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SubscribeElucidating the Design Space of Multimodal Protein Language Models
Multimodal protein language models (PLMs) integrate sequence and token-based structural information, serving as a powerful foundation for protein modeling, generation, and design. However, the reliance on tokenizing 3D structures into discrete tokens causes substantial loss of fidelity about fine-grained structural details and correlations. In this paper, we systematically elucidate the design space of multimodal PLMs to overcome their limitations. We identify tokenization loss and inaccurate structure token predictions by the PLMs as major bottlenecks. To address these, our proposed design space covers improved generative modeling, structure-aware architectures and representation learning, and data exploration. Our advancements approach finer-grained supervision, demonstrating that token-based multimodal PLMs can achieve robust structural modeling. The effective design methods dramatically improve the structure generation diversity, and notably, folding abilities of our 650M model by reducing the RMSD from 5.52 to 2.36 on PDB testset, even outperforming 3B baselines and on par with the specialized folding models.
Elucidating the solution space of extended reverse-time SDE for diffusion models
Diffusion models (DMs) demonstrate potent image generation capabilities in various generative modeling tasks. Nevertheless, their primary limitation lies in slow sampling speed, requiring hundreds or thousands of sequential function evaluations through large neural networks to generate high-quality images. Sampling from DMs can be seen alternatively as solving corresponding stochastic differential equations (SDEs) or ordinary differential equations (ODEs). In this work, we formulate the sampling process as an extended reverse-time SDE (ER SDE), unifying prior explorations into ODEs and SDEs. Leveraging the semi-linear structure of ER SDE solutions, we offer exact solutions and arbitrarily high-order approximate solutions for VP SDE and VE SDE, respectively. Based on the solution space of the ER SDE, we yield mathematical insights elucidating the superior performance of ODE solvers over SDE solvers in terms of fast sampling. Additionally, we unveil that VP SDE solvers stand on par with their VE SDE counterparts. Finally, we devise fast and training-free samplers, ER-SDE-Solvers, achieving state-of-the-art performance across all stochastic samplers. Experimental results demonstrate achieving 3.45 FID in 20 function evaluations and 2.24 FID in 50 function evaluations on the ImageNet 64times64 dataset.
Elucidating the design space of language models for image generation
The success of autoregressive (AR) language models in text generation has inspired the computer vision community to adopt Large Language Models (LLMs) for image generation. However, considering the essential differences between text and image modalities, the design space of language models for image generation remains underexplored. We observe that image tokens exhibit greater randomness compared to text tokens, which presents challenges when training with token prediction. Nevertheless, AR models demonstrate their potential by effectively learning patterns even from a seemingly suboptimal optimization problem. Our analysis also reveals that while all models successfully grasp the importance of local information in image generation, smaller models struggle to capture the global context. In contrast, larger models showcase improved capabilities in this area, helping to explain the performance gains achieved when scaling up model size. We further elucidate the design space of language models for vision generation, including tokenizer choice, model choice, model scalability, vocabulary design, and sampling strategy through extensive comparative experiments. Our work is the first to analyze the optimization behavior of language models in vision generation, and we believe it can inspire more effective designs when applying LMs to other domains. Finally, our elucidated language model for image generation, termed as ELM, achieves state-of-the-art performance on the ImageNet 256*256 benchmark. The code is available at https://github.com/Pepperlll/LMforImageGeneration.git.
Elucidating Discrepancy in Explanations of Predictive Models Developed using EMR
The lack of transparency and explainability hinders the clinical adoption of Machine learning (ML) algorithms. While explainable artificial intelligence (XAI) methods have been proposed, little research has focused on the agreement between these methods and expert clinical knowledge. This study applies current state-of-the-art explainability methods to clinical decision support algorithms developed for Electronic Medical Records (EMR) data to analyse the concordance between these factors and discusses causes for identified discrepancies from a clinical and technical perspective. Important factors for achieving trustworthy XAI solutions for clinical decision support are also discussed.
Elucidating The Design Space of Classifier-Guided Diffusion Generation
Guidance in conditional diffusion generation is of great importance for sample quality and controllability. However, existing guidance schemes are to be desired. On one hand, mainstream methods such as classifier guidance and classifier-free guidance both require extra training with labeled data, which is time-consuming and unable to adapt to new conditions. On the other hand, training-free methods such as universal guidance, though more flexible, have yet to demonstrate comparable performance. In this work, through a comprehensive investigation into the design space, we show that it is possible to achieve significant performance improvements over existing guidance schemes by leveraging off-the-shelf classifiers in a training-free fashion, enjoying the best of both worlds. Employing calibration as a general guideline, we propose several pre-conditioning techniques to better exploit pretrained off-the-shelf classifiers for guiding diffusion generation. Extensive experiments on ImageNet validate our proposed method, showing that state-of-the-art diffusion models (DDPM, EDM, DiT) can be further improved (up to 20%) using off-the-shelf classifiers with barely any extra computational cost. With the proliferation of publicly available pretrained classifiers, our proposed approach has great potential and can be readily scaled up to text-to-image generation tasks. The code is available at https://github.com/AlexMaOLS/EluCD/tree/main.
Elucidating the Exposure Bias in Diffusion Models
Diffusion models have demonstrated impressive generative capabilities, but their exposure bias problem, described as the input mismatch between training and sampling, lacks in-depth exploration. In this paper, we systematically investigate the exposure bias problem in diffusion models by first analytically modelling the sampling distribution, based on which we then attribute the prediction error at each sampling step as the root cause of the exposure bias issue. Furthermore, we discuss potential solutions to this issue and propose an intuitive metric for it. Along with the elucidation of exposure bias, we propose a simple, yet effective, training-free method called Epsilon Scaling to alleviate the exposure bias. We show that Epsilon Scaling explicitly moves the sampling trajectory closer to the vector field learned in the training phase by scaling down the network output (Epsilon), mitigating the input mismatch between training and sampling. Experiments on various diffusion frameworks (ADM, DDPM/DDIM, EDM, LDM), unconditional and conditional settings, and deterministic vs. stochastic sampling verify the effectiveness of our method. Remarkably, our ADM-ES, as a SOTA stochastic sampler, obtains 2.17 FID on CIFAR-10 under 100-step unconditional generation. The code is available at https://github.com/forever208/ADM-ES and https://github.com/forever208/EDM-ES.
Elucidation of Relaxation Dynamics Beyond Equilibrium Through AI-informed X-ray Photon Correlation Spectroscopy
Understanding and interpreting dynamics of functional materials in situ is a grand challenge in physics and materials science due to the difficulty of experimentally probing materials at varied length and time scales. X-ray photon correlation spectroscopy (XPCS) is uniquely well-suited for characterizing materials dynamics over wide-ranging time scales, however spatial and temporal heterogeneity in material behavior can make interpretation of experimental XPCS data difficult. In this work we have developed an unsupervised deep learning (DL) framework for automated classification and interpretation of relaxation dynamics from experimental data without requiring any prior physical knowledge of the system behavior. We demonstrate how this method can be used to rapidly explore large datasets to identify samples of interest, and we apply this approach to directly correlate bulk properties of a model system to microscopic dynamics. Importantly, this DL framework is material and process agnostic, marking a concrete step towards autonomous materials discovery.
ELUDE: Generating interpretable explanations via a decomposition into labelled and unlabelled features
Deep learning models have achieved remarkable success in different areas of machine learning over the past decade; however, the size and complexity of these models make them difficult to understand. In an effort to make them more interpretable, several recent works focus on explaining parts of a deep neural network through human-interpretable, semantic attributes. However, it may be impossible to completely explain complex models using only semantic attributes. In this work, we propose to augment these attributes with a small set of uninterpretable features. Specifically, we develop a novel explanation framework ELUDE (Explanation via Labelled and Unlabelled DEcomposition) that decomposes a model's prediction into two parts: one that is explainable through a linear combination of the semantic attributes, and another that is dependent on the set of uninterpretable features. By identifying the latter, we are able to analyze the "unexplained" portion of the model, obtaining insights into the information used by the model. We show that the set of unlabelled features can generalize to multiple models trained with the same feature space and compare our work to two popular attribute-oriented methods, Interpretable Basis Decomposition and Concept Bottleneck, and discuss the additional insights ELUDE provides.
mRAG: Elucidating the Design Space of Multi-modal Retrieval-Augmented Generation
Large Vision-Language Models (LVLMs) have made remarkable strides in multimodal tasks such as visual question answering, visual grounding, and complex reasoning. However, they remain limited by static training data, susceptibility to hallucinations, and inability to verify claims against up-to-date, external evidence, compromising their performance in dynamic real-world applications. Retrieval-Augmented Generation (RAG) offers a practical solution to mitigate these challenges by allowing the LVLMs to access large-scale knowledge databases via retrieval mechanisms, thereby grounding model outputs in factual, contextually relevant information. Here in this paper, we conduct the first systematic dissection of the multimodal RAG pipeline for LVLMs, explicitly investigating (1) the retrieval phase: on the modality configurations and retrieval strategies, (2) the re-ranking stage: on strategies to mitigate positional biases and improve the relevance of retrieved evidence, and (3) the generation phase: we further investigate how to best integrate retrieved candidates into the final generation process. Finally, we extend to explore a unified agentic framework that integrates re-ranking and generation through self-reflection, enabling LVLMs to select relevant evidence and suppress irrelevant context dynamically. Our full-stack exploration of RAG for LVLMs yields substantial insights, resulting in an average performance boost of 5% without any fine-tuning.
DiffSpectra: Molecular Structure Elucidation from Spectra using Diffusion Models
Molecular structure elucidation from spectra is a foundational problem in chemistry, with profound implications for compound identification, synthesis, and drug development. Traditional methods rely heavily on expert interpretation and lack scalability. Pioneering machine learning methods have introduced retrieval-based strategies, but their reliance on finite libraries limits generalization to novel molecules. Generative models offer a promising alternative, yet most adopt autoregressive SMILES-based architectures that overlook 3D geometry and struggle to integrate diverse spectral modalities. In this work, we present DiffSpectra, a generative framework that directly infers both 2D and 3D molecular structures from multi-modal spectral data using diffusion models. DiffSpectra formulates structure elucidation as a conditional generation process. Its denoising network is parameterized by Diffusion Molecule Transformer, an SE(3)-equivariant architecture that integrates topological and geometric information. Conditioning is provided by SpecFormer, a transformer-based spectral encoder that captures intra- and inter-spectral dependencies from multi-modal spectra. Extensive experiments demonstrate that DiffSpectra achieves high accuracy in structure elucidation, recovering exact structures with 16.01% top-1 accuracy and 96.86% top-20 accuracy through sampling. The model benefits significantly from 3D geometric modeling, SpecFormer pre-training, and multi-modal conditioning. These results highlight the effectiveness of spectrum-conditioned diffusion modeling in addressing the challenge of molecular structure elucidation. To our knowledge, DiffSpectra is the first framework to unify multi-modal spectral reasoning and joint 2D/3D generative modeling for de novo molecular structure elucidation.
Instruction-Tuned Video-Audio Models Elucidate Functional Specialization in the Brain
Recent voxel-wise multimodal brain encoding studies have shown that multimodal large language models (MLLMs) exhibit a higher degree of brain alignment compared to unimodal models in both unimodal and multimodal stimulus settings. More recently, instruction-tuned multimodal models have shown to generate task-specific representations that align strongly with brain activity. However, prior work evaluating the brain alignment of MLLMs has primarily focused on unimodal settings or relied on non-instruction-tuned multimodal models for multimodal stimuli. To address this gap, we investigated brain alignment, that is, measuring the degree of predictivity of neural activity recorded while participants were watching naturalistic movies (video along with audio) with representations derived from MLLMs. We utilized instruction-specific embeddings from six video and two audio instruction-tuned MLLMs. Experiments with 13 video task-specific instructions show that instruction-tuned video MLLMs significantly outperform non-instruction-tuned multimodal (by 15%) and unimodal models (by 20%). Our evaluation of MLLMs for both video and audio tasks using language-guided instructions shows clear disentanglement in task-specific representations from MLLMs, leading to precise differentiation of multimodal functional processing in the brain. We also find that MLLM layers align hierarchically with the brain, with early sensory areas showing strong alignment with early layers, while higher-level visual and language regions align more with middle to late layers. These findings provide clear evidence for the role of task-specific instructions in improving the alignment between brain activity and MLLMs, and open new avenues for mapping joint information processing in both the systems. We make the code publicly available [https://github.com/subbareddy248/mllm_videos].