamlessly incorporated into LLMs equipped with Rotary Position Embedding, such as LLaMA and GPT-NeoX, with negligible impact on training and inference latency. Experimental results reveal that CLEX can effectively extend the context window to over 4x or almost 8x training length, with no deterioration in performance. Furthermore, when evaluated on the practical LongBench benchmark, our model trained on a 4k length exhibits competitive performance against state-of-the-art open-source models trained on context lengths up to 32k.

The attention module, which is a crucial component in Transformer, cannot scale efficiently to long sequences due to its quadratic complexity. Many works focus on approximating the dot-then-exponentiate softmax function in the original attention, leading to sub-quadratic or even linear-complexity Transformer architectures. However, we show that these methods cannot be applied to more powerful attention modules that go beyond the dot-then-exponentiate style, e.g., Transformers with relative positional encoding (RPE). Since in many state-of-the-art models, relative positional encoding is used as default, designing efficient Transformers that can incorporate RPE is appealing. In this paper, we propose a novel way to accelerate attention calculation for Transformers with RPE on top of the kernelized attention. Based upon the observation that relative positional encoding forms a Toeplitz matrix, we mathematically show that kernelized attention with RPE can be calculated efficiently using Fast Fourier Transform (FFT). With FFT, our method achieves O(nlog n) time complexity. Interestingly, we further demonstrate that properly using relative positional encoding can mitigate the training instability problem of vanilla kernelized attention. On a wide range of tasks, we empirically show that our models can be trained from scratch without any optimization issues. The learned model performs better than many efficient Transformer variants and is faster than standard Transformer in the long-sequence regime.

Byte-pair encoding (BPE) is a ubiquitous algorithm in the subword tokenization process of language models as it provides multiple benefits. However, this process is solely based on pre-training data statistics, making it hard for the tokenizer to handle infrequent spellings. On the other hand, though robust to misspellings, pure character-level models often lead to unreasonably long sequences and make it harder for the model to learn meaningful words. To alleviate these challenges, we propose a character-based subword module (char2subword) that learns the subword embedding table in pre-trained models like BERT. Our char2subword module builds representations from characters out of the subword vocabulary, and it can be used as a drop-in replacement of the subword embedding table. The module is robust to character-level alterations such as misspellings, word inflection, casing, and punctuation. We integrate it further with BERT through pre-training while keeping BERT transformer parameters fixed--and thus, providing a practical method. Finally, we show that incorporating our module to mBERT significantly improves the performance on the social media linguistic code-switching evaluation (LinCE) benchmark.

In this paper, we propose P3D, the human part-wise motion context learning framework for sign language recognition. Our main contributions lie in two dimensions: learning the part-wise motion context and employing the pose ensemble to utilize 2D and 3D pose jointly. First, our empirical observation implies that part-wise context encoding benefits the performance of sign language recognition. While previous methods of sign language recognition learned motion context from the sequence of the entire pose, we argue that such methods cannot exploit part-specific motion context. In order to utilize part-wise motion context, we propose the alternating combination of a part-wise encoding Transformer (PET) and a whole-body encoding Transformer (WET). PET encodes the motion contexts from a part sequence, while WET merges them into a unified context. By learning part-wise motion context, our P3D achieves superior performance on WLASL compared to previous state-of-the-art methods. Second, our framework is the first to ensemble 2D and 3D poses for sign language recognition. Since the 3D pose holds rich motion context and depth information to distinguish the words, our P3D outperformed the previous state-of-the-art methods employing a pose ensemble.

Position bias has proven to be a prevalent issue of modern language models (LMs), where the models prioritize content based on its position within the given context. This bias often leads to unexpected model failures and hurts performance, robustness, and reliability across various applications. Our mechanistic analysis attributes the position bias to two components employed in nearly all state-of-the-art LMs: causal attention and relative positional encodings. Specifically, we find that causal attention generally causes models to favor distant content, while relative positional encodings like RoPE prefer nearby ones based on the analysis of retrieval-augmented question answering (QA). Further, our empirical study on object detection reveals that position bias is also present in vision-language models (VLMs). Based on the above analyses, we propose to ELIMINATE position bias caused by different input segment orders (e.g., options in LM-as-a-judge, retrieved documents in QA) in a TRAINING-FREE ZERO-SHOT manner. Our method changes the causal attention to bidirectional attention between segments and utilizes model attention values to decide the relative orders of segments instead of using the order provided in input prompts, therefore enabling Position-INvariant inferencE (PINE) at the segment level. By eliminating position bias, models achieve better performance and reliability in downstream tasks where position bias widely exists, such as LM-as-a-judge and retrieval-augmented QA. Notably, PINE is especially useful when adapting LMs for evaluating reasoning pairs: it consistently provides 8 to 10 percentage points performance gains in most cases, and makes Llama-3-70B-Instruct perform even better than GPT-4-0125-preview on the RewardBench reasoning subset.

Structural and Positional Encodings can significantly improve the performance of Graph Neural Networks in downstream tasks. Recent literature has begun to systematically investigate differences in the structural properties that these approaches encode, as well as performance trade-offs between them. However, the question of which structural properties yield the most effective encoding remains open. In this paper, we investigate this question from a geometric perspective. We propose a novel structural encoding based on discrete Ricci curvature (Local Curvature Profiles, short LCP) and show that it significantly outperforms existing encoding approaches. We further show that combining local structural encodings, such as LCP, with global positional encodings improves downstream performance, suggesting that they capture complementary geometric information. Finally, we compare different encoding types with (curvature-based) rewiring techniques. Rewiring has recently received a surge of interest due to its ability to improve the performance of Graph Neural Networks by mitigating over-smoothing and over-squashing effects. Our results suggest that utilizing curvature information for structural encodings delivers significantly larger performance increases than rewiring.

Extending context window sizes allows large language models (LLMs) to process longer sequences and handle more complex tasks. Rotary Positional Embedding (RoPE) has become the de facto standard due to its relative positional encoding properties that benefit long-context training. However, we observe that using RoPE with BFloat16 format results in numerical issues, causing it to deviate from its intended relative positional encoding, especially in long-context scenarios. This issue arises from BFloat16's limited precision and accumulates as context length increases, with the first token contributing significantly to this problem. To address this, we develop AnchorAttention, a plug-and-play attention method that alleviates numerical issues caused by BFloat16, improves long-context capabilities, and speeds up training. AnchorAttention reduces unnecessary attention computations, maintains semantic coherence, and boosts computational efficiency by treating the first token as a shared anchor with a consistent position ID, making it visible to all documents within the training context. Experiments on three types of LLMs demonstrate that AnchorAttention significantly improves long-context performance and reduces training time by over 50\% compared to standard full attention mechanisms, while preserving the original LLM's capabilities on general tasks. Our code is available at https://github.com/haonan3/AnchorContext.

Speculative decoding accelerates Large Language Model (LLM) inference by using a small draft model to predict multiple tokens, and a large target model to verify these tokens in parallel. Recent studies leverage the hidden state of the target model to enhance draft model prediction accuracy. However, existing methods suffer from the degrading quality of draft token predictions at later positions, due to error accumulation in draft model generated features. In this paper, we propose Position Specialists (PosS), which consist of multiple position-specialized draft layers to generate tokens at assigned position(s). Position specialists greatly improve token acceptance rate at later positions per drafting round, as each specialist only needs to focus on handling a certain level of draft model feature deviation. Experiment results on Llama-3-8B-Instruct and Llama-2-13B-chat across six datasets demonstrate that PosS effectively improves over baselines on average acceptance length and speed-up ratio. Our codebase is available at https://github.com/shrango/PosS.

Important information that relates to a specific topic in a document is often organized in tabular format to assist readers with information retrieval and comparison, which may be difficult to provide in natural language. However, tabular data in unstructured digital documents, e.g., Portable Document Format (PDF) and images, are difficult to parse into structured machine-readable format, due to complexity and diversity in their structure and style. To facilitate image-based table recognition with deep learning, we develop the largest publicly available table recognition dataset PubTabNet (https://github.com/ibm-aur-nlp/PubTabNet), containing 568k table images with corresponding structured HTML representation. PubTabNet is automatically generated by matching the XML and PDF representations of the scientific articles in PubMed Central Open Access Subset (PMCOA). We also propose a novel attention-based encoder-dual-decoder (EDD) architecture that converts images of tables into HTML code. The model has a structure decoder which reconstructs the table structure and helps the cell decoder to recognize cell content. In addition, we propose a new Tree-Edit-Distance-based Similarity (TEDS) metric for table recognition, which more appropriately captures multi-hop cell misalignment and OCR errors than the pre-established metric. The experiments demonstrate that the EDD model can accurately recognize complex tables solely relying on the image representation, outperforming the state-of-the-art by 9.7% absolute TEDS score.

Effectively training language models on long inputs poses many technical challenges. As a cost consideration, languages models are pretrained on a fixed sequence length before being adapted to longer sequences. We explore various methods for adapting models to longer inputs by training on segmented sequences and an interpolation-based method for extending absolute positional embeddings. We develop a training procedure to extend the input context size of pretrained models with no architectural changes and no additional memory costs than training on the original input lengths. By sub-sampling segments from long inputs while maintaining their original position the model is able to learn new positional interactions. Our method benefits both models trained with absolute positional embeddings, by extending their input contexts, as well as popular relative positional embedding methods showing a reduced perplexity on sequences longer than they were trained on. We demonstrate our method can extend input contexts by a factor of 4x while improving perplexity.

Since the introduction of the transformer model by Vaswani et al. (2017), a fundamental question has yet to be answered: how does a model achieve extrapolation at inference time for sequences that are longer than it saw during training? We first show that extrapolation can be enabled by simply changing the position representation method, though we find that current methods do not allow for efficient extrapolation. We therefore introduce a simpler and more efficient position method, Attention with Linear Biases (ALiBi). ALiBi does not add positional embeddings to word embeddings; instead, it biases query-key attention scores with a penalty that is proportional to their distance. We show that this method trains a 1.3 billion parameter model on input sequences of length 1024 that extrapolates to input sequences of length 2048, achieving the same perplexity as a sinusoidal position embedding model trained on inputs of length 2048 but training 11% faster and using 11% less memory. ALiBi's inductive bias towards recency also leads it to outperform multiple strong position methods on the WikiText-103 benchmark.

Conditional human motion generation is an important topic with many applications in virtual reality, gaming, and robotics. While prior works have focused on generating motion guided by text, music, or scenes, these typically result in isolated motions confined to short durations. Instead, we address the generation of long, continuous sequences guided by a series of varying textual descriptions. In this context, we introduce FlowMDM, the first diffusion-based model that generates seamless Human Motion Compositions (HMC) without any postprocessing or redundant denoising steps. For this, we introduce the Blended Positional Encodings, a technique that leverages both absolute and relative positional encodings in the denoising chain. More specifically, global motion coherence is recovered at the absolute stage, whereas smooth and realistic transitions are built at the relative stage. As a result, we achieve state-of-the-art results in terms of accuracy, realism, and smoothness on the Babel and HumanML3D datasets. FlowMDM excels when trained with only a single description per motion sequence thanks to its Pose-Centric Cross-ATtention, which makes it robust against varying text descriptions at inference time. Finally, to address the limitations of existing HMC metrics, we propose two new metrics: the Peak Jerk and the Area Under the Jerk, to detect abrupt transitions.

We introduce Perception Encoder (PE), a state-of-the-art encoder for image and video understanding trained via simple vision-language learning. Traditionally, vision encoders have relied on a variety of pretraining objectives, each tailored to specific downstream tasks such as classification, captioning, or localization. Surprisingly, after scaling our carefully tuned image pretraining recipe and refining with our robust video data engine, we find that contrastive vision-language training alone can produce strong, general embeddings for all of these downstream tasks. There is only one caveat: these embeddings are hidden within the intermediate layers of the network. To draw them out, we introduce two alignment methods, language alignment for multimodal language modeling, and spatial alignment for dense prediction. Together with the core contrastive checkpoint, our PE family of models achieves state-of-the-art performance on a wide variety of tasks, including zero-shot image and video classification and retrieval; document, image, and video Q&A; and spatial tasks such as detection, depth estimation, and tracking. To foster further research, we are releasing our models, code, and a novel dataset of synthetically and human-annotated videos.

Scene text recognition (STR) methods have struggled to attain high accuracy and fast inference speed. Autoregressive (AR)-based models implement the recognition in a character-by-character manner, showing superiority in accuracy but with slow inference speed. Alternatively, parallel decoding (PD)-based models infer all characters in a single decoding pass, offering faster inference speed but generally worse accuracy. We first present an empirical study of AR decoding in STR, and discover that the AR decoder not only models linguistic context, but also provides guidance on visual context perception. Consequently, we propose Context Perception Parallel Decoder (CPPD) to predict the character sequence in a PD pass. CPPD devises a character counting module to infer the occurrence count of each character, and a character ordering module to deduce the content-free reading order and placeholders. Meanwhile, the character prediction task associates the placeholders with characters. They together build a comprehensive recognition context. We construct a series of CPPD models and also plug the proposed modules into existing STR decoders. Experiments on both English and Chinese benchmarks demonstrate that the CPPD models achieve highly competitive accuracy while running approximately 8x faster than their AR-based counterparts. Moreover, the plugged models achieve significant accuracy improvements. Code is at https://github.com/PaddlePaddle/PaddleOCR/blob/dygraph/doc/doc_en/algorithm_rec_cppd_en.md{this https URL}.

State-of-the-art language models are autoregressive and operate on subword units known as tokens. Specifically, one must encode the conditioning string into a list of tokens before passing to the language models for next-token prediction. We show that popular encoding schemes, such as maximum prefix encoding (MPE) and byte-pair-encoding (BPE), induce a sampling bias that cannot be mitigated with more training or data. To counter this universal problem, for each encoding scheme above, we propose a novel algorithm to obtain unbiased estimates from any language model trained on tokenized data. Our methods do not require finetuning the model, and the complexity, defined as the number of model runs, scales linearly with the sequence length in the case of MPE. As a result, we show that one can simulate token-free behavior from a tokenized language model. We empirically verify the correctness of our method through a Markov-chain setup, where it accurately recovers the transition probabilities, as opposed to the conventional method of directly prompting tokens into the language model.

The prevalent use of Byte Pair Encoding (BPE) in Large Language Models (LLMs) facilitates robust handling of subword units and avoids issues of out-of-vocabulary words. Despite its success, a critical challenge persists: long tokens, rich in semantic information, have fewer occurrences in tokenized datasets compared to short tokens, which can result in imbalanced learning issue across different tokens. To address that, we propose LBPE, which prioritizes long tokens during the encoding process. LBPE generates tokens according to their reverse ranks of token length rather than their ranks in the vocabulary, granting longer tokens higher priority during the encoding process. Consequently, LBPE smooths the frequency differences between short and long tokens, and thus mitigates the learning imbalance. Extensive experiments across diverse language modeling tasks demonstrate that LBPE consistently outperforms the original BPE, well demonstrating its effectiveness.

The dominance of large decoder-only language models has overshadowed encoder-decoder architectures, despite their fundamental efficiency advantages in sequence processing. For small language models (SLMs) - those with 1 billion parameters or fewer - our systematic analysis across GPU, CPU, and NPU platforms reveals that encoder-decoder architectures achieve 47% lower first-token latency and 4.7x higher throughput compared to decoder-only models on edge devices. These gains may be attributed to encoder-decoder's one-time input processing and efficient separation of understanding and generation phases. We introduce a novel knowledge distillation framework that enables encoder-decoder models to leverage capabilities from large scalable decoder-only teachers while preserving their architectural advantages, achieving up to 6 average performance points improvement across diverse tasks, with significant gains in asymmetric sequence tasks where input and output distributions can benefit from different processing approaches. When combined with modern advances like Rotary Positional Embeddings (RoPE) and Vision encoders, our systematic investigation demonstrates that encoder-decoder architectures provide a more practical path toward deploying capable language models in resource-constrained environments. Our findings challenge the prevailing trend toward decoder-only scaling, showing that architectural choices become increasingly crucial as parameter budgets decrease, particularly for on-device and edge deployments where computational efficiency is paramount.

Recent image generation models show remarkable generation performance. However, they mirror strong location preference in datasets, which we call spatial bias. Therefore, generators render poor samples at unseen locations and scales. We argue that the generators rely on their implicit positional encoding to render spatial content. From our observations, the generator's implicit positional encoding is translation-variant, making the generator spatially biased. To address this issue, we propose injecting explicit positional encoding at each scale of the generator. By learning the spatially unbiased generator, we facilitate the robust use of generators in multiple tasks, such as GAN inversion, multi-scale generation, generation of arbitrary sizes and aspect ratios. Furthermore, we show that our method can also be applied to denoising diffusion probabilistic models.

Position encoding recently has shown effective in the transformer architecture. It enables valuable supervision for dependency modeling between elements at different positions of the sequence. In this paper, we first investigate various methods to integrate positional information into the learning process of transformer-based language models. Then, we propose a novel method named Rotary Position Embedding(RoPE) to effectively leverage the positional information. Specifically, the proposed RoPE encodes the absolute position with a rotation matrix and meanwhile incorporates the explicit relative position dependency in self-attention formulation. Notably, RoPE enables valuable properties, including the flexibility of sequence length, decaying inter-token dependency with increasing relative distances, and the capability of equipping the linear self-attention with relative position encoding. Finally, we evaluate the enhanced transformer with rotary position embedding, also called RoFormer, on various long text classification benchmark datasets. Our experiments show that it consistently overcomes its alternatives. Furthermore, we provide a theoretical analysis to explain some experimental results. RoFormer is already integrated into Huggingface: https://huggingface.co/docs/transformers/model_doc/roformer.

In this paper, we give an in-depth analysis on the mathematical problem formulations and the probabilistic optimization explorations for some of the key components in Transformer model [33] in the field of generative AI. We explore and discuss some potential further enhancement for current state of the art methods for some key underlying technologies of generative AI models from algorithmic and probabilistic optimization perspective. In particular, we present an optimal solution for sub-word encoding (SWE) based on similar initial settings as that of byte-pair encoding (BPE) algorithm in [9] with similar objectives as that of WordPiece approach in [28, 31] to maximize the likelihood of the training data. We also present cross entropy optimization method to optimize hyperparameters for word2vec model [17]. In addition, we propose a factored combination of rotary positional encoding (RoPE) [32] and attention with linear biases (ALiBi) [23] with a harmonic series. We also present a probabilistic FlashAttention [6, 7] (PrFlashAttention) method with a probability distribution over block distances in the matrix to decide which block is likely to participate in a given round of attention computation while maintaining the lower triangle shape of the tensor for autoregressive language models by re-shaping the tensors. Finally, we present staircase adaptive quantization (SAQ) of key-value (KV) cache for multi-query attention (MQA) based on the framework presented in [16] to have gradual quantization degradation while achieving reasonable model quality and cost savings.

We present SegFormer, a simple, efficient yet powerful semantic segmentation framework which unifies Transformers with lightweight multilayer perception (MLP) decoders. SegFormer has two appealing features: 1) SegFormer comprises a novel hierarchically structured Transformer encoder which outputs multiscale features. It does not need positional encoding, thereby avoiding the interpolation of positional codes which leads to decreased performance when the testing resolution differs from training. 2) SegFormer avoids complex decoders. The proposed MLP decoder aggregates information from different layers, and thus combining both local attention and global attention to render powerful representations. We show that this simple and lightweight design is the key to efficient segmentation on Transformers. We scale our approach up to obtain a series of models from SegFormer-B0 to SegFormer-B5, reaching significantly better performance and efficiency than previous counterparts. For example, SegFormer-B4 achieves 50.3% mIoU on ADE20K with 64M parameters, being 5x smaller and 2.2% better than the previous best method. Our best model, SegFormer-B5, achieves 84.0% mIoU on Cityscapes validation set and shows excellent zero-shot robustness on Cityscapes-C. Code will be released at: github.com/NVlabs/SegFormer.

Text-to-image (T2I) diffusion models rely on encoded prompts to guide the image generation process. Typically, these prompts are extended to a fixed length by adding padding tokens before text encoding. Despite being a default practice, the influence of padding tokens on the image generation process has not been investigated. In this work, we conduct the first in-depth analysis of the role padding tokens play in T2I models. We develop two causal techniques to analyze how information is encoded in the representation of tokens across different components of the T2I pipeline. Using these techniques, we investigate when and how padding tokens impact the image generation process. Our findings reveal three distinct scenarios: padding tokens may affect the model's output during text encoding, during the diffusion process, or be effectively ignored. Moreover, we identify key relationships between these scenarios and the model's architecture (cross or self-attention) and its training process (frozen or trained text encoder). These insights contribute to a deeper understanding of the mechanisms of padding tokens, potentially informing future model design and training practices in T2I systems.

Modern large language models (LLMs) that rely on attention mechanisms are typically trained with fixed context lengths which enforce upper limits on the length of input sequences that they can handle at evaluation time. To use these models on sequences longer than the train-time context length, one might employ techniques from the growing family of context length extrapolation methods -- most of which focus on modifying the system of positional encodings used in the attention mechanism to indicate where tokens or activations are located in the input sequence. We conduct a wide survey of existing methods of context length extrapolation on a base LLaMA or LLaMA 2 model, and introduce some of our own design as well -- in particular, a new truncation strategy for modifying the basis for the position encoding. We test these methods using three new evaluation tasks (FreeFormQA, AlteredNumericQA, and LongChat-Lines) as well as perplexity, which we find to be less fine-grained as a measure of long context performance of LLMs. We release the three tasks publicly as datasets on HuggingFace. We discover that linear scaling is the best method for extending context length, and show that further gains can be achieved by using longer scales at evaluation time. We also discover promising extrapolation capabilities in the truncated basis. To support further research in this area, we release three new 13B parameter long-context models which we call Giraffe: 4k and 16k context models trained from base LLaMA-13B, and a 32k context model trained from base LLaMA2-13B. We also release the code to replicate our results.

We introduce ARPG, a novel visual autoregressive model that enables randomized parallel generation, addressing the inherent limitations of conventional raster-order approaches, which hinder inference efficiency and zero-shot generalization due to their sequential, predefined token generation order. Our key insight is that effective random-order modeling necessitates explicit guidance for determining the position of the next predicted token. To this end, we propose a novel guided decoding framework that decouples positional guidance from content representation, encoding them separately as queries and key-value pairs. By directly incorporating this guidance into the causal attention mechanism, our approach enables fully random-order training and generation, eliminating the need for bidirectional attention. Consequently, ARPG readily generalizes to zero-shot tasks such as image inpainting, outpainting, and resolution expansion. Furthermore, it supports parallel inference by concurrently processing multiple queries using a shared KV cache. On the ImageNet-1K 256 benchmark, our approach attains an FID of 1.94 with only 64 sampling steps, achieving over a 20-fold increase in throughput while reducing memory consumption by over 75% compared to representative recent autoregressive models at a similar scale.

Neural Machine Translation (NMT) models have traditionally used Sinusoidal Positional Embeddings (PEs), which often struggle to capture long-range dependencies and are less efficient for handling extended context or document-level translation tasks. This work addresses the challenge of transitioning pre-trained NMT models from absolute sinusoidal PEs to relative PEs, such as Rotary Positional Embeddings (ROPE) and Attention with Linear Biases (ALIBI), without compromising performance. We demonstrate that parameter-efficient fine-tuning, using only a small amount of high-quality data, can successfully facilitate this transition. Experimental results indicate that switching from sinusoidal to relative PEs results in competitive translation quality on sentence-level evaluation benchmarks. Additionally, models trained with ROPE consistently outperform those using ALIBI and Sinusoidal PEs on document-level benchmarks across both string-based metrics and qualitative evaluations. Moreover, we find that a small amount of long-context data in a few languages is sufficient for cross-lingual length generalization, thereby inducing long-context capabilities.

This study investigates the existence of positional biases in Transformer-based models for text representation learning, particularly in the context of web document retrieval. We build on previous research that demonstrated loss of information in the middle of input sequences for causal language models, extending it to the domain of representation learning. We examine positional biases at various stages of training for an encoder-decoder model, including language model pre-training, contrastive pre-training, and contrastive fine-tuning. Experiments with the MS-MARCO document collection reveal that after contrastive pre-training the model already generates embeddings that better capture early contents of the input, with fine-tuning further aggravating this effect.

RNA plays a pivotal role in translating genetic instructions into functional outcomes, underscoring its importance in biological processes and disease mechanisms. Despite the emergence of numerous deep learning approaches for RNA, particularly universal RNA language models, there remains a significant lack of standardized benchmarks to assess the effectiveness of these methods. In this study, we introduce the first comprehensive RNA benchmark BEACON (BEnchmArk for COmprehensive RNA Task and Language Models). First, BEACON comprises 13 distinct tasks derived from extensive previous work covering structural analysis, functional studies, and engineering applications, enabling a comprehensive assessment of the performance of methods on various RNA understanding tasks. Second, we examine a range of models, including traditional approaches like CNNs, as well as advanced RNA foundation models based on language models, offering valuable insights into the task-specific performances of these models. Third, we investigate the vital RNA language model components from the tokenizer and positional encoding aspects. Notably, our findings emphasize the superiority of single nucleotide tokenization and the effectiveness of Attention with Linear Biases (ALiBi) over traditional positional encoding methods. Based on these insights, a simple yet strong baseline called BEACON-B is proposed, which can achieve outstanding performance with limited data and computational resources. The datasets and source code of our benchmark are available at https://github.com/terry-r123/RNABenchmark.

A major consideration in multilingual language modeling is how to best represent languages with diverse vocabularies and scripts. Although contemporary text encoding methods cover most of the world's writing systems, they exhibit bias towards the high-resource languages of the Global West. As a result, texts of underrepresented languages tend to be segmented into long sequences of linguistically meaningless units. To address the disparities, we introduce a new paradigm that encodes the same information with segments of consistent size across diverse languages. Our encoding convention (MYTE) is based on morphemes, as their inventories are more balanced across languages than characters, which are used in previous methods. We show that MYTE produces shorter encodings for all 99 analyzed languages, with the most notable improvements for non-European languages and non-Latin scripts. This, in turn, improves multilingual LM performance and diminishes the perplexity gap throughout diverse languages.

Recent studies have shown that, relative position encoding performs well in selective state space model scanning algorithms, and the architecture that balances SSM and Attention enhances the efficiency and effectiveness of the algorithm, while the sparse activation of the mixture of experts reduces the training cost. I studied the effectiveness of using different position encodings in structured state space dual algorithms, and the more effective SSD-Attn internal and external function mixing method, and designed a more efficient cross domain mixture of experts. I found that the same matrix is very wonderful in different algorithms, which allows us to establish a new hybrid sparse architecture: Cheems. Compared with other hybrid architectures, it is more efficient and more effective in language modeling tasks.

Causal transformer language models (LMs), such as GPT-3, typically require some form of positional encoding, such as positional embeddings. However, we show that LMs without any explicit positional encoding are still competitive with standard models, and that this phenomenon is robust across different datasets, model sizes, and sequence lengths. Probing experiments reveal that such models acquire an implicit notion of absolute positions throughout the network, effectively compensating for the missing information. We conjecture that causal attention enables the model to infer the number of predecessors that each token can attend to, thereby approximating its absolute position. Our findings indicate that causal LMs might derive positional awareness not only from the explicit positioning mechanism, but also from the effects of the causal mask.

Speculative decoding is a relatively new decoding framework that leverages small and efficient draft models to reduce the latency of LLMs. In this study, we introduce GliDe and CaPE, two low-hassle modifications to vanilla speculative decoding to further improve the decoding speed of a frozen LLM. Specifically, GliDe is a modified draft model architecture that reuses the cached keys and values from the target LLM, while CaPE is a proposal expansion method that uses the draft model's confidence scores to help select additional candidate tokens for verification. Extensive experiments on different benchmarks demonstrate that our proposed GliDe draft model significantly reduces the expected decoding latency. Additional evaluation using walltime reveals that GliDe can accelerate Vicuna models up to 2.17x and further extend the improvement to 2.61x with CaPE. We will release our code, data, and the trained draft models.

Position embedding is a core component of current Large Language Models (LLMs). Rotary position embedding (RoPE), a technique that encodes the position information with a rotation matrix, has been the de facto choice for position embedding in many LLMs, such as the Llama series. RoPE has been further utilized to extend long context capability, which is roughly based on adjusting the base parameter of RoPE to mitigate out-of-distribution (OOD) problems in position embedding. However, in this paper, we find that LLMs may obtain a superficial long-context ability based on the OOD theory. We revisit the role of RoPE in LLMs and propose a novel property of long-term decay, we derive that the base of RoPE bounds context length: there is an absolute lower bound for the base value to obtain certain context length capability. Our work reveals the relationship between context length and RoPE base both theoretically and empirically, which may shed light on future long context training.

We introduce a new neural architecture to learn the conditional probability of an output sequence with elements that are discrete tokens corresponding to positions in an input sequence. Such problems cannot be trivially addressed by existent approaches such as sequence-to-sequence and Neural Turing Machines, because the number of target classes in each step of the output depends on the length of the input, which is variable. Problems such as sorting variable sized sequences, and various combinatorial optimization problems belong to this class. Our model solves the problem of variable size output dictionaries using a recently proposed mechanism of neural attention. It differs from the previous attention attempts in that, instead of using attention to blend hidden units of an encoder to a context vector at each decoder step, it uses attention as a pointer to select a member of the input sequence as the output. We call this architecture a Pointer Net (Ptr-Net). We show Ptr-Nets can be used to learn approximate solutions to three challenging geometric problems -- finding planar convex hulls, computing Delaunay triangulations, and the planar Travelling Salesman Problem -- using training examples alone. Ptr-Nets not only improve over sequence-to-sequence with input attention, but also allow us to generalize to variable size output dictionaries. We show that the learnt models generalize beyond the maximum lengths they were trained on. We hope our results on these tasks will encourage a broader exploration of neural learning for discrete problems.

Large language models exhibit positional bias -- systematic neglect of information at specific context positions -- yet its interplay with linguistic diversity remains poorly understood. We present a cross-linguistic study across five typologically distinct languages (English, Russian, German, Hindi, Vietnamese), examining how positional bias interacts with model uncertainty, syntax, and prompting. Key findings: (1) Positional bias is model-driven, with language-specific variations -- Qwen2.5-7B favors late positions, challenging assumptions of early-token bias; (2) Explicit positional guidance (e.g., correct context is at position X) reduces accuracy across languages, undermining prompt-engineering practices; (3) Aligning context with positional bias increases entropy, yet minimal entropy does not predict accuracy. (4) We further uncover that LLMs differently impose dominant word order in free-word-order languages like Hindi.

Extending large language models (LLMs) to process longer inputs is crucial for numerous applications. However, the considerable computational cost of transformers, coupled with limited generalization of positional encoding, restricts the size of their context window. We introduce Context Expansion with Parallel Encoding (CEPE), a framework that can be applied to any existing decoder-only LLMs to extend their context window. CEPE adopts a small encoder to process long inputs chunk by chunk and enables the frozen decoder to leverage additional contexts via cross-attention. CEPE is efficient, generalizable, and versatile: trained with 8K-token documents, CEPE extends the context window of LLAMA-2 to 128K tokens, offering 10x the throughput with only 1/6 of the memory. CEPE yields strong performance on language modeling and in-context learning. CEPE also excels in retrieval-augmented applications, while existing long-context models degenerate with retrieved contexts. We further introduce a CEPE variant that can extend the context window of instruction-tuned models with only unlabeled data, and showcase its effectiveness on LLAMA-2-CHAT, leading to a strong instruction-following model that can leverage very long context on downstream tasks.

Implicit neural representations (INR) have gained significant popularity for signal and image representation for many end-tasks, such as superresolution, 3D modeling, and more. Most INR architectures rely on sinusoidal positional encoding, which accounts for high-frequency information in data. However, the finite encoding size restricts the model's representational power. Higher representational power is needed to go from representing a single given image to representing large and diverse datasets. Our approach addresses this gap by representing an image with a polynomial function and eliminates the need for positional encodings. Therefore, to achieve a progressively higher degree of polynomial representation, we use element-wise multiplications between features and affine-transformed coordinate locations after every ReLU layer. The proposed method is evaluated qualitatively and quantitatively on large datasets like ImageNet. The proposed Poly-INR model performs comparably to state-of-the-art generative models without any convolution, normalization, or self-attention layers, and with far fewer trainable parameters. With much fewer training parameters and higher representative power, our approach paves the way for broader adoption of INR models for generative modeling tasks in complex domains. The code is available at https://github.com/Rajhans0/Poly_INR

Generating accurate multilingual text with diffusion models has long been desired but remains challenging. Recent methods have made progress in rendering text in a single language, but rendering arbitrary languages is still an unexplored area. This paper introduces EasyText, a text rendering framework based on DiT (Diffusion Transformer), which connects denoising latents with multilingual character tokens encoded as character tokens. We propose character positioning encoding and position encoding interpolation techniques to achieve controllable and precise text rendering. Additionally, we construct a large-scale synthetic text image dataset with 1 million multilingual image-text annotations as well as a high-quality dataset of 20K annotated images, which are used for pretraining and fine-tuning respectively. Extensive experiments and evaluations demonstrate the effectiveness and advancement of our approach in multilingual text rendering, visual quality, and layout-aware text integration.

Predicting ATP-Protein Binding sites in genes is of great significance in the field of Biology and Medicine. The majority of research in this field has been conducted through time- and resource-intensive 'wet experiments' in laboratories. Over the years, researchers have been investigating computational methods computational methods to accomplish the same goals, utilising the strength of advanced Deep Learning and NLP algorithms. In this paper, we propose to develop methods to classify ATP-Protein binding sites. We conducted various experiments mainly using PSSMs and several word embeddings as features. We used 2D CNNs and LightGBM classifiers as our chief Deep Learning Algorithms. The MP3Vec and BERT models have also been subjected to testing in our study. The outcomes of our experiments demonstrated improvement over the state-of-the-art benchmarks.

In recent years, huge progress has been made on learning neural implicit representations from multi-view images for 3D reconstruction. As an additional input complementing coordinates, using sinusoidal functions as positional encodings plays a key role in revealing high frequency details with coordinate-based neural networks. However, high frequency positional encodings make the optimization unstable, which results in noisy reconstructions and artifacts in empty space. To resolve this issue in a general sense, we introduce to learn neural implicit representations with quantized coordinates, which reduces the uncertainty and ambiguity in the field during optimization. Instead of continuous coordinates, we discretize continuous coordinates into discrete coordinates using nearest interpolation among quantized coordinates which are obtained by discretizing the field in an extremely high resolution. We use discrete coordinates and their positional encodings to learn implicit functions through volume rendering. This significantly reduces the variations in the sample space, and triggers more multi-view consistency constraints on intersections of rays from different views, which enables to infer implicit function in a more effective way. Our quantized coordinates do not bring any computational burden, and can seamlessly work upon the latest methods. Our evaluations under the widely used benchmarks show our superiority over the state-of-the-art. Our code is available at https://github.com/MachinePerceptionLab/CQ-NIR.

We present a novel approach for the prediction of anticancer compound sensitivity by means of multi-modal attention-based neural networks (PaccMann). In our approach, we integrate three key pillars of drug sensitivity, namely, the molecular structure of compounds, transcriptomic profiles of cancer cells as well as prior knowledge about interactions among proteins within cells. Our models ingest a drug-cell pair consisting of SMILES encoding of a compound and the gene expression profile of a cancer cell and predicts an IC50 sensitivity value. Gene expression profiles are encoded using an attention-based encoding mechanism that assigns high weights to the most informative genes. We present and study three encoders for SMILES string of compounds: 1) bidirectional recurrent 2) convolutional 3) attention-based encoders. We compare our devised models against a baseline model that ingests engineered fingerprints to represent the molecular structure. We demonstrate that using our attention-based encoders, we can surpass the baseline model. The use of attention-based encoders enhance interpretability and enable us to identify genes, bonds and atoms that were used by the network to make a prediction.

Performance analyses based on videos are commonly used by coaches of athletes in various sports disciplines. In individual sports, these analyses mainly comprise the body posture. This paper focuses on the disciplines of triple, high, and long jump, which require fine-grained locations of the athlete's body. Typical human pose estimation datasets provide only a very limited set of keypoints, which is not sufficient in this case. Therefore, we propose a method to detect arbitrary keypoints on the whole body of the athlete by leveraging the limited set of annotated keypoints and auto-generated segmentation masks of body parts. Evaluations show that our model is capable of detecting keypoints on the head, torso, hands, feet, arms, and legs, including also bent elbows and knees. We analyze and compare different techniques to encode desired keypoints as the model's input and their embedding for the Transformer backbone.

We introduce a new method for learning a generative model of articulated 3D animal motions from raw, unlabeled online videos. Unlike existing approaches for 3D motion synthesis, our model requires no pose annotations or parametric shape models for training; it learns purely from a collection of unlabeled web video clips, leveraging semantic correspondences distilled from self-supervised image features. At the core of our method is a video Photo-Geometric Auto-Encoding framework that decomposes each training video clip into a set of explicit geometric and photometric representations, including a rest-pose 3D shape, an articulated pose sequence, and texture, with the objective of re-rendering the input video via a differentiable renderer. This decomposition allows us to learn a generative model over the underlying articulated pose sequences akin to a Variational Auto-Encoding (VAE) formulation, but without requiring any external pose annotations. At inference time, we can generate new motion sequences by sampling from the learned motion VAE, and create plausible 4D animations of an animal automatically within seconds given a single input image.

Context-augmented generation (CAG) techniques, including RAG and ICL, require the efficient combination of multiple contexts to generate responses to user queries. Directly inputting these contexts as a sequence introduces a considerable computational burden by re-encoding the combined selection of contexts for every request. To address this, we explore the promising potential of parallel encoding to independently pre-compute and cache each context's KV states. This approach enables the direct loading of cached states during inference while accommodating more contexts through position reuse across contexts. However, due to misalignments in attention distribution, directly applying parallel encoding results in a significant performance drop. To enable effective and efficient CAG, we propose Adaptive Parallel Encoding (APE), which brings shared prefix, attention temperature, and scaling factor to align the distribution of parallel encoding with sequential encoding. Results on RAG and ICL tasks demonstrate that APE can preserve 98% and 93% sequential encoding performance using the same inputs while outperforming parallel encoding by 3.6% and 7.9%, respectively. It also scales to many-shot CAG, effectively encoding hundreds of contexts in parallel. Efficiency evaluation shows that APE can achieve an end-to-end 4.5times speedup by reducing 28times prefilling time for a 128K-length context.

Recent advancements in diffusion models (DMs) have been propelled by alignment methods that post-train models to better conform to human preferences. However, these approaches typically require computation-intensive training of a base model and a reward model, which not only incurs substantial computational overhead but may also compromise model accuracy and training efficiency. To address these limitations, we propose Inversion-DPO, a novel alignment framework that circumvents reward modeling by reformulating Direct Preference Optimization (DPO) with DDIM inversion for DMs. Our method conducts intractable posterior sampling in Diffusion-DPO with the deterministic inversion from winning and losing samples to noise and thus derive a new post-training paradigm. This paradigm eliminates the need for auxiliary reward models or inaccurate appromixation, significantly enhancing both precision and efficiency of training. We apply Inversion-DPO to a basic task of text-to-image generation and a challenging task of compositional image generation. Extensive experiments show substantial performance improvements achieved by Inversion-DPO compared to existing post-training methods and highlight the ability of the trained generative models to generate high-fidelity compositionally coherent images. For the post-training of compostitional image geneation, we curate a paired dataset consisting of 11,140 images with complex structural annotations and comprehensive scores, designed to enhance the compositional capabilities of generative models. Inversion-DPO explores a new avenue for efficient, high-precision alignment in diffusion models, advancing their applicability to complex realistic generation tasks. Our code is available at https://github.com/MIGHTYEZ/Inversion-DPO

Masked image modelling (MIM) is a powerful self-supervised representation learning paradigm, whose potential has not been widely demonstrated in medical image analysis. In this work, we show the capacity of MIM to capture rich semantic representations of Haemotoxylin & Eosin (H&E)-stained images at the nuclear level. Inspired by Bidirectional Encoder representation from Image Transformers (BEiT), we split the images into smaller patches and generate corresponding discrete visual tokens. In addition to the regular grid-based patches, typically used in visual Transformers, we introduce patches of individual cell nuclei. We propose positional encoding of the irregular distribution of these structures within an image. We pre-train the model in a self-supervised manner on H&E-stained whole-slide images of diffuse large B-cell lymphoma, where cell nuclei have been segmented. The pre-training objective is to recover the original discrete visual tokens of the masked image on the one hand, and to reconstruct the visual tokens of the masked object instances on the other. Coupling these two pre-training tasks allows us to build powerful, context-aware representations of nuclei. Our model generalizes well and can be fine-tuned on downstream classification tasks, achieving improved cell classification accuracy on PanNuke dataset by more than 5% compared to current instance segmentation methods.

Data used for analytics and machine learning often take the form of tables with categorical entries. We introduce a family of lossless compression algorithms for such data that proceed in four steps: (i) Estimate latent variables associated to rows and columns; (ii) Partition the table in blocks according to the row/column latents; (iii) Apply a sequential (e.g. Lempel-Ziv) coder to each of the blocks; (iv) Append a compressed encoding of the latents. We evaluate it on several benchmark datasets, and study optimal compression in a probabilistic model for that tabular data, whereby latent values are independent and table entries are conditionally independent given the latent values. We prove that the model has a well defined entropy rate and satisfies an asymptotic equipartition property. We also prove that classical compression schemes such as Lempel-Ziv and finite-state encoders do not achieve this rate. On the other hand, the latent estimation strategy outlined above achieves the optimal rate.

Large-scale pre-trained language models, such as BERT and GPT-2, have achieved excellent performance in language representation learning and free-form text generation. However, these models cannot be directly employed to generate text under specified lexical constraints. To address this challenge, we present POINTER (PrOgressive INsertion-based TransformER), a simple yet novel insertion-based approach for hard-constrained text generation. The proposed method operates by progressively inserting new tokens between existing tokens in a parallel manner. This procedure is recursively applied until a sequence is completed. The resulting coarse-to-fine hierarchy makes the generation process intuitive and interpretable. We pre-train our model with the proposed progressive insertion-based objective on a 12GB Wikipedia dataset, and fine-tune it on downstream hard-constrained generation tasks. Non-autoregressive decoding yields an empirically logarithmic time complexity during inference time. Experimental results on both News and Yelp datasets demonstrate that POINTER achieves state-of-the-art performance on constrained text generation. We released the pre-trained models and the source code to facilitate future research (https://github.com/dreasysnail/POINTER).

Sample-and-rank is a key decoding strategy for modern generation-based dialogue systems. It helps achieve diverse and high-quality responses by selecting an answer from a small pool of generated candidates. The current state-of-the-art ranking methods mainly use an encoding paradigm called Cross-Encoder, which separately encodes each context-candidate pair and ranks the candidates according to their fitness scores. However, Cross-Encoder repeatedly encodes the same lengthy context for each candidate, resulting in high computational costs. Poly-Encoder addresses the above problems by reducing the interaction between context and candidates, but with a price of performance drop. In this work, we develop a new paradigm called Uni-Encoder, that keeps the full attention over each pair as in Cross-Encoder while only encoding the context once, as in Poly-Encoder. Uni-Encoder encodes all the candidates with the context in one forward pass. We use the same positional embedding for all candidates to ensure they are treated equally and design a new attention mechanism to avoid confusion. Our Uni-Encoder can simulate other ranking paradigms using different attention and response concatenation methods. Extensive experiments show that our proposed paradigm achieves new state-of-the-art results on four benchmark datasets with high computational efficiency. For instance, it improves R10@1 by 2.9% with an approximately 4X faster inference speed on the Ubuntu V2 dataset.

Transformer architectures rely on explicit position encodings in order to preserve a notion of word order. In this paper, we argue that existing work does not fully utilize position information. For example, the initial proposal of a sinusoid embedding is fixed and not learnable. In this paper, we first review absolute position embeddings and existing methods for relative position embeddings. We then propose new techniques that encourage increased interaction between query, key and relative position embeddings in the self-attention mechanism. Our most promising approach is a generalization of the absolute position embedding, improving results on SQuAD1.1 compared to previous position embeddings approaches. In addition, we address the inductive property of whether a position embedding can be robust enough to handle long sequences. We demonstrate empirically that our relative position embedding method is reasonably generalized and robust from the inductive perspective. Finally, we show that our proposed method can be adopted as a near drop-in replacement for improving the accuracy of large models with a small computational budget.

Decoding the linguistic intricacies of the genome is a crucial problem in biology, and pre-trained foundational models such as DNABERT and Nucleotide Transformer have made significant strides in this area. Existing works have largely hinged on k-mer, fixed-length permutations of A, T, C, and G, as the token of the genome language due to its simplicity. However, we argue that the computation and sample inefficiencies introduced by k-mer tokenization are primary obstacles in developing large genome foundational models. We provide conceptual and empirical insights into genome tokenization, building on which we propose to replace k-mer tokenization with Byte Pair Encoding (BPE), a statistics-based data compression algorithm that constructs tokens by iteratively merging the most frequent co-occurring genome segment in the corpus. We demonstrate that BPE not only overcomes the limitations of k-mer tokenization but also benefits from the computational efficiency of non-overlapping tokenization. Based on these insights, we introduce DNABERT-2, a refined genome foundation model that adapts an efficient tokenizer and employs multiple strategies to overcome input length constraints, reduce time and memory expenditure, and enhance model capability. Furthermore, we identify the absence of a comprehensive and standardized benchmark for genome understanding as another significant impediment to fair comparative analysis. In response, we propose the Genome Understanding Evaluation (GUE), a comprehensive multi-species genome classification dataset that amalgamates 28 distinct datasets across 7 tasks, with input lengths ranging from 70 to 1000. Through comprehensive experiments on the GUE benchmark, we demonstrate that DNABERT-2 achieves comparable performance to the state-of-the-art model with 21 times fewer parameters and approximately 56 times less GPU time in pre-training.

Diffusion models, such as Stable Diffusion, have made significant strides in visual generation, yet their paradigm remains fundamentally different from autoregressive language models, complicating the development of unified language-vision models. Recent efforts like LlamaGen have attempted autoregressive image generation using discrete VQVAE tokens, but the large number of tokens involved renders this approach inefficient and slow. In this work, we present Meissonic, which elevates non-autoregressive masked image modeling (MIM) text-to-image to a level comparable with state-of-the-art diffusion models like SDXL. By incorporating a comprehensive suite of architectural innovations, advanced positional encoding strategies, and optimized sampling conditions, Meissonic substantially improves MIM's performance and efficiency. Additionally, we leverage high-quality training data, integrate micro-conditions informed by human preference scores, and employ feature compression layers to further enhance image fidelity and resolution. Our model not only matches but often exceeds the performance of existing models like SDXL in generating high-quality, high-resolution images. Extensive experiments validate Meissonic's capabilities, demonstrating its potential as a new standard in text-to-image synthesis. We release a model checkpoint capable of producing 1024 times 1024 resolution images.

Large foundation models have recently emerged as a prominent focus of interest, attaining superior performance in widespread scenarios. Due to the scarcity of 3D data, many efforts have been made to adapt pre-trained transformers from vision to 3D domains. However, such 2D-to-3D approaches are still limited, due to the potential loss of spatial geometries and high computation cost. More importantly, their frameworks are mainly designed for 2D models, lacking a general any-to-3D paradigm. In this paper, we introduce Any2Point, a parameter-efficient method to empower any-modality large models (vision, language, audio) for 3D understanding. Given a frozen transformer from any source modality, we propose a 3D-to-any (1D or 2D) virtual projection strategy that correlates the input 3D points to the original 1D or 2D positions within the source modality. This mechanism enables us to assign each 3D token with a positional encoding paired with the pre-trained model, which avoids 3D geometry loss caused by the true projection and better motivates the transformer for 3D learning with 1D/2D positional priors. Then, within each transformer block, we insert an any-to-3D guided adapter module for parameter-efficient fine-tuning. The adapter incorporates prior spatial knowledge from the source modality to guide the local feature aggregation of 3D tokens, compelling the semantic adaption of any-modality transformers. We conduct extensive experiments to showcase the effectiveness and efficiency of our method. Code and models are released at https://github.com/Ivan-Tang-3D/Any2Point.

Large Language Models (LLMs) are increasingly applied in various real-world scenarios due to their excellent generalization capabilities and robust generative abilities. However, they exhibit position bias, also known as "lost in the middle", a phenomenon that is especially pronounced in long-context scenarios, which indicates the placement of the key information in different positions of a prompt can significantly affect accuracy. This paper first explores the micro-level manifestations of position bias, concluding that attention weights are a micro-level expression of position bias. It further identifies that, in addition to position embeddings, causal attention mask also contributes to position bias by creating position-specific hidden states. Based on these insights, we propose a method to mitigate position bias by scaling this positional hidden states. Experiments on the NaturalQuestions Multi-document QA, KV retrieval, LongBench and timeline reorder tasks, using various models including RoPE models, context windowextended models, and Alibi models, demonstrate the effectiveness and generalizability of our approach. Our method can improve performance by up to 15.2% by modifying just one dimension of hidden states. Our code is available at https://aka.ms/PositionalHidden.

We propose a new method for solving imaging inverse problems using text-to-image latent diffusion models as general priors. Existing methods using latent diffusion models for inverse problems typically rely on simple null text prompts, which can lead to suboptimal performance. To address this limitation, we introduce a method for prompt tuning, which jointly optimizes the text embedding on-the-fly while running the reverse diffusion process. This allows us to generate images that are more faithful to the diffusion prior. In addition, we propose a method to keep the evolution of latent variables within the range space of the encoder, by projection. This helps to reduce image artifacts, a major problem when using latent diffusion models instead of pixel-based diffusion models. Our combined method, called P2L, outperforms both image- and latent-diffusion model-based inverse problem solvers on a variety of tasks, such as super-resolution, deblurring, and inpainting.

Advancements in DNA sequencing technologies have significantly improved our ability to decode genomic sequences. However, the prediction and interpretation of these sequences remain challenging due to the intricate nature of genetic material. Large language models (LLMs) have introduced new opportunities for biological sequence analysis. Recent developments in genomic language models have underscored the potential of LLMs in deciphering DNA sequences. Nonetheless, existing models often face limitations in robustness and application scope, primarily due to constraints in model structure and training data scale. To address these limitations, we present GENERator, a generative genomic foundation model featuring a context length of 98k base pairs (bp) and 1.2B parameters. Trained on an expansive dataset comprising 386B bp of eukaryotic DNA, the GENERator demonstrates state-of-the-art performance across both established and newly proposed benchmarks. The model adheres to the central dogma of molecular biology, accurately generating protein-coding sequences that translate into proteins structurally analogous to known families. It also shows significant promise in sequence optimization, particularly through the prompt-responsive generation of promoter sequences with specific activity profiles. These capabilities position the GENERator as a pivotal tool for genomic research and biotechnological advancement, enhancing our ability to interpret and predict complex biological systems and enabling precise genomic interventions.

We investigate the CLIP image encoder by analyzing how individual model components affect the final representation. We decompose the image representation as a sum across individual image patches, model layers, and attention heads, and use CLIP's text representation to interpret the summands. Interpreting the attention heads, we characterize each head's role by automatically finding text representations that span its output space, which reveals property-specific roles for many heads (e.g. location or shape). Next, interpreting the image patches, we uncover an emergent spatial localization within CLIP. Finally, we use this understanding to remove spurious features from CLIP and to create a strong zero-shot image segmenter. Our results indicate that a scalable understanding of transformer models is attainable and can be used to repair and improve models.

Recently, there has been a surge in the popularity of pre trained large language models (LLMs) (such as GPT-4), sweeping across the entire Natural Language Processing (NLP) and Computer Vision (CV) communities. These LLMs have demonstrated advanced multi-modal understanding capabilities and showcased strong performance across various benchmarks. The LLM has started to embody traits of artificial general intelligence, which holds vital guidance for enhancing brain-like characteristics within visual encoding models. Hence, This paper proposes a new multi-modal training paradigm, aligning with LLM, for encoding fMRI activity in visual cortex. Based on this paradigm, we trained an encoding model in fMRI data named the LLM-Visual Encoding Model (LLM-VEM). Specifically, we utilize LLM (miniGPT4) to generate descriptive text for all stimulus images, forming a high-quality textual description set. Moreover, we use the pre-trained text encoder (CLIP) to process these detailed descriptions, obtaining the text embedding features. Next, we use the contrast loss function to minimize the distance between the image embedding features and the text embedding features to complete the alignment operation of the stimulus image and text information. With the assistance of the pre-trained LLM, this alignment process facilitates better learning of the visual encoding model, resulting in higher precision. The final experimental results indicate that our training paradigm has significantly aided in enhancing the performance of the visual encoding model.

The genome sequence contains the blueprint for governing cellular processes. While the availability of genomes has vastly increased over the last decades, experimental annotation of the various functional, non-coding and regulatory elements encoded in the DNA sequence remains both expensive and challenging. This has sparked interest in unsupervised language modeling of genomic DNA, a paradigm that has seen great success for protein sequence data. Although various DNA language models have been proposed, evaluation tasks often differ between individual works, and might not fully recapitulate the fundamental challenges of genome annotation, including the length, scale and sparsity of the data. In this study, we introduce BEND, a Benchmark for DNA language models, featuring a collection of realistic and biologically meaningful downstream tasks defined on the human genome. We find that embeddings from current DNA LMs can approach performance of expert methods on some tasks, but only capture limited information about long-range features. BEND is available at https://github.com/frederikkemarin/BEND.

Genomic (DNA) sequences encode an enormous amount of information for gene regulation and protein synthesis. Similar to natural language models, researchers have proposed foundation models in genomics to learn generalizable features from unlabeled genome data that can then be fine-tuned for downstream tasks such as identifying regulatory elements. Due to the quadratic scaling of attention, previous Transformer-based genomic models have used 512 to 4k tokens as context (<0.001% of the human genome), significantly limiting the modeling of long-range interactions in DNA. In addition, these methods rely on tokenizers to aggregate meaningful DNA units, losing single nucleotide resolution where subtle genetic variations can completely alter protein function via single nucleotide polymorphisms (SNPs). Recently, Hyena, a large language model based on implicit convolutions was shown to match attention in quality while allowing longer context lengths and lower time complexity. Leveraging Hyenas new long-range capabilities, we present HyenaDNA, a genomic foundation model pretrained on the human reference genome with context lengths of up to 1 million tokens at the single nucleotide-level, an up to 500x increase over previous dense attention-based models. HyenaDNA scales sub-quadratically in sequence length (training up to 160x faster than Transformer), uses single nucleotide tokens, and has full global context at each layer. We explore what longer context enables - including the first use of in-context learning in genomics for simple adaptation to novel tasks without updating pretrained model weights. On fine-tuned benchmarks from the Nucleotide Transformer, HyenaDNA reaches state-of-the-art (SotA) on 12 of 17 datasets using a model with orders of magnitude less parameters and pretraining data. On the GenomicBenchmarks, HyenaDNA surpasses SotA on all 8 datasets on average by +9 accuracy points.

Large Language Models (LLMs) have shown remarkable adaptability across domains beyond text, specifically electrocardiograms (ECGs). More specifically, there is a growing body of work exploring the task of generating text from a multi-channeled ECG and corresponding textual prompt. Current approaches typically involve pretraining an ECG-specific encoder with a self-supervised learning (SSL) objective and using the features output by the pretrained encoder to finetune a LLM for natural language generation (NLG). However, these methods are limited by 1) inefficiency from two-stage training and 2) interpretability challenges with encoder-generated features. To address these limitations, we introduce ECG-Byte, an adapted byte pair encoding (BPE) tokenizer pipeline for autoregressive language modeling of ECGs. This approach compresses and encodes ECG signals into tokens, enabling end-to-end LLM training by combining ECG and text tokens directly, while being much more interpretable since the ECG tokens can be directly mapped back to the original signal. Using ECG-Byte, we achieve competitive performance in NLG tasks in only half the time and ~48% of the data required by two-stage approaches.

Large Language Models (LLMs) are known to have limited extrapolation ability beyond their pre-trained context window, constraining their application in downstream tasks with lengthy inputs. Recent studies have sought to extend LLMs' context window by modifying rotary position embedding (RoPE), a popular position encoding method adopted by well-known LLMs such as LLaMA, PaLM, and GPT-NeoX. However, prior works like Position Interpolation (PI) and YaRN are resource-intensive and lack comparative experiments to assess their applicability. In this work, we identify the inherent need for LLMs' attention entropy (i.e. the information entropy of attention scores) to maintain stability and introduce a novel extension to RoPE which combines adjusting RoPE's base frequency and scaling the attention logits to help LLMs efficiently adapt to a larger context window. We validate the superiority of our method in both fine-tuning performance and robustness across different context window sizes on various context-demanding tasks. Notably, our method extends the context window of LLaMA-2-7B-Chat to 16,384 with only 100 samples and 6 training steps, showcasing extraordinary efficiency. Finally, we also explore how data compositions and training curricula affect context window extension for specific downstream tasks, suggesting fine-tuning LLMs with lengthy conversations as a good starting point. We release our code and SFT data at https://github.com/GAIR-NLP/Entropy-ABF.

Addressing the limitation of context length in large language models for code-related tasks is the primary focus of this paper. Existing LLMs are constrained by their pre-trained context lengths, leading to performance issues in handling long complex code sequences. Inspired by how human programmers navigate code, we introduce Hierarchical Rotary Position Embedding (HiRoPE), a novel approach that enhances the traditional rotary position embedding into a hierarchical format based on the hierarchical structure of source code. HiRoPE offers easy integration into existing LLMs without extra training costs. Our method is extensively evaluated with various LLMs, demonstrating stable performance in tasks such as language modeling and long code completion. We also introduce a new long code understanding task with real-world code projects, in hopes of promoting further development in this code-related field. Theoretically and experimentally, we find that HiRoPE also addresses the out-of-distribution issue in position encoding. Our HiRoPE significantly expands the context length capabilities of LLMs, enabling inference at lengths exponentially greater than the training length.

Pre-trained language models (PLMs) that use subword tokenization schemes can succeed at a variety of language tasks that require character-level information, despite lacking explicit access to the character composition of tokens. Here, studying a range of models (e.g., GPT- J, BERT, RoBERTa, GloVe), we probe what word pieces encode about character-level information by training classifiers to predict the presence or absence of a particular alphabetical character in a token, based on its embedding (e.g., probing whether the model embedding for "cat" encodes that it contains the character "a"). We find that these models robustly encode character-level information and, in general, larger models perform better at the task. We show that these results generalize to characters from non-Latin alphabets (Arabic, Devanagari, and Cyrillic). Then, through a series of experiments and analyses, we investigate the mechanisms through which PLMs acquire English-language character information during training and argue that this knowledge is acquired through multiple phenomena, including a systematic relationship between particular characters and particular parts of speech, as well as natural variability in the tokenization of related strings.

Implicit neural representations store videos as neural networks and have performed well for various vision tasks such as video compression and denoising. With frame index or positional index as input, implicit representations (NeRV, E-NeRV, \etc) reconstruct video from fixed and content-agnostic embeddings. Such embedding largely limits the regression capacity and internal generalization for video interpolation. In this paper, we propose a Hybrid Neural Representation for Videos (HNeRV), where a learnable encoder generates content-adaptive embeddings, which act as the decoder input. Besides the input embedding, we introduce HNeRV blocks, which ensure model parameters are evenly distributed across the entire network, such that higher layers (layers near the output) can have more capacity to store high-resolution content and video details. With content-adaptive embeddings and re-designed architecture, HNeRV outperforms implicit methods in video regression tasks for both reconstruction quality (+4.7 PSNR) and convergence speed (16times faster), and shows better internal generalization. As a simple and efficient video representation, HNeRV also shows decoding advantages for speed, flexibility, and deployment, compared to traditional codecs~(H.264, H.265) and learning-based compression methods. Finally, we explore the effectiveness of HNeRV on downstream tasks such as video compression and video inpainting. We provide project page at https://haochen-rye.github.io/HNeRV, and Code at https://github.com/haochen-rye/HNeRV

This paper introduces a novel framework for DNA sequence generation, comprising two key components: DiscDiff, a Latent Diffusion Model (LDM) tailored for generating discrete DNA sequences, and Absorb-Escape, a post-training algorithm designed to refine these sequences. Absorb-Escape enhances the realism of the generated sequences by correcting `round errors' inherent in the conversion process between latent and input spaces. Our approach not only sets new standards in DNA sequence generation but also demonstrates superior performance over existing diffusion models, in generating both short and long DNA sequences. Additionally, we introduce EPD-GenDNA, the first comprehensive, multi-species dataset for DNA generation, encompassing 160,000 unique sequences from 15 species. We hope this study will advance the generative modelling of DNA, with potential implications for gene therapy and protein production.

This study presents Latent Diffusion Autoencoder (LDAE), a novel encoder-decoder diffusion-based framework for efficient and meaningful unsupervised learning in medical imaging, focusing on Alzheimer disease (AD) using brain MR from the ADNI database as a case study. Unlike conventional diffusion autoencoders operating in image space, LDAE applies the diffusion process in a compressed latent representation, improving computational efficiency and making 3D medical imaging representation learning tractable. To validate the proposed approach, we explore two key hypotheses: (i) LDAE effectively captures meaningful semantic representations on 3D brain MR associated with AD and ageing, and (ii) LDAE achieves high-quality image generation and reconstruction while being computationally efficient. Experimental results support both hypotheses: (i) linear-probe evaluations demonstrate promising diagnostic performance for AD (ROC-AUC: 90%, ACC: 84%) and age prediction (MAE: 4.1 years, RMSE: 5.2 years); (ii) the learned semantic representations enable attribute manipulation, yielding anatomically plausible modifications; (iii) semantic interpolation experiments show strong reconstruction of missing scans, with SSIM of 0.969 (MSE: 0.0019) for a 6-month gap. Even for longer gaps (24 months), the model maintains robust performance (SSIM > 0.93, MSE < 0.004), indicating an ability to capture temporal progression trends; (iv) compared to conventional diffusion autoencoders, LDAE significantly increases inference throughput (20x faster) while also enhancing reconstruction quality. These findings position LDAE as a promising framework for scalable medical imaging applications, with the potential to serve as a foundation model for medical image analysis. Code available at https://github.com/GabrieleLozupone/LDAE

Rotary Position Embedding (RoPE) enables each attention head to capture multi-frequency information along the sequence dimension and is widely applied in foundation models. However, the nonlinearity introduced by RoPE complicates optimization of the key state in the Key-Value (KV) cache for RoPE-based attention. Existing KV cache compression methods typically store key state before rotation and apply the transformation during decoding, introducing additional computational overhead. This paper introduces EliteKV, a flexible modification framework for RoPE-based models supporting variable KV cache compression ratios. EliteKV first identifies the intrinsic frequency preference of each head using RoPElite, selectively restoring linearity to certain dimensions of key within attention computation. Building on this, joint low-rank compression of key and value enables partial cache sharing. Experimental results show that with minimal uptraining on only 0.6% of the original training data, RoPE-based models achieve a 75% reduction in KV cache size while preserving performance within a negligible margin. Furthermore, EliteKV consistently performs well across models of different scales within the same family.

Recent studies have introduced a new class of generative models for synthesizing implicit neural representations (INRs) that capture arbitrary continuous signals in various domains. These models opened the door for domain-agnostic generative models, but they often fail to achieve high-quality generation. We observed that the existing methods generate the weights of neural networks to parameterize INRs and evaluate the network with fixed positional embeddings (PEs). Arguably, this architecture limits the expressive power of generative models and results in low-quality INR generation. To address this limitation, we propose Domain-agnostic Latent Diffusion Model for INRs (DDMI) that generates adaptive positional embeddings instead of neural networks' weights. Specifically, we develop a Discrete-to-continuous space Variational AutoEncoder (D2C-VAE), which seamlessly connects discrete data and the continuous signal functions in the shared latent space. Additionally, we introduce a novel conditioning mechanism for evaluating INRs with the hierarchically decomposed PEs to further enhance expressive power. Extensive experiments across four modalities, e.g., 2D images, 3D shapes, Neural Radiance Fields, and videos, with seven benchmark datasets, demonstrate the versatility of DDMI and its superior performance compared to the existing INR generative models.

mRNA-based vaccines have become a major focus in the pharmaceutical industry. The coding sequence as well as the Untranslated Regions (UTRs) of an mRNA can strongly influence translation efficiency, stability, degradation, and other factors that collectively determine a vaccine's effectiveness. However, optimizing mRNA sequences for those properties remains a complex challenge. Existing deep learning models often focus solely on coding region optimization, overlooking the UTRs. We present Helix-mRNA, a structured state-space-based and attention hybrid model to address these challenges. In addition to a first pre-training, a second pre-training stage allows us to specialise the model with high-quality data. We employ single nucleotide tokenization of mRNA sequences with codon separation, ensuring prior biological and structural information from the original mRNA sequence is not lost. Our model, Helix-mRNA, outperforms existing methods in analysing both UTRs and coding region properties. It can process sequences 6x longer than current approaches while using only 10% of the parameters of existing foundation models. Its predictive capabilities extend to all mRNA regions. We open-source the model (https://github.com/helicalAI/helical) and model weights (https://huggingface.co/helical-ai/helix-mRNA).

Commonly-used transformer language models depend on a tokenization schema which sets an unchangeable subword vocabulary prior to pre-training, destined to be applied to all downstream tasks regardless of domain shift, novel word formations, or other sources of vocabulary mismatch. Recent work has shown that "token-free" models can be trained directly on characters or bytes, but training these models from scratch requires substantial computational resources, and this implies discarding the many domain-specific models that were trained on tokens. In this paper, we present XRayEmb, a method for retrofitting existing token-based models with character-level information. XRayEmb is composed of a character-level "encoder" that computes vector representations of character sequences, and a generative component that decodes from the internal representation to a character sequence. We show that incorporating XRayEmb's learned vectors into sequences of pre-trained token embeddings helps performance on both autoregressive and masked pre-trained transformer architectures and on both sequence-level and sequence tagging tasks, particularly on non-standard English text.

In this paper, we present CAD2Program, a new method for reconstructing 3D parametric models from 2D CAD drawings. Our proposed method is inspired by recent successes in vision-language models (VLMs), and departs from traditional methods which rely on task-specific data representations and/or algorithms. Specifically, on the input side, we simply treat the 2D CAD drawing as a raster image, regardless of its original format, and encode the image with a standard ViT model. We show that such an encoding scheme achieves competitive performance against existing methods that operate on vector-graphics inputs, while imposing substantially fewer restrictions on the 2D drawings. On the output side, our method auto-regressively predicts a general-purpose language describing 3D parametric models in text form. Compared to other sequence modeling methods for CAD which use domain-specific sequence representations with fixed-size slots, our text-based representation is more flexible, and can be easily extended to arbitrary geometric entities and semantic or functional properties. Experimental results on a large-scale dataset of cabinet models demonstrate the effectiveness of our method.

We introduce Brain-JEPA, a brain dynamics foundation model with the Joint-Embedding Predictive Architecture (JEPA). This pioneering model achieves state-of-the-art performance in demographic prediction, disease diagnosis/prognosis, and trait prediction through fine-tuning. Furthermore, it excels in off-the-shelf evaluations (e.g., linear probing) and demonstrates superior generalizability across different ethnic groups, surpassing the previous large model for brain activity significantly. Brain-JEPA incorporates two innovative techniques: Brain Gradient Positioning and Spatiotemporal Masking. Brain Gradient Positioning introduces a functional coordinate system for brain functional parcellation, enhancing the positional encoding of different Regions of Interest (ROIs). Spatiotemporal Masking, tailored to the unique characteristics of fMRI data, addresses the challenge of heterogeneous time-series patches. These methodologies enhance model performance and advance our understanding of the neural circuits underlying cognition. Overall, Brain-JEPA is paving the way to address pivotal questions of building brain functional coordinate system and masking brain activity at the AI-neuroscience interface, and setting a potentially new paradigm in brain activity analysis through downstream adaptation.

The assumption across nearly all language model (LM) tokenization schemes is that tokens should be subwords, i.e., contained within word boundaries. While providing a seemingly reasonable inductive bias, is this common practice limiting the potential of modern LMs? Whitespace is not a reliable delimiter of meaning, as evidenced by multi-word expressions (e.g., "by the way"), crosslingual variation in the number of words needed to express a concept (e.g., "spacesuit helmet" in German is "raumanzughelm"), and languages that do not use whitespace at all (e.g., Chinese). To explore the potential of tokenization beyond subwords, we introduce a "superword" tokenizer, SuperBPE, which incorporates a simple pretokenization curriculum into the byte-pair encoding (BPE) algorithm to first learn subwords, then superwords that bridge whitespace. This brings dramatic improvements in encoding efficiency: when fixing the vocabulary size to 200k, SuperBPE encodes a fixed piece of text with up to 33% fewer tokens than BPE on average. In experiments, we pretrain 8B transformer LMs from scratch while fixing the model size, vocabulary size, and train compute, varying *only* the algorithm for learning the vocabulary. Our model trained with SuperBPE achieves an average +4.0% absolute improvement over the BPE baseline across 30 downstream tasks (including +8.2% on MMLU), while simultaneously requiring 27% less compute at inference time. In analysis, we find that SuperBPE results in segmentations of text that are more uniform in per-token difficulty. Qualitatively, this may be because SuperBPE tokens often capture common multi-word expressions that function semantically as a single unit. SuperBPE is a straightforward, local modification to tokenization that improves both encoding efficiency and downstream performance, yielding better language models overall.

Existing codecs are designed to eliminate intrinsic redundancies to create a compact representation for compression. However, strong external priors from Multimodal Large Language Models (MLLMs) have not been explicitly explored in video compression. Herein, we introduce a unified paradigm for Cross-Modality Video Coding (CMVC), which is a pioneering approach to explore multimodality representation and video generative models in video coding. Specifically, on the encoder side, we disentangle a video into spatial content and motion components, which are subsequently transformed into distinct modalities to achieve very compact representation by leveraging MLLMs. During decoding, previously encoded components and video generation models are leveraged to create multiple encoding-decoding modes that optimize video reconstruction quality for specific decoding requirements, including Text-Text-to-Video (TT2V) mode to ensure high-quality semantic information and Image-Text-to-Video (IT2V) mode to achieve superb perceptual consistency. In addition, we propose an efficient frame interpolation model for IT2V mode via Low-Rank Adaption (LoRA) tuning to guarantee perceptual quality, which allows the generated motion cues to behave smoothly. Experiments on benchmarks indicate that TT2V achieves effective semantic reconstruction, while IT2V exhibits competitive perceptual consistency. These results highlight potential directions for future research in video coding.

Recent advancements in video generation have enabled models to synthesize high-quality, minute-long videos. However, generating even longer videos with temporal coherence remains a major challenge, and existing length extrapolation methods lead to temporal repetition or motion deceleration. In this work, we systematically analyze the role of frequency components in positional embeddings and identify an intrinsic frequency that primarily governs extrapolation behavior. Based on this insight, we propose RIFLEx, a minimal yet effective approach that reduces the intrinsic frequency to suppress repetition while preserving motion consistency, without requiring any additional modifications. RIFLEx offers a true free lunch--achieving high-quality 2times extrapolation on state-of-the-art video diffusion transformers in a completely training-free manner. Moreover, it enhances quality and enables 3times extrapolation by minimal fine-tuning without long videos. Project page and codes: https://riflex-video.github.io/{https://riflex-video.github.io/.}

Inspired by the success of unsupervised pre-training paradigms, researchers have applied these approaches to DNA pre-training. However, we argue that these approaches alone yield suboptimal results because pure DNA sequences lack sufficient information, since their functions are regulated by genomic profiles like chromatin accessibility. Here, we demonstrate that supervised training for genomic profile prediction serves as a more effective alternative to pure sequence pre-training. Furthermore, considering the multi-species and multi-profile nature of genomic profile prediction, we introduce our Species-Profile Adaptive Collaborative Experts (SPACE) that leverages Mixture of Experts (MoE) to better capture the relationships between DNA sequences across different species and genomic profiles, thereby learning more effective DNA representations. Through extensive experiments across various tasks, our model achieves state-of-the-art performance, establishing that DNA models trained with supervised genomic profiles serve as powerful DNA representation learners. The code is available at https://github.com/ZhuJiwei111/SPACE.

The abilities to perceive, learn, and use generalities, similarities, classes, i.e., semantic memory (SM), is central to cognition. Machine learning (ML), neural network, and AI research has been primarily driven by tasks requiring such abilities. However, another central facet of cognition, single-trial formation of permanent memories of experiences, i.e., episodic memory (EM), has had relatively little focus. Only recently has EM-like functionality been added to Deep Learning (DL) models, e.g., Neural Turing Machine, Memory Networks. However, in these cases: a) EM is implemented as a separate module, which entails substantial data movement (and so, time and power) between the DL net itself and EM; and b) individual items are stored localistically within the EM, precluding realizing the exponential representational efficiency of distributed over localist coding. We describe Sparsey, an unsupervised, hierarchical, spatial/spatiotemporal associative memory model differing fundamentally from mainstream ML models, most crucially, in its use of sparse distributed representations (SDRs), or, cell assemblies, which admits an extremely efficient, single-trial learning algorithm that maps input similarity into code space similarity (measured as intersection). SDRs of individual inputs are stored in superposition and because similarity is preserved, the patterns of intersections over the assigned codes reflect the similarity, i.e., statistical, structure, of all orders, not simply pairwise, over the inputs. Thus, SM, i.e., a generative model, is built as a computationally free side effect of the act of storing episodic memory traces of individual inputs, either spatial patterns or sequences. We report initial results on MNIST and on the Weizmann video event recognition benchmarks. While we have not yet attained SOTA class accuracy, learning takes only minutes on a single CPU.

With the recent advancements in single-image-based human mesh recovery, there is a growing interest in enhancing its performance in certain extreme scenarios, such as occlusion, while maintaining overall model accuracy. Although obtaining accurately annotated 3D human poses under occlusion is challenging, there is still a wealth of rich and precise 2D pose annotations that can be leveraged. However, existing works mostly focus on directly leveraging 2D pose coordinates to estimate 3D pose and mesh. In this paper, we present PostoMETRO(Pose token enhanced MEsh TRansfOrmer), which integrates occlusion-resilient 2D pose representation into transformers in a token-wise manner. Utilizing a specialized pose tokenizer, we efficiently condense 2D pose data to a compact sequence of pose tokens and feed them to the transformer together with the image tokens. This process not only ensures a rich depiction of texture from the image but also fosters a robust integration of pose and image information. Subsequently, these combined tokens are queried by vertex and joint tokens to decode 3D coordinates of mesh vertices and human joints. Facilitated by the robust pose token representation and the effective combination, we are able to produce more precise 3D coordinates, even under extreme scenarios like occlusion. Experiments on both standard and occlusion-specific benchmarks demonstrate the effectiveness of PostoMETRO. Qualitative results further illustrate the clarity of how 2D pose can help 3D reconstruction. Code will be made available.

Speculative decoding is an effective and lossless method for Large Language Model (LLM) inference acceleration. It employs a smaller model to generate a draft token sequence, which is then verified by the original base model. In multi-GPU systems, inference latency can be further reduced through tensor parallelism (TP), while the optimal TP size of the draft model is typically smaller than that of the base model, leading to GPU idling during the drafting stage. To solve this problem, we propose EasySpec, a layer-parallel speculation strategy that optimizes the efficiency of multi-GPU utilization.EasySpec breaks the sequential execution order of layers in the drafting model, enabling multi-layer parallelization across devices, albeit with some induced approximation errors. After each drafting-and-verification iteration, the draft model's key-value (KV) cache is calibrated in a single forward pass, preventing long-term error accumulation at minimal additional latency. We evaluated EasySpec on several mainstream open-source LLMs, using smaller versions of models from the same series as drafters. The results demonstrate that EasySpec can achieve a peak speedup of 4.17x compared to vanilla decoding, while preserving the original distribution of the base LLMs. Specifically, the drafting stage can be accelerated by up to 1.62x with a maximum accuracy drop of only 7%, requiring no training or fine-tuning on the draft models.

In healthcare, medical image segmentation is crucial for accurate disease diagnosis and the development of effective treatment strategies. Early detection can significantly aid in managing diseases and potentially prevent their progression. Machine learning, particularly deep convolutional neural networks, has emerged as a promising approach to addressing segmentation challenges. Traditional methods like U-Net use encoding blocks for local representation modeling and decoding blocks to uncover semantic relationships. However, these models often struggle with multi-scale objects exhibiting significant variations in texture and shape, and they frequently fail to capture long-range dependencies in the input data. Transformers designed for sequence-to-sequence predictions have been proposed as alternatives, utilizing global self-attention mechanisms. Yet, they can sometimes lack precise localization due to insufficient granular details. To overcome these limitations, we introduce TransDAE: a novel approach that reimagines the self-attention mechanism to include both spatial and channel-wise associations across the entire feature space, while maintaining computational efficiency. Additionally, TransDAE enhances the skip connection pathway with an inter-scale interaction module, promoting feature reuse and improving localization accuracy. Remarkably, TransDAE outperforms existing state-of-the-art methods on the Synaps multi-organ dataset, even without relying on pre-trained weights.

Recently, large language models (LLMs) have shown remarkable capabilities including understanding context, engaging in logical reasoning, and generating responses. However, this is achieved at the expense of stringent computational and memory requirements, hindering their ability to effectively support long input sequences. This survey provides an inclusive review of the recent techniques and methods devised to extend the sequence length in LLMs, thereby enhancing their capacity for long-context understanding. In particular, we review and categorize a wide range of techniques including architectural modifications, such as modified positional encoding and altered attention mechanisms, which are designed to enhance the processing of longer sequences while avoiding a proportional increase in computational requirements. The diverse methodologies investigated in this study can be leveraged across different phases of LLMs, i.e., training, fine-tuning and inference. This enables LLMs to efficiently process extended sequences. The limitations of the current methodologies is discussed in the last section along with the suggestions for future research directions, underscoring the importance of sequence length in the continued advancement of LLMs.

A critical component of a successful language generation pipeline is the decoding algorithm. However, the general principles that should guide the choice of decoding algorithm remain unclear. Previous works only compare decoding algorithms in narrow scenarios and their findings do not generalize across tasks. To better structure the discussion, we introduce a taxonomy that groups decoding strategies based on their implicit assumptions about how well the model's likelihood is aligned with the task-specific notion of utility. We argue that this taxonomy allows a broader view of the decoding problem and can lead to generalizable statements because it is grounded on the interplay between the decoding algorithms and the likelihood-utility misalignment. Specifically, by analyzing the correlation between the likelihood and the utility of predictions across a diverse set of tasks, we provide the first empirical evidence supporting the proposed taxonomy, and a set of principles to structure reasoning when choosing a decoding algorithm. Crucially, our analysis is the first one to relate likelihood-based decoding strategies with strategies that rely on external information such as value-guided methods and prompting, and covers the most diverse set of tasks up-to-date.

Encoder layer fusion (EncoderFusion) is a technique to fuse all the encoder layers (instead of the uppermost layer) for sequence-to-sequence (Seq2Seq) models, which has proven effective on various NLP tasks. However, it is still not entirely clear why and when EncoderFusion should work. In this paper, our main contribution is to take a step further in understanding EncoderFusion. Many of previous studies believe that the success of EncoderFusion comes from exploiting surface and syntactic information embedded in lower encoder layers. Unlike them, we find that the encoder embedding layer is more important than other intermediate encoder layers. In addition, the uppermost decoder layer consistently pays more attention to the encoder embedding layer across NLP tasks. Based on this observation, we propose a simple fusion method, SurfaceFusion, by fusing only the encoder embedding layer for the softmax layer. Experimental results show that SurfaceFusion outperforms EncoderFusion on several NLP benchmarks, including machine translation, text summarization, and grammatical error correction. It obtains the state-of-the-art performance on WMT16 Romanian-English and WMT14 English-French translation tasks. Extensive analyses reveal that SurfaceFusion learns more expressive bilingual word embeddings by building a closer relationship between relevant source and target embedding. Source code is freely available at https://github.com/SunbowLiu/SurfaceFusion.

The integration of Rotary Position Embedding (RoPE) in Multimodal Diffusion Transformer (MMDiT) has significantly enhanced text-to-image generation quality. However, the fundamental reliance of self-attention layers on positional embedding versus query-key similarity during generation remains an intriguing question. We present the first mechanistic analysis of RoPE-based MMDiT models (e.g., FLUX), introducing an automated probing strategy that disentangles positional information versus content dependencies by strategically manipulating RoPE during generation. Our analysis reveals distinct dependency patterns that do not straightforwardly correlate with depth, offering new insights into the layer-specific roles in RoPE-based MMDiT. Based on these findings, we propose a training-free, task-specific image editing framework that categorizes editing tasks into three types: position-dependent editing (e.g., object addition), content similarity-dependent editing (e.g., non-rigid editing), and region-preserved editing (e.g., background replacement). For each type, we design tailored key-value injection strategies based on the characteristics of the editing task. Extensive qualitative and quantitative evaluations demonstrate that our method outperforms state-of-the-art approaches, particularly in preserving original semantic content and achieving seamless modifications.

Whole-body pose estimation is a challenging task that requires simultaneous prediction of keypoints for the body, hands, face, and feet. Whole-body pose estimation aims to predict fine-grained pose information for the human body, including the face, torso, hands, and feet, which plays an important role in the study of human-centric perception and generation and in various applications. In this work, we present RTMW (Real-Time Multi-person Whole-body pose estimation models), a series of high-performance models for 2D/3D whole-body pose estimation. We incorporate RTMPose model architecture with FPN and HEM (Hierarchical Encoding Module) to better capture pose information from different body parts with various scales. The model is trained with a rich collection of open-source human keypoint datasets with manually aligned annotations and further enhanced via a two-stage distillation strategy. RTMW demonstrates strong performance on multiple whole-body pose estimation benchmarks while maintaining high inference efficiency and deployment friendliness. We release three sizes: m/l/x, with RTMW-l achieving a 70.2 mAP on the COCO-Wholebody benchmark, making it the first open-source model to exceed 70 mAP on this benchmark. Meanwhile, we explored the performance of RTMW in the task of 3D whole-body pose estimation, conducting image-based monocular 3D whole-body pose estimation in a coordinate classification manner. We hope this work can benefit both academic research and industrial applications. The code and models have been made publicly available at: https://github.com/open-mmlab/mmpose/tree/main/projects/rtmpose

Human motion prediction is a classical problem in computer vision and computer graphics, which has a wide range of practical applications. Previous effects achieve great empirical performance based on an encoding-decoding style. The methods of this style work by first encoding previous motions to latent representations and then decoding the latent representations into predicted motions. However, in practice, they are still unsatisfactory due to several issues, including complicated loss constraints, cumbersome training processes, and scarce switch of different categories of motions in prediction. In this paper, to address the above issues, we jump out of the foregoing style and propose a novel framework from a new perspective. Specifically, our framework works in a masked completion fashion. In the training stage, we learn a motion diffusion model that generates motions from random noise. In the inference stage, with a denoising procedure, we make motion prediction conditioning on observed motions to output more continuous and controllable predictions. The proposed framework enjoys promising algorithmic properties, which only needs one loss in optimization and is trained in an end-to-end manner. Additionally, it accomplishes the switch of different categories of motions effectively, which is significant in realistic tasks, e.g., the animation task. Comprehensive experiments on benchmarks confirm the superiority of the proposed framework. The project page is available at https://lhchen.top/Human-MAC.

Neural speech codecs have gained great attention for their outstanding reconstruction with discrete token representations. It is a crucial component in generative tasks such as speech coding and large language models (LLM). However, most works based on residual vector quantization perform worse with fewer tokens due to low coding efficiency for modeling complex coupled information. In this paper, we propose a neural speech codec named FreeCodec which employs a more effective encoding framework by decomposing intrinsic properties of speech into different components: 1) a global vector is extracted as the timbre information, 2) a prosody encoder with a long stride level is used to model the prosody information, 3) the content information is from a content encoder. Using different training strategies, FreeCodec achieves state-of-the-art performance in reconstruction and disentanglement scenarios. Results from subjective and objective experiments demonstrate that our framework outperforms existing methods.

Tokenization is fundamental to Natural Language Processing (NLP), directly impacting model efficiency and linguistic fidelity. While Byte Pair Encoding (BPE) is widely used in Large Language Models (LLMs), it often disregards morpheme boundaries, leading to suboptimal segmentation, particularly in morphologically rich languages. We introduce MorphBPE, a morphology-aware extension of BPE that integrates linguistic structure into subword tokenization while preserving statistical efficiency. Additionally, we propose two morphology-based evaluation metrics: (i) Morphological Consistency F1-Score, which quantifies the consistency between morpheme sharing and token sharing, contributing to LLM training convergence, and (ii) Morphological Edit Distance, which measures alignment between morphemes and tokens concerning interpretability. Experiments on English, Russian, Hungarian, and Arabic across 300M and 1B parameter LLMs demonstrate that MorphBPE consistently reduces cross-entropy loss, accelerates convergence, and improves morphological alignment scores. Fully compatible with existing LLM pipelines, MorphBPE requires minimal modifications for integration. The MorphBPE codebase and tokenizer playground will be available at: https://github.com/llm-lab-org/MorphBPE and https://tokenizer.llm-lab.org

In this paper, we propose a novel neural network model called RNN Encoder-Decoder that consists of two recurrent neural networks (RNN). One RNN encodes a sequence of symbols into a fixed-length vector representation, and the other decodes the representation into another sequence of symbols. The encoder and decoder of the proposed model are jointly trained to maximize the conditional probability of a target sequence given a source sequence. The performance of a statistical machine translation system is empirically found to improve by using the conditional probabilities of phrase pairs computed by the RNN Encoder-Decoder as an additional feature in the existing log-linear model. Qualitatively, we show that the proposed model learns a semantically and syntactically meaningful representation of linguistic phrases.

Byte-Pair Encoding (BPE) is a popular algorithm used for tokenizing data in NLP, despite being devised initially as a compression method. BPE appears to be a greedy algorithm at face value, but the underlying optimization problem that BPE seeks to solve has not yet been laid down. We formalize BPE as a combinatorial optimization problem. Via submodular functions, we prove that the iterative greedy version is a 1{{sigma(mu^star)}}(1-e^{-{sigma(mu^star)}})-approximation of an optimal merge sequence, where {sigma(mu^star)} is the total backward curvature with respect to the optimal merge sequence mu^star. Empirically the lower bound of the approximation is approx 0.37. We provide a faster implementation of BPE which improves the runtime complexity from Oleft(N Mright) to Oleft(N log Mright), where N is the sequence length and M is the merge count. Finally, we optimize the brute-force algorithm for optimal BPE using memoization.

Protein function prediction is a crucial task in bioinformatics, with significant implications for understanding biological processes and disease mechanisms. While the relationship between sequence and function has been extensively explored, translating protein structure to function continues to present substantial challenges. Various models, particularly, CNN and graph-based deep learning approaches that integrate structural and functional data, have been proposed to address these challenges. However, these methods often fall short in elucidating the functional significance of key residues essential for protein functionality, as they predominantly adopt a retrospective perspective, leading to suboptimal performance. Inspired by region proposal networks in computer vision, we introduce the Protein Region Proposal Network (ProteinRPN) for accurate protein function prediction. Specifically, the region proposal module component of ProteinRPN identifies potential functional regions (anchors) which are refined through the hierarchy-aware node drop pooling layer favoring nodes with defined secondary structures and spatial proximity. The representations of the predicted functional nodes are enriched using attention mechanisms and subsequently fed into a Graph Multiset Transformer, which is trained with supervised contrastive (SupCon) and InfoNCE losses on perturbed protein structures. Our model demonstrates significant improvements in predicting Gene Ontology (GO) terms, effectively localizing functional residues within protein structures. The proposed framework provides a robust, scalable solution for protein function annotation, advancing the understanding of protein structure-function relationships in computational biology.

We present AROMA (Attentive Reduced Order Model with Attention), a framework designed to enhance the modeling of partial differential equations (PDEs) using local neural fields. Our flexible encoder-decoder architecture can obtain smooth latent representations of spatial physical fields from a variety of data types, including irregular-grid inputs and point clouds. This versatility eliminates the need for patching and allows efficient processing of diverse geometries. The sequential nature of our latent representation can be interpreted spatially and permits the use of a conditional transformer for modeling the temporal dynamics of PDEs. By employing a diffusion-based formulation, we achieve greater stability and enable longer rollouts compared to conventional MSE training. AROMA's superior performance in simulating 1D and 2D equations underscores the efficacy of our approach in capturing complex dynamical behaviors.

Current vision systems typically assign fixed-length representations to images, regardless of the information content. This contrasts with human intelligence - and even large language models - which allocate varying representational capacities based on entropy, context and familiarity. Inspired by this, we propose an approach to learn variable-length token representations for 2D images. Our encoder-decoder architecture recursively processes 2D image tokens, distilling them into 1D latent tokens over multiple iterations of recurrent rollouts. Each iteration refines the 2D tokens, updates the existing 1D latent tokens, and adaptively increases representational capacity by adding new tokens. This enables compression of images into a variable number of tokens, ranging from 32 to 256. We validate our tokenizer using reconstruction loss and FID metrics, demonstrating that token count aligns with image entropy, familiarity and downstream task requirements. Recurrent token processing with increasing representational capacity in each iteration shows signs of token specialization, revealing potential for object / part discovery.

This article offers an empirical study on the different ways of encoding Chinese, Japanese, Korean (CJK) and English languages for text classification. Different encoding levels are studied, including UTF-8 bytes, characters, words, romanized characters and romanized words. For all encoding levels, whenever applicable, we provide comparisons with linear models, fastText and convolutional networks. For convolutional networks, we compare between encoding mechanisms using character glyph images, one-hot (or one-of-n) encoding, and embedding. In total there are 473 models, using 14 large-scale text classification datasets in 4 languages including Chinese, English, Japanese and Korean. Some conclusions from these results include that byte-level one-hot encoding based on UTF-8 consistently produces competitive results for convolutional networks, that word-level n-grams linear models are competitive even without perfect word segmentation, and that fastText provides the best result using character-level n-gram encoding but can overfit when the features are overly rich.

Given an input sequence (or prefix), modern language models often assign high probabilities to output sequences that are repetitive, incoherent, or irrelevant to the prefix; as such, model-generated text also contains such artifacts. To address these issues we present RankGen, a 1.2B parameter encoder model for English that scores model generations given a prefix. RankGen can be flexibly incorporated as a scoring function in beam search and used to decode from any pretrained language model. We train RankGen using large-scale contrastive learning to map a prefix close to the ground-truth sequence that follows it and far away from two types of negatives: (1) random sequences from the same document as the prefix, and (2) sequences generated from a large language model conditioned on the prefix. Experiments across four different language models (345M-11B parameters) and two domains show that RankGen significantly outperforms decoding algorithms like nucleus, top-k, and typical sampling, as well as contrastive decoding and search, on both automatic metrics (85.0 vs 77.3 MAUVE over nucleus) as well as human evaluations with English writers (74.5% human preference over nucleus sampling). Analysis reveals that RankGen outputs are more relevant to the prefix and improve continuity and coherence compared to baselines. We release our model checkpoints, code, and human preference data with explanations to facilitate future research.

We present a neural network architecture designed to naturally learn a positional embedding and overcome the spectral bias towards lower frequencies faced by conventional implicit neural representation networks. Our proposed architecture, SPDER, is a simple MLP that uses an activation function composed of a sinusoidal multiplied by a sublinear function, called the damping function. The sinusoidal enables the network to automatically learn the positional embedding of an input coordinate while the damping passes on the actual coordinate value by preventing it from being projected down to within a finite range of values. Our results indicate that SPDERs speed up training by 10x and converge to losses 1,500-50,000x lower than that of the state-of-the-art for image representation. SPDER is also state-of-the-art in audio representation. The superior representation capability allows SPDER to also excel on multiple downstream tasks such as image super-resolution and video frame interpolation. We provide intuition as to why SPDER significantly improves fitting compared to that of other INR methods while requiring no hyperparameter tuning or preprocessing.

Speculative decoding reduces the inference latency of a target large language model via utilizing a smaller and faster draft model. Its performance depends on a hyperparameter K -- the candidate length, i.e., the number of candidate tokens for the target model to verify in each round. However, previous methods often use simple heuristics to choose K, which may result in sub-optimal performance. We study the choice of the candidate length K and formulate it as a Markov Decision Process. We theoretically show that the optimal policy of this Markov decision process takes the form of a threshold policy, i.e., the current speculation should stop and be verified when the probability of getting a rejection exceeds a threshold value. Motivated by this theory, we propose SpecDec++, an enhanced version of speculative decoding that adaptively determines the candidate length on the fly. We augment the draft model with a trained acceptance prediction head to predict the conditional acceptance probability of the candidate tokens. SpecDec++ will stop the current speculation when the predicted probability that at least one token gets rejected exceeds a threshold. We implement SpecDec++ and apply it to the llama-2-chat 7B & 70B model pair. Our adaptive method achieves a 2.04x speedup on the Alpaca dataset (an additional 7.2% improvement over the baseline speculative decoding). On the GSM8K and HumanEval datasets, our method achieves a 2.26x speedup (9.4% improvement) and 2.23x speedup (11.1% improvement), respectively.

Large Language Models (LLMs) are primarily designed for batch processing. Existing methods for adapting LLMs to streaming rely either on expensive re-encoding or specialized architectures with limited scalability. This work identifies three key mismatches in adapting batch-oriented LLMs to streaming: (1) input-attention, (2) output-attention, and (3) position-ID mismatches. While it is commonly assumed that the latter two mismatches require frequent re-encoding, our analysis reveals that only the input-attention mismatch significantly impacts performance, indicating re-encoding outputs is largely unnecessary. To better understand this discrepancy with the common assumption, we provide the first comprehensive analysis of the impact of position encoding on LLMs in streaming, showing that preserving relative positions within source and target contexts is more critical than maintaining absolute order. Motivated by the above analysis, we introduce a group position encoding paradigm built on batch architectures to enhance consistency between streaming and batch modes. Extensive experiments on cross-lingual and cross-modal tasks demonstrate that our method outperforms existing approaches. Our method requires no architectural modifications, exhibits strong generalization in both streaming and batch modes. The code is available at repository https://github.com/EIT-NLP/StreamingLLM.

The success of pre-trained contextualized representations has prompted researchers to analyze them for the presence of linguistic information. Indeed, it is natural to assume that these pre-trained representations do encode some level of linguistic knowledge as they have brought about large empirical improvements on a wide variety of NLP tasks, which suggests they are learning true linguistic generalization. In this work, we focus on intrinsic probing, an analysis technique where the goal is not only to identify whether a representation encodes a linguistic attribute but also to pinpoint where this attribute is encoded. We propose a novel latent-variable formulation for constructing intrinsic probes and derive a tractable variational approximation to the log-likelihood. Our results show that our model is versatile and yields tighter mutual information estimates than two intrinsic probes previously proposed in the literature. Finally, we find empirical evidence that pre-trained representations develop a cross-lingually entangled notion of morphosyntax.

Understanding biological processes, drug development, and biotechnological advancements requires detailed analysis of protein structures and sequences, a task in protein research that is inherently complex and time-consuming when performed manually. To streamline this process, we introduce ProteinGPT, a state-of-the-art multi-modal protein chat system, that allows users to upload protein sequences and/or structures for comprehensive protein analysis and responsive inquiries. ProteinGPT seamlessly integrates protein sequence and structure encoders with linear projection layers for precise representation adaptation, coupled with a large language model (LLM) to generate accurate and contextually relevant responses. To train ProteinGPT, we construct a large-scale dataset of 132,092 proteins with annotations, and optimize the instruction-tuning process using GPT-4o. This innovative system ensures accurate alignment between the user-uploaded data and prompts, simplifying protein analysis. Experiments show that ProteinGPT can produce promising responses to proteins and their corresponding questions.

This short note is written for rapid communication of long context training and to share the idea of how to train it with low memory usage. In the note, we generalize the attention algorithm and neural network of Generative Pre-Trained Transformers and reinterpret it in Path integral formalism. First, the role of the transformer is understood as the time evolution of the token state and second, it is suggested that the all key-token states in the same time as the query-token can attend to the attention with the query token states. As a result of the repetitive time evolution, it is discussed that the token states in the past sequence meats the token states in the present sequence so that the attention between separated sequences becomes possible for maintaining infinite contextual information just by using low memory for limited size of sequence. For the experiment, the 12 input token window size was taken and one GPU with 24GB memory was used for the pre-training. It was confirmed that more than 150 length context is preserved. The sampling result of the training, the code and the other details will be included in the revised version of this note later.

Large-scale pre-trained models (PTMs) have been widely used in document-oriented NLP tasks, such as question answering. However, the encoding-task coupling requirement results in the repeated encoding of the same documents for different tasks and queries, which is highly computationally inefficient. To this end, we target to decouple document encoding from downstream tasks, and propose to represent each document as a plug-and-play document module, i.e., a document plugin, for PTMs (PlugD). By inserting document plugins into the backbone PTM for downstream tasks, we can encode a document one time to handle multiple tasks, which is more efficient than conventional encoding-task coupling methods that simultaneously encode documents and input queries using task-specific encoders. Extensive experiments on 8 datasets of 4 typical NLP tasks show that PlugD enables models to encode documents once and for all across different scenarios. Especially, PlugD can save 69% computational costs while achieving comparable performance to state-of-the-art encoding-task coupling methods. Additionally, we show that PlugD can serve as an effective post-processing way to inject knowledge into task-specific models, improving model performance without any additional model training.

While recent research has made significant progress in speech-driven talking face generation, the quality of the generated video still lags behind that of real recordings. One reason for this is the use of handcrafted intermediate representations like facial landmarks and 3DMM coefficients, which are designed based on human knowledge and are insufficient to precisely describe facial movements. Additionally, these methods require an external pretrained model for extracting these representations, whose performance sets an upper bound on talking face generation. To address these limitations, we propose a novel method called DAE-Talker that leverages data-driven latent representations obtained from a diffusion autoencoder (DAE). DAE contains an image encoder that encodes an image into a latent vector and a DDIM image decoder that reconstructs the image from it. We train our DAE on talking face video frames and then extract their latent representations as the training target for a Conformer-based speech2latent model. This allows DAE-Talker to synthesize full video frames and produce natural head movements that align with the content of speech, rather than relying on a predetermined head pose from a template video. We also introduce pose modelling in speech2latent for pose controllability. Additionally, we propose a novel method for generating continuous video frames with the DDIM image decoder trained on individual frames, eliminating the need for modelling the joint distribution of consecutive frames directly. Our experiments show that DAE-Talker outperforms existing popular methods in lip-sync, video fidelity, and pose naturalness. We also conduct ablation studies to analyze the effectiveness of the proposed techniques and demonstrate the pose controllability of DAE-Talker.

Linear position interpolation helps pre-trained models using rotary position embeddings (RoPE) to extrapolate to longer sequence lengths. We propose using linear position interpolation to extend the extrapolation range of models using Attention with Linear Biases (ALiBi). We find position interpolation significantly improves extrapolation capability on upstream language modelling and downstream summarization and retrieval tasks.

The 3D Human Pose Estimation (3D HPE) task uses 2D images or videos to predict human joint coordinates in 3D space. Despite recent advancements in deep learning-based methods, they mostly ignore the capability of coupling accessible texts and naturally feasible knowledge of humans, missing out on valuable implicit supervision to guide the 3D HPE task. Moreover, previous efforts often study this task from the perspective of the whole human body, neglecting fine-grained guidance hidden in different body parts. To this end, we present a new Fine-Grained Prompt-Driven Denoiser based on a diffusion model for 3D HPE, named FinePOSE. It consists of three core blocks enhancing the reverse process of the diffusion model: (1) Fine-grained Part-aware Prompt learning (FPP) block constructs fine-grained part-aware prompts via coupling accessible texts and naturally feasible knowledge of body parts with learnable prompts to model implicit guidance. (2) Fine-grained Prompt-pose Communication (FPC) block establishes fine-grained communications between learned part-aware prompts and poses to improve the denoising quality. (3) Prompt-driven Timestamp Stylization (PTS) block integrates learned prompt embedding and temporal information related to the noise level to enable adaptive adjustment at each denoising step. Extensive experiments on public single-human pose estimation datasets show that FinePOSE outperforms state-of-the-art methods. We further extend FinePOSE to multi-human pose estimation. Achieving 34.3mm average MPJPE on the EgoHumans dataset demonstrates the potential of FinePOSE to deal with complex multi-human scenarios. Code is available at https://github.com/PKU-ICST-MIPL/FinePOSE_CVPR2024.

Transformer models have advanced the state of the art in many Natural Language Processing (NLP) tasks. In this paper, we present a new Transformer architecture, Extended Transformer Construction (ETC), that addresses two key challenges of standard Transformer architectures, namely scaling input length and encoding structured inputs. To scale attention to longer inputs, we introduce a novel global-local attention mechanism between global tokens and regular input tokens. We also show that combining global-local attention with relative position encodings and a Contrastive Predictive Coding (CPC) pre-training objective allows ETC to encode structured inputs. We achieve state-of-the-art results on four natural language datasets requiring long and/or structured inputs.

Lip-reading aims to infer the speech content from the lip movement sequence and can be seen as a typical sequence-to-sequence (seq2seq) problem which translates the input image sequence of lip movements to the text sequence of the speech content. However, the traditional learning process of seq2seq models always suffers from two problems: the exposure bias resulted from the strategy of "teacher-forcing", and the inconsistency between the discriminative optimization target (usually the cross-entropy loss) and the final evaluation metric (usually the character/word error rate). In this paper, we propose a novel pseudo-convolutional policy gradient (PCPG) based method to address these two problems. On the one hand, we introduce the evaluation metric (refers to the character error rate in this paper) as a form of reward to optimize the model together with the original discriminative target. On the other hand, inspired by the local perception property of convolutional operation, we perform a pseudo-convolutional operation on the reward and loss dimension, so as to take more context around each time step into account to generate a robust reward and loss for the whole optimization. Finally, we perform a thorough comparison and evaluation on both the word-level and sentence-level benchmarks. The results show a significant improvement over other related methods, and report either a new state-of-the-art performance or a competitive accuracy on all these challenging benchmarks, which clearly proves the advantages of our approach.

Recent advances in text-to-motion generation using diffusion and autoregressive models have shown promising results. However, these models often suffer from a trade-off between real-time performance, high fidelity, and motion editability. To address this gap, we introduce MMM, a novel yet simple motion generation paradigm based on Masked Motion Model. MMM consists of two key components: (1) a motion tokenizer that transforms 3D human motion into a sequence of discrete tokens in latent space, and (2) a conditional masked motion transformer that learns to predict randomly masked motion tokens, conditioned on the pre-computed text tokens. By attending to motion and text tokens in all directions, MMM explicitly captures inherent dependency among motion tokens and semantic mapping between motion and text tokens. During inference, this allows parallel and iterative decoding of multiple motion tokens that are highly consistent with fine-grained text descriptions, therefore simultaneously achieving high-fidelity and high-speed motion generation. In addition, MMM has innate motion editability. By simply placing mask tokens in the place that needs editing, MMM automatically fills the gaps while guaranteeing smooth transitions between editing and non-editing parts. Extensive experiments on the HumanML3D and KIT-ML datasets demonstrate that MMM surpasses current leading methods in generating high-quality motion (evidenced by superior FID scores of 0.08 and 0.429), while offering advanced editing features such as body-part modification, motion in-betweening, and the synthesis of long motion sequences. In addition, MMM is two orders of magnitude faster on a single mid-range GPU than editable motion diffusion models. Our project page is available at https://exitudio.github.io/MMM-page.

In the field of instruction-following large vision-language models (LVLMs), the efficient deployment of these models faces challenges, notably due to the high memory demands of their key-value (KV) caches. Conventional cache management strategies for LLMs focus on cache eviction, which often fails to address the specific needs of multimodal instruction-following models. Recognizing this gap, in this paper, we introduce Elastic Cache, a novel approach that benefits from applying distinct acceleration methods for instruction encoding and output generation stages. We investigate the metrics of importance in different stages and propose an importance-driven cache merging strategy to prune redundancy caches. Instead of discarding less important caches, our strategy identifies important key/value vectors as anchor points. Surrounding less important caches are then merged with these anchors, enhancing the preservation of contextual information in the KV caches while yielding an arbitrary acceleration ratio. For instruction encoding, we utilize the frequency to evaluate the importance of caches. Regarding output generation, we prioritize tokens based on their distance with an offset, by which both the initial and most recent tokens are retained. Results on a range of LVLMs demonstrate that Elastic Cache not only boosts efficiency but also notably outperforms existing pruning methods in language generation across various tasks. Code is available at https://github.com/liuzuyan/ElasticCache

The rapid advancement of text-to-image (T2I) diffusion models has enabled them to generate unprecedented results from given texts. However, as text inputs become longer, existing encoding methods like CLIP face limitations, and aligning the generated images with long texts becomes challenging. To tackle these issues, we propose LongAlign, which includes a segment-level encoding method for processing long texts and a decomposed preference optimization method for effective alignment training. For segment-level encoding, long texts are divided into multiple segments and processed separately. This method overcomes the maximum input length limits of pretrained encoding models. For preference optimization, we provide decomposed CLIP-based preference models to fine-tune diffusion models. Specifically, to utilize CLIP-based preference models for T2I alignment, we delve into their scoring mechanisms and find that the preference scores can be decomposed into two components: a text-relevant part that measures T2I alignment and a text-irrelevant part that assesses other visual aspects of human preference. Additionally, we find that the text-irrelevant part contributes to a common overfitting problem during fine-tuning. To address this, we propose a reweighting strategy that assigns different weights to these two components, thereby reducing overfitting and enhancing alignment. After fine-tuning 512 times 512 Stable Diffusion (SD) v1.5 for about 20 hours using our method, the fine-tuned SD outperforms stronger foundation models in T2I alignment, such as PixArt-alpha and Kandinsky v2.2. The code is available at https://github.com/luping-liu/LongAlign.

The ability to accurately model the fitness landscape of protein sequences is critical to a wide range of applications, from quantifying the effects of human variants on disease likelihood, to predicting immune-escape mutations in viruses and designing novel biotherapeutic proteins. Deep generative models of protein sequences trained on multiple sequence alignments have been the most successful approaches so far to address these tasks. The performance of these methods is however contingent on the availability of sufficiently deep and diverse alignments for reliable training. Their potential scope is thus limited by the fact many protein families are hard, if not impossible, to align. Large language models trained on massive quantities of non-aligned protein sequences from diverse families address these problems and show potential to eventually bridge the performance gap. We introduce Tranception, a novel transformer architecture leveraging autoregressive predictions and retrieval of homologous sequences at inference to achieve state-of-the-art fitness prediction performance. Given its markedly higher performance on multiple mutants, robustness to shallow alignments and ability to score indels, our approach offers significant gain of scope over existing approaches. To enable more rigorous model testing across a broader range of protein families, we develop ProteinGym -- an extensive set of multiplexed assays of variant effects, substantially increasing both the number and diversity of assays compared to existing benchmarks.

Recent works have revealed the great potential of speculative decoding in accelerating the autoregressive generation process of large language models. The success of these methods relies on the alignment between draft candidates and the sampled outputs of the target model. Existing methods mainly achieve draft-target alignment with training-based methods, e.g., EAGLE, Medusa, involving considerable training costs. In this paper, we present a training-free alignment-augmented speculative decoding algorithm. We propose alignment sampling, which leverages output distribution obtained in the prefilling phase to provide more aligned draft candidates. To further benefit from high-quality but non-aligned draft candidates, we also introduce a simple yet effective flexible verification strategy. Through an adaptive probability threshold, our approach can improve generation accuracy while further improving inference efficiency. Experiments on 8 datasets (including question answering, summarization and code completion tasks) show that our approach increases the average generation score by 3.3 points for the LLaMA3 model. Our method achieves a mean acceptance length up to 2.39 and speed up generation by 2.23.

Micro-expression recognition (MER), a critical subfield of affective computing, presents greater challenges than macro-expression recognition due to its brief duration and low intensity. While incorporating prior knowledge has been shown to enhance MER performance, existing methods predominantly rely on simplistic, singular sources of prior knowledge, failing to fully exploit multi-source information. This paper introduces the Multi-Prior Fusion Network (MPFNet), leveraging a progressive training strategy to optimize MER tasks. We propose two complementary encoders: the Generic Feature Encoder (GFE) and the Advanced Feature Encoder (AFE), both based on Inflated 3D ConvNets (I3D) with Coordinate Attention (CA) mechanisms, to improve the model's ability to capture spatiotemporal and channel-specific features. Inspired by developmental psychology, we present two variants of MPFNet--MPFNet-P and MPFNet-C--corresponding to two fundamental modes of infant cognitive development: parallel and hierarchical processing. These variants enable the evaluation of different strategies for integrating prior knowledge. Extensive experiments demonstrate that MPFNet significantly improves MER accuracy while maintaining balanced performance across categories, achieving accuracies of 0.811, 0.924, and 0.857 on the SMIC, CASME II, and SAMM datasets, respectively. To the best of our knowledge, our approach achieves state-of-the-art performance on the SMIC and SAMM datasets.

Speculative decoding (SPD) aims to accelerate the auto-regressive token generation process of a target Large Language Model (LLM). Some approaches employ a draft model with multiple heads to predict a sequence of future tokens, where each head handles a token in the sequence. The target LLM verifies the predicted sequence and accepts aligned tokens, enabling efficient multi-token generation. However, existing methods assume that all tokens within a sequence are equally important, employing identical head structures and relying on a single-generation paradigm, either serial or parallel. To this end, we theoretically demonstrate that initial tokens in the draft sequence are more important than later ones. Building on this insight, we propose Gumiho, a hybrid model combining serial and parallel heads. Specifically, given the critical importance of early tokens, we employ a sophisticated Transformer architecture for the early draft heads in a serial configuration to improve accuracy. For later tokens, we utilize multiple lightweight MLP heads operating in parallel to enhance efficiency. By allocating more advanced model structures and longer running times to the early heads, Gumiho achieves improved overall performance. The experimental results demonstrate that our method outperforms existing approaches, fully validating its effectiveness.

Pipelined NLP systems have largely been superseded by end-to-end neural modeling, yet nearly all commonly-used models still require an explicit tokenization step. While recent tokenization approaches based on data-derived subword lexicons are less brittle than manually engineered tokenizers, these techniques are not equally suited to all languages, and the use of any fixed vocabulary may limit a model's ability to adapt. In this paper, we present CANINE, a neural encoder that operates directly on character sequences, without explicit tokenization or vocabulary, and a pre-training strategy that operates either directly on characters or optionally uses subwords as a soft inductive bias. To use its finer-grained input effectively and efficiently, CANINE combines downsampling, which reduces the input sequence length, with a deep transformer stack, which encodes context. CANINE outperforms a comparable mBERT model by 2.8 F1 on TyDi QA, a challenging multilingual benchmark, despite having 28% fewer model parameters.

Multistep instructions, such as recipes and how-to guides, greatly benefit from visual aids, such as a series of images that accompany the instruction steps. While Large Language Models (LLMs) have become adept at generating coherent textual steps, Large Vision/Language Models (LVLMs) are less capable of generating accompanying image sequences. The most challenging aspect is that each generated image needs to adhere to the relevant textual step instruction, as well as be visually consistent with earlier images in the sequence. To address this problem, we propose an approach for generating consistent image sequences, which integrates a Latent Diffusion Model (LDM) with an LLM to transform the sequence into a caption to maintain the semantic coherence of the sequence. In addition, to maintain the visual coherence of the image sequence, we introduce a copy mechanism to initialise reverse diffusion processes with a latent vector iteration from a previously generated image from a relevant step. Both strategies will condition the reverse diffusion process on the sequence of instruction steps and tie the contents of the current image to previous instruction steps and corresponding images. Experiments show that the proposed approach is preferred by humans in 46.6% of the cases against 26.6% for the second best method. In addition, automatic metrics showed that the proposed method maintains semantic coherence and visual consistency across steps in both domains.

This study examines the integration of Contrastive Predictive Coding (CPC) with Spiking Neural Networks (SNN). While CPC learns the predictive structure of data to generate meaningful representations, SNN mimics the computational processes of biological neural systems over time. In this study, the goal is to develop a predictive coding model with greater biological plausibility by processing inputs and outputs in a spike-based system. The proposed model was tested on the MNIST dataset and achieved a high classification rate in distinguishing positive sequential samples from non-sequential negative samples. The study demonstrates that CPC can be effectively combined with SNN, showing that an SNN trained for classification tasks can also function as an encoding mechanism. Project codes and detailed results can be accessed on our GitHub page: https://github.com/vnd-ogrenme/ongorusel-kodlama/tree/main/CPC_SNN

The Transformer architecture is shown to provide a powerful machine transduction framework for online handwritten gestures corresponding to glyph strokes of natural language sentences. The attention mechanism is successfully used to create latent representations of an end-to-end encoder-decoder model, solving multi-level segmentation while also learning some language features and syntax rules. The additional use of a large decoding space with some learned Byte-Pair-Encoding (BPE) is shown to provide robustness to ablated inputs and syntax rules. The encoder stack was directly fed with spatio-temporal data tokens potentially forming an infinitely large input vocabulary, an approach that finds applications beyond that of this work. Encoder transfer learning capabilities is also demonstrated on several languages resulting in faster optimisation and shared parameters. A new supervised dataset of online handwriting gestures suitable for generic handwriting recognition tasks was used to successfully train a small transformer model to an average normalised Levenshtein accuracy of 96% on English or German sentences and 94% in French.

Neural Implicit Representation (NIR) has recently gained significant attention due to its remarkable ability to encode complex and high-dimensional data into representation space and easily reconstruct it through a trainable mapping function. However, NIR methods assume a one-to-one mapping between the target data and representation models regardless of data relevancy or similarity. This results in poor generalization over multiple complex data and limits their efficiency and scalability. Motivated by continual learning, this work investigates how to accumulate and transfer neural implicit representations for multiple complex video data over sequential encoding sessions. To overcome the limitation of NIR, we propose a novel method, Progressive Fourier Neural Representation (PFNR), that aims to find an adaptive and compact sub-module in Fourier space to encode videos in each training session. This sparsified neural encoding allows the neural network to hold free weights, enabling an improved adaptation for future videos. In addition, when learning a representation for a new video, PFNR transfers the representation of previous videos with frozen weights. This design allows the model to continuously accumulate high-quality neural representations for multiple videos while ensuring lossless decoding that perfectly preserves the learned representations for previous videos. We validate our PFNR method on the UVG8/17 and DAVIS50 video sequence benchmarks and achieve impressive performance gains over strong continual learning baselines. The PFNR code is available at https://github.com/ihaeyong/PFNR.git.

The Segment Anything Model (SAM) has achieved remarkable successes in the realm of natural image segmentation, but its deployment in the medical imaging sphere has encountered challenges. Specifically, the model struggles with medical images that feature low contrast, faint boundaries, intricate morphologies, and small-sized objects. To address these challenges and enhance SAM's performance in the medical domain, we introduce a comprehensive modification. Firstly, we incorporate a frozen Convolutional Neural Network (CNN) branch as an image encoder, which synergizes with SAM's original Vision Transformer (ViT) encoder through a novel variational attention fusion module. This integration bolsters the model's capability to capture local spatial information, which is often paramount in medical imagery. Moreover, to further optimize SAM for medical imaging, we introduce feature and position adapters within the ViT branch, refining the encoder's representations. We see that compared to current prompting strategies to fine-tune SAM for ultrasound medical segmentation, the use of text descriptions that serve as text prompts for SAM helps significantly improve the performance. Leveraging ChatGPT's natural language understanding capabilities, we generate prompts that offer contextual information and guidance to SAM, enabling it to better understand the nuances of ultrasound medical images and improve its segmentation accuracy. Our method, in its entirety, represents a significant stride towards making universal image segmentation models more adaptable and efficient in the medical domain.

Innovations like protein diffusion have enabled significant progress in de novo protein design, which is a vital topic in life science. These methods typically depend on protein structure encoders to model residue backbone frames, where atoms do not exist. Most prior encoders rely on atom-wise features, such as angles and distances between atoms, which are not available in this context. Thus far, only several simple encoders, such as IPA, have been proposed for this scenario, exposing the frame modeling as a bottleneck. In this work, we proffer the Vector Field Network (VFN), which enables network layers to perform learnable vector computations between coordinates of frame-anchored virtual atoms, thus achieving a higher capability for modeling frames. The vector computation operates in a manner similar to a linear layer, with each input channel receiving 3D virtual atom coordinates instead of scalar values. The multiple feature vectors output by the vector computation are then used to update the residue representations and virtual atom coordinates via attention aggregation. Remarkably, VFN also excels in modeling both frames and atoms, as the real atoms can be treated as the virtual atoms for modeling, positioning VFN as a potential universal encoder. In protein diffusion (frame modeling), VFN exhibits an impressive performance advantage over IPA, excelling in terms of both designability (67.04% vs. 53.58%) and diversity (66.54% vs. 51.98%). In inverse folding (frame and atom modeling), VFN outperforms the previous SoTA model, PiFold (54.7% vs. 51.66%), on sequence recovery rate. We also propose a method of equipping VFN with the ESM model, which significantly surpasses the previous ESM-based SoTA (62.67% vs. 55.65%), LM-Design, by a substantial margin.

The recent advancements in large language models (LLMs) have been extraordinary, yet the escalating inference costs associated with them present challenges in real-world applications. To address these challenges, we propose a novel approach called Early-exiting Speculative Decoding (EESD) with lossless acceleration. Specifically, EESD utilizes a segment of the LLM to generate draft tokens, incorporating Early-exiting structures after the first N layers. To enhance the quality of draft tokens, a self-distillation method is integrated. This early-exiting design not only reduces deployment and training costs but also significantly accelerates the token generation speed. Moreover, we introduce a novel sampling mechanism that leverages Thompson Sampling to regulate the generation processes, automatically determining the quantity of draft tokens in each round. The original LLM is then employed to validate these draft tokens through a single forward pass, and thus guarantees that the final output text maintains a distribution consistent with vanilla auto-regressive decoding. The experimental results on both 13B and 70B models demonstrate that our approach decodes tokens at a markedly accelerated rate compared to prior methods, showing the effectiveness of our approach.

Distinguishing spatial relations is a basic part of human cognition which requires fine-grained perception on cross-instance. Although benchmarks like MME, MMBench and SEED comprehensively have evaluated various capabilities which already include visual spatial reasoning(VSR). There is still a lack of sufficient quantity and quality evaluation and optimization datasets for Vision Large Language Models(VLLMs) specifically targeting visual positional reasoning. To handle this, we first diagnosed current VLLMs with the VSR dataset and proposed a unified test set. We found current VLLMs to exhibit a contradiction of over-sensitivity to language instructions and under-sensitivity to visual positional information. By expanding the original benchmark from two aspects of tunning data and model structure, we mitigated this phenomenon. To our knowledge, we expanded spatially positioned image data controllably using diffusion models for the first time and integrated original visual encoding(CLIP) with other 3 powerful visual encoders(SigLIP, SAM and DINO). After conducting combination experiments on scaling data and models, we obtained a VLLM VSR Expert(VSRE) that not only generalizes better to different instructions but also accurately distinguishes differences in visual positional information. VSRE achieved over a 27\% increase in accuracy on the VSR test set. It becomes a performant VLLM on the position reasoning of both the VSR dataset and relevant subsets of other evaluation benchmarks. We open-sourced the expanded model with data and Appendix at https://github.com/peijin360/vsre and hope it will accelerate advancements in VLLM on VSR learning.

We present AnimaX, a feed-forward 3D animation framework that bridges the motion priors of video diffusion models with the controllable structure of skeleton-based animation. Traditional motion synthesis methods are either restricted to fixed skeletal topologies or require costly optimization in high-dimensional deformation spaces. In contrast, AnimaX effectively transfers video-based motion knowledge to the 3D domain, supporting diverse articulated meshes with arbitrary skeletons. Our method represents 3D motion as multi-view, multi-frame 2D pose maps, and enables joint video-pose diffusion conditioned on template renderings and a textual motion prompt. We introduce shared positional encodings and modality-aware embeddings to ensure spatial-temporal alignment between video and pose sequences, effectively transferring video priors to motion generation task. The resulting multi-view pose sequences are triangulated into 3D joint positions and converted into mesh animation via inverse kinematics. Trained on a newly curated dataset of 160,000 rigged sequences, AnimaX achieves state-of-the-art results on VBench in generalization, motion fidelity, and efficiency, offering a scalable solution for category-agnostic 3D animation. Project page: https://anima-x.github.io/{https://anima-x.github.io/}.

Recent advances in language modeling have demonstrated the effectiveness of State Space Models (SSMs) for efficient sequence modeling. While hybrid architectures such as Samba and the decoder-decoder architecture, YOCO, have shown promising performance gains over Transformers, prior works have not investigated the efficiency potential of representation sharing between SSM layers. In this paper, we introduce the Gated Memory Unit (GMU), a simple yet effective mechanism for efficient memory sharing across layers. We apply it to create SambaY, a decoder-hybrid-decoder architecture that incorporates GMUs in the cross-decoder to share memory readout states from a Samba-based self-decoder. SambaY significantly enhances decoding efficiency, preserves linear pre-filling time complexity, and boosts long-context performance, all while eliminating the need for explicit positional encoding. Through extensive scaling experiments, we demonstrate that our model exhibits a significantly lower irreducible loss compared to a strong YOCO baseline, indicating superior performance scalability under large-scale compute regimes. Our largest model enhanced with Differential Attention, Phi4-mini-Flash-Reasoning, achieves significantly better performance than Phi4-mini-Reasoning on reasoning tasks such as Math500, AIME24/25, and GPQA Diamond without any reinforcement learning, while delivering up to 10x higher decoding throughput on 2K-length prompts with 32K generation length under the vLLM inference framework. We release our training codebase on open-source data at https://github.com/microsoft/ArchScale.

Large language models (LLMs) exhibit exceptional performance across a wide range of tasks; however, their token-by-token autoregressive generation process significantly hinders inference speed. Speculative decoding presents a promising draft-then-verify framework that reduces generation latency while maintaining output distribution fidelity. Nevertheless, the draft model introduces additional computational overhead, becoming a performance bottleneck and increasing the time to first token (TTFT). Previous approaches to mitigate draft model overhead have primarily relied on heuristics and generally failed to match the quality of the draft language models. To address these challenges, we propose DuoDecoding, a novel approach that strategically deploys the draft and target models on the CPU and GPU respectively, enabling parallel decoding while preserving draft quality. Our method incorporates a hardware-aware optimal draft budget to minimize idle times and employs dynamic multi-sequence drafting to enhance draft quality. Extensive experiments across seven tasks show that DuoDecoding achieves up to 2.61x speedup in generation latency, while reducing TTFT to 83% of that in conventional speculative decoding. The Code is available at https://github.com/KaiLv69/DuoDecoding.

Post-training quantization (PTQ) is the go-to compression technique for large generative models, such as stable diffusion or large language models. PTQ methods commonly keep the softmax activation in higher precision as it has been shown to be very sensitive to quantization noise. However, this can lead to a significant runtime and power overhead during inference on resource-constraint edge devices. In this work, we investigate the source of the softmax sensitivity to quantization and show that the quantization operation leads to a large bias in the softmax output, causing accuracy degradation. To overcome this issue, we propose an offline bias correction technique that improves the quantizability of softmax without additional compute during deployment, as it can be readily absorbed into the quantization parameters. We demonstrate the effectiveness of our method on stable diffusion v1.5 and 125M-size OPT language model, achieving significant accuracy improvement for 8-bit quantized softmax.

The success of transformers in computer vision has led to several attempts to adapt them for mobile devices, but their performance remains unsatisfactory in some real-world applications. To address this issue, we propose PP-MobileSeg, a semantic segmentation model that achieves state-of-the-art performance on mobile devices. PP-MobileSeg comprises three novel parts: the StrideFormer backbone, the Aggregated Attention Module (AAM), and the Valid Interpolate Module (VIM). The four-stage StrideFormer backbone is built with MV3 blocks and strided SEA attention, and it is able to extract rich semantic and detailed features with minimal parameter overhead. The AAM first filters the detailed features through semantic feature ensemble voting and then combines them with semantic features to enhance the semantic information. Furthermore, we proposed VIM to upsample the downsampled feature to the resolution of the input image. It significantly reduces model latency by only interpolating classes present in the final prediction, which is the most significant contributor to overall model latency. Extensive experiments show that PP-MobileSeg achieves a superior tradeoff between accuracy, model size, and latency compared to other methods. On the ADE20K dataset, PP-MobileSeg achieves 1.57% higher accuracy in mIoU than SeaFormer-Base with 32.9% fewer parameters and 42.3% faster acceleration on Qualcomm Snapdragon 855. Source codes are available at https://github.com/PaddlePaddle/PaddleSeg/tree/release/2.8.

Large language models have shown remarkable performance across a wide range of language tasks, owing to their exceptional capabilities in context modeling. The most commonly used method of context modeling is full self-attention, as seen in standard decoder-only Transformers. Although powerful, this method can be inefficient for long sequences and may overlook inherent input structures. To address these problems, an alternative approach is parallel context encoding, which splits the context into sub-pieces and encodes them parallelly. Because parallel patterns are not encountered during training, naively applying parallel encoding leads to performance degradation. However, the underlying reasons and potential mitigations are unclear. In this work, we provide a detailed analysis of this issue and identify that unusually high attention entropy can be a key factor. Furthermore, we adopt two straightforward methods to reduce attention entropy by incorporating attention sinks and selective mechanisms. Experiments on various tasks reveal that these methods effectively lower irregular attention entropy and narrow performance gaps. We hope this study can illuminate ways to enhance context modeling mechanisms.

Designing biological sequences is an important challenge that requires satisfying complex constraints and thus is a natural problem to address with deep generative modeling. Diffusion generative models have achieved considerable success in many applications. Score-based generative stochastic differential equations (SDE) model is a continuous-time diffusion model framework that enjoys many benefits, but the originally proposed SDEs are not naturally designed for modeling discrete data. To develop generative SDE models for discrete data such as biological sequences, here we introduce a diffusion process defined in the probability simplex space with stationary distribution being the Dirichlet distribution. This makes diffusion in continuous space natural for modeling discrete data. We refer to this approach as Dirchlet diffusion score model. We demonstrate that this technique can generate samples that satisfy hard constraints using a Sudoku generation task. This generative model can also solve Sudoku, including hard puzzles, without additional training. Finally, we applied this approach to develop the first human promoter DNA sequence design model and showed that designed sequences share similar properties with natural promoter sequences.

Parameter-efficient finetuning (PEFT) has become ubiquitous to adapt foundation models to downstream task requirements while retaining their generalization ability. However, the amount of additionally introduced parameters and compute for successful adaptation and hyperparameter searches can explode quickly, especially when deployed at scale to serve numerous individual requests. To ensure effective, parameter-efficient, and hyperparameter-robust adaptation, we propose the ETHER transformation family, which performs Efficient fineTuning via HypErplane Reflections. By design, ETHER transformations require a minimal number of parameters, are less likely to deteriorate model performance, and exhibit robustness to hyperparameter and learning rate choices. In particular, we introduce ETHER and its relaxation ETHER+, which match or outperform existing PEFT methods with significantly fewer parameters (sim10-100 times lower than LoRA or OFT) across multiple image synthesis and natural language tasks without exhaustive hyperparameter tuning. Finally, we investigate the recent emphasis on Hyperspherical Energy retention for adaptation and raise questions on its practical utility. The code is available at https://github.com/mwbini/ether.

As Large Language Models (LLMs) can now process extremely long contexts, efficient inference over these extended inputs has become increasingly important, especially for emerging applications like LLM agents that highly depend on this capability. Speculative decoding (SD) offers a promising lossless acceleration technique compared to lossy alternatives such as quantization and model cascades. However, most state-of-the-art SD methods are trained on short texts (typically fewer than 4k tokens), making them unsuitable for long-context scenarios. Specifically, adapting these methods to long contexts presents three key challenges: (1) the excessive memory demands posed by draft models due to large Key-Value (KV) cache; (2) performance degradation resulting from the mismatch between short-context training and long-context inference; and (3) inefficiencies in tree attention mechanisms when managing long token sequences. This work introduces LongSpec, a framework that addresses these challenges through three core innovations: a memory-efficient draft model with a constant-sized KV cache; novel position indices that mitigate the training-inference mismatch; and an attention aggregation strategy that combines fast prefix computation with standard tree attention to enable efficient decoding. Experimental results confirm the effectiveness of LongSpec, achieving up to a 3.26x speedup over strong Flash Attention baselines across five long-context understanding datasets, as well as a 2.25x reduction in wall-clock time on the AIME24 long reasoning task with the QwQ model, demonstrating significant latency improvements for long-context applications. The code is available at https://github.com/sail-sg/LongSpec.

Tables organize valuable content in a concise and compact representation. This content is extremely valuable for systems such as search engines, Knowledge Graph's, etc, since they enhance their predictive capabilities. Unfortunately, tables come in a large variety of shapes and sizes. Furthermore, they can have complex column/row-header configurations, multiline rows, different variety of separation lines, missing entries, etc. As such, the correct identification of the table-structure from an image is a non-trivial task. In this paper, we present a new table-structure identification model. The latter improves the latest end-to-end deep learning model (i.e. encoder-dual-decoder from PubTabNet) in two significant ways. First, we introduce a new object detection decoder for table-cells. In this way, we can obtain the content of the table-cells from programmatic PDF's directly from the PDF source and avoid the training of the custom OCR decoders. This architectural change leads to more accurate table-content extraction and allows us to tackle non-english tables. Second, we replace the LSTM decoders with transformer based decoders. This upgrade improves significantly the previous state-of-the-art tree-editing-distance-score (TEDS) from 91% to 98.5% on simple tables and from 88.7% to 95% on complex tables.

Despite extensive progress on image generation, common deep generative model architectures are not easily applied to lossless compression. For example, VAEs suffer from a compression cost overhead due to their latent variables. This overhead can only be partially eliminated with elaborate schemes such as bits-back coding, often resulting in poor single-sample compression rates. To overcome such problems, we establish a new class of tractable lossless compression models that permit efficient encoding and decoding: Probabilistic Circuits (PCs). These are a class of neural networks involving |p| computational units that support efficient marginalization over arbitrary subsets of the D feature dimensions, enabling efficient arithmetic coding. We derive efficient encoding and decoding schemes that both have time complexity O (log(D) cdot |p|), where a naive scheme would have linear costs in D and |p|, making the approach highly scalable. Empirically, our PC-based (de)compression algorithm runs 5-40 times faster than neural compression algorithms that achieve similar bitrates. By scaling up the traditional PC structure learning pipeline, we achieve state-of-the-art results on image datasets such as MNIST. Furthermore, PCs can be naturally integrated with existing neural compression algorithms to improve the performance of these base models on natural image datasets. Our results highlight the potential impact that non-standard learning architectures may have on neural data compression.

In Transformer architectures, tokens\textemdash discrete units derived from raw data\textemdash are formed by segmenting inputs into fixed-length chunks. Each token is then mapped to an embedding, enabling parallel attention computations while preserving the input's essential information. Due to the quadratic computational complexity of transformer self-attention mechanisms, token reduction has primarily been used as an efficiency strategy. This is especially true in single vision and language domains, where it helps balance computational costs, memory usage, and inference latency. Despite these advances, this paper argues that token reduction should transcend its traditional efficiency-oriented role in the era of large generative models. Instead, we position it as a fundamental principle in generative modeling, critically influencing both model architecture and broader applications. Specifically, we contend that across vision, language, and multimodal systems, token reduction can: (i) facilitate deeper multimodal integration and alignment, (ii) mitigate "overthinking" and hallucinations, (iii) maintain coherence over long inputs, and (iv) enhance training stability, etc. We reframe token reduction as more than an efficiency measure. By doing so, we outline promising future directions, including algorithm design, reinforcement learning-guided token reduction, token optimization for in-context learning, and broader ML and scientific domains. We highlight its potential to drive new model architectures and learning strategies that improve robustness, increase interpretability, and better align with the objectives of generative modeling.

Pre-trained large language models demonstrate potential in extracting information from DNA sequences, yet adapting to a variety of tasks and data modalities remains a challenge. To address this, we propose DNAGPT, a generalized DNA pre-training model trained on over 200 billion base pairs from all mammals. By enhancing the classic GPT model with a binary classification task (DNA sequence order), a numerical regression task (guanine-cytosine content prediction), and a comprehensive token language, DNAGPT can handle versatile DNA analysis tasks while processing both sequence and numerical data. Our evaluation of genomic signal and region recognition, mRNA abundance regression, and artificial genomes generation tasks demonstrates DNAGPT's superior performance compared to existing models designed for specific downstream tasks, benefiting from pre-training using the newly designed model structure.