Daily Papers

We present a novel dual-head deep learning architecture for protein-protein interaction modeling that enables simultaneous prediction of binding affinity (ΔG) and mutation-induced affinity changes (ΔΔG) using only protein sequence information. Our approach offers a significant advancement over existing methods by employing specialized prediction heads that operate on a shared representation network, allowing direct and optimized prediction of both values. To ensure robust generalization, we integrated complementary datasets from SKEMPI v2 and PDBbind with a rigorous protein domain-based splitting strategy that prevents information leakage between training and validation sets. Our architecture combines transformer-based encoders with a novel cross-attention mechanism that processes paired protein sequences directly, without requiring any structural information. The network embeds input sequences using ESM3 representations, then employs a learnable sliced window embedding layer to manage variable-length sequences efficiently. A multi-layer transformer encoder with bidirectional self-attention captures intra-protein patterns, while cross-attention layers enable explicit modeling of interactions between protein pairs. This shared representation network feeds into separate ΔG and ΔΔG prediction heads, allowing task-specific optimization while leveraging common features. The model achieves ΔΔG validation of Pearson correlation at 0.485, while maintaining strong ΔG predictions (Pearson: 0.638). While existing approaches require protein structure data and binding interface information, our model eliminates these constraints. This provides a critical advantage for the numerous proteins with unknown structures or those challenging to crystallize, such as viral and intrinsically disordered proteins.

Proteins are essential to life's processes, underpinning evolution and diversity. Advances in sequencing technology have revealed millions of proteins, underscoring the need for sophisticated pre-trained protein models for biological analysis and AI development. Facebook's ESM2, the most advanced protein language model to date, leverages a masked prediction task for unsupervised learning, crafting amino acid representations with notable biochemical accuracy. Yet, it lacks in delivering functional protein insights, signaling an opportunity for enhancing representation quality.Our study addresses this gap by incorporating protein family classification into ESM2's training.This approach, augmented with Community Propagation-Based Clustering Algorithm, improves global protein representations, while a contextual prediction task fine-tunes local amino acid accuracy. Significantly, our model achieved state-of-the-art results in several downstream experiments, demonstrating the power of combining global and local methodologies to substantially boost protein representation quality.

Learning effective protein representations is critical in a variety of tasks in biology such as predicting protein functions. Recent sequence representation learning methods based on Protein Language Models (PLMs) excel in sequence-based tasks, but their direct adaptation to tasks involving protein structures remains a challenge. In contrast, structure-based methods leverage 3D structural information with graph neural networks and geometric pre-training methods show potential in function prediction tasks, but still suffers from the limited number of available structures. To bridge this gap, our study undertakes a comprehensive exploration of joint protein representation learning by integrating a state-of-the-art PLM (ESM-2) with distinct structure encoders (GVP, GearNet, CDConv). We introduce three representation fusion strategies and explore different pre-training techniques. Our method achieves significant improvements over existing sequence- and structure-based methods, setting new state-of-the-art for function annotation. This study underscores several important design choices for fusing protein sequence and structure information. Our implementation is available at https://github.com/DeepGraphLearning/ESM-GearNet.

Hallucination is a common issue in Multimodal Large Language Models (MLLMs), yet the underlying principles remain poorly understood. In this paper, we investigate which components of MLLMs contribute to object hallucinations. To analyze image representations while completely avoiding the influence of all other factors other than the image representation itself, we propose a parametric-free representation alignment metric (Pfram) that can measure the similarities between any two representation systems without requiring additional training parameters. Notably, Pfram can also assess the alignment of a neural representation system with the human representation system, represented by ground-truth annotations of images. By evaluating the alignment with object annotations, we demonstrate that this metric shows strong and consistent correlations with object hallucination across a wide range of state-of-the-art MLLMs, spanning various model architectures and sizes. Furthermore, using this metric, we explore other key issues related to image representations in MLLMs, such as the role of different modules, the impact of textual instructions, and potential improvements including the use of alternative visual encoders. Our code is available at: https://github.com/yellow-binary-tree/Pfram.

Crystal structures are characterized by atomic bases within a primitive unit cell that repeats along a regular lattice throughout 3D space. The periodic and infinite nature of crystals poses unique challenges for geometric graph representation learning. Specifically, constructing graphs that effectively capture the complete geometric information of crystals and handle chiral crystals remains an unsolved and challenging problem. In this paper, we introduce a novel approach that utilizes the periodic patterns of unit cells to establish the lattice-based representation for each atom, enabling efficient and expressive graph representations of crystals. Furthermore, we propose ComFormer, a SE(3) transformer designed specifically for crystalline materials. ComFormer includes two variants; namely, iComFormer that employs invariant geometric descriptors of Euclidean distances and angles, and eComFormer that utilizes equivariant vector representations. Experimental results demonstrate the state-of-the-art predictive accuracy of ComFormer variants on various tasks across three widely-used crystal benchmarks. Our code is publicly available as part of the AIRS library (https://github.com/divelab/AIRS).

In many computer vision applications, images are acquired with arbitrary or random rotations and translations, and in such setups, it is desirable to obtain semantic representations disentangled from the image orientation. Examples of such applications include semiconductor wafer defect inspection, plankton microscope images, and inference on single-particle cryo-electron microscopy (cryo-EM) micro-graphs. In this work, we propose Invariant Representation Learning with Implicit Neural Representation (IRL-INR), which uses an implicit neural representation (INR) with a hypernetwork to obtain semantic representations disentangled from the orientation of the image. We show that IRL-INR can effectively learn disentangled semantic representations on more complex images compared to those considered in prior works and show that these semantic representations synergize well with SCAN to produce state-of-the-art unsupervised clustering results.

We present SAM4EM, a novel approach for 3D segmentation of complex neural structures in electron microscopy (EM) data by leveraging the Segment Anything Model (SAM) alongside advanced fine-tuning strategies. Our contributions include the development of a prompt-free adapter for SAM using two stage mask decoding to automatically generate prompt embeddings, a dual-stage fine-tuning method based on Low-Rank Adaptation (LoRA) for enhancing segmentation with limited annotated data, and a 3D memory attention mechanism to ensure segmentation consistency across 3D stacks. We further release a unique benchmark dataset for the segmentation of astrocytic processes and synapses. We evaluated our method on challenging neuroscience segmentation benchmarks, specifically targeting mitochondria, glia, and synapses, with significant accuracy improvements over state-of-the-art (SOTA) methods, including recent SAM-based adapters developed for the medical domain and other vision transformer-based approaches. Experimental results indicate that our approach outperforms existing solutions in the segmentation of complex processes like glia and post-synaptic densities. Our code and models are available at https://github.com/Uzshah/SAM4EM.

Accurately predicting protein melting temperature changes (Delta Tm) is fundamental for assessing protein stability and guiding protein engineering. Leveraging multi-modal protein representations has shown great promise in capturing the complex relationships among protein sequences, structures, and functions. In this study, we develop models based on powerful protein language models, including ESM-2, ESM-3 and AlphaFold, using various feature extraction methods to enhance prediction accuracy. By utilizing the ESM-3 model, we achieve a new state-of-the-art performance on the s571 test dataset, obtaining a Pearson correlation coefficient (PCC) of 0.50. Furthermore, we conduct a fair evaluation to compare the performance of different protein language models in the Delta Tm prediction task. Our results demonstrate that integrating multi-modal protein representations could advance the prediction of protein melting temperatures.

Protein language models have demonstrated significant potential in the field of protein engineering. However, current protein language models primarily operate at the residue scale, which limits their ability to provide information at the atom level. This limitation prevents us from fully exploiting the capabilities of protein language models for applications involving both proteins and small molecules. In this paper, we propose ESM-AA (ESM All-Atom), a novel approach that enables atom-scale and residue-scale unified molecular modeling. ESM-AA achieves this by pre-training on multi-scale code-switch protein sequences and utilizing a multi-scale position encoding to capture relationships among residues and atoms. Experimental results indicate that ESM-AA surpasses previous methods in protein-molecule tasks, demonstrating the full utilization of protein language models. Further investigations reveal that through unified molecular modeling, ESM-AA not only gains molecular knowledge but also retains its understanding of proteins. The source codes of ESM-AA are publicly released at https://github.com/zhengkangjie/ESM-AA.

Transformer-based self-supervised speech models (S3Ms) are often described as contextualized, yet what this entails remains unclear. Here, we focus on how a single frame-level S3M representation can encode phones and their surrounding context. Prior work has shown that S3Ms represent phones compositionally; for example, phonological vectors such as voicing, bilabiality, and nasality vectors are superposed in the S3M representation of [m]. We extend this view by proposing that phonological information from a sequence of neighboring phones is also compositionally encoded in a single frame, such that vectors corresponding to previous, current, and next phones are superposed within a single frame-level representation. We show that this structure has several properties, including orthogonality between relative positions, and emergence of implicit phonetic boundaries. Together, our findings advance our understanding of context-dependent S3M representations.

Multimodal protein language models deliver strong performance on mutation-effect prediction, but training such models from scratch demands substantial computational resources. In this paper, we propose a fine-tuning framework called InstructPLM-mu and try to answer a question: Can multimodal fine-tuning of a pretrained, sequence-only protein language model match the performance of models trained end-to-end? Surprisingly, our experiments show that fine-tuning ESM2 with structural inputs can reach performance comparable to ESM3. To understand how this is achieved, we systematically compare three different feature-fusion designs and fine-tuning recipes. Our results reveal that both the fusion method and the tuning strategy strongly affect final accuracy, indicating that the fine-tuning process is not trivial. We hope this work offers practical guidance for injecting structure into pretrained protein language models and motivates further research on better fusion mechanisms and fine-tuning protocols.

We provide a construction for categorical representation learning and introduce the foundations of "categorifier". The central theme in representation learning is the idea of everything to vector. Every object in a dataset S can be represented as a vector in R^n by an encoding map E: Obj(S)toR^n. More importantly, every morphism can be represented as a matrix E: Hom(S)toR^{n}_{n}. The encoding map E is generally modeled by a deep neural network. The goal of representation learning is to design appropriate tasks on the dataset to train the encoding map (assuming that an encoding is optimal if it universally optimizes the performance on various tasks). However, the latter is still a set-theoretic approach. The goal of the current article is to promote the representation learning to a new level via a category-theoretic approach. As a proof of concept, we provide an example of a text translator equipped with our technology, showing that our categorical learning model outperforms the current deep learning models by 17 times. The content of the current article is part of the recent US patent proposal (patent application number: 63110906).

Large language models have demonstrated remarkable reasoning capabilities across diverse natural language tasks. However, comparable breakthroughs in scientific discovery are more limited, because understanding complex physical phenomena demands multifaceted representations far beyond language alone. A compelling example is the design of functional materials such as MOFs-critical for a range of impactful applications like carbon capture and hydrogen storage. Navigating their vast and intricate design space in language-based representations interpretable by LLMs is challenging due to the numerous possible three-dimensional atomic arrangements and strict reticular rules of coordination geometry and topology. Despite promising early results in LLM-assisted discovery for simpler materials systems, MOF design remains heavily reliant on tacit human expertise rarely codified in textual information alone. To overcome this barrier, we introduce L2M3OF, the first multimodal LLM for MOFs. L2M3OF integrates crystal representation learning with language understanding to process structural, textual, and knowledge modalities jointly. L2M3OF employs a pre-trained crystal encoder with a lightweight projection layer to compress structural information into a token space, enabling efficient alignment with language instructions. To facilitate training and evaluation, we curate a structure-property-knowledge database of crystalline materials and benchmark L2M3OF against state-of-the-art closed-source LLMs such as GPT-5, Gemini-2.5-Pro and DeepSeek-R1. Experiments show that L2M3OF outperforms leading text-based closed-source LLMs in property prediction and knowledge generation tasks, despite using far fewer parameters. These results highlight the importance of multimodal approaches for porous material understanding and establish L2M3OF as a foundation for next-generation AI systems in materials discovery.

Large multimodal models (LMMs) combine unimodal encoders and large language models (LLMs) to perform multimodal tasks. Despite recent advancements towards the interpretability of these models, understanding internal representations of LMMs remains largely a mystery. In this paper, we present a novel framework for the interpretation of LMMs. We propose a dictionary learning based approach, applied to the representation of tokens. The elements of the learned dictionary correspond to our proposed concepts. We show that these concepts are well semantically grounded in both vision and text. Thus we refer to these as ``multi-modal concepts''. We qualitatively and quantitatively evaluate the results of the learnt concepts. We show that the extracted multimodal concepts are useful to interpret representations of test samples. Finally, we evaluate the disentanglement between different concepts and the quality of grounding concepts visually and textually. Our code is publicly available at https://github.com/mshukor/xl-vlms

Quantitative microstructural characterization is fundamental to materials science, where electron micrograph (EM) provides indispensable high-resolution insights. However, progress in deep learning-based EM characterization has been hampered by the scarcity of large-scale, diverse, and expert-annotated datasets, due to acquisition costs, privacy concerns, and annotation complexity. To address this issue, we introduce UniEM-3M, the first large-scale and multimodal EM dataset for instance-level understanding. It comprises 5,091 high-resolution EMs, about 3 million instance segmentation labels, and image-level attribute-disentangled textual descriptions, a subset of which will be made publicly available. Furthermore, we are also releasing a text-to-image diffusion model trained on the entire collection to serve as both a powerful data augmentation tool and a proxy for the complete data distribution. To establish a rigorous benchmark, we evaluate various representative instance segmentation methods on the complete UniEM-3M and present UniEM-Net as a strong baseline model. Quantitative experiments demonstrate that this flow-based model outperforms other advanced methods on this challenging benchmark. Our multifaceted release of a partial dataset, a generative model, and a comprehensive benchmark -- available at huggingface -- will significantly accelerate progress in automated materials analysis.

High-throughput data generation methods and machine learning (ML) algorithms have given rise to a new era of computational materials science by learning relationships among composition, structure, and properties and by exploiting such relations for design. However, to build these connections, materials data must be translated into a numerical form, called a representation, that can be processed by a machine learning model. Datasets in materials science vary in format (ranging from images to spectra), size, and fidelity. Predictive models vary in scope and property of interests. Here, we review context-dependent strategies for constructing representations that enable the use of materials as inputs or outputs of machine learning models. Furthermore, we discuss how modern ML techniques can learn representations from data and transfer chemical and physical information between tasks. Finally, we outline high-impact questions that have not been fully resolved and thus, require further investigation.

Learned representations are a central component in modern ML systems, serving a multitude of downstream tasks. When training such representations, it is often the case that computational and statistical constraints for each downstream task are unknown. In this context rigid, fixed capacity representations can be either over or under-accommodating to the task at hand. This leads us to ask: can we design a flexible representation that can adapt to multiple downstream tasks with varying computational resources? Our main contribution is Matryoshka Representation Learning (MRL) which encodes information at different granularities and allows a single embedding to adapt to the computational constraints of downstream tasks. MRL minimally modifies existing representation learning pipelines and imposes no additional cost during inference and deployment. MRL learns coarse-to-fine representations that are at least as accurate and rich as independently trained low-dimensional representations. The flexibility within the learned Matryoshka Representations offer: (a) up to 14x smaller embedding size for ImageNet-1K classification at the same level of accuracy; (b) up to 14x real-world speed-ups for large-scale retrieval on ImageNet-1K and 4K; and (c) up to 2% accuracy improvements for long-tail few-shot classification, all while being as robust as the original representations. Finally, we show that MRL extends seamlessly to web-scale datasets (ImageNet, JFT) across various modalities -- vision (ViT, ResNet), vision + language (ALIGN) and language (BERT). MRL code and pretrained models are open-sourced at https://github.com/RAIVNLab/MRL.

The rapid progress of Multimodal Large Language Models(MLLMs) has transformed the AI landscape. These models combine pre-trained LLMs with various modality encoders. This integration requires a systematic understanding of how different modalities connect to the language backbone. Our survey presents an LLM-centric analysis of current approaches. We examine methods for transforming and aligning diverse modal inputs into the language embedding space. This addresses a significant gap in existing literature. We propose a classification framework for MLLMs based on three key dimensions. First, we examine architectural strategies for modality integration. This includes both the specific integration mechanisms and the fusion level. Second, we categorize representation learning techniques as either joint or coordinate representations. Third, we analyze training paradigms, including training strategies and objective functions. By examining 125 MLLMs developed between 2021 and 2025, we identify emerging patterns in the field. Our taxonomy provides researchers with a structured overview of current integration techniques. These insights aim to guide the development of more robust multimodal integration strategies for future models built on pre-trained foundations.

Self-supervised speech models (S3Ms) are known to encode rich phonetic information, yet how this information is structured remains underexplored. We conduct a comprehensive study across 96 languages to analyze the underlying structure of S3M representations, with particular attention to phonological vectors. We first show that there exist linear directions within the model's representation space that correspond to phonological features. We further demonstrate that the scale of these phonological vectors correlate to the degree of acoustic realization of their corresponding phonological features in a continuous manner. For example, the difference between [d] and [t] yields a voicing vector: adding this vector to [p] produces [b], while scaling it results in a continuum of voicing. Together, these findings indicate that S3Ms encode speech using phonologically interpretable and compositional vectors, demonstrating phonological vector arithmetic. All code and interactive demos are available at https://github.com/juice500ml/phonetic-arithmetic .

Developing equivariant neural networks for the E(3) group plays an important role in modeling 3D data across real-world applications. Enforcing this equivariance primarily involves the tensor products of irreducible representations (irreps). However, the computational complexity of such operations increases significantly as higher-order tensors are used. In this work, we propose a systematic approach to substantially accelerate the computation of the tensor products of irreps. We mathematically connect the commonly used Clebsch-Gordan coefficients to the Gaunt coefficients, which are integrals of products of three spherical harmonics. Through Gaunt coefficients, the tensor product of irreps becomes equivalent to the multiplication between spherical functions represented by spherical harmonics. This perspective further allows us to change the basis for the equivariant operations from spherical harmonics to a 2D Fourier basis. Consequently, the multiplication between spherical functions represented by a 2D Fourier basis can be efficiently computed via the convolution theorem and Fast Fourier Transforms. This transformation reduces the complexity of full tensor products of irreps from O(L^6) to O(L^3), where L is the max degree of irreps. Leveraging this approach, we introduce the Gaunt Tensor Product, which serves as a new method to construct efficient equivariant operations across different model architectures. Our experiments on the Open Catalyst Project and 3BPA datasets demonstrate both the increased efficiency and improved performance of our approach.

Effectively representing materials as text has the potential to leverage the vast advancements of large language models (LLMs) for discovering new materials. While LLMs have shown remarkable success in various domains, their application to materials science remains underexplored. A fundamental challenge is the lack of understanding of how to best utilize text-based representations for materials modeling. This challenge is further compounded by the absence of a comprehensive benchmark to rigorously evaluate the capabilities and limitations of these text representations in capturing the complexity of material systems. To address this gap, we propose MatText, a suite of benchmarking tools and datasets designed to systematically evaluate the performance of language models in modeling materials. MatText encompasses nine distinct text-based representations for material systems, including several novel representations. Each representation incorporates unique inductive biases that capture relevant information and integrate prior physical knowledge about materials. Additionally, MatText provides essential tools for training and benchmarking the performance of language models in the context of materials science. These tools include standardized dataset splits for each representation, probes for evaluating sensitivity to geometric factors, and tools for seamlessly converting crystal structures into text. Using MatText, we conduct an extensive analysis of the capabilities of language models in modeling materials. Our findings reveal that current language models consistently struggle to capture the geometric information crucial for materials modeling across all representations. Instead, these models tend to leverage local information, which is emphasized in some of our novel representations. Our analysis underscores MatText's ability to reveal shortcomings of text-based methods for materials design.

Understanding how humans conceptualize and categorize natural objects offers critical insights into perception and cognition. With the advent of Large Language Models (LLMs), a key question arises: can these models develop human-like object representations from linguistic and multimodal data? In this study, we combined behavioral and neuroimaging analyses to explore the relationship between object concept representations in LLMs and human cognition. We collected 4.7 million triplet judgments from LLMs and Multimodal LLMs (MLLMs) to derive low-dimensional embeddings that capture the similarity structure of 1,854 natural objects. The resulting 66-dimensional embeddings were stable, predictive, and exhibited semantic clustering similar to human mental representations. Remarkably, the dimensions underlying these embeddings were interpretable, suggesting that LLMs and MLLMs develop human-like conceptual representations of objects. Further analysis showed strong alignment between model embeddings and neural activity patterns in brain regions such as EBA, PPA, RSC, and FFA. This provides compelling evidence that the object representations in LLMs, while not identical to human ones, share fundamental similarities that reflect key aspects of human conceptual knowledge. Our findings advance the understanding of machine intelligence and inform the development of more human-like artificial cognitive systems.

The fundamental units of internal representations in large language models (LLMs) remain undefined, limiting further understanding of their mechanisms. Neurons or features are often regarded as such units, yet neurons suffer from polysemy, while features face concerns of unreliable reconstruction and instability. To address this issue, we propose the Atoms Theory, which defines such units as atoms. We introduce the atomic inner product (AIP) to correct representation shifting, formally define atoms, and prove the conditions that atoms satisfy the Restricted Isometry Property (RIP), ensuring stable sparse representations over atom set and linking to compressed sensing. Under stronger conditions, we further establish the uniqueness and exact ell_1 recoverability of the sparse representations, and provide guarantees that single-layer sparse autoencoders (SAEs) with threshold activations can reliably identify the atoms. To validate the Atoms Theory, we train threshold-activated SAEs on Gemma2-2B, Gemma2-9B, and Llama3.1-8B, achieving 99.9% sparse reconstruction across layers on average, and more than 99.8% of atoms satisfy the uniqueness condition, compared to 0.5% for neurons and 68.2% for features, showing that atoms more faithfully capture intrinsic representations of LLMs. Scaling experiments further reveal the link between SAEs size and recovery capacity. Overall, this work systematically introduces and validates Atoms Theory of LLMs, providing a theoretical framework for understanding internal representations and a foundation for mechanistic interpretability. Code available at https://github.com/ChenhuiHu/towards_atoms.

Large-scale pre-trained Vision-Language Models (VLMs) have become essential for transfer learning across diverse tasks. However, adapting these models with limited few-shot data often leads to overfitting, diminishing their performance on new tasks. To tackle this issue, we propose a novel Multi-Modal Representation Learning (MMRL) framework that introduces a shared, learnable, and modality-agnostic representation space. MMRL projects the space tokens to text and image representation tokens, facilitating more effective multi-modal interactions. Unlike previous approaches that solely optimize class token features, MMRL integrates representation tokens at higher layers of the encoders--where dataset-specific features are more prominent--while preserving generalized knowledge in the lower layers. During training, both representation and class features are optimized, with trainable projection layer applied to the representation tokens, whereas the class token projection layer remains frozen to retain pre-trained knowledge. Furthermore, a regularization term is introduced to align the class features and text features with the zero-shot features from the frozen VLM, thereby safeguarding the model's generalization capacity. For inference, a decoupling strategy is employed, wherein both representation and class features are utilized for base classes, while only the class features, which retain more generalized knowledge, are used for new tasks. Extensive experiments across 15 datasets demonstrate that MMRL outperforms state-of-the-art methods, achieving a balanced trade-off between task-specific adaptation and generalization. Code is available at https://github.com/yunncheng/MMRL.

Recent advances in Large Multimodal Models (LMMs) lead to significant breakthroughs in both academia and industry. One question that arises is how we, as humans, can understand their internal neural representations. This paper takes an initial step towards addressing this question by presenting a versatile framework to identify and interpret the semantics within LMMs. Specifically, 1) we first apply a Sparse Autoencoder(SAE) to disentangle the representations into human understandable features. 2) We then present an automatic interpretation framework to interpreted the open-semantic features learned in SAE by the LMMs themselves. We employ this framework to analyze the LLaVA-NeXT-8B model using the LLaVA-OV-72B model, demonstrating that these features can effectively steer the model's behavior. Our results contribute to a deeper understanding of why LMMs excel in specific tasks, including EQ tests, and illuminate the nature of their mistakes along with potential strategies for their rectification. These findings offer new insights into the internal mechanisms of LMMs and suggest parallels with the cognitive processes of the human brain.

As SE(3)-equivariant graph neural networks mature as a core tool for 3D atomistic modeling, improving their efficiency, expressivity, and physical consistency has become a central challenge for large-scale applications. In this work, we introduce EquiformerV3, the third generation of the SE(3)-equivariant graph attention Transformer, designed to advance all three dimensions: efficiency, expressivity, and generality. Building on EquiformerV2, we have the following three key advances. First, we optimize the software implementation, achieving 1.75times speedup. Second, we introduce simple and effective modifications to EquiformerV2, including equivariant merged layer normalization, improved feedforward network hyper-parameters, and attention with smooth radius cutoff. Third, we propose SwiGLU-S^2 activations to incorporate many-body interactions for better theoretical expressivity and to preserve strict equivariance while reducing the complexity of sampling S^2 grids. Together, SwiGLU-S^2 activations and smooth-cutoff attention enable accurate modeling of smoothly varying potential energy surfaces (PES), generalizing EquiformerV3 to tasks requiring energy-conserving simulations and higher-order derivatives of PES. With these improvements, EquiformerV3 trained with the auxiliary task of denoising non-equilibrium structures (DeNS) achieves state-of-the-art results on OC20, OMat24, and Matbench Discovery.

Recently, triple decomposition has attracted increasing attention for decomposing third-order tensors into three factor tensors. However, this approach is limited to third-order tensors and enforces uniformity in the lower dimensions across all factor tensors, which restricts its flexibility and applicability. To address these issues, we propose the Multiple decomposition, a novel framework that generalizes triple decomposition to arbitrary order tensors and allows the short dimensions of the factor tensors to differ. We establish its connections with other classical tensor decompositions. Furthermore, implicit neural representation (INR) is employed to continuously represent the factor tensors in Multiple decomposition, enabling the method to generalize to non-grid data. We refer to this INR-based Multiple decomposition as Implicit Multiple Tensor Decomposition (IMTD). Then, the Proximal Alternating Least Squares (PALS) algorithm is utilized to solve the IMTD-based tensor reconstruction models. Since the objective function in IMTD-based models often lacks the Kurdyka-Lojasiewicz (KL) property, we establish a KL-free convergence analysis for the algorithm. Finally, extensive numerical experiments further validate the effectiveness of the proposed method.

The rising importance of 3D representation learning, pivotal in computer vision, autonomous driving, and robotics, is evident. However, a prevailing trend, which straightforwardly resorted to transferring 2D alignment strategies to the 3D domain, encounters three distinct challenges: (1) Information Degradation: This arises from the alignment of 3D data with mere single-view 2D images and generic texts, neglecting the need for multi-view images and detailed subcategory texts. (2) Insufficient Synergy: These strategies align 3D representations to image and text features individually, hampering the overall optimization for 3D models. (3) Underutilization: The fine-grained information inherent in the learned representations is often not fully exploited, indicating a potential loss in detail. To address these issues, we introduce JM3D, a comprehensive approach integrating point cloud, text, and image. Key contributions include the Structured Multimodal Organizer (SMO), enriching vision-language representation with multiple views and hierarchical text, and the Joint Multi-modal Alignment (JMA), combining language understanding with visual representation. Our advanced model, JM3D-LLM, marries 3D representation with large language models via efficient fine-tuning. Evaluations on ModelNet40 and ScanObjectNN establish JM3D's superiority. The superior performance of JM3D-LLM further underscores the effectiveness of our representation transfer approach. Our code and models are available at https://github.com/Mr-Neko/JM3D.

When manipulating three-dimensional data, it is possible to ensure that rotational and translational symmetries are respected by applying so-called SE(3)-equivariant models. Protein structure prediction is a prominent example of a task which displays these symmetries. Recent work in this area has successfully made use of an SE(3)-equivariant model, applying an iterative SE(3)-equivariant attention mechanism. Motivated by this application, we implement an iterative version of the SE(3)-Transformer, an SE(3)-equivariant attention-based model for graph data. We address the additional complications which arise when applying the SE(3)-Transformer in an iterative fashion, compare the iterative and single-pass versions on a toy problem, and consider why an iterative model may be beneficial in some problem settings. We make the code for our implementation available to the community.

Recent years have witnessed a surge in the development of protein structural tokenization methods, which chunk protein 3D structures into discrete or continuous representations. Structure tokenization enables the direct application of powerful techniques like language modeling for protein structures, and large multimodal models to integrate structures with protein sequences and functional texts. Despite the progress, the capabilities and limitations of these methods remain poorly understood due to the lack of a unified evaluation framework. We first introduce StructTokenBench, a framework that comprehensively evaluates the quality and efficiency of structure tokenizers, focusing on fine-grained local substructures rather than global structures, as typical in existing benchmarks. Our evaluations reveal that no single model dominates all benchmarking perspectives. Observations of codebook under-utilization led us to develop AminoAseed, a simple yet effective strategy that enhances codebook gradient updates and optimally balances codebook size and dimension for improved tokenizer utilization and quality. Compared to the leading model ESM3, our method achieves an average of 6.31% performance improvement across 24 supervised tasks, with sensitivity and utilization rates increased by 12.83% and 124.03%, respectively. Source code and model weights are available at https://github.com/KatarinaYuan/StructTokenBench

Large-scale Protein Language Models (PLMs) have improved performance in protein prediction tasks, ranging from 3D structure prediction to various function predictions. In particular, AlphaFold, a ground-breaking AI system, could potentially reshape structural biology. However, the utility of the PLM module in AlphaFold, Evoformer, has not been explored beyond structure prediction. In this paper, we investigate the representation ability of three popular PLMs: ESM-1b (single sequence), MSA-Transformer (multiple sequence alignment) and Evoformer (structural), with a special focus on Evoformer. Specifically, we aim to answer the following key questions: (i) Does the Evoformer trained as part of AlphaFold produce representations amenable to predicting protein function? (ii) If yes, can Evoformer replace ESM-1b and MSA-Transformer? (ii) How much do these PLMs rely on evolution-related protein data? In this regard, are they complementary to each other? We compare these models by empirical study along with new insights and conclusions. All code and datasets for reproducibility are available at https://github.com/elttaes/Revisiting-PLMs.

Large-scale pretrained language models (LMs) are said to ``lack the ability to connect utterances to the world'' (Bender and Koller, 2020), because they do not have ``mental models of the world' '(Mitchell and Krakauer, 2023). If so, one would expect LM representations to be unrelated to representations induced by vision models. We present an empirical evaluation across four families of LMs (BERT, GPT-2, OPT and LLaMA-2) and three vision model architectures (ResNet, SegFormer, and MAE). Our experiments show that LMs partially converge towards representations isomorphic to those of vision models, subject to dispersion, polysemy and frequency. This has important implications for both multi-modal processing and the LM understanding debate (Mitchell and Krakauer, 2023).

We investigate the internal representations of vision-and-language models (VLMs) and how they encode task representations. We consider tasks specified through examples or instructions, using either text or image inputs. Surprisingly, we find that conceptually similar tasks are mapped to similar task vector representations, regardless of how they are specified. Our findings suggest that to output answers, tokens in VLMs undergo three distinct phases: input, task, and answer, a process which is consistent across different modalities and specifications. The task vectors we identify in VLMs are general enough to be derived in one modality (e.g., text) and transferred to another (e.g., image). Additionally, we find that ensembling exemplar and instruction based task vectors produce better task representations. Taken together, these insights shed light on the underlying mechanisms of VLMs, particularly their ability to represent tasks in a shared manner across different modalities and task specifications. Project page: https://task-vectors-are-cross-modal.github.io.

Equivariant Transformers such as Equiformer have demonstrated the efficacy of applying Transformers to the domain of 3D atomistic systems. However, they are still limited to small degrees of equivariant representations due to their computational complexity. In this paper, we investigate whether these architectures can scale well to higher degrees. Starting from Equiformer, we first replace SO(3) convolutions with eSCN convolutions to efficiently incorporate higher-degree tensors. Then, to better leverage the power of higher degrees, we propose three architectural improvements -- attention re-normalization, separable S^2 activation and separable layer normalization. Putting this all together, we propose EquiformerV2, which outperforms previous state-of-the-art methods on the large-scale OC20 dataset by up to 12% on forces, 4% on energies, offers better speed-accuracy trade-offs, and 2times reduction in DFT calculations needed for computing adsorption energies.

Proteins are fundamental to biology, executing diverse functions through complex physicochemical interactions, and they hold transformative potential across medicine, materials science, and environmental applications. Protein Language Models (pLMs) aim to unlock insights from the vast space of unlabeled protein sequences by learning rich, semantic representations from primary sequences via masked language modeling. However, these models typically exhibit limited generative capacity. In this work, we introduce the Diffusion Sequence Model (DSM), a novel pLM trained with masked diffusion to enable both high-quality representation learning and generative protein design. DSM builds upon the ESM2 architecture by incorporating a masked forward diffusion process inspired by the LLaDA framework. After training, DSM is capable of generating diverse, biomimetic sequences that align with expected amino acid compositions, secondary structures, and predicted functions, even with 90\% token corruption. Furthermore, DSM's learned representations match or exceed those of similarly sized pLMs on downstream tasks. We also introduce DSM(ppi), a variant fine-tuned to generate protein binders by attending to target sequences. We demonstrate DSM(ppi)'s effectiveness on the challenging Bench-tested Binder Benchmark (BenchBB), where both DSM and DSM(ppi) produce candidates with superior predicted binding affinity compared to known binders. Our results establish masked diffusion as a powerful paradigm for unifying protein representation and generation in a single framework.

We demonstrate that the inference operations of several open-weight large language models (LLMs) can be mapped to an exactly equivalent linear system for an input sequence without modifying the model weights or altering output predictions. Extending techniques from image diffusion models that exhibit local or piecewise linearity, we strategically alter the gradient computation with respect to a given input sequence for a next-token prediction such that the Jacobian of the model nearly exactly reproduces the forward prediction with a linear system. We demonstrate this approach across models (Llama 3, Gemma 3, Qwen 3, Phi 4, Mistral Ministral and OLMo 2, up to Llama 3.3 70B Q4) and show through the singular value decomposition of the detached Jacobian that these LLMs operate in extremely low-dimensional subspaces where many of the largest singular vectors decode to concepts related to the most-likely output token. This approach also allows us to examine the operation of each successive layer (and its attention and MLP components) as nearly-exact linear systems and observe the emergence of semantic concepts. Despite their expressive power and global nonlinearity, modern LLMs can be interpreted through nearly-exact locally linear decompositions that provide insights into their internal representations and reveal interpretable semantic structures in the next-token prediction process.

Encoder-free architectures have been preliminarily explored in the 2D visual domain, yet it remains an open question whether they can be effectively applied to 3D understanding scenarios. In this paper, we present the first comprehensive investigation into the potential of encoder-free architectures to overcome the challenges of encoder-based 3D Large Multimodal Models (LMMs). These challenges include the failure to adapt to varying point cloud resolutions and the point features from the encoder not meeting the semantic needs of Large Language Models (LLMs). We identify key aspects for 3D LMMs to remove the encoder and enable the LLM to assume the role of the 3D encoder: 1) We propose the LLM-embedded Semantic Encoding strategy in the pre-training stage, exploring the effects of various point cloud self-supervised losses. And we present the Hybrid Semantic Loss to extract high-level semantics. 2) We introduce the Hierarchical Geometry Aggregation strategy in the instruction tuning stage. This incorporates inductive bias into the LLM early layers to focus on the local details of the point clouds. To the end, we present the first Encoder-free 3D LMM, ENEL. Our 7B model rivals the current state-of-the-art model, ShapeLLM-13B, achieving 55.0%, 50.92%, and 42.7% on the classification, captioning, and VQA tasks, respectively. Our results demonstrate that the encoder-free architecture is highly promising for replacing encoder-based architectures in the field of 3D understanding. The code is released at https://github.com/Ivan-Tang-3D/ENEL

A key requirement for the development of effective learning representations is their evaluation and comparison to representations we know to be effective. In natural sensory domains, the community has viewed the brain as a source of inspiration and as an implicit benchmark for success. However, it has not been possible to directly test representational learning algorithms directly against the representations contained in neural systems. Here, we propose a new benchmark for visual representations on which we have directly tested the neural representation in multiple visual cortical areas in macaque (utilizing data from [Majaj et al., 2012]), and on which any computer vision algorithm that produces a feature space can be tested. The benchmark measures the effectiveness of the neural or machine representation by computing the classification loss on the ordered eigendecomposition of a kernel matrix [Montavon et al., 2011]. In our analysis we find that the neural representation in visual area IT is superior to visual area V4. In our analysis of representational learning algorithms, we find that three-layer models approach the representational performance of V4 and the algorithm in [Le et al., 2012] surpasses the performance of V4. Impressively, we find that a recent supervised algorithm [Krizhevsky et al., 2012] achieves performance comparable to that of IT for an intermediate level of image variation difficulty, and surpasses IT at a higher difficulty level. We believe this result represents a major milestone: it is the first learning algorithm we have found that exceeds our current estimate of IT representation performance. We hope that this benchmark will assist the community in matching the representational performance of visual cortex and will serve as an initial rallying point for further correspondence between representations derived in brains and machines.

Embedding models have been crucial in enabling various downstream tasks such as semantic similarity, information retrieval, and clustering. Recently, there has been a surge of interest in developing universal text embedding models that can generalize across tasks (e.g., MTEB). However, progress in learning universal multimodal embedding models has been relatively slow despite their importance. In this work, we aim to explore the potential for building universal embeddings capable of handling a wide range of downstream tasks. Our contributions are twofold: (1) MMEB (Massive Multimodal Embedding Benchmark), which covers 4 meta-tasks (i.e. classification, visual question answering, multimodal retrieval, and visual grounding) and 36 datasets, including 20 training and 16 evaluation datasets, and (2) VLM2Vec (Vision-Language Model -> Vector), a contrastive training framework that converts any state-of-the-art vision-language model into an embedding model via training on MMEB. Unlike previous models such as CLIP and BLIP, VLM2Vec can process any combination of images and text to generate a fixed-dimensional vector based on task instructions. We build a series of VLM2Vec models on Phi-3.5-V and evaluate them on MMEB's evaluation split. Our results show that \model achieves an absolute average improvement of 10% to 20% over existing multimodal embedding models on both in-distribution and out-of-distribution datasets in MMEB.

The integration of molecule and language has garnered increasing attention in molecular science. Recent advancements in Language Models (LMs) have demonstrated potential for the comprehensive modeling of molecule and language. However, existing works exhibit notable limitations. Most existing works overlook the modeling of 3D information, which is crucial for understanding molecular structures and also functions. While some attempts have been made to leverage external structure encoding modules to inject the 3D molecular information into LMs, there exist obvious difficulties that hinder the integration of molecular structure and language text, such as modality alignment and separate tuning. To bridge this gap, we propose 3D-MolT5, a unified framework designed to model both 1D molecular sequence and 3D molecular structure. The key innovation lies in our methodology for mapping fine-grained 3D substructure representations (based on 3D molecular fingerprints) to a specialized 3D token vocabulary for 3D-MolT5. This 3D structure token vocabulary enables the seamless combination of 1D sequence and 3D structure representations in a tokenized format, allowing 3D-MolT5 to encode molecular sequence (SELFIES), molecular structure, and text sequences within a unified architecture. Alongside, we further introduce 1D and 3D joint pre-training to enhance the model's comprehension of these diverse modalities in a joint representation space and better generalize to various tasks for our foundation model. Through instruction tuning on multiple downstream datasets, our proposed 3D-MolT5 shows superior performance than existing methods in molecular property prediction, molecule captioning, and text-based molecule generation tasks. Our code will be available on GitHub soon.

Large-scale pre-trained Vision-Language Models (VLMs) have significantly advanced transfer learning across diverse tasks. However, adapting these models with limited few-shot data often leads to overfitting, undermining their ability to generalize to new tasks. To address this, we propose Multi-Modal Representation Learning (MMRL), which introduces a shared, learnable, modality-agnostic representation space. MMRL generates space tokens projected into both text and image encoders as representation tokens, enabling more effective cross-modal interactions. Unlike prior methods that mainly optimize class token features, MMRL inserts representation tokens into higher encoder layers--where task-specific features are more prominent--while preserving general knowledge in the lower layers. During training, both class and representation features are jointly optimized: a trainable projection layer is applied to representation tokens for task adaptation, while the projection layer for class token remains frozen to retain pre-trained knowledge. To further promote generalization, we introduce a regularization term aligning class and text features with the frozen VLM's zero-shot features. At inference, a decoupling strategy uses both class and representation features for base tasks, but only class features for novel tasks due to their stronger generalization. Building upon this, we propose MMRL++, a parameter-efficient and interaction-aware extension that significantly reduces trainable parameters and enhances intra-modal interactions--particularly across the layers of representation tokens--allowing gradient sharing and instance-specific information to propagate more effectively through the network. Extensive experiments on 15 datasets demonstrate that MMRL and MMRL++ consistently outperform state-of-the-art methods, achieving a strong balance between task-specific adaptation and generalization.

Unlike the predictable scaling laws in natural language processing and computer vision, protein language models (PLMs) scale poorly: for many tasks, models within the same family plateau or even decrease in performance, with mid-sized models often outperforming the largest in the family. We introduce Reverse Distillation, a principled framework that decomposes large PLM representations into orthogonal subspaces guided by smaller models of the same family. The resulting embeddings have a nested, Matryoshka-style structure: the first k dimensions of a larger model's embedding are exactly the representation from the smaller model. This ensures that larger reverse-distilled models consistently outperform smaller ones. A motivating intuition is that smaller models, constrained by capacity, preferentially encode broadly-shared protein features. Reverse distillation isolates these shared features and orthogonally extracts additional contributions from larger models, preventing interference between the two. On ProteinGym benchmarks, reverse-distilled ESM-2 variants outperform their respective baselines at the same embedding dimensionality, with the reverse-distilled 15 billion parameter model achieving the strongest performance. Our framework is generalizable to any model family where scaling challenges persist. Code and trained models are available at https://github.com/rohitsinghlab/plm_reverse_distillation.

Graph neural networks that model 3D data, such as point clouds or atoms, are typically desired to be SO(3) equivariant, i.e., equivariant to 3D rotations. Unfortunately equivariant convolutions, which are a fundamental operation for equivariant networks, increase significantly in computational complexity as higher-order tensors are used. In this paper, we address this issue by reducing the SO(3) convolutions or tensor products to mathematically equivalent convolutions in SO(2) . This is accomplished by aligning the node embeddings' primary axis with the edge vectors, which sparsifies the tensor product and reduces the computational complexity from O(L^6) to O(L^3), where L is the degree of the representation. We demonstrate the potential implications of this improvement by proposing the Equivariant Spherical Channel Network (eSCN), a graph neural network utilizing our novel approach to equivariant convolutions, which achieves state-of-the-art results on the large-scale OC-20 and OC-22 datasets.

We investigate the internal representations of vision-language models (VLMs) to address hallucinations, a persistent challenge despite advances in model size and training. We project VLMs' internal image representations to their language vocabulary and observe more confident output probabilities on real objects than hallucinated objects. We additionally use these output probabilities to spatially localize real objects. Building on this approach, we introduce a knowledge erasure algorithm that removes hallucinations by linearly orthogonalizing image features with respect to hallucinated object features. We show that targeted edits to a model's latent representations can reduce hallucinations by up to 25.7% on the COCO2014 dataset while preserving performance. Our findings demonstrate how a deeper understanding of VLMs' latent representations can enhance reliability and enable novel capabilities, such as zero-shot segmentation.

Predicting protein function from amino acid sequence remains a central challenge in data-scarce (low-N) regimes, limiting machine learning-guided protein design when only small amounts of assay-labeled sequence-function data are available. Protein language models (pLMs) have advanced the field by providing evolutionary-informed embeddings and sparse autoencoders (SAEs) have enabled decomposition of these embeddings into interpretable latent variables that capture structural and functional features. However, the effectiveness of SAEs for low-N function prediction and protein design has not been systematically studied. Herein, we evaluate SAEs trained on fine-tuned ESM2 embeddings across diverse fitness extrapolation and protein engineering tasks. We show that SAEs, with as few as 24 sequences, consistently outperform or compete with their ESM2 baselines in fitness prediction, indicating that their sparse latent space encodes compact and biologically meaningful representations that generalize more effectively from limited data. Moreover, steering predictive latents exploits biological motifs in pLM representations, yielding top-fitness variants in 83% of cases compared to designing with ESM2 alone.

Multi-modal Large Language Models (MLLMs) have recently exhibited impressive general-purpose capabilities by leveraging vision foundation models to encode the core concepts of images into representations. These are then combined with instructions and processed by the language model to generate high-quality responses. Despite significant progress in enhancing the language component, challenges persist in optimally fusing visual encodings within the language model for task-specific adaptability. Recent research has focused on improving this fusion through modality adaptation modules but at the cost of significantly increased model complexity and training data needs. In this paper, we propose EMMA (Efficient Multi-Modal Adaptation), a lightweight cross-modality module designed to efficiently fuse visual and textual encodings, generating instruction-aware visual representations for the language model. Our key contributions include: (1) an efficient early fusion mechanism that integrates vision and language representations with minimal added parameters (less than 0.2% increase in model size), (2) an in-depth interpretability analysis that sheds light on the internal mechanisms of the proposed method; (3) comprehensive experiments that demonstrate notable improvements on both specialized and general benchmarks for MLLMs. Empirical results show that EMMA boosts performance across multiple tasks by up to 9.3% while significantly improving robustness against hallucinations. Our code is available at https://github.com/SaraGhazanfari/EMMA

Multi-view transformers such as DUSt3R are revolutionizing 3D vision by solving 3D tasks in a feed-forward manner. However, contrary to previous optimization-based pipelines, the inner mechanisms of multi-view transformers are unclear. Their black-box nature makes further improvements beyond data scaling challenging and complicates usage in safety- and reliability-critical applications. Here, we present an approach for probing and visualizing 3D representations from the residual connections of the multi-view transformers' layers. In this manner, we investigate a variant of the DUSt3R model, shedding light on the development of its latent state across blocks, the role of the individual layers, and suggest how it differs from methods with stronger inductive biases of explicit global pose. Finally, we show that the investigated variant of DUSt3R estimates correspondences that are refined with reconstructed geometry. The code used for the analysis is available at https://github.com/JulienGaubil/und3rstand .

Electron microscopy (EM) enables the reconstruction of neural circuits at the level of individual synapses, which has been transformative for scientific discoveries. However, due to the complex morphology, an accurate reconstruction of cortical axons has become a major challenge. Worse still, there is no publicly available large-scale EM dataset from the cortex that provides dense ground truth segmentation for axons, making it difficult to develop and evaluate large-scale axon reconstruction methods. To address this, we introduce the AxonEM dataset, which consists of two 30x30x30 um^3 EM image volumes from the human and mouse cortex, respectively. We thoroughly proofread over 18,000 axon instances to provide dense 3D axon instance segmentation, enabling large-scale evaluation of axon reconstruction methods. In addition, we densely annotate nine ground truth subvolumes for training, per each data volume. With this, we reproduce two published state-of-the-art methods and provide their evaluation results as a baseline. We publicly release our code and data at https://connectomics-bazaar.github.io/proj/AxonEM/index.html to foster the development of advanced methods.

The extent to which text-only language models (LMs) learn to represent features of the non-linguistic world is an open question. Prior work has shown that pretrained LMs can be taught to caption images when a vision model's parameters are optimized to encode images in the language space. We test a stronger hypothesis: that the conceptual representations learned by frozen text-only models and vision-only models are similar enough that this can be achieved with a linear map. We show that the image representations from vision models can be transferred as continuous prompts to frozen LMs by training only a single linear projection. Using these to prompt the LM achieves competitive performance on captioning and visual question answering tasks compared to models that tune both the image encoder and text decoder (such as the MAGMA model). We compare three image encoders with increasing amounts of linguistic supervision seen during pretraining: BEIT (no linguistic information), NF-ResNET (lexical category information), and CLIP (full natural language descriptions). We find that all three encoders perform equally well at transferring visual property information to the language model (e.g., whether an animal is large or small), but that image encoders pretrained with linguistic supervision more saliently encode category information (e.g., distinguishing hippo vs. elephant) and thus perform significantly better on benchmark language-and-vision tasks. Our results indicate that LMs encode conceptual information structurally similarly to vision-based models, even those that are solely trained on images. Code is available here: https://github.com/jmerullo/limber

Recent advances in scene understanding have leveraged multimodal large language models (MLLMs) for 3D reasoning by capitalizing on their strong 2D pretraining. However, the lack of explicit 3D data during MLLM pretraining limits 3D representation capability. In this paper, we investigate the 3D-awareness of MLLMs by evaluating multi-view correspondence and reveal a strong positive correlation between the quality of 3D-aware representation and downstream task performance. Motivated by this, we propose 3DRS, a framework that enhances MLLM 3D representation learning by introducing supervision from pretrained 3D foundation models. Our approach aligns MLLM visual features with rich 3D knowledge distilled from 3D models, effectively improving scene understanding. Extensive experiments across multiple benchmarks and MLLMs -- including visual grounding, captioning, and question answering -- demonstrate consistent performance gains. Project page: https://visual-ai.github.io/3drs

Multimodal large language models (MLLMs) have shown promising advancements in general visual and language understanding. However, the representation of multimodal information using MLLMs remains largely unexplored. In this work, we introduce a new framework, E5-V, designed to adapt MLLMs for achieving universal multimodal embeddings. Our findings highlight the significant potential of MLLMs in representing multimodal inputs compared to previous approaches. By leveraging MLLMs with prompts, E5-V effectively bridges the modality gap between different types of inputs, demonstrating strong performance in multimodal embeddings even without fine-tuning. We propose a single modality training approach for E5-V, where the model is trained exclusively on text pairs. This method demonstrates significant improvements over traditional multimodal training on image-text pairs, while reducing training costs by approximately 95%. Additionally, this approach eliminates the need for costly multimodal training data collection. Extensive experiments across four types of tasks demonstrate the effectiveness of E5-V. As a universal multimodal model, E5-V not only achieves but often surpasses state-of-the-art performance in each task, despite being trained on a single modality.

Multimodal Attributed Graphs (MAGs) are ubiquitous in real-world applications, encompassing extensive knowledge through multimodal attributes attached to nodes (e.g., texts and images) and topological structure representing node interactions. Despite its potential to advance diverse research fields like social networks and e-commerce, MAG representation learning (MAGRL) remains underexplored due to the lack of standardized datasets and evaluation frameworks. In this paper, we first propose MAGB, a comprehensive MAG benchmark dataset, featuring curated graphs from various domains with both textual and visual attributes. Based on MAGB dataset, we further systematically evaluate two mainstream MAGRL paradigms: GNN-as-Predictor, which integrates multimodal attributes via Graph Neural Networks (GNNs), and VLM-as-Predictor, which harnesses Vision Language Models (VLMs) for zero-shot reasoning. Extensive experiments on MAGB reveal following critical insights: (i) Modality significances fluctuate drastically with specific domain characteristics. (ii) Multimodal embeddings can elevate the performance ceiling of GNNs. However, intrinsic biases among modalities may impede effective training, particularly in low-data scenarios. (iii) VLMs are highly effective at generating multimodal embeddings that alleviate the imbalance between textual and visual attributes. These discoveries, which illuminate the synergy between multimodal attributes and graph topologies, contribute to reliable benchmarks, paving the way for future MAG research. The MAGB dataset and evaluation pipeline are publicly available at https://github.com/sktsherlock/MAGB.

Self-supervised models have revolutionized speech processing, achieving new levels of performance in a wide variety of tasks with limited resources. However, the inner workings of these models are still opaque. In this paper, we aim to analyze the encoded contextual representation of these foundation models based on their inter- and intra-model similarity, independent of any external annotation and task-specific constraint. We examine different SSL models varying their training paradigm -- Contrastive (Wav2Vec2.0) and Predictive models (HuBERT); and model sizes (base and large). We explore these models on different levels of localization/distributivity of information including (i) individual neurons; (ii) layer representation; (iii) attention weights and (iv) compare the representations with their finetuned counterparts.Our results highlight that these models converge to similar representation subspaces but not to similar neuron-localized concepts\footnote{A concept represents a coherent fragment of knowledge, such as ``a class containing certain objects as elements, where the objects have certain properties. We made the code publicly available for facilitating further research, we publicly released our code.

Research on 3D Vision-Language Models (3D-VLMs) is gaining increasing attention, which is crucial for developing embodied AI within 3D scenes, such as visual navigation and embodied question answering. Due to the high density of visual features, especially in large 3D scenes, accurately locating task-relevant visual information is challenging. Existing works attempt to segment all objects and consider their features as scene representations. However, these task-agnostic object features include much redundant information and missing details for the task-relevant area. To tackle these problems, we propose LSceneLLM, an adaptive framework that automatically identifies task-relevant areas by leveraging LLM's visual preference for different tasks, followed by a plug-and-play scene magnifier module to capture fine-grained details in focused areas. Specifically, a dense token selector examines the attention map of LLM to identify visual preferences for the instruction input. It then magnifies fine-grained details of the focusing area. An adaptive self-attention module is leveraged to fuse the coarse-grained and selected fine-grained visual information. To comprehensively evaluate the large scene understanding ability of 3D-VLMs, we further introduce a cross-room understanding benchmark, XR-Scene, which contains a series of large scene understanding tasks including XR-QA, XR-EmbodiedPlanning, and XR-SceneCaption. Experiments show that our method surpasses existing methods on both large scene understanding and existing scene understanding benchmarks. Plunging our scene magnifier module into the existing 3D-VLMs also brings significant improvement.

Common approaches rely on fixed-length embedding vectors from language models as sentence embeddings for downstream tasks such as semantic textual similarity (STS). Such methods are limited in their flexibility due to unknown computational constraints and budgets across various applications. Matryoshka Representation Learning (MRL) (Kusupati et al., 2022) encodes information at finer granularities, i.e., with lower embedding dimensions, to adaptively accommodate ad hoc tasks. Similar accuracy can be achieved with a smaller embedding size, leading to speedups in downstream tasks. Despite its improved efficiency, MRL still requires traversing all Transformer layers before obtaining the embedding, which remains the dominant factor in time and memory consumption. This prompts consideration of whether the fixed number of Transformer layers affects representation quality and whether using intermediate layers for sentence representation is feasible. In this paper, we introduce a novel sentence embedding model called Two-dimensional Matryoshka Sentence Embedding (2DMSE). It supports elastic settings for both embedding sizes and Transformer layers, offering greater flexibility and efficiency than MRL. We conduct extensive experiments on STS tasks and downstream applications. The experimental results demonstrate the effectiveness of our proposed model in dynamically supporting different embedding sizes and Transformer layers, allowing it to be highly adaptable to various scenarios.

Despite significant advancements in Multimodal Large Language Models (MLLMs) for understanding complex human intentions through cross-modal interactions, capturing intricate image details remains challenging. Previous methods integrating multiple vision encoders to enhance visual detail introduce redundancy and computational overhead. We observe that most MLLMs utilize only the last-layer feature map of the vision encoder for visual representation, neglecting the rich fine-grained information in shallow feature maps. To address this issue, we propose \modelname, a simple yet effective multi-layer feature fuser that efficiently integrates deep and shallow features from Vision Transformers (ViTs). Specifically, it leverages semantically aligned deep features as queries to dynamically extract missing details from shallow features, thus preserving semantic alignment while enriching the representation with fine-grained information. Applied to the LLaVA-1.5 model, \modelname~achieves significant improvements in visual representation and benchmark performance, providing a more flexible and lightweight solution compared to multi-encoder ensemble methods. The code and model have been released at https://github.com/yuecao0119/MMFuser.

Shape assembly aims to reassemble parts (or fragments) into a complete object, which is a common task in our daily life. Different from the semantic part assembly (e.g., assembling a chair's semantic parts like legs into a whole chair), geometric part assembly (e.g., assembling bowl fragments into a complete bowl) is an emerging task in computer vision and robotics. Instead of semantic information, this task focuses on geometric information of parts. As the both geometric and pose space of fractured parts are exceptionally large, shape pose disentanglement of part representations is beneficial to geometric shape assembly. In our paper, we propose to leverage SE(3) equivariance for such shape pose disentanglement. Moreover, while previous works in vision and robotics only consider SE(3) equivariance for the representations of single objects, we move a step forward and propose leveraging SE(3) equivariance for representations considering multi-part correlations, which further boosts the performance of the multi-part assembly. Experiments demonstrate the significance of SE(3) equivariance and our proposed method for geometric shape assembly. Project page: https://crtie.github.io/SE-3-part-assembly/

Projecting visual features into word embedding space has become a significant fusion strategy adopted by Multimodal Large Language Models (MLLMs). However, its internal mechanisms have yet to be explored. Inspired by multilingual research, we identify domain-specific neurons in multimodal large language models. Specifically, we investigate the distribution of domain-specific neurons and the mechanism of how MLLMs process features from diverse domains. Furthermore, we propose a three-stage framework for language model modules in MLLMs when handling projected image features, and verify this hypothesis using logit lens. Extensive experiments indicate that while current MLLMs exhibit Visual Question Answering (VQA) capability, they may not fully utilize domain-specific information. Manipulating domain-specific neurons properly will result in a 10\% change of accuracy at most, shedding light on the development of cross-domain, all-encompassing MLLMs in the future. Our code will be released upon paper notification.

The capabilities of large language models (LLMs) have sparked debate over whether such systems just learn an enormous collection of superficial statistics or a coherent model of the data generating process -- a world model. We find evidence for the latter by analyzing the learned representations of three spatial datasets (world, US, NYC places) and three temporal datasets (historical figures, artworks, news headlines) in the Llama-2 family of models. We discover that LLMs learn linear representations of space and time across multiple scales. These representations are robust to prompting variations and unified across different entity types (e.g. cities and landmarks). In addition, we identify individual ``space neurons'' and ``time neurons'' that reliably encode spatial and temporal coordinates. Our analysis demonstrates that modern LLMs acquire structured knowledge about fundamental dimensions such as space and time, supporting the view that they learn not merely superficial statistics, but literal world models.

Crystal symmetry plays a fundamental role in determining its physical, chemical, and electronic properties such as electrical and thermal conductivity, optical and polarization behavior, and mechanical strength. Almost all known crystalline materials have internal symmetry. However, this is often inadequately addressed by existing generative models, making the consistent generation of stable and symmetrically valid crystal structures a significant challenge. We introduce WyFormer, a generative model that directly tackles this by formally conditioning on space group symmetry. It achieves this by using Wyckoff positions as the basis for an elegant, compressed, and discrete structure representation. To model the distribution, we develop a permutation-invariant autoregressive model based on the Transformer encoder and an absence of positional encoding. Extensive experimentation demonstrates WyFormer's compelling combination of attributes: it achieves best-in-class symmetry-conditioned generation, incorporates a physics-motivated inductive bias, produces structures with competitive stability, predicts material properties with competitive accuracy even without atomic coordinates, and exhibits unparalleled inference speed.

Latent diffusion models (LDMs) exhibit an impressive ability to produce realistic images, yet the inner workings of these models remain mysterious. Even when trained purely on images without explicit depth information, they typically output coherent pictures of 3D scenes. In this work, we investigate a basic interpretability question: does an LDM create and use an internal representation of simple scene geometry? Using linear probes, we find evidence that the internal activations of the LDM encode linear representations of both 3D depth data and a salient-object / background distinction. These representations appear surprisingly early in the denoising process-well before a human can easily make sense of the noisy images. Intervention experiments further indicate these representations play a causal role in image synthesis, and may be used for simple high-level editing of an LDM's output. Project page: https://yc015.github.io/scene-representation-diffusion-model/

Language Models (LMs) have greatly influenced diverse domains. However, their inherent limitation in comprehending 3D molecular structures has considerably constrained their potential in the biomolecular domain. To bridge this gap, we focus on 3D molecule-text interpretation, and propose 3D-MoLM: 3D-Molecular Language Modeling. Specifically, 3D-MoLM enables an LM to interpret and analyze 3D molecules by equipping the LM with a 3D molecular encoder. This integration is achieved by a 3D molecule-text projector, bridging the 3D molecular encoder's representation space and the LM's input space. Moreover, to enhance 3D-MoLM's ability of cross-modal molecular understanding and instruction following, we meticulously curated a 3D molecule-centric instruction tuning dataset -- 3D-MoIT. Through 3D molecule-text alignment and 3D molecule-centric instruction tuning, 3D-MoLM establishes an integration of 3D molecular encoder and LM. It significantly surpasses existing baselines on downstream tasks, including molecule-text retrieval, molecule captioning, and more challenging open-text molecular QA tasks, especially focusing on 3D-dependent properties.

Recent studies in interpretability have explored the inner workings of transformer models trained on tasks across various domains, often discovering that these networks naturally develop highly structured representations. When such representations comprehensively reflect the task domain's structure, they are commonly referred to as "World Models" (WMs). In this work, we identify WMs in transformers trained on maze-solving tasks. By using Sparse Autoencoders (SAEs) and analyzing attention patterns, we examine the construction of WMs and demonstrate consistency between SAE feature-based and circuit-based analyses. By subsequently intervening on isolated features to confirm their causal role, we find that it is easier to activate features than to suppress them. Furthermore, we find that models can reason about mazes involving more simultaneously active features than they encountered during training; however, when these same mazes (with greater numbers of connections) are provided to models via input tokens instead, the models fail. Finally, we demonstrate that positional encoding schemes appear to influence how World Models are structured within the model's residual stream.

Spherical equivariant graph neural networks (EGNNs) provide a principled framework for learning on three-dimensional molecular and biomolecular systems, where predictions must respect the rotational symmetries inherent in physics. These models extend traditional message-passing GNNs and Transformers by representing node and edge features as spherical tensors that transform under irreducible representations of the rotation group SO(3), ensuring that predictions change in physically meaningful ways under rotations of the input. This guide develops a complete, intuitive foundation for spherical equivariant modeling - from group representations and spherical harmonics, to tensor products, Clebsch-Gordan decomposition, and the construction of SO(3)-equivariant kernels. Building on this foundation, we construct the Tensor Field Network and SE(3)-Transformer architectures and explain how they perform equivariant message-passing and attention on geometric graphs. Through clear mathematical derivations and annotated code excerpts, this guide serves as a self-contained introduction for researchers and learners seeking to understand or implement spherical EGNNs for applications in chemistry, molecular property prediction, protein structure modeling, and generative modeling.

Equivariant Graph Neural Networks (EGNNs) have become a widely used approach for modeling 3D atomistic systems. However, mainstream architectures face critical scalability bottlenecks due to the explicit construction of geometric features or dense tensor products on every edge. To overcome this, we introduce E2Former-V2, a scalable architecture that integrates algebraic sparsity with hardware-aware execution. We first propose Equivariant Axis-Aligned Sparsification (EAAS). EAAS builds on Wigner-6j convolution by exploiting an SO(3) rightarrow SO(2) change of basis to transform computationally expensive dense tensor contractions into efficient, sparse parity re-indexing operations. Building on this representation, we introduce On-the-Fly Equivariant Attention, a fully node-centric mechanism implemented via a custom fused Triton kernel. By eliminating materialized edge tensors and maximizing SRAM utilization, our kernel achieves a 20times improvement in TFLOPS compared to standard implementations. Extensive experiments on the SPICE and OMol25 datasets demonstrate that E2Former-V2 maintains comparable predictive performance while notably accelerating inference. This work demonstrates that large equivariant transformers can be trained efficiently using widely accessible GPU platforms. The code is avalible at https://github.com/IQuestLab/UBio-MolFM/tree/e2formerv2.

We introduce Qwen3-VL, the most capable vision-language model in the Qwen series to date, achieving superior performance across a broad range of multimodal benchmarks. It natively supports interleaved contexts of up to 256K tokens, seamlessly integrating text, images, and video. The model family includes both dense (2B/4B/8B/32B) and mixture-of-experts (30B-A3B/235B-A22B) variants to accommodate diverse latency-quality trade-offs. Qwen3-VL delivers three core pillars: (i) markedly stronger pure-text understanding, surpassing comparable text-only backbones in several cases; (ii) robust long-context comprehension with a native 256K-token window for both text and interleaved multimodal inputs, enabling faithful retention, retrieval, and cross-referencing across long documents and videos; and (iii) advanced multimodal reasoning across single-image, multi-image, and video tasks, demonstrating leading performance on comprehensive evaluations such as MMMU and visual-math benchmarks (e.g., MathVista and MathVision). Architecturally, we introduce three key upgrades: (i) an enhanced interleaved-MRoPE for stronger spatial-temporal modeling across images and video; (ii) DeepStack integration, which effectively leverages multi-level ViT features to tighten vision-language alignment; and (iii) text-based time alignment for video, evolving from T-RoPE to explicit textual timestamp alignment for more precise temporal grounding. Under comparable token budgets and latency constraints, Qwen3-VL achieves superior performance in both dense and Mixture-of-Experts (MoE) architectures. We envision Qwen3-VL serving as a foundational engine for image-grounded reasoning, agentic decision-making, and multimodal code intelligence in real-world workflows.

Language models~(LMs) gradually become general-purpose interfaces in the interactive and embodied world, where the understanding of physical concepts is an essential prerequisite. However, it is not yet clear whether LMs can understand physical concepts in the human world. To investigate this, we design a benchmark VEC that covers the tasks of (i) Visual concepts, such as the shape and material of objects, and (ii) Embodied Concepts, learned from the interaction with the world such as the temperature of objects. Our zero (few)-shot prompting results show that the understanding of certain visual concepts emerges as scaling up LMs, but there are still basic concepts to which the scaling law does not apply. For example, OPT-175B performs close to humans with a zero-shot accuracy of 85\% on the material concept, yet behaves like random guessing on the mass concept. Instead, vision-augmented LMs such as CLIP and BLIP achieve a human-level understanding of embodied concepts. Analysis indicates that the rich semantics in visual representation can serve as a valuable source of embodied knowledge. Inspired by this, we propose a distillation method to transfer embodied knowledge from VLMs to LMs, achieving performance gain comparable with that by scaling up the parameters of LMs 134x. Our dataset is available at https://github.com/TobiasLee/VEC

We show that protein sequences can be thought of as sentences in natural language processing and can be parsed using the existing Quantum Natural Language framework into parameterized quantum circuits of reasonable qubits, which can be trained to solve various protein-related machine-learning problems. We classify proteins based on their subcellular locations, a pivotal task in bioinformatics that is key to understanding biological processes and disease mechanisms. Leveraging the quantum-enhanced processing capabilities, we demonstrate that Quantum Tensor Networks (QTN) can effectively handle the complexity and diversity of protein sequences. We present a detailed methodology that adapts QTN architectures to the nuanced requirements of protein data, supported by comprehensive experimental results. We demonstrate two distinct QTNs, inspired by classical recurrent neural networks (RNN) and convolutional neural networks (CNN), to solve the binary classification task mentioned above. Our top-performing quantum model has achieved a 94% accuracy rate, which is comparable to the performance of a classical model that uses the ESM2 protein language model embeddings. It's noteworthy that the ESM2 model is extremely large, containing 8 million parameters in its smallest configuration, whereas our best quantum model requires only around 800 parameters. We demonstrate that these hybrid models exhibit promising performance, showcasing their potential to compete with classical models of similar complexity.

This work introduces a diffusion model for molecule generation in 3D that is equivariant to Euclidean transformations. Our E(3) Equivariant Diffusion Model (EDM) learns to denoise a diffusion process with an equivariant network that jointly operates on both continuous (atom coordinates) and categorical features (atom types). In addition, we provide a probabilistic analysis which admits likelihood computation of molecules using our model. Experimentally, the proposed method significantly outperforms previous 3D molecular generative methods regarding the quality of generated samples and efficiency at training time.

Multimodal representation learning models have demonstrated successful operation across complex tasks, and the integration of vision-language models (VLMs) has further enabled embedding models with instruction-following capabilities. However, existing embedding models lack visual-interactive capabilities to specify regions of interest from users (e.g., point, bounding box, mask), which have been explored in generative models to broaden their human-interactive applicability. Equipping embedding models with visual interactions not only would unlock new applications with localized grounding of user intent, which remains unexplored, but also enable the models to learn entity-level information within images to complement their global representations for conventional embedding tasks. In this paper, we propose a novel Visual-InteRactive Text-Image Universal Embedder (VIRTUE) that extends the capabilities of the segmentation model and the vision-language model to the realm of representation learning. In VIRTUE, the segmentation model can process visual prompts that pinpoint specific regions within an image, thereby enabling the embedder to handle complex and ambiguous scenarios more precisely. To evaluate the visual-interaction ability of VIRTUE, we introduce a large-scale Segmentation-and-Scene Caption Retrieval (SCaR) benchmark comprising 1M samples that aims to retrieve the text caption by jointly considering the entity with a specific object and image scene. VIRTUE consistently achieves a state-of-the-art performance with significant improvements across 36 universal MMEB (3.1%-8.5%) and five visual-interactive SCaR (15.2%-20.3%) tasks.

Despite rapid adoption and deployment of large language models (LLMs), the internal computations of these models remain opaque and poorly understood. In this work, we seek to understand how high-level human-interpretable features are represented within the internal neuron activations of LLMs. We train k-sparse linear classifiers (probes) on these internal activations to predict the presence of features in the input; by varying the value of k we study the sparsity of learned representations and how this varies with model scale. With k=1, we localize individual neurons which are highly relevant for a particular feature, and perform a number of case studies to illustrate general properties of LLMs. In particular, we show that early layers make use of sparse combinations of neurons to represent many features in superposition, that middle layers have seemingly dedicated neurons to represent higher-level contextual features, and that increasing scale causes representational sparsity to increase on average, but there are multiple types of scaling dynamics. In all, we probe for over 100 unique features comprising 10 different categories in 7 different models spanning 70 million to 6.9 billion parameters.

The ability to translate diverse patterns of inputs into structured patterns of behavior has been thought to rest on both humans' and machines' ability to learn robust representations of relevant concepts. The rapid advancement of transformer-based large language models (LLMs) has led to a diversity of computational ingredients -- architectures, fine tuning methods, and training datasets among others -- but it remains unclear which of these ingredients are most crucial for building models that develop human-like representations. Further, most current LLM benchmarks are not suited to measuring representational alignment between humans and models, making benchmark scores unreliable for assessing if current LLMs are making progress towards becoming useful cognitive models. We address these limitations by first evaluating a set of over 70 models that widely vary in their computational ingredients on a triplet similarity task, a method well established in the cognitive sciences for measuring human conceptual representations, using concepts from the THINGS database. Comparing human and model representations, we find that models that undergo instruction-finetuning and which have larger dimensionality of attention heads are among the most human aligned, while multimodal pretraining and parameter size have limited bearing on alignment. Correlations between alignment scores and scores on existing benchmarks reveal that while some benchmarks (e.g., MMLU) are better suited than others (e.g., MUSR) for capturing representational alignment, no existing benchmark is capable of fully accounting for the variance of alignment scores, demonstrating their insufficiency in capturing human-AI alignment. Taken together, our findings help highlight the computational ingredients most essential for advancing LLMs towards models of human conceptual representation and address a key benchmarking gap in LLM evaluation.

Multimodal LLMs have reached remarkable levels of proficiency in understanding multimodal inputs, driving extensive research to develop increasingly powerful models. However, much less attention has been paid to understanding and explaining the underlying mechanisms of these models. Most existing explainability research examines these models only in their final states, overlooking the dynamic representational shifts that occur during training. In this work, we systematically analyze the evolution of hidden state representations to reveal how fine-tuning alters the internal structure of a model to specialize in new multimodal tasks. Using a concept-based approach, we map hidden states to interpretable visual and textual concepts, enabling us to trace changes in encoded concepts across modalities as training progresses. We also demonstrate the use of shift vectors to capture these concepts changes. These shift vectors allow us to recover fine-tuned concepts by shifting those in the original model. Finally, we explore the practical impact of our findings on model steering, showing that we can adjust multimodal LLMs behaviors without any training, such as modifying answer types, captions style, or biasing the model toward specific responses. Our work sheds light on how multimodal representations evolve through fine-tuning and offers a new perspective for interpreting model adaptation in multimodal tasks. The code for this project is publicly available at https://github.com/mshukor/xl-vlms.

This study is dedicated to assessing the capabilities of large language models (LLMs) such as GPT-3.5-Turbo, GPT-4, and GPT-4-Turbo in extracting structured information from scientific documents in materials science. To this end, we primarily focus on two critical tasks of information extraction: (i) a named entity recognition (NER) of studied materials and physical properties and (ii) a relation extraction (RE) between these entities. Due to the evident lack of datasets within Materials Informatics (MI), we evaluated using SuperMat, based on superconductor research, and MeasEval, a generic measurement evaluation corpus. The performance of LLMs in executing these tasks is benchmarked against traditional models based on the BERT architecture and rule-based approaches (baseline). We introduce a novel methodology for the comparative analysis of intricate material expressions, emphasising the standardisation of chemical formulas to tackle the complexities inherent in materials science information assessment. For NER, LLMs fail to outperform the baseline with zero-shot prompting and exhibit only limited improvement with few-shot prompting. However, a GPT-3.5-Turbo fine-tuned with the appropriate strategy for RE outperforms all models, including the baseline. Without any fine-tuning, GPT-4 and GPT-4-Turbo display remarkable reasoning and relationship extraction capabilities after being provided with merely a couple of examples, surpassing the baseline. Overall, the results suggest that although LLMs demonstrate relevant reasoning skills in connecting concepts, specialised models are currently a better choice for tasks requiring extracting complex domain-specific entities like materials. These insights provide initial guidance applicable to other materials science sub-domains in future work.

Current Large Language Models (LLMs) for understanding proteins primarily treats amino acid sequences as a text modality. Meanwhile, Protein Language Models (PLMs), such as ESM-2, have learned massive sequential evolutionary knowledge from the universe of natural protein sequences. Furthermore, structure-based encoders like ProteinMPNN learn the structural information of proteins through Graph Neural Networks. However, whether the incorporation of protein encoders can enhance the protein understanding of LLMs has not been explored. To bridge this gap, we propose EvoLlama, a multimodal framework that connects a structure-based encoder, a sequence-based protein encoder and an LLM for protein understanding. EvoLlama consists of a ProteinMPNN structure encoder, an ESM-2 protein sequence encoder, a multimodal projector to align protein and text representations and a Llama-3 text decoder. To train EvoLlama, we fine-tune it on protein-oriented instructions and protein property prediction datasets verbalized via natural language instruction templates. Our experiments show that EvoLlama's protein understanding capabilities have been significantly enhanced, outperforming other fine-tuned protein-oriented LLMs in zero-shot settings by an average of 1%-8% and surpassing the state-of-the-art baseline with supervised fine-tuning by an average of 6%. On protein property prediction datasets, our approach achieves promising results that are competitive with state-of-the-art task-specific baselines. We will release our code in a future version.

Learning compatible representations enables the interchangeable use of semantic features as models are updated over time. This is particularly relevant in search and retrieval systems where it is crucial to avoid reprocessing of the gallery images with the updated model. While recent research has shown promising empirical evidence, there is still a lack of comprehensive theoretical understanding about learning compatible representations. In this paper, we demonstrate that the stationary representations learned by the d-Simplex fixed classifier optimally approximate compatibility representation according to the two inequality constraints of its formal definition. This not only establishes a solid foundation for future works in this line of research but also presents implications that can be exploited in practical learning scenarios. An exemplary application is the now-standard practice of downloading and fine-tuning new pre-trained models. Specifically, we show the strengths and critical issues of stationary representations in the case in which a model undergoing sequential fine-tuning is asynchronously replaced by downloading a better-performing model pre-trained elsewhere. Such a representation enables seamless delivery of retrieval service (i.e., no reprocessing of gallery images) and offers improved performance without operational disruptions during model replacement. Code available at: https://github.com/miccunifi/iamcl2r.

Large Language Models (LLMs) have demonstrated exceptional text understanding. Existing works explore their application in text embedding tasks. However, there are few works utilizing LLMs to assist multimodal representation tasks. In this work, we investigate the potential of LLMs to enhance multimodal representation in multimodal item-to-item (I2I) recommendations. One feasible method is the transfer of Multimodal Large Language Models (MLLMs) for representation tasks. However, pre-training MLLMs usually requires collecting high-quality, web-scale multimodal data, resulting in complex training procedures and high costs. This leads the community to rely heavily on open-source MLLMs, hindering customized training for representation scenarios. Therefore, we aim to design an end-to-end training method that customizes the integration of any existing LLMs and vision encoders to construct efficient multimodal representation models. Preliminary experiments show that fine-tuned LLMs in this end-to-end method tend to overlook image content. To overcome this challenge, we propose a novel training framework, NoteLLM-2, specifically designed for multimodal representation. We propose two ways to enhance the focus on visual information. The first method is based on the prompt viewpoint, which separates multimodal content into visual content and textual content. NoteLLM-2 adopts the multimodal In-Content Learning method to teach LLMs to focus on both modalities and aggregate key information. The second method is from the model architecture, utilizing a late fusion mechanism to directly fuse visual information into textual information. Extensive experiments have been conducted to validate the effectiveness of our method.

Recent advancements in Multimodal Large Language Models (MLLMs) underscore the significance of scalable models and data to boost performance, yet this often incurs substantial computational costs. Although the Mixture of Experts (MoE) architecture has been employed to efficiently scale large language and image-text models, these efforts typically involve fewer experts and limited modalities. To address this, our work presents the pioneering attempt to develop a unified MLLM with the MoE architecture, named Uni-MoE that can handle a wide array of modalities. Specifically, it features modality-specific encoders with connectors for a unified multimodal representation. We also implement a sparse MoE architecture within the LLMs to enable efficient training and inference through modality-level data parallelism and expert-level model parallelism. To enhance the multi-expert collaboration and generalization, we present a progressive training strategy: 1) Cross-modality alignment using various connectors with different cross-modality data, 2) Training modality-specific experts with cross-modality instruction data to activate experts' preferences, and 3) Tuning the Uni-MoE framework utilizing Low-Rank Adaptation (LoRA) on mixed multimodal instruction data. We evaluate the instruction-tuned Uni-MoE on a comprehensive set of multimodal datasets. The extensive experimental results demonstrate Uni-MoE's principal advantage of significantly reducing performance bias in handling mixed multimodal datasets, alongside improved multi-expert collaboration and generalization. Our findings highlight the substantial potential of MoE frameworks in advancing MLLMs and the code is available at https://github.com/HITsz-TMG/UMOE-Scaling-Unified-Multimodal-LLMs.

Recent progress has been made towards learning invariant or equivariant representations with self-supervised learning. While invariant methods are evaluated on large scale datasets, equivariant ones are evaluated in smaller, more controlled, settings. We aim at bridging the gap between the two in order to learn more diverse representations that are suitable for a wide range of tasks. We start by introducing a dataset called 3DIEBench, consisting of renderings from 3D models over 55 classes and more than 2.5 million images where we have full control on the transformations applied to the objects. We further introduce a predictor architecture based on hypernetworks to learn equivariant representations with no possible collapse to invariance. We introduce SIE (Split Invariant-Equivariant) which combines the hypernetwork-based predictor with representations split in two parts, one invariant, the other equivariant, to learn richer representations. We demonstrate significant performance gains over existing methods on equivariance related tasks from both a qualitative and quantitative point of view. We further analyze our introduced predictor and show how it steers the learned latent space. We hope that both our introduced dataset and approach will enable learning richer representations without supervision in more complex scenarios. Code and data are available at https://github.com/facebookresearch/SIE.

Multi-modal Large Language Models (MLLMs) have introduced a novel dimension to document understanding, i.e., they endow large language models with visual comprehension capabilities; however, how to design a suitable image-text pre-training task for bridging the visual and language modality in document-level MLLMs remains underexplored. In this study, we introduce a novel visual-language alignment method that casts the key issue as a Visual Question Answering with Mask generation (VQAMask) task, optimizing two tasks simultaneously: VQA-based text parsing and mask generation. The former allows the model to implicitly align images and text at the semantic level. The latter introduces an additional mask generator (discarded during inference) to explicitly ensure alignment between visual texts within images and their corresponding image regions at a spatially-aware level. Together, they can prevent model hallucinations when parsing visual text and effectively promote spatially-aware feature representation learning. To support the proposed VQAMask task, we construct a comprehensive image-mask generation pipeline and provide a large-scale dataset with 6M data (MTMask6M). Subsequently, we demonstrate that introducing the proposed mask generation task yields competitive document-level understanding performance. Leveraging the proposed VQAMask, we introduce Marten, a training-efficient MLLM tailored for document-level understanding. Extensive experiments show that our Marten consistently achieves significant improvements among 8B-MLLMs in document-centric tasks. Code and datasets are available at https://github.com/PriNing/Marten.

Large language models (LLMs) have demonstrated remarkable prediction performance for a growing array of tasks. However, their rapid proliferation and increasing opaqueness have created a growing need for interpretability. Here, we ask whether we can automatically obtain natural language explanations for black box text modules. A "text module" is any function that maps text to a scalar continuous value, such as a submodule within an LLM or a fitted model of a brain region. "Black box" indicates that we only have access to the module's inputs/outputs. We introduce Summarize and Score (SASC), a method that takes in a text module and returns a natural language explanation of the module's selectivity along with a score for how reliable the explanation is. We study SASC in 3 contexts. First, we evaluate SASC on synthetic modules and find that it often recovers ground truth explanations. Second, we use SASC to explain modules found within a pre-trained BERT model, enabling inspection of the model's internals. Finally, we show that SASC can generate explanations for the response of individual fMRI voxels to language stimuli, with potential applications to fine-grained brain mapping. All code for using SASC and reproducing results is made available on Github.

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

Invariance-based and generative methods have shown a conspicuous performance for 3D self-supervised representation learning (SSRL). However, the former relies on hand-crafted data augmentations that introduce bias not universally applicable to all downstream tasks, and the latter indiscriminately reconstructs masked regions, resulting in irrelevant details being saved in the representation space. To solve the problem above, we introduce 3D-JEPA, a novel non-generative 3D SSRL framework. Specifically, we propose a multi-block sampling strategy that produces a sufficiently informative context block and several representative target blocks. We present the context-aware decoder to enhance the reconstruction of the target blocks. Concretely, the context information is fed to the decoder continuously, facilitating the encoder in learning semantic modeling rather than memorizing the context information related to target blocks. Overall, 3D-JEPA predicts the representation of target blocks from a context block using the encoder and context-aware decoder architecture. Various downstream tasks on different datasets demonstrate 3D-JEPA's effectiveness and efficiency, achieving higher accuracy with fewer pretraining epochs, e.g., 88.65% accuracy on PB_T50_RS with 150 pretraining epochs.

Crystalline materials often exhibit a high level of symmetry. However, most generative models do not account for symmetry, but rather model each atom without any constraints on its position or element. We propose a generative model, Wyckoff Diffusion (WyckoffDiff), which generates symmetry-based descriptions of crystals. This is enabled by considering a crystal structure representation that encodes all symmetry, and we design a novel neural network architecture which enables using this representation inside a discrete generative model framework. In addition to respecting symmetry by construction, the discrete nature of our model enables fast generation. We additionally present a new metric, Fr\'echet Wrenformer Distance, which captures the symmetry aspects of the materials generated, and we benchmark WyckoffDiff against recently proposed generative models for crystal generation. Code is available online at https://github.com/httk/wyckoffdiff

The goal of protein representation learning is to extract knowledge from protein databases that can be applied to various protein-related downstream tasks. Although protein sequence, structure, and function are the three key modalities for a comprehensive understanding of proteins, existing methods for protein representation learning have utilized only one or two of these modalities due to the difficulty of capturing the asymmetric interrelationships between them. To account for this asymmetry, we introduce our novel asymmetric multi-modal masked autoencoder (AMMA). AMMA adopts (1) a unified multi-modal encoder to integrate all three modalities into a unified representation space and (2) asymmetric decoders to ensure that sequence latent features reflect structural and functional information. The experiments demonstrate that the proposed AMMA is highly effective in learning protein representations that exhibit well-aligned inter-modal relationships, which in turn makes it effective for various downstream protein-related tasks.

While LLMs are powerful embedding backbones, their application in training-free settings faces two structural challenges: causal attention restricts early tokens from accessing subsequent context, and the next-token prediction objective biases representations toward generation rather than semantic compression. To address these limitations, we propose KV-Embedding, a framework that activates the latent representation power of frozen LLMs. Our method leverages the observation that the key-value (KV) states of the final token at each layer encode a compressed view of the sequence. By re-routing these states as a prepended prefix, we enable all tokens to access sequence-level context within a single forward pass. To ensure model-agnostic applicability, we introduce an automated layer selection strategy based on intrinsic dimensionality. Evaluations on MTEB across Qwen, Mistral, and Llama backbones show that KV-Embedding outperforms existing training-free baselines by up to 10%, while maintaining robust performance on sequences up to 4,096 tokens. These results demonstrate that internal state manipulation offers an efficient alternative to input modification, and we hope this work encourages further exploration of LLM internals for representation learning.

Recent advancements in multimodal fusion have witnessed the remarkable success of vision-language (VL) models, which excel in various multimodal applications such as image captioning and visual question answering. However, building VL models requires substantial hardware resources, where efficiency is restricted by two key factors: the extended input sequence of the language model with vision features demands more computational operations, and a large number of additional learnable parameters increase memory complexity. These challenges significantly restrict the broader applicability of such models. To bridge this gap, we propose ADEM-VL, an efficient vision-language method that tunes VL models based on pretrained large language models (LLMs) by adopting a parameter-free cross-attention mechanism for similarity measurements in multimodal fusion. This approach only requires embedding vision features into the language space, significantly reducing the number of trainable parameters and accelerating both training and inference speeds. To enhance representation learning in fusion module, we introduce an efficient multiscale feature generation scheme that requires only a single forward pass through the vision encoder. Moreover, we propose an adaptive fusion scheme that dynamically discards less relevant visual information for each text token based on its attention score. This ensures that the fusion process prioritizes the most pertinent visual features. With experiments on various tasks including visual question answering, image captioning, and instruction-following, we demonstrate that our framework outperforms existing approaches. Specifically, our method surpasses existing methods by an average accuracy of 0.77% on ScienceQA dataset, with reduced training and inference latency, demonstrating the superiority of our framework. The code is available at https://github.com/Hao840/ADEM-VL.

Characterizing materials with electron micrographs poses significant challenges for automated labeling due to the complex nature of nanomaterial structures. To address this, we introduce a fully automated, end-to-end pipeline that leverages recent advances in Generative AI. It is designed for analyzing and understanding the microstructures of semiconductor materials with effectiveness comparable to that of human experts, contributing to the pursuit of Artificial General Intelligence (AGI) in nanomaterial identification. Our approach utilizes Large MultiModal Models (LMMs) such as GPT-4V, alongside text-to-image models like DALLE-3. We integrate a GPT-4 guided Visual Question Answering (VQA) method to analyze nanomaterial images, generate synthetic nanomaterial images via DALLE-3, and employ in-context learning with few-shot prompting in GPT-4V for accurate nanomaterial identification. Our method surpasses traditional techniques by enhancing the precision of nanomaterial identification and optimizing the process for high-throughput screening.

Multimodal Large Language Models (MLLMs) exhibit impressive capabilities across a variety of tasks, especially when equipped with carefully designed visual prompts. However, existing studies primarily focus on logical reasoning and visual understanding, while the capability of MLLMs to operate effectively in 3D vision remains an ongoing area of exploration. In this paper, we introduce a novel visual prompting method, called 3DAxisPrompt, to elicit the 3D understanding capabilities of MLLMs in real-world scenes. More specifically, our method leverages the 3D coordinate axis and masks generated from the Segment Anything Model (SAM) to provide explicit geometric priors to MLLMs and then extend their impressive 2D grounding and reasoning ability to real-world 3D scenarios. Besides, we first provide a thorough investigation of the potential visual prompting formats and conclude our findings to reveal the potential and limits of 3D understanding capabilities in GPT-4o, as a representative of MLLMs. Finally, we build evaluation environments with four datasets, i.e., ScanRefer, ScanNet, FMB, and nuScene datasets, covering various 3D tasks. Based on this, we conduct extensive quantitative and qualitative experiments, which demonstrate the effectiveness of the proposed method. Overall, our study reveals that MLLMs, with the help of 3DAxisPrompt, can effectively perceive an object's 3D position in real-world scenarios. Nevertheless, a single prompt engineering approach does not consistently achieve the best outcomes for all 3D tasks. This study highlights the feasibility of leveraging MLLMs for 3D vision grounding/reasoning with prompt engineering techniques.

Modern large language models (LLMs) achieve impressive performance on some tasks, while exhibiting distinctly non-human-like behaviors on others. This raises the question of how well the LLM's learned representations align with human representations. In this work, we introduce a novel approach to study representation alignment: we adopt a method from research on activation steering to identify neurons responsible for specific concepts (e.g., ''cat'') and then analyze the corresponding activation patterns. We find that LLM representations captured this way closely align with human representations inferred from behavioral data, matching inter-human alignment levels. Our approach significantly outperforms the alignment captured by word embeddings, which have been the focus of prior work on human-LLM alignment. Additionally, our approach enables a more granular view of how LLMs represent concepts -- we show that LLMs organize concepts in a way that mirrors human concept organization.

Do machines and humans process language in similar ways? A recent line of research has hinted in the affirmative, demonstrating that human brain signals can be effectively predicted using the internal representations of language models (LMs). This is thought to reflect shared computational principles between LMs and human language processing. However, there are also clear differences in how LMs and humans acquire and use language, even if the final task they are performing is the same. Despite this, there is little work exploring systematic differences between human and machine language processing using brain data. To address this question, we examine the differences between LM representations and the human brain's responses to language, specifically by examining a dataset of Magnetoencephalography (MEG) responses to a written narrative. In doing so we identify three phenomena that, in prior work, LMs have been found to not capture well: emotional understanding, figurative language processing, and physical commonsense. By fine-tuning LMs on datasets related to these phenomena, we observe that fine-tuned LMs show improved alignment with human brain responses across these tasks. Our study implies that the observed divergences between LMs and human brains may stem from LMs' inadequate representation of these specific types of knowledge.

Based on the foundation of Large Language Models (LLMs), Multilingual Large Language Models (MLLMs) have been developed to address the challenges of multilingual natural language processing tasks, hoping to achieve knowledge transfer from high-resource to low-resource languages. However, significant limitations and challenges still exist, such as language imbalance, multilingual alignment, and inherent bias. In this paper, we aim to provide a comprehensive analysis of MLLMs, delving deeply into discussions surrounding these critical issues. First of all, we start by presenting an overview of MLLMs, covering their evolution, key techniques, and multilingual capacities. Secondly, we explore widely utilized multilingual corpora for MLLMs' training and multilingual datasets oriented for downstream tasks that are crucial for enhancing the cross-lingual capability of MLLMs. Thirdly, we survey the existing studies on multilingual representations and investigate whether the current MLLMs can learn a universal language representation. Fourthly, we discuss bias on MLLMs including its category and evaluation metrics, and summarize the existing debiasing techniques. Finally, we discuss existing challenges and point out promising research directions. By demonstrating these aspects, this paper aims to facilitate a deeper understanding of MLLMs and their potentiality in various domains.

The generation of plausible crystal structures is often the first step in predicting the structure and properties of a material from its chemical composition. Quickly generating and predicting inorganic crystal structures is important for the discovery of new materials, which can target applications such as energy or electronic devices. However, most current methods for crystal structure prediction are computationally expensive, slowing the pace of innovation. Seeding structure prediction algorithms with quality generated candidates can overcome a major bottleneck. Here, we introduce CrystaLLM, a methodology for the versatile generation of crystal structures, based on the autoregressive large language modeling (LLM) of the Crystallographic Information File (CIF) format. Trained on millions of CIF files, CrystaLLM focuses on modeling crystal structures through text. CrystaLLM can produce plausible crystal structures for a wide range of inorganic compounds unseen in training, as demonstrated by ab initio simulations. The integration with predictors of formation energy permits the use of a Monte Carlo Tree Search algorithm to improve the generation of meaningful structures. Our approach challenges conventional representations of crystals, and demonstrates the potential of LLMs for learning effective 'world models' of crystal chemistry, which will lead to accelerated discovery and innovation in materials science.

Developing robust representations of chemical structures that enable models to learn topological inductive biases is challenging. In this manuscript, we present a representation of atomistic systems. We begin by proving that our representation satisfies all structural, geometric, efficiency, and generalizability constraints. Afterward, we provide a general algorithm to encode any atomistic system. Finally, we report performance comparable to state-of-the-art methods on numerous tasks. We open-source all code and datasets. The code and data are available at https://github.com/rahulkhorana/PolyatomicComplexes.

E(3)-equivariant neural networks have demonstrated success across a wide range of 3D modelling tasks. A fundamental operation in these networks is the tensor product, which interacts two geometric features in an equivariant manner to create new features. Due to the high computational complexity of the tensor product, significant effort has been invested to optimize the runtime of this operation. For example, Luo et al. (2024) recently proposed the Gaunt tensor product (GTP) which promises a significant speedup. In this work, we provide a careful, systematic analysis of a number of tensor product operations. In particular, we emphasize that different tensor products are not performing the same operation. The reported speedups typically come at the cost of expressivity. We introduce measures of expressivity and interactability to characterize these differences. In addition, we realized the original implementation of GTP can be greatly simplified by directly using a spherical grid at no cost in asymptotic runtime. This spherical grid approach is faster on our benchmarks and in actual training of the MACE interatomic potential by 30%. Finally, we provide the first systematic microbenchmarks of the various tensor product operations. We find that the theoretical runtime guarantees can differ wildly from empirical performance, demonstrating the need for careful application-specific benchmarking. Code is available at https://github.com/atomicarchitects/PriceofFreedom.

Brain Signals, such as Electroencephalography (EEG), and human languages have been widely explored independently for many downstream tasks, however, the connection between them has not been well explored. In this study, we explore the relationship and dependency between EEG and language. To study at the representation level, we introduced MTAM, a Multimodal Transformer Alignment Model, to observe coordinated representations between the two modalities. We used various relationship alignment-seeking techniques, such as Canonical Correlation Analysis and Wasserstein Distance, as loss functions to transfigure features. On downstream applications, sentiment analysis and relation detection, we achieved new state-of-the-art results on two datasets, ZuCo and K-EmoCon. Our method achieved an F1-score improvement of 1.7% on K-EmoCon and 9.3% on Zuco datasets for sentiment analysis, and 7.4% on ZuCo for relation detection. In addition, we provide interpretations of the performance improvement: (1) feature distribution shows the effectiveness of the alignment module for discovering and encoding the relationship between EEG and language; (2) alignment weights show the influence of different language semantics as well as EEG frequency features; (3) brain topographical maps provide an intuitive demonstration of the connectivity in the brain regions. Our code is available at https://github.com/Jason-Qiu/EEG_Language_Alignment.

Motivated by the hypothesis that neural network representations encode abstract, interpretable features as linearly accessible, approximately orthogonal directions, sparse autoencoders (SAEs) have become a popular tool in interpretability. However, recent work has demonstrated phenomenology of model representations that lies outside the scope of this hypothesis, showing signatures of hierarchical, nonlinear, and multi-dimensional features. This raises the question: do SAEs represent features that possess structure at odds with their motivating hypothesis? If not, does avoiding this mismatch help identify said features and gain further insights into neural network representations? To answer these questions, we take a construction-based approach and re-contextualize the popular matching pursuits (MP) algorithm from sparse coding to design MP-SAE -- an SAE that unrolls its encoder into a sequence of residual-guided steps, allowing it to capture hierarchical and nonlinearly accessible features. Comparing this architecture with existing SAEs on a mixture of synthetic and natural data settings, we show: (i) hierarchical concepts induce conditionally orthogonal features, which existing SAEs are unable to faithfully capture, and (ii) the nonlinear encoding step of MP-SAE recovers highly meaningful features, helping us unravel shared structure in the seemingly dichotomous representation spaces of different modalities in a vision-language model, hence demonstrating the assumption that useful features are solely linearly accessible is insufficient. We also show that the sequential encoder principle of MP-SAE affords an additional benefit of adaptive sparsity at inference time, which may be of independent interest. Overall, we argue our results provide credence to the idea that interpretability should begin with the phenomenology of representations, with methods emerging from assumptions that fit it.

The rapid advancement of Multimodal Large Language Models (MLLMs) has significantly impacted various multimodal tasks. However, these models face challenges in tasks that require spatial understanding within 3D environments. Efforts to enhance MLLMs, such as incorporating point cloud features, have been made, yet a considerable gap remains between the models' learned representations and the inherent complexity of 3D scenes. This discrepancy largely stems from the training of MLLMs on predominantly 2D data, which restricts their effectiveness in comprehending 3D spaces. To address this issue, in this paper, we propose a novel generalist model, i.e., Video-3D LLM, for 3D scene understanding. By treating 3D scenes as dynamic videos and incorporating 3D position encoding into these representations, our Video-3D LLM aligns video representations with real-world spatial contexts more accurately. Additionally, we have implemented a maximum coverage sampling technique to optimize the balance between computational costs and performance efficiency. Extensive experiments demonstrate that our model achieves state-of-the-art performance on several 3D scene understanding benchmarks, including ScanRefer, Multi3DRefer, Scan2Cap, ScanQA, and SQA3D.

Statistics of grain sizes and orientations in metals correlate to the material's mechanical properties. Reproducing representative volume elements for further analysis of deformation and failure in metals, like 316L stainless steel, is particularly important due to their wide use in manufacturing goods today. Two approaches, initially created for video games, were considered for the procedural generation of representative grain microstructures. The first is the Wave Function Collapse (WFC) algorithm, and the second is constraint propagation and probabilistic inference through Markov Junior, a free and open-source software. This study aimed to investigate these two algorithms' effectiveness in using reference electron backscatter diffraction (EBSD) maps and recreating a statistically similar one that could be used in further research. It utilized two stainless steel EBSD maps as references to test both algorithms. First, the WFC algorithm was too constricting and, thus, incapable of producing images that resembled EBSDs. The second, MarkovJunior, was much more effective in creating a Voronoi tessellation that could be used to create an EBSD map in Python. When comparing the results between the reference and the generated EBSD, we discovered that the orientation and volume fractions were extremely similar. With the study, it was concluded that MarkovJunior is an effective machine learning tool that can reproduce representative grain microstructures.

We address the problem of performing backpropagation for computation graphs involving 3D transformation groups SO(3), SE(3), and Sim(3). 3D transformation groups are widely used in 3D vision and robotics, but they do not form vector spaces and instead lie on smooth manifolds. The standard backpropagation approach, which embeds 3D transformations in Euclidean spaces, suffers from numerical difficulties. We introduce a new library, which exploits the group structure of 3D transformations and performs backpropagation in the tangent spaces of manifolds. We show that our approach is numerically more stable, easier to implement, and beneficial to a diverse set of tasks. Our plug-and-play PyTorch library is available at https://github.com/princeton-vl/lietorch.

We introduce InternVL3, a significant advancement in the InternVL series featuring a native multimodal pre-training paradigm. Rather than adapting a text-only large language model (LLM) into a multimodal large language model (MLLM) that supports visual inputs, InternVL3 jointly acquires multimodal and linguistic capabilities from both diverse multimodal data and pure-text corpora during a single pre-training stage. This unified training paradigm effectively addresses the complexities and alignment challenges commonly encountered in conventional post-hoc training pipelines for MLLMs. To further improve performance and scalability, InternVL3 incorporates variable visual position encoding (V2PE) to support extended multimodal contexts, employs advanced post-training techniques such as supervised fine-tuning (SFT) and mixed preference optimization (MPO), and adopts test-time scaling strategies alongside an optimized training infrastructure. Extensive empirical evaluations demonstrate that InternVL3 delivers superior performance across a wide range of multi-modal tasks. In particular, InternVL3-78B achieves a score of 72.2 on the MMMU benchmark, setting a new state-of-the-art among open-source MLLMs. Its capabilities remain highly competitive with leading proprietary models, including ChatGPT-4o, Claude 3.5 Sonnet, and Gemini 2.5 Pro, while also maintaining strong pure-language proficiency. In pursuit of open-science principles, we will publicly release both the training data and model weights to foster further research and development in next-generation MLLMs.

Vision-Language Models (VLMs) leverage aligned visual encoders to transform images into visual tokens, allowing them to be processed similarly to text by the backbone large language model (LLM). This unified input paradigm enables VLMs to excel in vision-language tasks such as visual question answering (VQA). To improve fine-grained visual reasoning, recent advancements in vision-language modeling introduce image cropping techniques that feed all encoded sub-images into the model. However, this approach significantly increases the number of visual tokens, leading to inefficiency and potential distractions for the LLM. To address the generalization challenges of image representation in VLMs, we propose a lightweight, universal framework that seamlessly integrates with existing VLMs to enhance their ability to process finegrained details. Our method leverages textual semantics to identify key visual areas, improving VQA performance without requiring any retraining of the VLM. Additionally, it incorporates textual signals into the visual encoding process, enhancing both efficiency and effectiveness. The proposed method, SEMCLIP, strengthens the visual understanding of a 7B VLM, LLaVA-1.5 by 3.3% on average across 7 benchmarks, and particularly by 5.3% on the challenging detailed understanding benchmark V*.

This paper demonstrates an approach for learning highly semantic image representations without relying on hand-crafted data-augmentations. We introduce the Image-based Joint-Embedding Predictive Architecture (I-JEPA), a non-generative approach for self-supervised learning from images. The idea behind I-JEPA is simple: from a single context block, predict the representations of various target blocks in the same image. A core design choice to guide I-JEPA towards producing semantic representations is the masking strategy; specifically, it is crucial to (a) sample target blocks with sufficiently large scale (semantic), and to (b) use a sufficiently informative (spatially distributed) context block. Empirically, when combined with Vision Transformers, we find I-JEPA to be highly scalable. For instance, we train a ViT-Huge/14 on ImageNet using 16 A100 GPUs in under 72 hours to achieve strong downstream performance across a wide range of tasks, from linear classification to object counting and depth prediction.

Large language models (LLMs) have achieved remarkable success and demonstrated superior performance across various tasks, including natural language processing (NLP), weather forecasting, biological protein folding, text generation, and solving mathematical problems. However, many real-world data exhibit highly non-Euclidean latent hierarchical anatomy, such as protein networks, transportation networks, financial networks, brain networks, and linguistic structures or syntactic trees in natural languages. Effectively learning intrinsic semantic entailment and hierarchical relationships from these raw, unstructured input data using LLMs remains an underexplored area. Due to its effectiveness in modeling tree-like hierarchical structures, hyperbolic geometry -- a non-Euclidean space -- has rapidly gained popularity as an expressive latent representation space for complex data modeling across domains such as graphs, images, languages, and multi-modal data. Here, we provide a comprehensive and contextual exposition of recent advancements in LLMs that leverage hyperbolic geometry as a representation space to enhance semantic representation learning and multi-scale reasoning. Specifically, the paper presents a taxonomy of the principal techniques of Hyperbolic LLMs (HypLLMs) in terms of four main categories: (1) hyperbolic LLMs through exp/log maps; (2) hyperbolic fine-tuned models; (3) fully hyperbolic LLMs, and (4) hyperbolic state-space models. We also explore crucial potential applications and outline future research directions. A repository of key papers, models, datasets, and code implementations is available at https://github.com/sarangp2402/Hyperbolic-LLM-Models/tree/main.

We analyse perception and memory, using mathematical models for knowledge graphs and tensors, to gain insights into the corresponding functionalities of the human mind. Our discussion is based on the concept of propositional sentences consisting of subject-predicate-object (SPO) triples for expressing elementary facts. SPO sentences are the basis for most natural languages but might also be important for explicit perception and declarative memories, as well as intra-brain communication and the ability to argue and reason. A set of SPO sentences can be described as a knowledge graph, which can be transformed into an adjacency tensor. We introduce tensor models, where concepts have dual representations as indices and associated embeddings, two constructs we believe are essential for the understanding of implicit and explicit perception and memory in the brain. We argue that a biological realization of perception and memory imposes constraints on information processing. In particular, we propose that explicit perception and declarative memories require a semantic decoder, which, in a simple realization, is based on four layers: First, a sensory memory layer, as a buffer for sensory input, second, an index layer representing concepts, third, a memoryless representation layer for the broadcasting of information ---the "blackboard", or the "canvas" of the brain--- and fourth, a working memory layer as a processing center and data buffer. We discuss the operations of the four layers and relate them to the global workspace theory. In a Bayesian brain interpretation, semantic memory defines the prior for observable triple statements. We propose that ---in evolution and during development--- semantic memory, episodic memory, and natural language evolved as emergent properties in agents' process to gain a deeper understanding of sensory information.

Despite Multi-modal Large Language Models (MM-LLMs) have made exciting strides recently, they are still struggling to efficiently model the interactions among multi-modal inputs and the generation in non-textual modalities. In this work, we propose TEAL (Tokenize and Embed ALl)}, an approach to treat the input from any modality as a token sequence and learn a joint embedding space for all modalities. Specifically, for the input from any modality, TEAL first discretizes it into a token sequence with the off-the-shelf tokenizer and embeds the token sequence into a joint embedding space with a learnable embedding matrix. MM-LLMs just need to predict the multi-modal tokens autoregressively as the textual LLMs do. Finally, the corresponding de-tokenizer is applied to generate the output in each modality based on the predicted token sequence. With the joint embedding space, TEAL enables the frozen LLMs to perform both understanding and generation tasks involving non-textual modalities, such as image and audio. Thus, the textual LLM can just work as an interface and maintain its high performance in textual understanding and generation. Experiments show that TEAL achieves substantial improvements in multi-modal understanding, and implements a simple scheme for multi-modal generations.

Effectively representing 3D scenes for Multimodal Large Language Models (MLLMs) is crucial yet challenging. Existing approaches commonly only rely on 2D image features and use varied tokenization approaches. This work presents a rigorous study of 3D token structures, systematically comparing video-based and point-based representations while maintaining consistent model backbones and parameters. We propose a novel approach that enriches visual tokens by incorporating 3D point cloud features from a Sonata pretrained Point Transformer V3 encoder. Our experiments demonstrate that merging explicit 3D features significantly boosts performance. Furthermore, we show that point-based token structures can rival video-based ones when the points are cleverly sampled and ordered. Our best models from both structures achieve state-of-the-art results on multiple 3D understanding benchmarks. We emphasize our analysis of token structures as a key contribution, alongside transparent reporting of results averaged over multiple seeds, a practice we believe is vital for robust progress in the field.

Knowledge graph (KG) embeddings learn low-dimensional representations of entities and relations to predict missing facts. KGs often exhibit hierarchical and logical patterns which must be preserved in the embedding space. For hierarchical data, hyperbolic embedding methods have shown promise for high-fidelity and parsimonious representations. However, existing hyperbolic embedding methods do not account for the rich logical patterns in KGs. In this work, we introduce a class of hyperbolic KG embedding models that simultaneously capture hierarchical and logical patterns. Our approach combines hyperbolic reflections and rotations with attention to model complex relational patterns. Experimental results on standard KG benchmarks show that our method improves over previous Euclidean- and hyperbolic-based efforts by up to 6.1% in mean reciprocal rank (MRR) in low dimensions. Furthermore, we observe that different geometric transformations capture different types of relations while attention-based transformations generalize to multiple relations. In high dimensions, our approach yields new state-of-the-art MRRs of 49.6% on WN18RR and 57.7% on YAGO3-10.

Recent developments in Multimodal Large Language Models (MLLMs) have shown rapid progress, moving towards the goal of creating versatile MLLMs that understand inputs from various modalities. However, existing methods typically rely on joint training with paired multimodal instruction data, which is resource-intensive and challenging to extend to new modalities. In this paper, we propose a new paradigm through the model composition of existing MLLMs to create a new model that retains the modal understanding capabilities of each original model. Our basic implementation, NaiveMC, demonstrates the effectiveness of this paradigm by reusing modality encoders and merging LLM parameters. Furthermore, we introduce DAMC to address parameter interference and mismatch issues during the merging process, thereby enhancing the model performance. To facilitate research in this area, we propose MCUB, a benchmark for assessing ability of MLLMs to understand inputs from diverse modalities. Experiments on this benchmark and four other multimodal understanding tasks show significant improvements over baselines, proving that model composition can create a versatile model capable of processing inputs from multiple modalities.

Hyperdimensional computing (HDC) is a biologically-inspired framework which represents symbols with high-dimensional vectors, and uses vector operations to manipulate them. The ensemble of a particular vector space and a prescribed set of vector operations (including one addition-like for "bundling" and one outer-product-like for "binding") form a *vector symbolic architecture* (VSA). While VSAs have been employed in numerous applications and have been studied empirically, many theoretical questions about VSAs remain open. We analyze the *representation capacities* of four common VSAs: MAP-I, MAP-B, and two VSAs based on sparse binary vectors. "Representation capacity' here refers to bounds on the dimensions of the VSA vectors required to perform certain symbolic tasks, such as testing for set membership i in S and estimating set intersection sizes |X cap Y| for two sets of symbols X and Y, to a given degree of accuracy. We also analyze the ability of a novel variant of a Hopfield network (a simple model of associative memory) to perform some of the same tasks that are typically asked of VSAs. In addition to providing new bounds on VSA capacities, our analyses establish and leverage connections between VSAs, "sketching" (dimensionality reduction) algorithms, and Bloom filters.

Protein language models are a powerful tool for learning protein representations through pre-training on vast protein sequence datasets. However, traditional protein language models lack explicit structural supervision, despite its relevance to protein function. To address this issue, we introduce the integration of remote homology detection to distill structural information into protein language models without requiring explicit protein structures as input. We evaluate the impact of this structure-informed training on downstream protein function prediction tasks. Experimental results reveal consistent improvements in function annotation accuracy for EC number and GO term prediction. Performance on mutant datasets, however, varies based on the relationship between targeted properties and protein structures. This underscores the importance of considering this relationship when applying structure-aware training to protein function prediction tasks. Code and model weights are available at https://github.com/DeepGraphLearning/esm-s.

Self-supervised neural language models have recently achieved unprecedented success, from natural language processing to learning the languages of biological sequences and organic molecules. These models have demonstrated superior performance in the generation, structure classification, and functional predictions for proteins and molecules with learned representations. However, most of the masking-based pre-trained language models are not designed for generative design, and their black-box nature makes it difficult to interpret their design logic. Here we propose BLMM Crystal Transformer, a neural network based probabilistic generative model for generative and tinkering design of inorganic materials. Our model is built on the blank filling language model for text generation and has demonstrated unique advantages in learning the "materials grammars" together with high-quality generation, interpretability, and data efficiency. It can generate chemically valid materials compositions with as high as 89.7\% charge neutrality and 84.8\% balanced electronegativity, which are more than 4 and 8 times higher compared to a pseudo random sampling baseline. The probabilistic generation process of BLMM allows it to recommend tinkering operations based on learned materials chemistry and makes it useful for materials doping. Combined with the TCSP crysal structure prediction algorithm, We have applied our model to discover a set of new materials as validated using DFT calculations. Our work thus brings the unsupervised transformer language models based generative artificial intelligence to inorganic materials. A user-friendly web app has been developed for computational materials doping and can be accessed freely at www.materialsatlas.org/blmtinker.

Understanding what defines a good representation in large language models (LLMs) is fundamental to both theoretical understanding and practical applications. In this paper, we investigate the quality of intermediate representations in various LLM architectures, including Transformers and State Space Models (SSMs). We find that intermediate layers often yield more informative representations for downstream tasks than the final layers. To measure the representation quality, we adapt and apply a suite of metrics - such as prompt entropy, curvature, and augmentation-invariance - originally proposed in other contexts. Our empirical study reveals significant architectural differences, how representations evolve throughout training, and how factors like input randomness and prompt length affect each layer. Notably, we observe a bimodal pattern in the entropy of some intermediate layers and consider potential explanations tied to training data. Overall, our results illuminate the internal mechanics of LLMs and guide strategies for architectural optimization and training.

Automated and semi-automated techniques in biomedical electron microscopy (EM) enable the acquisition of large datasets at a high rate. Segmentation methods are therefore essential to analyze and interpret these large volumes of data, which can no longer completely be labeled manually. In recent years, deep learning algorithms achieved impressive results in both pixel-level labeling (semantic segmentation) and the labeling of separate instances of the same class (instance segmentation). In this review, we examine how these algorithms were adapted to the task of segmenting cellular and sub-cellular structures in EM images. The special challenges posed by such images and the network architectures that overcame some of them are described. Moreover, a thorough overview is also provided on the notable datasets that contributed to the proliferation of deep learning in EM. Finally, an outlook of current trends and future prospects of EM segmentation is given, especially in the area of label-free learning.

Vision Language Models (VLMs) encode multimodal inputs over large, complex, and difficult-to-interpret architectures, which limit transparency and trust. We propose a Multimodal Inversion for Model Interpretation and Conceptualization (MIMIC) framework to visualize the internal representations of VLMs by synthesizing visual concepts corresponding to internal encodings. MIMIC uses a joint VLM-based inversion and a feature alignment objective to account for VLM's autoregressive processing. It additionally includes a triplet of regularizers for spatial alignment, natural image smoothness, and semantic realism. We quantitatively and qualitatively evaluate MIMIC by inverting visual concepts over a range of varying-length free-form VLM output texts. Reported results include both standard visual quality metrics as well as semantic text-based metrics. To the best of our knowledge, this is the first model inversion approach addressing visual interpretations of VLM concepts.

With the bloom of Large Language Models (LLMs), Multimodal Large Language Models (MLLMs) that incorporate LLMs with pre-trained vision models have recently demonstrated impressive performance across diverse vision-language tasks. However, they fall short to comprehend context involving multiple images. A primary reason for this shortcoming is that the visual features for each images are encoded individually by frozen encoders before feeding into the LLM backbone, lacking awareness of other images and the multimodal instructions. We term this issue as prior-LLM modality isolation and propose a two phase paradigm, browse-and-concentrate, to enable in-depth multimodal context fusion prior to feeding the features into LLMs. This paradigm initially "browses" through the inputs for essential insights, and then revisits the inputs to "concentrate" on crucial details, guided by these insights, to achieve a more comprehensive understanding of the multimodal inputs. Additionally, we develop training strategies specifically to enhance the understanding of multi-image inputs. Our method markedly boosts the performance on 7 multi-image scenarios, contributing to increments on average accuracy by 2.13% and 7.60% against strong MLLMs baselines with 3B and 11B LLMs, respectively.

Large Language Models (LLMs) have demonstrated impressive performance on multimodal tasks, without any multimodal finetuning. They are the building block for Large Multimodal Models, yet, we still lack a proper understanding of their success. In this work, we expose frozen LLMs to image, video, audio and text inputs and analyse their internal representation aiming to understand their generalization beyond textual inputs. Findings. Perceptual tokens (1) are easily distinguishable from textual ones inside LLMs, with significantly different representations, and complete translation to textual tokens does not exist. Yet, (2) both perceptual and textual tokens activate similar LLM weights. Despite being different, (3) perceptual and textual tokens are implicitly aligned inside LLMs, we call this the implicit multimodal alignment (IMA), and argue that this is linked to architectural design, helping LLMs to generalize. This provide more evidence to believe that the generalization of LLMs to multimodal inputs is mainly due to their architecture. Implications. (1) We find a positive correlation between the implicit alignment score and the task performance, suggesting that this could act as a proxy metric for model evaluation and selection. (2) A negative correlation exists regarding hallucinations, revealing that this problem is mainly due to misalignment between the internal perceptual and textual representations. (3) Perceptual tokens change slightly throughout the model, thus, we propose different approaches to skip computations (e.g. in FFN layers), and significantly reduce the inference cost. (4) Due to the slowly changing embeddings across layers, and the high overlap between textual and multimodal activated weights, we compress LLMs by keeping only 1 subnetwork that works well across a wide range of multimodal tasks. Paper code: https://github.com/mshukor/ima-lmms.

Large language models (LLMs) have recently shown strong potential in audio-visual speech recognition (AVSR), but their high computational demands and sensitivity to token granularity limit their practicality in resource-constrained settings. Token compression methods can reduce inference cost, but they require fixing a compression rate in advance and produce a single fixed-length output, offering no flexibility to balance information density and efficiency at inference time. Matryoshka representation learning (MRL) addresses this by enabling a single model to operate across multiple token granularities, allowing compression rates to be adjusted dynamically. However, current MRL-based methods treat each scale independently during training, limiting cross-scale generalization, robustness at high compression, and interpretability. To overcome these limitations, we propose MoME (Mixture of Matryoshka Experts), a novel framework that integrates sparse Mixture-of-Experts (MoE) into MRL-based LLMs for AVSR. MoME augments a frozen LLM with top-k routed and shared experts, allowing dynamic capacity allocation across scales and modalities. A shared router promotes consistent expert activation across granularities, enabling compressed sequences to benefit from representations learned at lower compression. Experiments on LRS2 and LRS3 demonstrate that MoME achieves state-of-the-art performance across AVSR, ASR, and VSR tasks, while requiring significantly fewer parameters and maintaining robustness under noise. MoME unifies the adaptability of MRL with the efficiency of MoE, offering a scalable and interpretable solution for resource-aware speech recognition.

Vision-language models (VLMs) are typically composed of a vision encoder, e.g. CLIP, and a language model (LM) that interprets the encoded features to solve downstream tasks. Despite remarkable progress, VLMs are subject to several shortcomings due to the limited capabilities of vision encoders, e.g. "blindness" to certain image features, visual hallucination, etc. To address these issues, we study broadening the visual encoding capabilities of VLMs. We first comprehensively benchmark several vision encoders with different inductive biases for solving VLM tasks. We observe that there is no single encoding configuration that consistently achieves top performance across different tasks, and encoders with different biases can perform surprisingly similarly. Motivated by this, we introduce a method, named BRAVE, that consolidates features from multiple frozen encoders into a more versatile representation that can be directly fed as the input to a frozen LM. BRAVE achieves state-of-the-art performance on a broad range of captioning and VQA benchmarks and significantly reduces the aforementioned issues of VLMs, while requiring a smaller number of trainable parameters than existing methods and having a more compressed representation. Our results highlight the potential of incorporating different visual biases for a more broad and contextualized visual understanding of VLMs.

We investigate compositional structures in data embeddings from pre-trained vision-language models (VLMs). Traditionally, compositionality has been associated with algebraic operations on embeddings of words from a pre-existing vocabulary. In contrast, we seek to approximate representations from an encoder as combinations of a smaller set of vectors in the embedding space. These vectors can be seen as "ideal words" for generating concepts directly within the embedding space of the model. We first present a framework for understanding compositional structures from a geometric perspective. We then explain what these compositional structures entail probabilistically in the case of VLM embeddings, providing intuitions for why they arise in practice. Finally, we empirically explore these structures in CLIP's embeddings and we evaluate their usefulness for solving different vision-language tasks such as classification, debiasing, and retrieval. Our results show that simple linear algebraic operations on embedding vectors can be used as compositional and interpretable methods for regulating the behavior of VLMs.