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Sep 25

Long-context Protein Language Model

Self-supervised training of language models (LMs) has seen great success for protein sequences in learning meaningful representations and for generative drug design. Most protein LMs are based on the Transformer architecture trained on individual proteins with short context lengths. Such protein LMs cannot extrapolate to longer proteins and protein complexes well. They also fail to account for the underlying biological mechanisms carried out by biomolecular interactions and dynamics i.e., proteins often interact with other proteins, molecules, and pathways in complex biological systems. In this work, we propose LC-PLM based on an alternative protein LM architecture, BiMamba-S, built off selective structured state-space models, to learn high-quality universal protein representations at the amino acid token level using masked language modeling. We also introduce its graph-contextual variant, LC-PLM-G, which contextualizes protein-protein interaction (PPI) graphs for a second stage of training. LC-PLM demonstrates favorable neural scaling laws, better length extrapolation capability, and a 7% to 34% improvement on protein downstream tasks than Transformer-based ESM-2. LC-PLM-G further trained within the context of PPI graphs shows promising results on protein structure and function prediction tasks. Our study demonstrates the benefit of increasing the context size with computationally efficient LM architecture (e.g. structured state space models) in learning universal protein representations and incorporating molecular interaction context contained in biological graphs.

Mamba: Linear-Time Sequence Modeling with Selective State Spaces

Foundation models, now powering most of the exciting applications in deep learning, are almost universally based on the Transformer architecture and its core attention module. Many subquadratic-time architectures such as linear attention, gated convolution and recurrent models, and structured state space models (SSMs) have been developed to address Transformers' computational inefficiency on long sequences, but they have not performed as well as attention on important modalities such as language. We identify that a key weakness of such models is their inability to perform content-based reasoning, and make several improvements. First, simply letting the SSM parameters be functions of the input addresses their weakness with discrete modalities, allowing the model to selectively propagate or forget information along the sequence length dimension depending on the current token. Second, even though this change prevents the use of efficient convolutions, we design a hardware-aware parallel algorithm in recurrent mode. We integrate these selective SSMs into a simplified end-to-end neural network architecture without attention or even MLP blocks (Mamba). Mamba enjoys fast inference (5times higher throughput than Transformers) and linear scaling in sequence length, and its performance improves on real data up to million-length sequences. As a general sequence model backbone, Mamba achieves state-of-the-art performance across several modalities such as language, audio, and genomics. On language modeling, our Mamba-3B model outperforms Transformers of the same size and matches Transformers twice its size, both in pretraining and downstream evaluation.

Graph Mamba: Towards Learning on Graphs with State Space Models

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.

Selective Structured State-Spaces for Long-Form Video Understanding

Effective modeling of complex spatiotemporal dependencies in long-form videos remains an open problem. The recently proposed Structured State-Space Sequence (S4) model with its linear complexity offers a promising direction in this space. However, we demonstrate that treating all image-tokens equally as done by S4 model can adversely affect its efficiency and accuracy. To address this limitation, we present a novel Selective S4 (i.e., S5) model that employs a lightweight mask generator to adaptively select informative image tokens resulting in more efficient and accurate modeling of long-term spatiotemporal dependencies in videos. Unlike previous mask-based token reduction methods used in transformers, our S5 model avoids the dense self-attention calculation by making use of the guidance of the momentum-updated S4 model. This enables our model to efficiently discard less informative tokens and adapt to various long-form video understanding tasks more effectively. However, as is the case for most token reduction methods, the informative image tokens could be dropped incorrectly. To improve the robustness and the temporal horizon of our model, we propose a novel long-short masked contrastive learning (LSMCL) approach that enables our model to predict longer temporal context using shorter input videos. We present extensive comparative results using three challenging long-form video understanding datasets (LVU, COIN and Breakfast), demonstrating that our approach consistently outperforms the previous state-of-the-art S4 model by up to 9.6% accuracy while reducing its memory footprint by 23%.

Spatial-Mamba: Effective Visual State Space Models via Structure-aware State Fusion

Selective state space models (SSMs), such as Mamba, highly excel at capturing long-range dependencies in 1D sequential data, while their applications to 2D vision tasks still face challenges. Current visual SSMs often convert images into 1D sequences and employ various scanning patterns to incorporate local spatial dependencies. However, these methods are limited in effectively capturing the complex image spatial structures and the increased computational cost caused by the lengthened scanning paths. To address these limitations, we propose Spatial-Mamba, a novel approach that establishes neighborhood connectivity directly in the state space. Instead of relying solely on sequential state transitions, we introduce a structure-aware state fusion equation, which leverages dilated convolutions to capture image spatial structural dependencies, significantly enhancing the flow of visual contextual information. Spatial-Mamba proceeds in three stages: initial state computation in a unidirectional scan, spatial context acquisition through structure-aware state fusion, and final state computation using the observation equation. Our theoretical analysis shows that Spatial-Mamba unifies the original Mamba and linear attention under the same matrix multiplication framework, providing a deeper understanding of our method. Experimental results demonstrate that Spatial-Mamba, even with a single scan, attains or surpasses the state-of-the-art SSM-based models in image classification, detection and segmentation. Source codes and trained models can be found at https://github.com/EdwardChasel/Spatial-Mamba.

MambaMIM: Pre-training Mamba with State Space Token Interpolation and its Application to Medical Image Segmentation

Recently, the state space model Mamba has demonstrated efficient long-sequence modeling capabilities, particularly for addressing long-sequence visual tasks in 3D medical imaging. However, existing generative self-supervised learning methods have not yet fully unleashed Mamba's potential for handling long-range dependencies because they overlook the inherent causal properties of state space sequences in masked modeling. To address this challenge, we propose a general-purpose pre-training framework called MambaMIM, a masked image modeling method based on a novel TOKen-Interpolation strategy (TOKI) for the selective structure state space sequence, which learns causal relationships of state space within the masked sequence. Further, MambaMIM introduces a bottom-up 3D hybrid masking strategy to maintain a masking consistency across different architectures and can be used on any single or hybrid Mamba architecture to enhance its multi-scale and long-range representation capability. We pre-train MambaMIM on a large-scale dataset of 6.8K CT scans and evaluate its performance across eight public medical segmentation benchmarks. Extensive downstream experiments reveal the feasibility and advancement of using Mamba for medical image pre-training. In particular, when we apply the MambaMIM to a customized architecture that hybridizes MedNeXt and Vision Mamba, we consistently obtain the state-of-the-art segmentation performance. The code is available at: https://github.com/FengheTan9/MambaMIM.

Res-VMamba: Fine-Grained Food Category Visual Classification Using Selective State Space Models with Deep Residual Learning

Food classification is the foundation for developing food vision tasks and plays a key role in the burgeoning field of computational nutrition. Due to the complexity of food requiring fine-grained classification, recent academic research mainly modifies Convolutional Neural Networks (CNNs) and/or Vision Transformers (ViTs) to perform food category classification. However, to learn fine-grained features, the CNN backbone needs additional structural design, whereas ViT, containing the self-attention module, has increased computational complexity. In recent months, a new Sequence State Space (S4) model, through a Selection mechanism and computation with a Scan (S6), colloquially termed Mamba, has demonstrated superior performance and computation efficiency compared to the Transformer architecture. The VMamba model, which incorporates the Mamba mechanism into image tasks (such as classification), currently establishes the state-of-the-art (SOTA) on the ImageNet dataset. In this research, we introduce an academically underestimated food dataset CNFOOD-241, and pioneer the integration of a residual learning framework within the VMamba model to concurrently harness both global and local state features inherent in the original VMamba architectural design. The research results show that VMamba surpasses current SOTA models in fine-grained and food classification. The proposed Res-VMamba further improves the classification accuracy to 79.54\% without pretrained weight. Our findings elucidate that our proposed methodology establishes a new benchmark for SOTA performance in food recognition on the CNFOOD-241 dataset. The code can be obtained on GitHub: https://github.com/ChiShengChen/ResVMamba.

Demystifying the Token Dynamics of Deep Selective State Space Models

Selective state space models (SSM), such as Mamba, have gained prominence for their effectiveness in modeling sequential data. Despite their outstanding empirical performance, a comprehensive theoretical understanding of deep selective SSM remains elusive, hindering their further development and adoption for applications that need high fidelity. In this paper, we investigate the dynamical properties of tokens in a pre-trained Mamba model. In particular, we derive the dynamical system governing the continuous-time limit of the Mamba model and characterize the asymptotic behavior of its solutions. In the one-dimensional case, we prove that only one of the following two scenarios happens: either all tokens converge to zero, or all tokens diverge to infinity. We provide criteria based on model parameters to determine when each scenario occurs. For the convergent scenario, we empirically verify that this scenario negatively impacts the model's performance. For the divergent scenario, we prove that different tokens will diverge to infinity at different rates, thereby contributing unequally to the updates during model training. Based on these investigations, we propose two refinements for the model: excluding the convergent scenario and reordering tokens based on their importance scores, both aimed at improving practical performance. Our experimental results validate these refinements, offering insights into enhancing Mamba's effectiveness in real-world applications.

Structured State Space Models for In-Context Reinforcement Learning

Structured state space sequence (S4) models have recently achieved state-of-the-art performance on long-range sequence modeling tasks. These models also have fast inference speeds and parallelisable training, making them potentially useful in many reinforcement learning settings. We propose a modification to a variant of S4 that enables us to initialise and reset the hidden state in parallel, allowing us to tackle reinforcement learning tasks. We show that our modified architecture runs asymptotically faster than Transformers in sequence length and performs better than RNN's on a simple memory-based task. We evaluate our modified architecture on a set of partially-observable environments and find that, in practice, our model outperforms RNN's while also running over five times faster. Then, by leveraging the model's ability to handle long-range sequences, we achieve strong performance on a challenging meta-learning task in which the agent is given a randomly-sampled continuous control environment, combined with a randomly-sampled linear projection of the environment's observations and actions. Furthermore, we show the resulting model can adapt to out-of-distribution held-out tasks. Overall, the results presented in this paper show that structured state space models are fast and performant for in-context reinforcement learning tasks. We provide code at https://github.com/luchris429/popjaxrl.

A Survey on Structured State Space Sequence (S4) Models

Recent advancements in sequence modeling have led to the emergence of Structured State Space Models (SSMs) as an efficient alternative to Recurrent Neural Networks (RNNs) and Transformers, addressing challenges in long-range dependency modeling and computational efficiency. While RNNs suffer from vanishing gradients and sequential inefficiencies, and Transformers face quadratic complexity, SSMs leverage structured recurrence and state-space representations to achieve superior long-sequence processing with linear or near-linear complexity. This survey provides a comprehensive review of SSMs, tracing their evolution from the foundational S4 model to its successors like Mamba, Simplified Structured State Space Sequence Model (S5), and Jamba, highlighting their improvements in computational efficiency, memory optimization, and inference speed. By comparing SSMs with traditional sequence models across domains such as natural language processing (NLP), speech recognition, vision, and time-series forecasting, we demonstrate their advantages in handling long-range dependencies while reducing computational overhead. Despite their potential, challenges remain in areas such as training optimization, hybrid modeling, and interpretability. This survey serves as a structured guide for researchers and practitioners, detailing the advancements, trade-offs, and future directions of SSM-based architectures in AI and deep learning.

Efficiently Modeling Long Sequences with Structured State Spaces

A central goal of sequence modeling is designing a single principled model that can address sequence data across a range of modalities and tasks, particularly on long-range dependencies. Although conventional models including RNNs, CNNs, and Transformers have specialized variants for capturing long dependencies, they still struggle to scale to very long sequences of 10000 or more steps. A promising recent approach proposed modeling sequences by simulating the fundamental state space model (SSM) \( x'(t) = Ax(t) + Bu(t), y(t) = Cx(t) + Du(t) \), and showed that for appropriate choices of the state matrix \( A \), this system could handle long-range dependencies mathematically and empirically. However, this method has prohibitive computation and memory requirements, rendering it infeasible as a general sequence modeling solution. We propose the Structured State Space sequence model (S4) based on a new parameterization for the SSM, and show that it can be computed much more efficiently than prior approaches while preserving their theoretical strengths. Our technique involves conditioning \( A \) with a low-rank correction, allowing it to be diagonalized stably and reducing the SSM to the well-studied computation of a Cauchy kernel. S4 achieves strong empirical results across a diverse range of established benchmarks, including (i) 91\% accuracy on sequential CIFAR-10 with no data augmentation or auxiliary losses, on par with a larger 2-D ResNet, (ii) substantially closing the gap to Transformers on image and language modeling tasks, while performing generation 60times faster (iii) SoTA on every task from the Long Range Arena benchmark, including solving the challenging Path-X task of length 16k that all prior work fails on, while being as efficient as all competitors.

On the Parameterization and Initialization of Diagonal State Space Models

State space models (SSM) have recently been shown to be very effective as a deep learning layer as a promising alternative to sequence models such as RNNs, CNNs, or Transformers. The first version to show this potential was the S4 model, which is particularly effective on tasks involving long-range dependencies by using a prescribed state matrix called the HiPPO matrix. While this has an interpretable mathematical mechanism for modeling long dependencies, it introduces a custom representation and algorithm that can be difficult to implement. On the other hand, a recent variant of S4 called DSS showed that restricting the state matrix to be fully diagonal can still preserve the performance of the original model when using a specific initialization based on approximating S4's matrix. This work seeks to systematically understand how to parameterize and initialize such diagonal state space models. While it follows from classical results that almost all SSMs have an equivalent diagonal form, we show that the initialization is critical for performance. We explain why DSS works mathematically, by showing that the diagonal restriction of S4's matrix surprisingly recovers the same kernel in the limit of infinite state dimension. We also systematically describe various design choices in parameterizing and computing diagonal SSMs, and perform a controlled empirical study ablating the effects of these choices. Our final model S4D is a simple diagonal version of S4 whose kernel computation requires just 2 lines of code and performs comparably to S4 in almost all settings, with state-of-the-art results for image, audio, and medical time-series domains, and averaging 85\% on the Long Range Arena benchmark.

How to Train Your HiPPO: State Space Models with Generalized Orthogonal Basis Projections

Linear time-invariant state space models (SSM) are a classical model from engineering and statistics, that have recently been shown to be very promising in machine learning through the Structured State Space sequence model (S4). A core component of S4 involves initializing the SSM state matrix to a particular matrix called a HiPPO matrix, which was empirically important for S4's ability to handle long sequences. However, the specific matrix that S4 uses was actually derived in previous work for a particular time-varying dynamical system, and the use of this matrix as a time-invariant SSM had no known mathematical interpretation. Consequently, the theoretical mechanism by which S4 models long-range dependencies actually remains unexplained. We derive a more general and intuitive formulation of the HiPPO framework, which provides a simple mathematical interpretation of S4 as a decomposition onto exponentially-warped Legendre polynomials, explaining its ability to capture long dependencies. Our generalization introduces a theoretically rich class of SSMs that also lets us derive more intuitive S4 variants for other bases such as the Fourier basis, and explains other aspects of training S4, such as how to initialize the important timescale parameter. These insights improve S4's performance to 86% on the Long Range Arena benchmark, with 96% on the most difficult Path-X task.

Robustifying State-space Models for Long Sequences via Approximate Diagonalization

State-space models (SSMs) have recently emerged as a framework for learning long-range sequence tasks. An example is the structured state-space sequence (S4) layer, which uses the diagonal-plus-low-rank structure of the HiPPO initialization framework. However, the complicated structure of the S4 layer poses challenges; and, in an effort to address these challenges, models such as S4D and S5 have considered a purely diagonal structure. This choice simplifies the implementation, improves computational efficiency, and allows channel communication. However, diagonalizing the HiPPO framework is itself an ill-posed problem. In this paper, we propose a general solution for this and related ill-posed diagonalization problems in machine learning. We introduce a generic, backward-stable "perturb-then-diagonalize" (PTD) methodology, which is based on the pseudospectral theory of non-normal operators, and which may be interpreted as the approximate diagonalization of the non-normal matrices defining SSMs. Based on this, we introduce the S4-PTD and S5-PTD models. Through theoretical analysis of the transfer functions of different initialization schemes, we demonstrate that the S4-PTD/S5-PTD initialization strongly converges to the HiPPO framework, while the S4D/S5 initialization only achieves weak convergences. As a result, our new models show resilience to Fourier-mode noise-perturbed inputs, a crucial property not achieved by the S4D/S5 models. In addition to improved robustness, our S5-PTD model averages 87.6% accuracy on the Long-Range Arena benchmark, demonstrating that the PTD methodology helps to improve the accuracy of deep learning models.

Chimera: Effectively Modeling Multivariate Time Series with 2-Dimensional State Space Models

Modeling multivariate time series is a well-established problem with a wide range of applications from healthcare to financial markets. Traditional State Space Models (SSMs) are classical approaches for univariate time series modeling due to their simplicity and expressive power to represent linear dependencies. They, however, have fundamentally limited expressive power to capture non-linear dependencies, are slow in practice, and fail to model the inter-variate information flow. Despite recent attempts to improve the expressive power of SSMs by using deep structured SSMs, the existing methods are either limited to univariate time series, fail to model complex patterns (e.g., seasonal patterns), fail to dynamically model the dependencies of variate and time dimensions, and/or are input-independent. We present Chimera that uses two input-dependent 2-D SSM heads with different discretization processes to learn long-term progression and seasonal patterns. To improve the efficiency of complex 2D recurrence, we present a fast training using a new 2-dimensional parallel selective scan. We further present and discuss 2-dimensional Mamba and Mamba-2 as the spacial cases of our 2D SSM. Our experimental evaluation shows the superior performance of Chimera on extensive and diverse benchmarks, including ECG and speech time series classification, long-term and short-term time series forecasting, and time series anomaly detection.

Mamba-FSCIL: Dynamic Adaptation with Selective State Space Model for Few-Shot Class-Incremental Learning

Few-shot class-incremental learning (FSCIL) confronts the challenge of integrating new classes into a model with minimal training samples while preserving the knowledge of previously learned classes. Traditional methods widely adopt static adaptation relying on a fixed parameter space to learn from data that arrive sequentially, prone to overfitting to the current session. Existing dynamic strategies require the expansion of the parameter space continually, leading to increased complexity. To address these challenges, we integrate the recently proposed selective state space model (SSM) into FSCIL. Concretely, we propose a dual selective SSM projector that dynamically adjusts the projection parameters based on the intermediate features for dynamic adaptation. The dual design enables the model to maintain the robust features of base classes, while adaptively learning distinctive feature shifts for novel classes. Additionally, we develop a class-sensitive selective scan mechanism to guide dynamic adaptation. It minimizes the disruption to base-class representations caused by training on novel data, and meanwhile, forces the selective scan to perform in distinct patterns between base and novel classes. Experiments on miniImageNet, CUB-200, and CIFAR-100 demonstrate that our framework outperforms the existing state-of-the-art methods. The code is available at https://github.com/xiaojieli0903/Mamba-FSCIL.

Is Mamba Effective for Time Series Forecasting?

In the realm of time series forecasting (TSF), it is imperative for models to adeptly discern and distill hidden patterns within historical time series data to forecast future states. Transformer-based models exhibit formidable efficacy in TSF, primarily attributed to their advantage in apprehending these patterns. However, the quadratic complexity of the Transformer leads to low computational efficiency and high costs, which somewhat hinders the deployment of the TSF model in real-world scenarios. Recently, Mamba, a selective state space model, has gained traction due to its ability to process dependencies in sequences while maintaining near-linear complexity. For TSF tasks, these characteristics enable Mamba to comprehend hidden patterns as the Transformer and reduce computational overhead compared to the Transformer. Therefore, we propose a Mamba-based model named Simple-Mamba (S-Mamba) for TSF. Specifically, we tokenize the time points of each variate autonomously via a linear layer. A bidirectional Mamba layer is utilized to extract inter-variate correlations and a Feed-Forward Network is set to learn temporal dependencies. Finally, the generation of forecast outcomes through a linear mapping layer. Experiments on thirteen public datasets prove that S-Mamba maintains low computational overhead and achieves leading performance. Furthermore, we conduct extensive experiments to explore Mamba's potential in TSF tasks. Our code is available at https://github.com/wzhwzhwzh0921/S-D-Mamba.

Effectively Modeling Time Series with Simple Discrete State Spaces

Time series modeling is a well-established problem, which often requires that methods (1) expressively represent complicated dependencies, (2) forecast long horizons, and (3) efficiently train over long sequences. State-space models (SSMs) are classical models for time series, and prior works combine SSMs with deep learning layers for efficient sequence modeling. However, we find fundamental limitations with these prior approaches, proving their SSM representations cannot express autoregressive time series processes. We thus introduce SpaceTime, a new state-space time series architecture that improves all three criteria. For expressivity, we propose a new SSM parameterization based on the companion matrix -- a canonical representation for discrete-time processes -- which enables SpaceTime's SSM layers to learn desirable autoregressive processes. For long horizon forecasting, we introduce a "closed-loop" variation of the companion SSM, which enables SpaceTime to predict many future time-steps by generating its own layer-wise inputs. For efficient training and inference, we introduce an algorithm that reduces the memory and compute of a forward pass with the companion matrix. With sequence length ell and state-space size d, we go from O(d ell) na\"ively to O(d + ell). In experiments, our contributions lead to state-of-the-art results on extensive and diverse benchmarks, with best or second-best AUROC on 6 / 7 ECG and speech time series classification, and best MSE on 14 / 16 Informer forecasting tasks. Furthermore, we find SpaceTime (1) fits AR(p) processes that prior deep SSMs fail on, (2) forecasts notably more accurately on longer horizons than prior state-of-the-art, and (3) speeds up training on real-world ETTh1 data by 73% and 80% relative wall-clock time over Transformers and LSTMs.

Birdie: Advancing State Space Models with Reward-Driven Objectives and Curricula

Efficient state space models (SSMs), such as linear recurrent neural networks and linear attention variants, offer computational advantages over Transformers but struggle with tasks requiring long-range in-context retrieval-like text copying, associative recall, and question answering over long contexts. Previous efforts to address these challenges have focused on architectural modifications, often reintroducing computational inefficiencies. In this paper, we propose a novel training procedure, Birdie, that significantly enhances the in-context retrieval capabilities of SSMs without altering their architecture. Our approach combines bidirectional input processing with dynamic mixtures of specialized pre-training objectives, optimized via reinforcement learning. We introduce a new bidirectional SSM architecture that seamlessly transitions from bidirectional context processing to causal generation. Experimental evaluations demonstrate that Birdie markedly improves performance on retrieval-intensive tasks such as multi-number phone book lookup, long paragraph question-answering, and infilling. This narrows the performance gap with Transformers, while retaining computational efficiency. Our findings highlight the importance of training procedures in leveraging the fixed-state capacity of SSMs, offering a new direction to advance their capabilities. All code and pre-trained models are available at https://www.github.com/samblouir/birdie, with support for JAX and PyTorch.

Sparse Modular Activation for Efficient Sequence Modeling

Linear State Space Models (SSMs) have demonstrated strong performance in a variety of sequence modeling tasks due to their efficient encoding of the recurrent structure. However, in more comprehensive tasks like language modeling and machine translation, self-attention-based models still outperform SSMs. Hybrid models employing both SSM and self-attention generally show promising performance, but current approaches apply attention modules statically and uniformly to all elements in the input sequences, leading to sub-optimal quality-efficiency trade-offs. In this work, we introduce Sparse Modular Activation (SMA), a general mechanism enabling neural networks to sparsely and dynamically activate sub-modules for sequence elements in a differentiable manner. Through allowing each element to skip non-activated sub-modules, SMA reduces computation and memory consumption at both training and inference stages of sequence modeling. As a specific instantiation of SMA, we design a novel neural architecture, SeqBoat, which employs SMA to sparsely activate a Gated Attention Unit (GAU) based on the state representations learned from an SSM. By constraining the GAU to only conduct local attention on the activated inputs, SeqBoat can achieve linear inference complexity with theoretically infinite attention span, and provide substantially better quality-efficiency trade-off than the chunking-based models. With experiments on a wide range of tasks, including language modeling, speech classification and long-range arena, SeqBoat brings new state-of-the-art results among hybrid models with linear complexity and reveals the amount of attention needed for each task through the learned sparse activation patterns.

What's the Magic Word? A Control Theory of LLM Prompting

Prompt engineering is crucial for deploying LLMs but is poorly understood mathematically. We formalize LLM systems as a class of discrete stochastic dynamical systems to explore prompt engineering through the lens of control theory. We investigate the reachable set of output token sequences R_y(mathbf x_0) for which there exists a control input sequence mathbf u for each mathbf y in R_y(mathbf x_0) that steers the LLM to output mathbf y from initial state sequence mathbf x_0. We offer analytic analysis on the limitations on the controllability of self-attention in terms of reachable set, where we prove an upper bound on the reachable set of outputs R_y(mathbf x_0) as a function of the singular values of the parameter matrices. We present complementary empirical analysis on the controllability of a panel of LLMs, including Falcon-7b, Llama-7b, and Falcon-40b. Our results demonstrate a lower bound on the reachable set of outputs R_y(mathbf x_0) w.r.t. initial state sequences mathbf x_0 sampled from the Wikitext dataset. We find that the correct next Wikitext token following sequence mathbf x_0 is reachable over 97% of the time with prompts of kleq 10 tokens. We also establish that the top 75 most likely next tokens, as estimated by the LLM itself, are reachable at least 85% of the time with prompts of kleq 10 tokens. Intriguingly, short prompt sequences can dramatically alter the likelihood of specific outputs, even making the least likely tokens become the most likely ones. This control-centric analysis of LLMs demonstrates the significant and poorly understood role of input sequences in steering output probabilities, offering a foundational perspective for enhancing language model system capabilities.

Hierarchical State Space Models for Continuous Sequence-to-Sequence Modeling

Reasoning from sequences of raw sensory data is a ubiquitous problem across fields ranging from medical devices to robotics. These problems often involve using long sequences of raw sensor data (e.g. magnetometers, piezoresistors) to predict sequences of desirable physical quantities (e.g. force, inertial measurements). While classical approaches are powerful for locally-linear prediction problems, they often fall short when using real-world sensors. These sensors are typically non-linear, are affected by extraneous variables (e.g. vibration), and exhibit data-dependent drift. For many problems, the prediction task is exacerbated by small labeled datasets since obtaining ground-truth labels requires expensive equipment. In this work, we present Hierarchical State-Space Models (HiSS), a conceptually simple, new technique for continuous sequential prediction. HiSS stacks structured state-space models on top of each other to create a temporal hierarchy. Across six real-world sensor datasets, from tactile-based state prediction to accelerometer-based inertial measurement, HiSS outperforms state-of-the-art sequence models such as causal Transformers, LSTMs, S4, and Mamba by at least 23% on MSE. Our experiments further indicate that HiSS demonstrates efficient scaling to smaller datasets and is compatible with existing data-filtering techniques. Code, datasets and videos can be found on https://hiss-csp.github.io.

Combining Recurrent, Convolutional, and Continuous-time Models with Linear State-Space Layers

Recurrent neural networks (RNNs), temporal convolutions, and neural differential equations (NDEs) are popular families of deep learning models for time-series data, each with unique strengths and tradeoffs in modeling power and computational efficiency. We introduce a simple sequence model inspired by control systems that generalizes these approaches while addressing their shortcomings. The Linear State-Space Layer (LSSL) maps a sequence u mapsto y by simply simulating a linear continuous-time state-space representation x = Ax + Bu, y = Cx + Du. Theoretically, we show that LSSL models are closely related to the three aforementioned families of models and inherit their strengths. For example, they generalize convolutions to continuous-time, explain common RNN heuristics, and share features of NDEs such as time-scale adaptation. We then incorporate and generalize recent theory on continuous-time memorization to introduce a trainable subset of structured matrices A that endow LSSLs with long-range memory. Empirically, stacking LSSL layers into a simple deep neural network obtains state-of-the-art results across time series benchmarks for long dependencies in sequential image classification, real-world healthcare regression tasks, and speech. On a difficult speech classification task with length-16000 sequences, LSSL outperforms prior approaches by 24 accuracy points, and even outperforms baselines that use hand-crafted features on 100x shorter sequences.

Hydra: A 1.6B-Parameter State-Space Language Model with Sparse Attention, Mixture-of-Experts, and Memory

We present Hydra as an architectural proposal for hybrid long-context language models that combine conditional computation, long-context memory mechanisms, and sparse mixture-of-experts within an approximately 1.6B parameter design envelope. Hydra integrates a Mamba-style Structured State Space Model (SSM) backbone with intermittent sparse global attention, chunk-level MoE feed-forward routing, and dual (workspace plus factual PKM) memories. We formalize the component interfaces, give transparent parameter and complexity accounting, and outline a staged curriculum intended to stably activate the parts. We accompany the specification with illustrative toy-scale prototype measurements (tens of millions of parameters on synthetic data) whose sole purpose is to demonstrate implementation feasibility and qualitative scaling behaviors (for example, long-context throughput crossover and controllable expert routing), not to claim competitive full-scale performance. We explicitly delineate assumptions and open risks (training complexity, memory utilization, specialization dynamics) and position Hydra as a blueprint to stimulate empirical follow-up rather than a finished system. By combining SSM efficiency, selective sparse attention, MoE capacity, and learnable memory, Hydra sketches a path toward modular, input-adaptive long-context language models; validating end-task gains at target scale remains future work.

Mamba-360: Survey of State Space Models as Transformer Alternative for Long Sequence Modelling: Methods, Applications, and Challenges

Sequence modeling is a crucial area across various domains, including Natural Language Processing (NLP), speech recognition, time series forecasting, music generation, and bioinformatics. Recurrent Neural Networks (RNNs) and Long Short Term Memory Networks (LSTMs) have historically dominated sequence modeling tasks like Machine Translation, Named Entity Recognition (NER), etc. However, the advancement of transformers has led to a shift in this paradigm, given their superior performance. Yet, transformers suffer from O(N^2) attention complexity and challenges in handling inductive bias. Several variations have been proposed to address these issues which use spectral networks or convolutions and have performed well on a range of tasks. However, they still have difficulty in dealing with long sequences. State Space Models(SSMs) have emerged as promising alternatives for sequence modeling paradigms in this context, especially with the advent of S4 and its variants, such as S4nd, Hippo, Hyena, Diagnol State Spaces (DSS), Gated State Spaces (GSS), Linear Recurrent Unit (LRU), Liquid-S4, Mamba, etc. In this survey, we categorize the foundational SSMs based on three paradigms namely, Gating architectures, Structural architectures, and Recurrent architectures. This survey also highlights diverse applications of SSMs across domains such as vision, video, audio, speech, language (especially long sequence modeling), medical (including genomics), chemical (like drug design), recommendation systems, and time series analysis, including tabular data. Moreover, we consolidate the performance of SSMs on benchmark datasets like Long Range Arena (LRA), WikiText, Glue, Pile, ImageNet, Kinetics-400, sstv2, as well as video datasets such as Breakfast, COIN, LVU, and various time series datasets. The project page for Mamba-360 work is available on this webpage.https://github.com/badripatro/mamba360.

FlowState: Sampling Rate Invariant Time Series Forecasting

Foundation models (FMs) have transformed natural language processing, but their success has not yet translated to time series forecasting. Existing time series foundation models (TSFMs), often based on transformer variants, struggle with generalization across varying context and target lengths, lack adaptability to different sampling rates, and are computationally inefficient. We introduce FlowState, a novel TSFM architecture that addresses these challenges through two key innovations: a state space model (SSM) based encoder and a functional basis decoder. This design enables continuous-time modeling and dynamic time-scale adjustment, allowing FlowState to inherently generalize across all possible temporal resolutions, and dynamically adjust the forecasting horizons. In contrast to other state-of-the-art TSFMs, which require training data across all possible sampling rates to memorize patterns at each scale, FlowState inherently adapts its internal dynamics to the input scale, enabling smaller models, reduced data requirements, and improved efficiency. We further propose an efficient pretraining strategy that improves robustness and accelerates training. Despite being the smallest model, FlowState outperforms all other models and is state-of-the-art for the GIFT-ZS and the Chronos-ZS benchmarks. Ablation studies confirm the effectiveness of its components, and we demonstrate its unique ability to adapt online to varying input sampling rates.

Solving robust MDPs as a sequence of static RL problems

Designing control policies whose performance level is guaranteed to remain above a given threshold in a span of environments is a critical feature for the adoption of reinforcement learning (RL) in real-world applications. The search for such robust policies is a notoriously difficult problem, related to the so-called dynamic model of transition function uncertainty, where the environment dynamics are allowed to change at each time step. But in practical cases, one is rather interested in robustness to a span of static transition models throughout interaction episodes. The static model is known to be harder to solve than the dynamic one, and seminal algorithms, such as robust value iteration, as well as most recent works on deep robust RL, build upon the dynamic model. In this work, we propose to revisit the static model. We suggest an analysis of why solving the static model under some mild hypotheses is a reasonable endeavor, based on an equivalence with the dynamic model, and formalize the general intuition that robust MDPs can be solved by tackling a series of static problems. We introduce a generic meta-algorithm called IWOCS, which incrementally identifies worst-case transition models so as to guide the search for a robust policy. Discussion on IWOCS sheds light on new ways to decouple policy optimization and adversarial transition functions and opens new perspectives for analysis. We derive a deep RL version of IWOCS and demonstrate it is competitive with state-of-the-art algorithms on classical benchmarks.

Disentangling Shape and Pose for Object-Centric Deep Active Inference Models

Active inference is a first principles approach for understanding the brain in particular, and sentient agents in general, with the single imperative of minimizing free energy. As such, it provides a computational account for modelling artificial intelligent agents, by defining the agent's generative model and inferring the model parameters, actions and hidden state beliefs. However, the exact specification of the generative model and the hidden state space structure is left to the experimenter, whose design choices influence the resulting behaviour of the agent. Recently, deep learning methods have been proposed to learn a hidden state space structure purely from data, alleviating the experimenter from this tedious design task, but resulting in an entangled, non-interpreteable state space. In this paper, we hypothesize that such a learnt, entangled state space does not necessarily yield the best model in terms of free energy, and that enforcing different factors in the state space can yield a lower model complexity. In particular, we consider the problem of 3D object representation, and focus on different instances of the ShapeNet dataset. We propose a model that factorizes object shape, pose and category, while still learning a representation for each factor using a deep neural network. We show that models, with best disentanglement properties, perform best when adopted by an active agent in reaching preferred observations.

Foundation Inference Models for Markov Jump Processes

Markov jump processes are continuous-time stochastic processes which describe dynamical systems evolving in discrete state spaces. These processes find wide application in the natural sciences and machine learning, but their inference is known to be far from trivial. In this work we introduce a methodology for zero-shot inference of Markov jump processes (MJPs), on bounded state spaces, from noisy and sparse observations, which consists of two components. First, a broad probability distribution over families of MJPs, as well as over possible observation times and noise mechanisms, with which we simulate a synthetic dataset of hidden MJPs and their noisy observation process. Second, a neural network model that processes subsets of the simulated observations, and that is trained to output the initial condition and rate matrix of the target MJP in a supervised way. We empirically demonstrate that one and the same (pretrained) model can infer, in a zero-shot fashion, hidden MJPs evolving in state spaces of different dimensionalities. Specifically, we infer MJPs which describe (i) discrete flashing ratchet systems, which are a type of Brownian motors, and the conformational dynamics in (ii) molecular simulations, (iii) experimental ion channel data and (iv) simple protein folding models. What is more, we show that our model performs on par with state-of-the-art models which are finetuned to the target datasets.

A Low-complexity Structured Neural Network to Realize States of Dynamical Systems

Data-driven learning is rapidly evolving and places a new perspective on realizing state-space dynamical systems. However, dynamical systems derived from nonlinear ordinary differential equations (ODEs) suffer from limitations in computational efficiency. Thus, this paper stems from data-driven learning to advance states of dynamical systems utilizing a structured neural network (StNN). The proposed learning technique also seeks to identify an optimal, low-complexity operator to solve dynamical systems, the so-called Hankel operator, derived from time-delay measurements. Thus, we utilize the StNN based on the Hankel operator to solve dynamical systems as an alternative to existing data-driven techniques. We show that the proposed StNN reduces the number of parameters and computational complexity compared with the conventional neural networks and also with the classical data-driven techniques, such as Sparse Identification of Nonlinear Dynamics (SINDy) and Hankel Alternative view of Koopman (HAVOK), which is commonly known as delay-Dynamic Mode Decomposition(DMD) or Hankel-DMD. More specifically, we present numerical simulations to solve dynamical systems utilizing the StNN based on the Hankel operator beginning from the fundamental Lotka-Volterra model, where we compare the StNN with the LEarning Across Dynamical Systems (LEADS), and extend our analysis to highly nonlinear and chaotic Lorenz systems, comparing the StNN with conventional neural networks, SINDy, and HAVOK. Hence, we show that the proposed StNN paves the way for realizing state-space dynamical systems with a low-complexity learning algorithm, enabling prediction and understanding of future states.

Overcoming Long-Context Limitations of State-Space Models via Context-Dependent Sparse Attention

Efficient long-context modeling remains a critical challenge for natural language processing (NLP), as the time complexity of the predominant Transformer architecture scales quadratically with the sequence length. While state-space models (SSMs) offer alternative sub-quadratic solutions, they struggle to capture long-range dependencies effectively. In this work, we focus on analyzing and improving the long-context modeling capabilities of SSMs. We show that the widely used synthetic task, associative recall, which requires a model to recall a value associated with a single key without context, insufficiently represents the complexities of real-world long-context modeling. To address this limitation, we extend the associative recall to a novel synthetic task, joint recall, which requires a model to recall the value associated with a key given in a specified context. Theoretically, we prove that SSMs do not have the expressiveness to solve multi-query joint recall in sub-quadratic time complexity. To resolve this issue, we propose a solution based on integrating SSMs with Context-Dependent Sparse Attention (CDSA), which has the expressiveness to solve multi-query joint recall with sub-quadratic computation. To bridge the gap between theoretical analysis and real-world applications, we propose locality-sensitive Hashing Attention with sparse Key Selection (HAX), which instantiates the theoretical solution and is further tailored to natural language domains. Extensive experiments on both synthetic and real-world long-context benchmarks show that HAX consistently outperforms SSM baselines and SSMs integrated with context-independent sparse attention (CISA).

Provable Benefits of Multi-task RL under Non-Markovian Decision Making Processes

In multi-task reinforcement learning (RL) under Markov decision processes (MDPs), the presence of shared latent structures among multiple MDPs has been shown to yield significant benefits to the sample efficiency compared to single-task RL. In this paper, we investigate whether such a benefit can extend to more general sequential decision making problems, such as partially observable MDPs (POMDPs) and more general predictive state representations (PSRs). The main challenge here is that the large and complex model space makes it hard to identify what types of common latent structure of multi-task PSRs can reduce the model complexity and improve sample efficiency. To this end, we posit a joint model class for tasks and use the notion of eta-bracketing number to quantify its complexity; this number also serves as a general metric to capture the similarity of tasks and thus determines the benefit of multi-task over single-task RL. We first study upstream multi-task learning over PSRs, in which all tasks share the same observation and action spaces. We propose a provably efficient algorithm UMT-PSR for finding near-optimal policies for all PSRs, and demonstrate that the advantage of multi-task learning manifests if the joint model class of PSRs has a smaller eta-bracketing number compared to that of individual single-task learning. We also provide several example multi-task PSRs with small eta-bracketing numbers, which reap the benefits of multi-task learning. We further investigate downstream learning, in which the agent needs to learn a new target task that shares some commonalities with the upstream tasks via a similarity constraint. By exploiting the learned PSRs from the upstream, we develop a sample-efficient algorithm that provably finds a near-optimal policy.

LongMamba: Enhancing Mamba's Long Context Capabilities via Training-Free Receptive Field Enlargement

State space models (SSMs) have emerged as an efficient alternative to Transformer models for language modeling, offering linear computational complexity and constant memory usage as context length increases. However, despite their efficiency in handling long contexts, recent studies have shown that SSMs, such as Mamba models, generally underperform compared to Transformers in long-context understanding tasks. To address this significant shortfall and achieve both efficient and accurate long-context understanding, we propose LongMamba, a training-free technique that significantly enhances the long-context capabilities of Mamba models. LongMamba builds on our discovery that the hidden channels in Mamba can be categorized into local and global channels based on their receptive field lengths, with global channels primarily responsible for long-context capability. These global channels can become the key bottleneck as the input context lengthens. Specifically, when input lengths largely exceed the training sequence length, global channels exhibit limitations in adaptively extend their receptive fields, leading to Mamba's poor long-context performance. The key idea of LongMamba is to mitigate the hidden state memory decay in these global channels by preventing the accumulation of unimportant tokens in their memory. This is achieved by first identifying critical tokens in the global channels and then applying token filtering to accumulate only those critical tokens. Through extensive benchmarking across synthetic and real-world long-context scenarios, LongMamba sets a new standard for Mamba's long-context performance, significantly extending its operational range without requiring additional training. Our code is available at https://github.com/GATECH-EIC/LongMamba.

An Overview of Diffusion Models: Applications, Guided Generation, Statistical Rates and Optimization

Diffusion models, a powerful and universal generative AI technology, have achieved tremendous success in computer vision, audio, reinforcement learning, and computational biology. In these applications, diffusion models provide flexible high-dimensional data modeling, and act as a sampler for generating new samples under active guidance towards task-desired properties. Despite the significant empirical success, theory of diffusion models is very limited, potentially slowing down principled methodological innovations for further harnessing and improving diffusion models. In this paper, we review emerging applications of diffusion models, understanding their sample generation under various controls. Next, we overview the existing theories of diffusion models, covering their statistical properties and sampling capabilities. We adopt a progressive routine, beginning with unconditional diffusion models and connecting to conditional counterparts. Further, we review a new avenue in high-dimensional structured optimization through conditional diffusion models, where searching for solutions is reformulated as a conditional sampling problem and solved by diffusion models. Lastly, we discuss future directions about diffusion models. The purpose of this paper is to provide a well-rounded theoretical exposure for stimulating forward-looking theories and methods of diffusion models.

STree: Speculative Tree Decoding for Hybrid State-Space Models

Speculative decoding is a technique to leverage hardware concurrency to improve the efficiency of large-scale autoregressive (AR) Transformer models by enabling multiple steps of token generation in a single forward pass. State-space models (SSMs) are already more efficient than AR Transformers, since their state summarizes all past data with no need to cache or re-process tokens in the sliding window context. However, their state can also comprise thousands of tokens; so, speculative decoding has recently been extended to SSMs. Existing approaches, however, do not leverage the tree-based verification methods, since current SSMs lack the means to compute a token tree efficiently. We propose the first scalable algorithm to perform tree-based speculative decoding in state-space models (SSMs) and hybrid architectures of SSMs and Transformer layers. We exploit the structure of accumulated state transition matrices to facilitate tree-based speculative decoding with minimal overhead to current SSM state update implementations. With the algorithm, we describe a hardware-aware implementation that improves naive application of AR Transformer tree-based speculative decoding methods to SSMs. Furthermore, we outperform vanilla speculative decoding with SSMs even with a baseline drafting model and tree structure on three different benchmarks, opening up opportunities for further speed up with SSM and hybrid model inference. Code will be released upon paper acceptance.

An Empirical Study of Mamba-based Language Models

Selective state-space models (SSMs) like Mamba overcome some of the shortcomings of Transformers, such as quadratic computational complexity with sequence length and large inference-time memory requirements from the key-value cache. Moreover, recent studies have shown that SSMs can match or exceed the language modeling capabilities of Transformers, making them an attractive alternative. In a controlled setting (e.g., same data), however, studies so far have only presented small scale experiments comparing SSMs to Transformers. To understand the strengths and weaknesses of these architectures at larger scales, we present a direct comparison between 8B-parameter Mamba, Mamba-2, and Transformer models trained on the same datasets of up to 3.5T tokens. We also compare these models to a hybrid architecture consisting of 43% Mamba-2, 7% attention, and 50% MLP layers (Mamba-2-Hybrid). Using a diverse set of tasks, we answer the question of whether Mamba models can match Transformers at larger training budgets. Our results show that while pure SSMs match or exceed Transformers on many tasks, they lag behind Transformers on tasks which require strong copying or in-context learning abilities (e.g., 5-shot MMLU, Phonebook) or long-context reasoning. In contrast, we find that the 8B Mamba-2-Hybrid exceeds the 8B Transformer on all 12 standard tasks we evaluated (+2.65 points on average) and is predicted to be up to 8x faster when generating tokens at inference time. To validate long-context capabilities, we provide additional experiments evaluating variants of the Mamba-2-Hybrid and Transformer extended to support 16K, 32K, and 128K sequences. On an additional 23 long-context tasks, the hybrid model continues to closely match or exceed the Transformer on average. To enable further study, we release the checkpoints as well as the code used to train our models as part of NVIDIA's Megatron-LM project.

Almost-Linear RNNs Yield Highly Interpretable Symbolic Codes in Dynamical Systems Reconstruction

Dynamical systems (DS) theory is fundamental for many areas of science and engineering. It can provide deep insights into the behavior of systems evolving in time, as typically described by differential or recursive equations. A common approach to facilitate mathematical tractability and interpretability of DS models involves decomposing nonlinear DS into multiple linear DS separated by switching manifolds, i.e. piecewise linear (PWL) systems. PWL models are popular in engineering and a frequent choice in mathematics for analyzing the topological properties of DS. However, hand-crafting such models is tedious and only possible for very low-dimensional scenarios, while inferring them from data usually gives rise to unnecessarily complex representations with very many linear subregions. Here we introduce Almost-Linear Recurrent Neural Networks (AL-RNNs) which automatically and robustly produce most parsimonious PWL representations of DS from time series data, using as few PWL nonlinearities as possible. AL-RNNs can be efficiently trained with any SOTA algorithm for dynamical systems reconstruction (DSR), and naturally give rise to a symbolic encoding of the underlying DS that provably preserves important topological properties. We show that for the Lorenz and R\"ossler systems, AL-RNNs discover, in a purely data-driven way, the known topologically minimal PWL representations of the corresponding chaotic attractors. We further illustrate on two challenging empirical datasets that interpretable symbolic encodings of the dynamics can be achieved, tremendously facilitating mathematical and computational analysis of the underlying systems.

Accelerating Distributed Stochastic Optimization via Self-Repellent Random Walks

We study a family of distributed stochastic optimization algorithms where gradients are sampled by a token traversing a network of agents in random-walk fashion. Typically, these random-walks are chosen to be Markov chains that asymptotically sample from a desired target distribution, and play a critical role in the convergence of the optimization iterates. In this paper, we take a novel approach by replacing the standard linear Markovian token by one which follows a nonlinear Markov chain - namely the Self-Repellent Radom Walk (SRRW). Defined for any given 'base' Markov chain, the SRRW, parameterized by a positive scalar {\alpha}, is less likely to transition to states that were highly visited in the past, thus the name. In the context of MCMC sampling on a graph, a recent breakthrough in Doshi et al. (2023) shows that the SRRW achieves O(1/{\alpha}) decrease in the asymptotic variance for sampling. We propose the use of a 'generalized' version of the SRRW to drive token algorithms for distributed stochastic optimization in the form of stochastic approximation, termed SA-SRRW. We prove that the optimization iterate errors of the resulting SA-SRRW converge to zero almost surely and prove a central limit theorem, deriving the explicit form of the resulting asymptotic covariance matrix corresponding to iterate errors. This asymptotic covariance is always smaller than that of an algorithm driven by the base Markov chain and decreases at rate O(1/{\alpha}^2) - the performance benefit of using SRRW thereby amplified in the stochastic optimization context. Empirical results support our theoretical findings.

State and parameter learning with PaRIS particle Gibbs

Non-linear state-space models, also known as general hidden Markov models, are ubiquitous in statistical machine learning, being the most classical generative models for serial data and sequences in general. The particle-based, rapid incremental smoother PaRIS is a sequential Monte Carlo (SMC) technique allowing for efficient online approximation of expectations of additive functionals under the smoothing distribution in these models. Such expectations appear naturally in several learning contexts, such as likelihood estimation (MLE) and Markov score climbing (MSC). PARIS has linear computational complexity, limited memory requirements and comes with non-asymptotic bounds, convergence results and stability guarantees. Still, being based on self-normalised importance sampling, the PaRIS estimator is biased. Our first contribution is to design a novel additive smoothing algorithm, the Parisian particle Gibbs PPG sampler, which can be viewed as a PaRIS algorithm driven by conditional SMC moves, resulting in bias-reduced estimates of the targeted quantities. We substantiate the PPG algorithm with theoretical results, including new bounds on bias and variance as well as deviation inequalities. Our second contribution is to apply PPG in a learning framework, covering MLE and MSC as special examples. In this context, we establish, under standard assumptions, non-asymptotic bounds highlighting the value of bias reduction and the implicit Rao--Blackwellization of PPG. These are the first non-asymptotic results of this kind in this setting. We illustrate our theoretical results with numerical experiments supporting our claims.

A Discriminative Approach to Bayesian Filtering with Applications to Human Neural Decoding

Given a stationary state-space model that relates a sequence of hidden states and corresponding measurements or observations, Bayesian filtering provides a principled statistical framework for inferring the posterior distribution of the current state given all measurements up to the present time. For example, the Apollo lunar module implemented a Kalman filter to infer its location from a sequence of earth-based radar measurements and land safely on the moon. To perform Bayesian filtering, we require a measurement model that describes the conditional distribution of each observation given state. The Kalman filter takes this measurement model to be linear, Gaussian. Here we show how a nonlinear, Gaussian approximation to the distribution of state given observation can be used in conjunction with Bayes' rule to build a nonlinear, non-Gaussian measurement model. The resulting approach, called the Discriminative Kalman Filter (DKF), retains fast closed-form updates for the posterior. We argue there are many cases where the distribution of state given measurement is better-approximated as Gaussian, especially when the dimensionality of measurements far exceeds that of states and the Bernstein-von Mises theorem applies. Online neural decoding for brain-computer interfaces provides a motivating example, where filtering incorporates increasingly detailed measurements of neural activity to provide users control over external devices. Within the BrainGate2 clinical trial, the DKF successfully enabled three volunteers with quadriplegia to control an on-screen cursor in real-time using mental imagery alone. Participant "T9" used the DKF to type out messages on a tablet PC.

Quamba2: A Robust and Scalable Post-training Quantization Framework for Selective State Space Models

State Space Models (SSMs) are emerging as a compelling alternative to Transformers because of their consistent memory usage and high performance. Despite this, scaling up SSMs on cloud services or limited-resource devices is challenging due to their storage requirements and computational power. To overcome this, quantizing SSMs with low bit-width data formats can reduce model size and benefit from hardware acceleration. As SSMs are prone to quantization-induced errors, recent efforts have focused on optimizing a particular model or bit-width for efficiency without sacrificing performance. However, distinct bit-width configurations are essential for different scenarios, like W4A8 for boosting large-batch decoding speed, and W4A16 for enhancing generation speed in short prompt applications for a single user. To this end, we present Quamba2, compatible with W8A8, W4A8, and W4A16 for both Mamba1 and Mamba2 backbones, addressing the growing demand for SSM deployment on various platforms. Based on the channel order preserving and activation persistence of SSMs, we propose an offline approach to quantize inputs of a linear recurrence in 8-bit by sorting and clustering for input x, combined with a per-state-group quantization for input-dependent parameters B and C. To ensure compute-invariance in the SSM output, we rearrange weights offline according to the clustering sequence. The experiments show that Quamba2-8B outperforms several state-of-the-art SSM quantization methods and delivers 1.3times and 3times speed-ups in the pre-filling and generation stages, respectively, while offering 4times memory reduction with only a 1.6% average accuracy drop. The evaluation on MMLU shows the generalizability and robustness of our framework. The code and quantized models will be released at: https://github.com/enyac-group/Quamba.

Denotational validation of higher-order Bayesian inference

We present a modular semantic account of Bayesian inference algorithms for probabilistic programming languages, as used in data science and machine learning. Sophisticated inference algorithms are often explained in terms of composition of smaller parts. However, neither their theoretical justification nor their implementation reflects this modularity. We show how to conceptualise and analyse such inference algorithms as manipulating intermediate representations of probabilistic programs using higher-order functions and inductive types, and their denotational semantics. Semantic accounts of continuous distributions use measurable spaces. However, our use of higher-order functions presents a substantial technical difficulty: it is impossible to define a measurable space structure over the collection of measurable functions between arbitrary measurable spaces that is compatible with standard operations on those functions, such as function application. We overcome this difficulty using quasi-Borel spaces, a recently proposed mathematical structure that supports both function spaces and continuous distributions. We define a class of semantic structures for representing probabilistic programs, and semantic validity criteria for transformations of these representations in terms of distribution preservation. We develop a collection of building blocks for composing representations. We use these building blocks to validate common inference algorithms such as Sequential Monte Carlo and Markov Chain Monte Carlo. To emphasize the connection between the semantic manipulation and its traditional measure theoretic origins, we use Kock's synthetic measure theory. We demonstrate its usefulness by proving a quasi-Borel counterpart to the Metropolis-Hastings-Green theorem.

Understanding the differences in Foundation Models: Attention, State Space Models, and Recurrent Neural Networks

Softmax attention is the principle backbone of foundation models for various artificial intelligence applications, yet its quadratic complexity in sequence length can limit its inference throughput in long-context settings. To address this challenge, alternative architectures such as linear attention, State Space Models (SSMs), and Recurrent Neural Networks (RNNs) have been considered as more efficient alternatives. While connections between these approaches exist, such models are commonly developed in isolation and there is a lack of theoretical understanding of the shared principles underpinning these architectures and their subtle differences, greatly influencing performance and scalability. In this paper, we introduce the Dynamical Systems Framework (DSF), which allows a principled investigation of all these architectures in a common representation. Our framework facilitates rigorous comparisons, providing new insights on the distinctive characteristics of each model class. For instance, we compare linear attention and selective SSMs, detailing their differences and conditions under which both are equivalent. We also provide principled comparisons between softmax attention and other model classes, discussing the theoretical conditions under which softmax attention can be approximated. Additionally, we substantiate these new insights with empirical validations and mathematical arguments. This shows the DSF's potential to guide the systematic development of future more efficient and scalable foundation models.

A Markov Categorical Framework for Language Modeling

Auto-regressive language models factorize sequence probabilities and are trained by minimizing the negative log-likelihood (NLL) objective. While empirically powerful, a deep theoretical understanding of why this simple objective yields such versatile representations remains elusive. This work introduces a unifying analytical framework using Markov Categories (MCs) to deconstruct the AR generation process and the NLL objective. We model the single-step generation map as a composition of Markov kernels in the category Stoch. This compositional view, when enriched with statistical divergences, allows us to dissect information flow and learned geometry. Our framework makes three main contributions. First, we provide a formal, information-theoretic rationale for the success of modern speculative decoding methods like EAGLE, quantifying the information surplus in hidden states that these methods exploit. Second, we formalize how NLL minimization forces the model to learn not just the next token, but the data's intrinsic conditional stochasticity, a process we analyze using categorical entropy. Third, and most centrally, we prove that NLL training acts as an implicit form of spectral contrastive learning. By analyzing the information geometry of the model's prediction head, we show that NLL implicitly forces the learned representation space to align with the eigenspectrum of a predictive similarity operator, thereby learning a geometrically structured space without explicit contrastive pairs. This compositional and information-geometric perspective reveals the deep structural principles underlying the effectiveness of modern LMs. Project Page: https://github.com/asiresearch/lm-theory

Modeling Inter-Dependence Between Time and Mark in Multivariate Temporal Point Processes

Temporal Point Processes (TPP) are probabilistic generative frameworks. They model discrete event sequences localized in continuous time. Generally, real-life events reveal descriptive information, known as marks. Marked TPPs model time and marks of the event together for practical relevance. Conditioned on past events, marked TPPs aim to learn the joint distribution of the time and the mark of the next event. For simplicity, conditionally independent TPP models assume time and marks are independent given event history. They factorize the conditional joint distribution of time and mark into the product of individual conditional distributions. This structural limitation in the design of TPP models hurt the predictive performance on entangled time and mark interactions. In this work, we model the conditional inter-dependence of time and mark to overcome the limitations of conditionally independent models. We construct a multivariate TPP conditioning the time distribution on the current event mark in addition to past events. Besides the conventional intensity-based models for conditional joint distribution, we also draw on flexible intensity-free TPP models from the literature. The proposed TPP models outperform conditionally independent and dependent models in standard prediction tasks. Our experimentation on various datasets with multiple evaluation metrics highlights the merit of the proposed approach.

TimeGraphs: Graph-based Temporal Reasoning

Many real-world systems exhibit temporal, dynamic behaviors, which are captured as time series of complex agent interactions. To perform temporal reasoning, current methods primarily encode temporal dynamics through simple sequence-based models. However, in general these models fail to efficiently capture the full spectrum of rich dynamics in the input, since the dynamics is not uniformly distributed. In particular, relevant information might be harder to extract and computing power is wasted for processing all individual timesteps, even if they contain no significant changes or no new information. Here we propose TimeGraphs, a novel approach that characterizes dynamic interactions as a hierarchical temporal graph, diverging from traditional sequential representations. Our approach models the interactions using a compact graph-based representation, enabling adaptive reasoning across diverse time scales. Adopting a self-supervised method, TimeGraphs constructs a multi-level event hierarchy from a temporal input, which is then used to efficiently reason about the unevenly distributed dynamics. This construction process is scalable and incremental to accommodate streaming data. We evaluate TimeGraphs on multiple datasets with complex, dynamic agent interactions, including a football simulator, the Resistance game, and the MOMA human activity dataset. The results demonstrate both robustness and efficiency of TimeGraphs on a range of temporal reasoning tasks. Our approach obtains state-of-the-art performance and leads to a performance increase of up to 12.2% on event prediction and recognition tasks over current approaches. Our experiments further demonstrate a wide array of capabilities including zero-shot generalization, robustness in case of data sparsity, and adaptability to streaming data flow.