Daily Papers

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

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.

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.

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.

In this work, we propose aligning pretrained visual encoders to serve as tokenizers for latent diffusion models in image generation. Unlike training a variational autoencoder (VAE) from scratch, which primarily emphasizes low-level details, our approach leverages the rich semantic structure of foundation encoders. We introduce a three-stage alignment strategy: (1) freeze the encoder and train an adapter and a decoder to establish a semantic latent space; (2) jointly optimize all components with an additional semantic preservation loss, enabling the encoder to capture perceptual details while retaining high-level semantics; and (3) refine the decoder for improved reconstruction quality. This alignment yields semantically rich image tokenizers that benefit diffusion models. On ImageNet 256times256, our tokenizer accelerates the convergence of diffusion models, reaching a gFID of 1.90 within just 64 epochs, and improves generation both with and without classifier-free guidance. Scaling to LAION, a 2B-parameter text-to-image model trained with our tokenizer consistently outperforms FLUX VAE under the same training steps. Overall, our method is simple, scalable, and establishes a semantically grounded paradigm for continuous tokenizer design.

Vision-Language Models (VLMs) encode images into lengthy sequences of visual tokens, leading to excessive computational overhead and limited inference efficiency. While prior efforts prune or merge tokens to address this issue, they often rely on special tokens (e.g., CLS) or require task-specific training, hindering scalability across architectures. In this paper, we propose HiPrune, a training-free and model-agnostic token Pruning framework that exploits the Hierarchical attention structure within vision encoders. We identify that middle layers attend to object-centric regions, while deep layers capture global contextual features. Based on this observation, HiPrune selects three types of informative tokens: (1) Anchor tokens with high attention in object-centric layers, (2) Buffer tokens adjacent to anchors for spatial continuity, and (3) Register tokens with strong attention in deep layers for global summarization. Our method requires no retraining and integrates seamlessly with any ViT-based VLM. Extensive experiments on LLaVA-1.5, LLaVA-NeXT, and Qwen2.5-VL demonstrate that HiPrune achieves state-of-the-art pruning performance, preserving up to 99.3% task accuracy with only 33.3% tokens, and maintaining 99.5% accuracy with just 11.1% tokens. Meanwhile, it reduces inference FLOPs and latency by up to 9times, showcasing strong generalization across models and tasks. Code is available at https://github.com/Danielement321/HiPrune.

Aligned text-image encoders such as CLIP have become the de facto model for vision-language tasks. Furthermore, modality-specific encoders achieve impressive performances in their respective domains. This raises a central question: does an alignment exist between uni-modal vision and language encoders since they fundamentally represent the same physical world? Analyzing the latent spaces structure of vision and language models on image-caption benchmarks using the Centered Kernel Alignment (CKA), we find that the representation spaces of unaligned and aligned encoders are semantically similar. In the absence of statistical similarity in aligned encoders like CLIP, we show that a possible matching of unaligned encoders exists without any training. We frame this as a seeded graph-matching problem exploiting the semantic similarity between graphs and propose two methods - a Fast Quadratic Assignment Problem optimization, and a novel localized CKA metric-based matching/retrieval. We demonstrate the effectiveness of this on several downstream tasks including cross-lingual, cross-domain caption matching and image classification. Code available at github.com/mayug/0-shot-llm-vision.

Autonomous driving requires understanding infrastructure elements, such as lanes and crosswalks. To navigate safely, this understanding must be derived from sensor data in real-time and needs to be represented in vectorized form. Learned Bird's-Eye View (BEV) encoders are commonly used to combine a set of camera images from multiple views into one joint latent BEV grid. Traditionally, from this latent space, an intermediate raster map is predicted, providing dense spatial supervision but requiring post-processing into the desired vectorized form. More recent models directly derive infrastructure elements as polylines using vectorized map decoders, providing instance-level information. Our approach, Augmentation Map Network (AugMapNet), proposes latent BEV feature grid augmentation, a novel technique that significantly enhances the latent BEV representation. AugMapNet combines vector decoding and dense spatial supervision more effectively than existing architectures while remaining easy to integrate compared to other hybrid approaches. It additionally benefits from extra processing on its latent BEV features. Experiments on nuScenes and Argoverse2 datasets demonstrate significant improvements on vectorized map prediction of up to 13.3% over the StreamMapNet baseline on 60 m range and greater improvements on larger ranges. We confirm transferability by applying our method to another baseline, SQD-MapNet, and find similar improvements. A detailed analysis of the latent BEV grid confirms a more structured latent space of AugMapNet and shows the value of our novel concept beyond pure performance improvement. The code can be found at https://github.com/tmonnin/augmapnet

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.

To address the challenges of table structure recognition, we propose a novel Split-Merge-based top-down model optimized for large, densely populated tables. Our approach formulates row and column splitting as sequence labeling tasks, utilizing dual Transformer encoders to capture feature interactions. The merging process is framed as a grid cell classification task, leveraging an additional Transformer encoder to ensure accurate and coherent merging. By eliminating unstable bounding box predictions, our method reduces resolution loss and computational complexity, achieving high accuracy while maintaining fast processing speed. Extensive experiments on FinTabNet and PubTabNet demonstrate the superiority of our model over existing approaches, particularly in real-world applications. Our method offers a robust, scalable, and efficient solution for large-scale table recognition, making it well-suited for industrial deployment.

Despite significant advances in Multimodal Large Language Models (MLLMs), understanding complex temporal dynamics in videos remains a major challenge. Our experiments show that current Video Large Language Model (Video-LLM) architectures have critical limitations in temporal understanding, struggling with tasks that require detailed comprehension of action sequences and temporal progression. In this work, we propose a Video-LLM architecture that introduces stacked temporal attention modules directly within the vision encoder. This design incorporates a temporal attention in vision encoder, enabling the model to better capture the progression of actions and the relationships between frames before passing visual tokens to the LLM. Our results show that this approach significantly improves temporal reasoning and outperforms existing models in video question answering tasks, specifically in action recognition. We improve on benchmarks including VITATECS, MVBench, and Video-MME by up to +5.5%. By enhancing the vision encoder with temporal structure, we address a critical gap in video understanding for Video-LLMs. Project page and code are available at: https://alirasekh.github.io/STAVEQ2/.

Recent work has shown how denoising and contractive autoencoders implicitly capture the structure of the data-generating density, in the case where the corruption noise is Gaussian, the reconstruction error is the squared error, and the data is continuous-valued. This has led to various proposals for sampling from this implicitly learned density function, using Langevin and Metropolis-Hastings MCMC. However, it remained unclear how to connect the training procedure of regularized auto-encoders to the implicit estimation of the underlying data-generating distribution when the data are discrete, or using other forms of corruption process and reconstruction errors. Another issue is the mathematical justification which is only valid in the limit of small corruption noise. We propose here a different attack on the problem, which deals with all these issues: arbitrary (but noisy enough) corruption, arbitrary reconstruction loss (seen as a log-likelihood), handling both discrete and continuous-valued variables, and removing the bias due to non-infinitesimal corruption noise (or non-infinitesimal contractive penalty).

Representation alignment (REPA) guides generative training by distilling representations from a strong, pretrained vision encoder to intermediate diffusion features. We investigate a fundamental question: what aspect of the target representation matters for generation, its global semantic information (e.g., measured by ImageNet-1K accuracy) or its spatial structure (i.e. pairwise cosine similarity between patch tokens)? Prevalent wisdom holds that stronger global semantic performance leads to better generation as a target representation. To study this, we first perform a large-scale empirical analysis across 27 different vision encoders and different model scales. The results are surprising; spatial structure, rather than global performance, drives the generation performance of a target representation. To further study this, we introduce two straightforward modifications, which specifically accentuate the transfer of spatial information. We replace the standard MLP projection layer in REPA with a simple convolution layer and introduce a spatial normalization layer for the external representation. Surprisingly, our simple method (implemented in <4 lines of code), termed iREPA, consistently improves convergence speed of REPA, across a diverse set of vision encoders, model sizes, and training variants (such as REPA, REPA-E, Meanflow, JiT etc). %, etc. Our work motivates revisiting the fundamental working mechanism of representational alignment and how it can be leveraged for improved training of generative models. The code and project page are available at https://end2end-diffusion.github.io/irepa

A major goal of neuroscience is to understand brain computations during visual processing in naturalistic settings. A dominant approach is to use image-computable deep neural networks trained with different task objectives as a basis for linear encoding models. However, in addition to requiring tuning a large number of parameters, the linear encoding approach ignores the structure of the feature maps both in the brain and the models. Recently proposed alternatives have focused on decomposing the linear mapping to spatial and feature components but focus on finding static receptive fields for units that are applicable only in early visual areas. In this work, we employ the attention mechanism used in the transformer architecture to study how retinotopic visual features can be dynamically routed to category-selective areas in high-level visual processing. We show that this computational motif is significantly more powerful than alternative methods in predicting brain activity during natural scene viewing, across different feature basis models and modalities. We also show that this approach is inherently more interpretable, without the need to create importance maps, by interpreting the attention routing signal for different high-level categorical areas. Our approach proposes a mechanistic model of how visual information from retinotopic maps can be routed based on the relevance of the input content to different category-selective regions.

We propose the Wasserstein Auto-Encoder (WAE)---a new algorithm for building a generative model of the data distribution. WAE minimizes a penalized form of the Wasserstein distance between the model distribution and the target distribution, which leads to a different regularizer than the one used by the Variational Auto-Encoder (VAE). This regularizer encourages the encoded training distribution to match the prior. We compare our algorithm with several other techniques and show that it is a generalization of adversarial auto-encoders (AAE). Our experiments show that WAE shares many of the properties of VAEs (stable training, encoder-decoder architecture, nice latent manifold structure) while generating samples of better quality, as measured by the FID score.

What do auto-encoders learn about the underlying data generating distribution? Recent work suggests that some auto-encoder variants do a good job of capturing the local manifold structure of data. This paper clarifies some of these previous observations by showing that minimizing a particular form of regularized reconstruction error yields a reconstruction function that locally characterizes the shape of the data generating density. We show that the auto-encoder captures the score (derivative of the log-density with respect to the input). It contradicts previous interpretations of reconstruction error as an energy function. Unlike previous results, the theorems provided here are completely generic and do not depend on the parametrization of the auto-encoder: they show what the auto-encoder would tend to if given enough capacity and examples. These results are for a contractive training criterion we show to be similar to the denoising auto-encoder training criterion with small corruption noise, but with contraction applied on the whole reconstruction function rather than just encoder. Similarly to score matching, one can consider the proposed training criterion as a convenient alternative to maximum likelihood because it does not involve a partition function. Finally, we show how an approximate Metropolis-Hastings MCMC can be setup to recover samples from the estimated distribution, and this is confirmed in sampling experiments.

In line with recent advances in neural drug design and sensitivity prediction, we propose a novel architecture for interpretable prediction of anticancer compound sensitivity using a multimodal attention-based convolutional encoder. Our model is based on the three key pillars of drug sensitivity: compounds' structure in the form of a SMILES sequence, gene expression profiles of tumors and prior knowledge on intracellular interactions from protein-protein interaction networks. We demonstrate that our multiscale convolutional attention-based (MCA) encoder significantly outperforms a baseline model trained on Morgan fingerprints, a selection of encoders based on SMILES as well as previously reported state of the art for multimodal drug sensitivity prediction (R2 = 0.86 and RMSE = 0.89). Moreover, the explainability of our approach is demonstrated by a thorough analysis of the attention weights. We show that the attended genes significantly enrich apoptotic processes and that the drug attention is strongly correlated with a standard chemical structure similarity index. Finally, we report a case study of two receptor tyrosine kinase (RTK) inhibitors acting on a leukemia cell line, showcasing the ability of the model to focus on informative genes and submolecular regions of the two compounds. The demonstrated generalizability and the interpretability of our model testify its potential for in-silico prediction of anticancer compound efficacy on unseen cancer cells, positioning it as a valid solution for the development of personalized therapies as well as for the evaluation of candidate compounds in de novo drug design.

Unified generation of sequence and structure for scientific data (e.g., materials, molecules, proteins) is a critical task. Existing approaches primarily rely on either autoregressive sequence models or diffusion models, each offering distinct advantages and facing notable limitations. Autoregressive models, such as GPT, Llama, and Phi-4, have demonstrated remarkable success in natural language generation and have been extended to multimodal tasks (e.g., image, video, and audio) using advanced encoders like VQ-VAE to represent complex modalities as discrete sequences. However, their direct application to scientific domains is challenging due to the high precision requirements and the diverse nature of scientific data. On the other hand, diffusion models excel at generating high-dimensional scientific data, such as protein, molecule, and material structures, with remarkable accuracy. Yet, their inability to effectively model sequences limits their potential as general-purpose multimodal foundation models. To address these challenges, we propose UniGenX, a unified framework that combines autoregressive next-token prediction with conditional diffusion models. This integration leverages the strengths of autoregressive models to ease the training of conditional diffusion models, while diffusion-based generative heads enhance the precision of autoregressive predictions. We validate the effectiveness of UniGenX on material and small molecule generation tasks, achieving a significant leap in state-of-the-art performance for material crystal structure prediction and establishing new state-of-the-art results for small molecule structure prediction, de novo design, and conditional generation. Notably, UniGenX demonstrates significant improvements, especially in handling long sequences for complex structures, showcasing its efficacy as a versatile tool for scientific data generation.

Leaf-lesion segmentation is topology-sensitive: small merges, splits, or false holes can be biologically meaningful descriptors of biochemical pathways, yet they are weakly penalized by standard pixel-wise losses in Euclidean latents. I explore HyperTopo-Adapters, a lightweight, parameter-efficient head trained on top of a frozen vision encoder, which embeds features on a product manifold -- hyperbolic + Euclidean + spherical (H + E + S) -- to encourage hierarchical separation (H), local linear detail (E), and global closure (S). A topology prior complements Dice/BCE in two forms: (i) persistent-homology (PH) distance for evaluation and selection, and (ii) a differentiable surrogate that combines a soft Euler-characteristic match with total variation regularization for stable training. I introduce warm-ups for both the hyperbolic contrastive term and the topology prior, per-sample evaluation of structure-aware metrics (Boundary-F1, Betti errors, PD distance), and a min-PD within top-K Dice rule for checkpoint selection. On a Kaggle leaf-lesion dataset (N=2,940), early results show consistent gains in boundary and topology metrics (reducing Delta beta_1 hole error by 9%) while Dice/IoU remain competitive. The study is diagnostic by design: I report controlled ablations (curvature learning, latent dimensions, contrastive temperature, surrogate settings), and ongoing tests varying encoder strength (ResNet-50, DeepLabV3, DINOv2/v3), input resolution, PH weight, and partial unfreezing of late blocks. The contribution is an open, reproducible train/eval suite (available at https://github.com/ChimdiWalter/HyperTopo-Adapters) that isolates geometric/topological priors and surfaces failure modes to guide stronger, topology-preserving architectures.

Multimodal models have demonstrated powerful capabilities in complex tasks requiring multimodal alignment including zero-shot classification and cross-modal retrieval. However, existing models typically rely on millions of paired multimodal samples, which are prohibitively expensive or infeasible to obtain in many domains. In this work, we explore the feasibility of building multimodal models with limited amount of paired data by aligning pretrained unimodal foundation models. We show that high-quality alignment is possible with as few as tens of thousands of paired samplesx2013less than 1% of the data typically used in the field. To achieve this, we introduce STRUCTURE, an effective regularization technique that preserves the neighborhood geometry of the latent space of unimodal encoders. Additionally, we show that aligning last layers is often suboptimal and demonstrate the benefits of aligning the layers with the highest representational similarity across modalities. These two components can be readily incorporated into existing alignment methods, yielding substantial gains across 24 zero-shot image classification and retrieval benchmarks, with average relative improvement of 51.6% in classification and 91.8% in retrieval tasks. Our results highlight the effectiveness and broad applicability of our framework for limited-sample multimodal learning and offer a promising path forward for resource-constrained domains.

Molecular representations are inherently task-dependent, yet most pre-trained molecular encoders are not. Task conditioning promises representations that reorganize based on task descriptions, but existing approaches rely on expensive labeled data. We show that weak supervision on programmatically derived molecular motifs is sufficient. Our Adaptive Chemical Embedding Model (ACE-Mol) learns from hundreds of motifs paired with natural language descriptors that are cheap to compute, trivial to scale. Conventional encoders slowly search the embedding space for task-relevant structure, whereas ACE-Mol immediately aligns its representations with the task. ACE-Mol achieves state-of-the-art performance across molecular property prediction benchmarks with interpretable, chemically meaningful representations.

Expanding multimodal representations to novel modalities is constrained by reliance on large-scale paired datasets (e.g., text-image, text-audio, text-3D, text-molecule), which are costly and often infeasible in domains requiring expert annotation such as medical imaging and molecular analysis. We introduce TextME, the first text-only modality expansion framework, to the best of our knowledge, projecting diverse modalities into LLM embedding space as a unified anchor. Our approach exploits the geometric structure of pretrained contrastive encoders to enable zero-shot cross-modal transfer using only text descriptions, without paired supervision. We empirically validate that such consistent modality gaps exist across image, video, audio, 3D, X-ray, and molecular domains, demonstrating that text-only training can preserve substantial performance of pretrained encoders. We further show that our framework enables emergent cross-modal retrieval between modality pairs not explicitly aligned during training (e.g., audio-to-image, 3D-to-image). These results establish text-only training as a practical alternative to paired supervision for modality expansion.

Recent studies have shown that code language models at scale demonstrate significant performance gains on downstream tasks, i.e., code generation. However, most of the existing works on code representation learning train models at a hundred million parameter scale using very limited pretraining corpora. In this work, we fuel code representation learning with a vast amount of code data via a two-stage pretraining scheme. We first train the encoders via a mix that leverages both randomness in masking language modeling and the structure aspect of programming language. We then enhance the representations via contrastive learning with hard negative and hard positive constructed in an unsupervised manner. We establish an off-the-shelf encoder model that persistently outperforms the existing models on a wide variety of downstream tasks by large margins. To comprehend the factors contributing to successful code representation learning, we conduct detailed ablations and share our findings on (i) a customized and effective token-level denoising scheme for source code; (ii) the importance of hard negatives and hard positives; (iii) how the proposed bimodal contrastive learning boost the cross-lingual semantic search performance; and (iv) how the pretraining schemes decide the downstream task performance scales with the model size.

Generating music that temporally aligns with video events is challenging for existing text-to-music models, which lack fine-grained temporal control. We introduce V2M-Zero, a zero-pair video-to-music generation approach that outputs time-aligned music for video. Our method is motivated by a key observation: temporal synchronization requires matching when and how much change occurs, not what changes. While musical and visual events differ semantically, they exhibit shared temporal structure that can be captured independently within each modality. We capture this structure through event curves computed from intra-modal similarity using pretrained music and video encoders. By measuring temporal change within each modality independently, these curves provide comparable representations across modalities. This enables a simple training strategy: fine-tune a text-to-music model on music-event curves, then substitute video-event curves at inference without cross-modal training or paired data. Across OES-Pub, MovieGenBench-Music, and AIST++, V2M-Zero achieves substantial gains over paired-data baselines: 5-21% higher audio quality, 13-15% better semantic alignment, 21-52% improved temporal synchronization, and 28% higher beat alignment on dance videos. We find similar results via a large crowd-source subjective listening test. Overall, our results validate that temporal alignment through within-modality features, rather than paired cross-modal supervision, is effective for video-to-music generation. Results are available at https://genjib.github.io/v2m_zero/

This paper investigates the fundamental discontinuity between the latest two Segment Anything Models: SAM2 and SAM3. We explain why the expertise in prompt-based segmentation of SAM2 does not transfer to the multimodal concept-driven paradigm of SAM3. SAM2 operates through spatial prompts points, boxes, and masks yielding purely geometric and temporal segmentation. In contrast, SAM3 introduces a unified vision-language architecture capable of open-vocabulary reasoning, semantic grounding, contrastive alignment, and exemplar-based concept understanding. We structure this analysis through five core components: (1) a Conceptual Break Between Prompt-Based and Concept-Based Segmentation, contrasting spatial prompt semantics of SAM2 with multimodal fusion and text-conditioned mask generation of SAM3; (2) Architectural Divergence, detailing pure vision-temporal design of SAM2 versus integration of vision-language encoders, geometry and exemplar encoders, fusion modules, DETR-style decoders, object queries, and ambiguity-handling via Mixture-of-Experts in SAM3; (3) Dataset and Annotation Differences, contrasting SA-V video masks with multimodal concept-annotated corpora of SAM3; (4) Training and Hyperparameter Distinctions, showing why SAM2 optimization knowledge does not apply to SAM3; and (5) Evaluation, Metrics, and Failure Modes, outlining the transition from geometric IoU metrics to semantic, open-vocabulary evaluation. Together, these analyses establish SAM3 as a new class of segmentation foundation model and chart future directions for the emerging concept-driven segmentation era.

Vision-language models (VLMs) have advanced rapidly, but their ability to capture spatial relationships remains a blindspot. Current VLMs are typically built with contrastive language-image pretraining (CLIP) style image encoders. The training recipe often flattens images into 1D patch sequences, discarding the 2D structure necessary for spatial reasoning. We argue that this lack of spatial awareness is a missing dimension in VLM design and a bottleneck for applications requiring spatial grounding, such as robotics and embodied AI. To address this, we investigate (i) image encoders trained with alternative objectives and (ii) 2D positional encodings. Our experiments show that these architectural choices can lead to improved spatial reasoning on several benchmarks.

Flow-matching methods for 3D shape assembly learn point-wise velocity fields that transport parts toward assembled configurations, yet they receive no explicit guidance about which cross-part interactions should drive the motion. We introduce TORA, a topology-first representation alignment framework that distills relational structure from a frozen pretrained 3D encoder into the flow-matching backbone during training. We first realize this via simple instantiation, token-wise cosine matching, which injects the learned geometric descriptors from the teacher representation. We then extend to employ a Centered Kernel Alignment (CKA) loss to match the similarity structure between student and teacher representations for enhanced topological alignment. Through systematic probing of diverse 3D encoders, we show that geometry- and contact-centric teacher properties, not semantic classification ability, govern alignment effectiveness, and that alignment is most beneficial at later transformer layers where spatial structure naturally emerges. TORA introduces zero inference overhead while yielding two consistent benefits: faster convergence (up to 6.9times) and improved accuracy in-distribution, along with greater robustness under domain shift. Experiments on five benchmarks spanning geometric, semantic, and inter-object assembly demonstrate state-of-the-art performance, with particularly pronounced gains in zero-shot transfer to unseen real-world and synthetic datasets. Project page: https://nahyuklee.github.io/tora.

Adversarial diffusion and diffusion-inversion methods have advanced unpaired image-to-image translation, but each faces key limitations. Adversarial approaches require target-domain adversarial loss during training, which can limit generalization to unseen data, while diffusion-inversion methods often produce low-fidelity translations due to imperfect inversion into noise-latent representations. In this work, we propose the Self-Supervised Semantic Bridge (SSB), a versatile framework that integrates external semantic priors into diffusion bridge models to enable spatially faithful translation without cross-domain supervision. Our key idea is to leverage self-supervised visual encoders to learn representations that are invariant to appearance changes but capture geometric structure, forming a shared latent space that conditions the diffusion bridges. Extensive experiments show that SSB outperforms strong prior methods for challenging medical image synthesis in both in-domain and out-of-domain settings, and extends easily to high-quality text-guided editing.

X-ray images play a vital role in the intraoperative processes due to their high resolution and fast imaging speed and greatly promote the subsequent segmentation, registration and reconstruction. However, over-dosed X-rays superimpose potential risks to human health to some extent. Data-driven algorithms from volume scans to X-ray images are restricted by the scarcity of paired X-ray and volume data. Existing methods are mainly realized by modelling the whole X-ray imaging procedure. In this study, we propose a learning-based approach termed CT2X-GAN to synthesize the X-ray images in an end-to-end manner using the content and style disentanglement from three different image domains. Our method decouples the anatomical structure information from CT scans and style information from unpaired real X-ray images/ digital reconstructed radiography (DRR) images via a series of decoupling encoders. Additionally, we introduce a novel consistency regularization term to improve the stylistic resemblance between synthesized X-ray images and real X-ray images. Meanwhile, we also impose a supervised process by computing the similarity of computed real DRR and synthesized DRR images. We further develop a pose attention module to fully strengthen the comprehensive information in the decoupled content code from CT scans, facilitating high-quality multi-view image synthesis in the lower 2D space. Extensive experiments were conducted on the publicly available CTSpine1K dataset and achieved 97.8350, 0.0842 and 3.0938 in terms of FID, KID and defined user-scored X-ray similarity, respectively. In comparison with 3D-aware methods (pi-GAN, EG3D), CT2X-GAN is superior in improving the synthesis quality and realistic to the real X-ray images.

Recent advancements in Multimodal Large Language Models (MLLMs) have significantly enhanced performance on 2D visual tasks. However, improving their spatial intelligence remains a challenge. Existing 3D MLLMs always rely on additional 3D or 2.5D data to incorporate spatial awareness, restricting their utility in scenarios with only 2D inputs, such as images or videos. In this paper, we present Spatial-MLLM, a novel framework for visual-based spatial reasoning from purely 2D observations. Unlike conventional video MLLMs which rely on CLIP-based visual encoders optimized for semantic understanding, our key insight is to unleash the strong structure prior from the feed-forward visual geometry foundation model. Specifically, we propose a dual-encoder architecture: a pretrained 2D visual encoder to extract semantic features, and a spatial encoder-initialized from the backbone of the visual geometry model-to extract 3D structure features. A connector then integrates both features into unified visual tokens for enhanced spatial understanding. Furthermore, we propose a space-aware frame sampling strategy at inference time, which selects the spatially informative frames of a video sequence, ensuring that even under limited token length, the model focuses on frames critical for spatial reasoning. Beyond architecture improvements, we construct the Spatial-MLLM-120k dataset and train the model on it using supervised fine-tuning and GRPO. Extensive experiments on various real-world datasets demonstrate that our spatial-MLLM achieves state-of-the-art performance in a wide range of visual-based spatial understanding and reasoning tasks. Project page: https://diankun-wu.github.io/Spatial-MLLM/.

Sparse autoencoders (SAEs) have emerged as a promising method for interpreting neural network representations by decomposing activations into sparse combinations of dictionary atoms. However, SAEs assume that features combine additively through linear reconstruction, an assumption that cannot capture compositional structure: linear models cannot distinguish whether "Starbucks" arises from the composition of "star" and "coffee" features or merely their co-occurrence. This forces SAEs to allocate monolithic features for compound concepts rather than decomposing them into interpretable constituents. We introduce PolySAE, which extends the SAE decoder with higher-order terms to model feature interactions while preserving the linear encoder essential for interpretability. Through low-rank tensor factorization on a shared projection subspace, PolySAE captures pairwise and triple feature interactions with small parameter overhead (3% on GPT2). Across four language models and three SAE variants, PolySAE achieves an average improvement of approximately 8% in probing F1 while maintaining comparable reconstruction error, and produces 2-10times larger Wasserstein distances between class-conditional feature distributions. Critically, learned interaction weights exhibit negligible correlation with co-occurrence frequency (r = 0.06 vs. r = 0.82 for SAE feature covariance), suggesting that polynomial terms capture compositional structure, such as morphological binding and phrasal composition, largely independent of surface statistics.

Transformer models are deployed in a wide range of settings, from multi-accelerator clusters to standalone mobile phones. The diverse inference constraints in these scenarios necessitate practitioners to train foundation models such as PaLM 2, Llama, & ViTs as a series of models of varying sizes. Due to significant training costs, only a select few model sizes are trained and supported, limiting more fine-grained control over relevant tradeoffs, including latency, cost, and accuracy. This work introduces MatFormer, a nested Transformer architecture designed to offer elasticity in a variety of deployment constraints. Each Feed Forward Network (FFN) block of a MatFormer model is jointly optimized with a few nested smaller FFN blocks. This training procedure allows for the Mix'n'Match of model granularities across layers -- i.e., a trained universal MatFormer model enables extraction of hundreds of accurate smaller models, which were never explicitly optimized. We empirically demonstrate MatFormer's effectiveness across different model classes (decoders & encoders), modalities (language & vision), and scales (up to 2.6B parameters). We find that a 2.6B decoder-only MatFormer language model (MatLM) allows us to extract smaller models spanning from 1.5B to 2.6B, each exhibiting comparable validation loss and one-shot downstream evaluations to their independently trained counterparts. Furthermore, we observe that smaller encoders extracted from a universal MatFormer-based ViT (MatViT) encoder preserve the metric-space structure for adaptive large-scale retrieval. Finally, we showcase that speculative decoding with the accurate and consistent submodels extracted from MatFormer can further reduce inference latency.

Generative domain adaptation has achieved remarkable progress, enabling us to adapt a pre-trained generator to a new target domain. However, existing methods simply adapt the generator to a single target domain and are limited to a single modality, either text-driven or image-driven. Moreover, they are prone to overfitting domain-specific attributes, which inevitably compromises cross-domain consistency. In this paper, we propose UniHDA, a unified and versatile framework for generative hybrid domain adaptation with multi-modal references from multiple domains. We use CLIP encoder to project multi-modal references into a unified embedding space and then linear interpolate the direction vectors from multiple target domains to achieve hybrid domain adaptation. To ensure the cross-domain consistency, we propose a novel cross-domain spatial structure (CSS) loss that maintains detailed spatial structure information between source and target generator. Experiments show that the adapted generator can synthesise realistic images with various attribute compositions. Additionally, our framework is versatile to multiple generators, \eg, StyleGAN2 and Diffusion Models.

Pre-trained Transformer language models (LM) have become go-to text representation encoders. Prior research fine-tunes deep LMs to encode text sequences such as sentences and passages into single dense vector representations for efficient text comparison and retrieval. However, dense encoders require a lot of data and sophisticated techniques to effectively train and suffer in low data situations. This paper finds a key reason is that standard LMs' internal attention structure is not ready-to-use for dense encoders, which needs to aggregate text information into the dense representation. We propose to pre-train towards dense encoder with a novel Transformer architecture, Condenser, where LM prediction CONditions on DENSE Representation. Our experiments show Condenser improves over standard LM by large margins on various text retrieval and similarity tasks.

Large language models (LLMs) trained purely on text ostensibly lack any direct perceptual experience, yet their internal representations are implicitly shaped by multimodal regularities encoded in language. We test the hypothesis that explicit sensory prompting can surface this latent structure, bringing a text-only LLM into closer representational alignment with specialist vision and audio encoders. When a sensory prompt tells the model to 'see' or 'hear', it cues the model to resolve its next-token predictions as if they were conditioned on latent visual or auditory evidence that is never actually supplied. Our findings reveal that lightweight prompt engineering can reliably activate modality-appropriate representations in purely text-trained LLMs.

We introduce Playground v3 (PGv3), our latest text-to-image model that achieves state-of-the-art (SoTA) performance across multiple testing benchmarks, excels in graphic design abilities and introduces new capabilities. Unlike traditional text-to-image generative models that rely on pre-trained language models like T5 or CLIP text encoders, our approach fully integrates Large Language Models (LLMs) with a novel structure that leverages text conditions exclusively from a decoder-only LLM. Additionally, to enhance image captioning quality-we developed an in-house captioner, capable of generating captions with varying levels of detail, enriching the diversity of text structures. We also introduce a new benchmark CapsBench to evaluate detailed image captioning performance. Experimental results demonstrate that PGv3 excels in text prompt adherence, complex reasoning, and accurate text rendering. User preference studies indicate the super-human graphic design ability of our model for common design applications, such as stickers, posters, and logo designs. Furthermore, PGv3 introduces new capabilities, including precise RGB color control and robust multilingual understanding.

Visual imitation learning frameworks allow robots to learn manipulation skills from expert demonstrations. While existing approaches mainly focus on policy design, they often neglect the structure and capacity of visual encoders, limiting spatial understanding and generalization. Inspired by biological vision systems, which rely on both visual and proprioceptive cues for robust control, we propose VGGT-DP, a visuomotor policy framework that integrates geometric priors from a pretrained 3D perception model with proprioceptive feedback. We adopt the Visual Geometry Grounded Transformer (VGGT) as the visual encoder and introduce a proprioception-guided visual learning strategy to align perception with internal robot states, improving spatial grounding and closed-loop control. To reduce inference latency, we design a frame-wise token reuse mechanism that compacts multi-view tokens into an efficient spatial representation. We further apply random token pruning to enhance policy robustness and reduce overfitting. Experiments on challenging MetaWorld tasks show that VGGT-DP significantly outperforms strong baselines such as DP and DP3, particularly in precision-critical and long-horizon scenarios.

Perception systems in modern autonomous driving vehicles typically take inputs from complementary multi-modal sensors, e.g., LiDAR and cameras. However, in real-world applications, sensor corruptions and failures lead to inferior performances, thus compromising autonomous safety. In this paper, we propose a robust framework, called MetaBEV, to address extreme real-world environments involving overall six sensor corruptions and two extreme sensor-missing situations. In MetaBEV, signals from multiple sensors are first processed by modal-specific encoders. Subsequently, a set of dense BEV queries are initialized, termed meta-BEV. These queries are then processed iteratively by a BEV-Evolving decoder, which selectively aggregates deep features from either LiDAR, cameras, or both modalities. The updated BEV representations are further leveraged for multiple 3D prediction tasks. Additionally, we introduce a new M2oE structure to alleviate the performance drop on distinct tasks in multi-task joint learning. Finally, MetaBEV is evaluated on the nuScenes dataset with 3D object detection and BEV map segmentation tasks. Experiments show MetaBEV outperforms prior arts by a large margin on both full and corrupted modalities. For instance, when the LiDAR signal is missing, MetaBEV improves 35.5% detection NDS and 17.7% segmentation mIoU upon the vanilla BEVFusion model; and when the camera signal is absent, MetaBEV still achieves 69.2% NDS and 53.7% mIoU, which is even higher than previous works that perform on full-modalities. Moreover, MetaBEV performs fairly against previous methods in both canonical perception and multi-task learning settings, refreshing state-of-the-art nuScenes BEV map segmentation with 70.4% mIoU.

The analysis of 3D medical images is crucial for modern healthcare, yet traditional task-specific models are becoming increasingly inadequate due to limited generalizability across diverse clinical scenarios. Multimodal large language models (MLLMs) offer a promising solution to these challenges. However, existing MLLMs have limitations in fully leveraging the rich, hierarchical information embedded in 3D medical images. Inspired by clinical practice, where radiologists focus on both 3D spatial structure and 2D planar content, we propose Med-2E3, a novel MLLM for 3D medical image analysis that integrates 3D and 2D encoders. To aggregate 2D features more effectively, we design a Text-Guided Inter-Slice (TG-IS) scoring module, which scores the attention of each 2D slice based on slice contents and task instructions. To the best of our knowledge, Med-2E3 is the first MLLM to integrate both 3D and 2D features for 3D medical image analysis. Experiments on a large-scale, open-source 3D medical multimodal benchmark demonstrate that Med-2E3 exhibits task-specific attention distribution and significantly outperforms current state-of-the-art models, with a 14% improvement in report generation and a 5% gain in medical visual question answering (VQA), highlighting the model's potential in addressing complex multimodal clinical tasks. The code will be released upon acceptance.

Speech understanding as an element of the more generic video understanding using audio-visual large language models (av-LLMs) is a crucial yet understudied aspect. This paper proposes video-SALMONN, a single end-to-end av-LLM for video processing, which can understand not only visual frame sequences, audio events and music, but speech as well. To obtain fine-grained temporal information required by speech understanding, while keeping efficient for other video elements, this paper proposes a novel multi-resolution causal Q-Former (MRC Q-Former) structure to connect pre-trained audio-visual encoders and the backbone large language model. Moreover, dedicated training approaches including the diversity loss and the unpaired audio-visual mixed training scheme are proposed to avoid frames or modality dominance. On the introduced speech-audio-visual evaluation benchmark, video-SALMONN achieves more than 25\% absolute accuracy improvements on the video-QA task and over 30\% absolute accuracy improvements on audio-visual QA tasks with human speech. In addition, video-SALMONN demonstrates remarkable video comprehension and reasoning abilities on tasks that are unprecedented by other av-LLMs. Our training code and model checkpoints are available at \url{https://github.com/bytedance/SALMONN/}.

Concatenating quantum error correction codes scales error correction capability by driving logical error rates down double-exponentially across levels. However, the noise structure shifts under concatenation, making it hard to choose an optimal code sequence. We automate this choice by estimating the effective noise channel after each level and selecting the next code accordingly. In particular, we use learning-based methods to tailor small, non-additive encoders when the noise exhibits sufficient structure, then switch to standard codes once the noise is nearly uniform. In simulations, this level-wise adaptation achieves a target logical error rate with far fewer qubits than concatenating stabilizer codes alone--reducing qubit counts by up to two orders of magnitude for strongly structured noise. Therefore, this hybrid, learning-based strategy offers a promising tool for early fault-tolerant quantum computing.

We study sentence-level identification of the 19 values in the Schwartz motivational continuum as a concrete formulation of human value detection in text. The setting - out-of-context sentences from news and political manifestos - features sparse moral cues and severe class imbalance. This combination makes fine-grained sentence-level value detection intrinsically difficult, even for strong modern neural models. We first operationalize a binary moral presence task ("does any value appear?") and show that it is learnable from single sentences (positive-class F1 approx 0.74 with calibrated thresholds). We then compare a presence-gated hierarchy to a direct multi-label classifier under matched compute, both based on DeBERTa-base and augmented with lightweight signals (prior-sentence context, LIWC-22/eMFD/MJD lexica, and topic features). The hierarchy does not outperform direct prediction, indicating that gate recall limits downstream gains. We also benchmark instruction-tuned LLMs - Gemma 2 9B, Llama 3.1 8B, Mistral 8B, and Qwen 2.5 7B - in zero-/few-shot and QLoRA setups and build simple ensembles; a soft-vote supervised ensemble reaches macro-F1 0.332, significantly surpassing the best single supervised model and exceeding prior English-only baselines. Overall, in this scenario, lightweight signals and small ensembles yield the most reliable improvements, while hierarchical gating offers limited benefit. We argue that, under an 8 GB single-GPU constraint and at the 7-9B scale, carefully tuned supervised encoders remain a strong and compute-efficient baseline for structured human value detection, and we outline how richer value structure and sentence-in-document context could further improve performance.

Multimodal foundation models (MFMs) have revolutionized sequential recommender systems through advanced representation learning. While Parameter-efficient Fine-tuning (PEFT) is commonly used to adapt these models, studies often prioritize parameter efficiency, neglecting GPU memory and training speed. To address this, we introduced the IISAN framework, significantly enhancing efficiency. However, IISAN was limited to symmetrical MFMs and identical text and image encoders, preventing the use of state-of-the-art Large Language Models. To overcome this, we developed IISAN-Versa, a versatile plug-and-play architecture compatible with both symmetrical and asymmetrical MFMs. IISAN-Versa employs a Decoupled PEFT structure and utilizes both intra- and inter-modal adaptation. It effectively handles asymmetry through a simple yet effective combination of group layer-dropping and dimension transformation alignment. Our research demonstrates that IISAN-Versa effectively adapts large text encoders, and we further identify a scaling effect where larger encoders generally perform better. IISAN-Versa also demonstrates strong versatility in our defined multimodal scenarios, which include raw titles and captions generated from images and videos. Additionally, IISAN-Versa achieved state-of-the-art performance on the Microlens public benchmark. We release our code at https://github.com/GAIR-Lab/IISAN.

This paper investigates the capability of plain Vision Transformers (ViTs) for semantic segmentation using the encoder-decoder framework and introduces SegViTv2. In this study, we introduce a novel Attention-to-Mask (\atm) module to design a lightweight decoder effective for plain ViT. The proposed ATM converts the global attention map into semantic masks for high-quality segmentation results. Our decoder outperforms the popular decoder UPerNet using various ViT backbones while consuming only about 5% of the computational cost. For the encoder, we address the concern of the relatively high computational cost in the ViT-based encoders and propose a Shrunk++ structure that incorporates edge-aware query-based down-sampling (EQD) and query-based upsampling (QU) modules. The Shrunk++ structure reduces the computational cost of the encoder by up to 50% while maintaining competitive performance. Furthermore, we propose to adapt SegViT for continual semantic segmentation, demonstrating nearly zero forgetting of previously learned knowledge. Experiments show that our proposed SegViTv2 surpasses recent segmentation methods on three popular benchmarks including ADE20k, COCO-Stuff-10k and PASCAL-Context datasets. The code is available through the following link: https://github.com/zbwxp/SegVit.

The integration of Large Language Models (LLMs) into autonomous driving has attracted growing interest for their strong reasoning and semantic understanding abilities, which are essential for handling complex decision-making and long-tail scenarios. However, existing methods typically feed LLMs with tokens from multi-view and multi-frame images independently, leading to redundant computation and limited spatial consistency. This separation in visual processing hinders accurate 3D spatial reasoning and fails to maintain geometric coherence across views. On the other hand, Bird's-Eye View (BEV) representations learned from geometrically annotated tasks (e.g., object detection) provide spatial structure but lack the semantic richness of foundation vision encoders. To bridge this gap, we propose BEVLM, a framework that connects a spatially consistent and semantically distilled BEV representation with LLMs. Through extensive experiments, we show that BEVLM enables LLMs to reason more effectively in cross-view driving scenes, improving accuracy by 46%, by leveraging BEV features as unified inputs. Furthermore, by distilling semantic knowledge from LLMs into BEV representations, BEVLM significantly improves closed-loop end-to-end driving performance by 29% in safety-critical scenarios.

Universally modeling all typical information extraction tasks (UIE) with one generative language model (GLM) has revealed great potential by the latest study, where various IE predictions are unified into a linearized hierarchical expression under a GLM. Syntactic structure information, a type of effective feature which has been extensively utilized in IE community, should also be beneficial to UIE. In this work, we propose a novel structure-aware GLM, fully unleashing the power of syntactic knowledge for UIE. A heterogeneous structure inductor is explored to unsupervisedly induce rich heterogeneous structural representations by post-training an existing GLM. In particular, a structural broadcaster is devised to compact various latent trees into explicit high-order forests, helping to guide a better generation during decoding. We finally introduce a task-oriented structure fine-tuning mechanism, further adjusting the learned structures to most coincide with the end-task's need. Over 12 IE benchmarks across 7 tasks our system shows significant improvements over the baseline UIE system. Further in-depth analyses show that our GLM learns rich task-adaptive structural bias that greatly resolves the UIE crux, the long-range dependence issue and boundary identifying. Source codes are open at https://github.com/ChocoWu/LasUIE.

Predicting drug-target interaction (DTI) is critical in the drug discovery process. Despite remarkable advances in recent DTI models through the integration of representations from diverse drug and target encoders, such models often struggle to capture the fine-grained interactions between drugs and protein, i.e. the binding of specific drug atoms (or substructures) and key amino acids of proteins, which is crucial for understanding the binding mechanisms and optimising drug design. To address this issue, this paper introduces a novel model, called FusionDTI, which uses a token-level Fusion module to effectively learn fine-grained information for Drug-Target Interaction. In particular, our FusionDTI model uses the SELFIES representation of drugs to mitigate sequence fragment invalidation and incorporates the structure-aware (SA) vocabulary of target proteins to address the limitation of amino acid sequences in structural information, additionally leveraging pre-trained language models extensively trained on large-scale biomedical datasets as encoders to capture the complex information of drugs and targets. Experiments on three well-known benchmark datasets show that our proposed FusionDTI model achieves the best performance in DTI prediction compared with seven existing state-of-the-art baselines. Furthermore, our case study indicates that FusionDTI could highlight the potential binding sites, enhancing the explainability of the DTI prediction.

Structure information is critical for understanding the semantics of text-rich images, such as documents, tables, and charts. Existing Multimodal Large Language Models (MLLMs) for Visual Document Understanding are equipped with text recognition ability but lack general structure understanding abilities for text-rich document images. In this work, we emphasize the importance of structure information in Visual Document Understanding and propose the Unified Structure Learning to boost the performance of MLLMs. Our Unified Structure Learning comprises structure-aware parsing tasks and multi-grained text localization tasks across 5 domains: document, webpage, table, chart, and natural image. To better encode structure information, we design a simple and effective vision-to-text module H-Reducer, which can not only maintain the layout information but also reduce the length of visual features by merging horizontal adjacent patches through convolution, enabling the LLM to understand high-resolution images more efficiently. Furthermore, by constructing structure-aware text sequences and multi-grained pairs of texts and bounding boxes for publicly available text-rich images, we build a comprehensive training set DocStruct4M to support structure learning. Finally, we construct a small but high-quality reasoning tuning dataset DocReason25K to trigger the detailed explanation ability in the document domain. Our model DocOwl 1.5 achieves state-of-the-art performance on 10 visual document understanding benchmarks, improving the SOTA performance of MLLMs with a 7B LLM by more than 10 points in 5/10 benchmarks. Our codes, models, and datasets are publicly available at https://github.com/X-PLUG/mPLUG-DocOwl/tree/main/DocOwl1.5.

There has been a recent surge of interest in automating software engineering tasks using deep learning. This paper addresses the problem of code generation, where the goal is to generate target code given source code in a different language or a natural language description. Most state-of-the-art deep learning models for code generation use training strategies primarily designed for natural language. However, understanding and generating code requires a more rigorous comprehension of the code syntax and semantics. With this motivation, we develop an encoder-decoder Transformer model where both the encoder and decoder are explicitly trained to recognize the syntax and data flow in the source and target codes, respectively. We not only make the encoder structure-aware by leveraging the source code's syntax tree and data flow graph, but we also support the decoder in preserving the syntax and data flow of the target code by introducing two novel auxiliary tasks: AST (Abstract Syntax Tree) paths prediction and data flow prediction. To the best of our knowledge, this is the first work to introduce a structure-aware Transformer decoder that models both syntax and data flow to enhance the quality of generated code. The proposed StructCoder model achieves state-of-the-art performance on code translation and text-to-code generation tasks in the CodeXGLUE benchmark, and improves over baselines of similar size on the APPS code generation benchmark. Our code is publicly available at https://github.com/reddy-lab-code-research/StructCoder/.

Pre-trained models for programming languages have recently demonstrated great success on code intelligence. To support both code-related understanding and generation tasks, recent works attempt to pre-train unified encoder-decoder models. However, such encoder-decoder framework is sub-optimal for auto-regressive tasks, especially code completion that requires a decoder-only manner for efficient inference. In this paper, we present UniXcoder, a unified cross-modal pre-trained model for programming language. The model utilizes mask attention matrices with prefix adapters to control the behavior of the model and leverages cross-modal contents like AST and code comment to enhance code representation. To encode AST that is represented as a tree in parallel, we propose a one-to-one mapping method to transform AST in a sequence structure that retains all structural information from the tree. Furthermore, we propose to utilize multi-modal contents to learn representation of code fragment with contrastive learning, and then align representations among programming languages using a cross-modal generation task. We evaluate UniXcoder on five code-related tasks over nine datasets. To further evaluate the performance of code fragment representation, we also construct a dataset for a new task, called zero-shot code-to-code search. Results show that our model achieves state-of-the-art performance on most tasks and analysis reveals that comment and AST can both enhance UniXcoder.

Graph contrastive learning (GCL) has become a powerful tool for learning graph data, but its scalability remains a significant challenge. In this work, we propose a simple yet effective training framework called Structural Compression (StructComp) to address this issue. Inspired by a sparse low-rank approximation on the diffusion matrix, StructComp trains the encoder with the compressed nodes. This allows the encoder not to perform any message passing during the training stage, and significantly reduces the number of sample pairs in the contrastive loss. We theoretically prove that the original GCL loss can be approximated with the contrastive loss computed by StructComp. Moreover, StructComp can be regarded as an additional regularization term for GCL models, resulting in a more robust encoder. Empirical studies on seven benchmark datasets show that StructComp greatly reduces the time and memory consumption while improving model performance compared to the vanilla GCL models and scalable training methods.

Learning effective protein representations is critical in a variety of tasks in biology such as predicting protein function or structure. Existing approaches usually pretrain protein language models on a large number of unlabeled amino acid sequences and then finetune the models with some labeled data in downstream tasks. Despite the effectiveness of sequence-based approaches, the power of pretraining on known protein structures, which are available in smaller numbers only, has not been explored for protein property prediction, though protein structures are known to be determinants of protein function. In this paper, we propose to pretrain protein representations according to their 3D structures. We first present a simple yet effective encoder to learn the geometric features of a protein. We pretrain the protein graph encoder by leveraging multiview contrastive learning and different self-prediction tasks. Experimental results on both function prediction and fold classification tasks show that our proposed pretraining methods outperform or are on par with the state-of-the-art sequence-based methods, while using much less pretraining data. Our implementation is available at https://github.com/DeepGraphLearning/GearNet.

Linear sequences of words are implicitly represented in our brains by hierarchical structures that organize the composition of words in sentences. Linguists formalize different frameworks to model this hierarchy; two of the most common syntactic frameworks are Constituency and Dependency. Constituency represents sentences as nested groups of phrases, while dependency represents a sentence by assigning relations between its words. Recently, the pursuit of intelligent machines has produced Language Models (LMs) capable of solving many language tasks with a human-level performance. Many studies now question whether LMs implicitly represent syntactic hierarchies. This thesis focuses on producing constituency and dependency structures from LMs in an unsupervised setting. I review the critical methods in this field and highlight a line of work that utilizes a numerical representation for binary constituency trees (Syntactic Distance). I present a detailed study on StructFormer (SF) (Shen et al., 2021), which retrofits a transformer encoder architecture with a parser network to produce constituency and dependency structures. I present six experiments to analyze and address this field's challenges; experiments include investigating the effect of repositioning the parser network within the SF architecture, evaluating subword-based induced trees, and benchmarking the models developed in the thesis experiments on linguistic tasks. Models benchmarking is performed by participating in the BabyLM challenge, published at CoNLL 2023 (Momen et al., 2023). The results of this thesis encourage further development in the direction of retrofitting transformer-based models to induce syntactic structures, supported by the acceptable performance of SF in different experimental settings and the observed limitations that require innovative solutions to advance the state of syntactic structure induction.

Protein structure tokenization converts 3D structures into discrete or vectorized representations, enabling the integration of structural and sequence data. Despite many recent works on structure tokenization, the properties of the underlying discrete representations are not well understood. In this work, we first demonstrate that the successful utilization of structural tokens in a language model for structure prediction depends on using rich, pre-trained sequence embeddings to bridge the semantic gap between the sequence and structural "language". The analysis of the structural vocabulary itself then reveals significant semantic redundancy, where multiple distinct tokens correspond to nearly identical local geometries, acting as "structural synonyms". This redundancy, rather than being a flaw, can be exploited with a simple "synonym swap" strategy to generate diverse conformational ensembles by perturbing a predicted structure with its structural synonyms. This computationally lightweight method accurately recapitulates protein flexibility, performing competitively with state-of-the-art models. Our study provides fundamental insights into the nature of discrete protein structure representations and introduces a powerful, near-instantaneous method for modeling protein dynamics. Source code is available in https://github.com/IDEA-XL/TokenMD.

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

Pre-trained models for programming language have achieved dramatic empirical improvements on a variety of code-related tasks such as code search, code completion, code summarization, etc. However, existing pre-trained models regard a code snippet as a sequence of tokens, while ignoring the inherent structure of code, which provides crucial code semantics and would enhance the code understanding process. We present GraphCodeBERT, a pre-trained model for programming language that considers the inherent structure of code. Instead of taking syntactic-level structure of code like abstract syntax tree (AST), we use data flow in the pre-training stage, which is a semantic-level structure of code that encodes the relation of "where-the-value-comes-from" between variables. Such a semantic-level structure is neat and does not bring an unnecessarily deep hierarchy of AST, the property of which makes the model more efficient. We develop GraphCodeBERT based on Transformer. In addition to using the task of masked language modeling, we introduce two structure-aware pre-training tasks. One is to predict code structure edges, and the other is to align representations between source code and code structure. We implement the model in an efficient way with a graph-guided masked attention function to incorporate the code structure. We evaluate our model on four tasks, including code search, clone detection, code translation, and code refinement. Results show that code structure and newly introduced pre-training tasks can improve GraphCodeBERT and achieves state-of-the-art performance on the four downstream tasks. We further show that the model prefers structure-level attentions over token-level attentions in the task of code search.

Recent techniques such as retrieval-augmented generation or chain-of-thought reasoning have led to longer contexts and increased inference costs. Context compression techniques can reduce these costs, but the most effective approaches require fine-tuning the target model or even modifying its architecture. This can degrade its general abilities when not used for this specific purpose. Here we explore an alternative approach: an encoder that compresses the context into continuous representations which replace token embeddings in decoder LLMs. First, we perform a systematic study of training strategies and architecture choices for the encoder. Our findings led to the design of an Adaptable text Representations Compressor, named ARC-Encoder, which outputs x-times fewer continuous representations (typically x!in!{4,8}) than text tokens. We evaluate ARC-Encoder across a variety of LLM usage scenarios, ranging from in-context learning to context window extension, on both instruct and base decoders. Results show that ARC-Encoder achieves state-of-the-art performance on several benchmarks while improving computational efficiency at inference. Finally, we demonstrate that our models can be adapted to multiple decoders simultaneously, allowing a single encoder to generalize across different decoder LLMs. This makes ARC-Encoder a flexible and efficient solution for portable encoders that work seamlessly with multiple LLMs. We release a training code at https://github.com/kyutai-labs/ARC-Encoder , fine-tuning dataset and pretrained models are available at https://huggingface.co/collections/kyutai/arc-encoders-68ee18787301407d60a57047 .

Predictor-based methods have substantially enhanced Neural Architecture Search (NAS) optimization. The efficacy of these predictors is largely influenced by the method of encoding neural network architectures. While traditional encodings used an adjacency matrix describing the graph structure of a neural network, novel encodings embrace a variety of approaches from unsupervised pretraining of latent representations to vectors of zero-cost proxies. In this paper, we categorize and investigate neural encodings from three main types: structural, learned, and score-based. Furthermore, we extend these encodings and introduce unified encodings, that extend NAS predictors to multiple search spaces. Our analysis draws from experiments conducted on over 1.5 million neural network architectures on NAS spaces such as NASBench-101 (NB101), NB201, NB301, Network Design Spaces (NDS), and TransNASBench-101. Building on our study, we present our predictor FLAN: Flow Attention for NAS. FLAN integrates critical insights on predictor design, transfer learning, and unified encodings to enable more than an order of magnitude cost reduction for training NAS accuracy predictors. Our implementation and encodings for all neural networks are open-sourced at https://github.com/abdelfattah-lab/flan_nas{https://github.com/abdelfattah-lab/flan\_nas}.

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.

Building huge and highly capable language models has been a trend in the past years. Despite their great performance, they incur high computational cost. A common solution is to apply model compression or choose light-weight architectures, which often need a separate fixed-size model for each desirable computational budget, and may lose performance in case of heavy compression. This paper proposes an effective dynamic inference approach, called E-LANG, which distributes the inference between large accurate Super-models and light-weight Swift models. To this end, a decision making module routes the inputs to Super or Swift models based on the energy characteristics of the representations in the latent space. This method is easily adoptable and architecture agnostic. As such, it can be applied to black-box pre-trained models without a need for architectural manipulations, reassembling of modules, or re-training. Unlike existing methods that are only applicable to encoder-only backbones and classification tasks, our method also works for encoder-decoder structures and sequence-to-sequence tasks such as translation. The E-LANG performance is verified through a set of experiments with T5 and BERT backbones on GLUE, SuperGLUE, and WMT. In particular, we outperform T5-11B with an average computations speed-up of 3.3times on GLUE and 2.9times on SuperGLUE. We also achieve BERT-based SOTA on GLUE with 3.2times less computations. Code and demo are available in the supplementary materials.

Deep encoder-decoder based CNNs have advanced image inpainting methods for hole filling. While existing methods recover structures and textures step-by-step in the hole regions, they typically use two encoder-decoders for separate recovery. The CNN features of each encoder are learned to capture either missing structures or textures without considering them as a whole. The insufficient utilization of these encoder features limit the performance of recovering both structures and textures. In this paper, we propose a mutual encoder-decoder CNN for joint recovery of both. We use CNN features from the deep and shallow layers of the encoder to represent structures and textures of an input image, respectively. The deep layer features are sent to a structure branch and the shallow layer features are sent to a texture branch. In each branch, we fill holes in multiple scales of the CNN features. The filled CNN features from both branches are concatenated and then equalized. During feature equalization, we reweigh channel attentions first and propose a bilateral propagation activation function to enable spatial equalization. To this end, the filled CNN features of structure and texture mutually benefit each other to represent image content at all feature levels. We use the equalized feature to supplement decoder features for output image generation through skip connections. Experiments on the benchmark datasets show the proposed method is effective to recover structures and textures and performs favorably against state-of-the-art approaches.

In recent years, exploiting the domain-specific underlying structure of data and its generative factors for representation learning has shown success in various use-case agnostic applications. However, the diversity and complexity of tabular data have made it challenging to represent these structures in a latent space through multi-dimensional vectors. We design an autoencoder-based framework for building general purpose embeddings, we assess the performance of different autoencoder architectures, and show simpler models outperform complex ones in embedding highly complex tabular data. We apply our framework to produce plug-and-play, rich, and anonymized embeddings representing AWS customers for usage in any model, saving up to 45% of development time, and observe significant improvements in downstream models. Moreover, we propose a significant improvement to the calculation of reconstruction loss for multi-layer contractive autoencoders (CAE) by calculating the Jacobian of the entire encoder leading to a 15% improvement in reconstruction quality when compared to a stacked CAE.

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

Vision encoders are increasingly used in modern applications, from vision-only models to multimodal systems such as vision-language models. Despite their remarkable success, it remains unclear how these architectures represent features internally. Here, we propose a novel approach for interpreting vision features via image reconstruction. We compare two related model families, SigLIP and SigLIP2, which differ only in their training objective, and show that encoders pre-trained on image-based tasks retain significantly more image information than those trained on non-image tasks such as contrastive learning. We further apply our method to a range of vision encoders, ranking them by the informativeness of their feature representations. Finally, we demonstrate that manipulating the feature space yields predictable changes in reconstructed images, revealing that orthogonal rotations (rather than spatial transformations) control color encoding. Our approach can be applied to any vision encoder, shedding light on the inner structure of its feature space. The code and model weights to reproduce the experiments are available in GitHub.

Neural networks are trained by choosing an architecture and training the parameters. The choice of architecture is often by trial and error or with Neural Architecture Search (NAS) methods. While NAS provides some automation, it often relies on discrete steps that optimize the architecture and then train the parameters. We introduce a novel neural network training framework that fundamentally transforms the process by learning architecture and parameters simultaneously with gradient descent. With the appropriate setting of the loss function, it can discover sparse and compact neural networks for given datasets. Central to our approach is a multi-scale encoder-decoder, in which the encoder embeds pairs of neural networks with similar functionalities close to each other (irrespective of their architectures and weights). To train a neural network with a given dataset, we randomly sample a neural network embedding in the embedding space and then perform gradient descent using our custom loss function, which incorporates a sparsity penalty to encourage compactness. The decoder generates a neural network corresponding to the embedding. Experiments demonstrate that our framework can discover sparse and compact neural networks maintaining a high performance.

The rapid expansion of genomic sequence data calls for new methods to achieve robust sequence representations. Existing techniques often neglect intricate structural details, emphasizing mainly contextual information. To address this, we developed k-mer embeddings that merge contextual and structural string information by enhancing De Bruijn graphs with structural similarity connections. Subsequently, we crafted a self-supervised method based on Contrastive Learning that employs a heterogeneous Graph Convolutional Network encoder and constructs positive pairs based on node similarities. Our embeddings consistently outperform prior techniques for Edit Distance Approximation and Closest String Retrieval tasks.

Managing extensive context remains a critical bottleneck for Large Language Models (LLMs), particularly in applications like long-document question answering and autonomous agents where lengthy inputs incur high computational costs and introduce noise. Existing compression techniques often disrupt local coherence through discrete token removal or rely on implicit latent encoding that suffers from positional bias and incompatibility with closed-source APIs. To address these limitations, we introduce the EDU-based Context Compressor, a novel explicit compression framework designed to preserve both global structure and fine-grained details. Our approach reformulates context compression as a structure-then-select process. First, our LingoEDU transforms linear text into a structural relation tree of Elementary Discourse Units (EDUs) which are anchored strictly to source indices to eliminate hallucination. Second, a lightweight ranking module selects query-relevant sub-trees for linearization. To rigorously evaluate structural understanding, we release StructBench, a manually annotated dataset of 248 diverse documents. Empirical results demonstrate that our method achieves state-of-the-art structural prediction accuracy and significantly outperforms frontier LLMs while reducing costs. Furthermore, our structure-aware compression substantially enhances performance across downstream tasks ranging from long-context tasks to complex Deep Search scenarios.

Recent years have seen a paradigm shift in NLP towards using pretrained language models ({PLM}) for a wide range of tasks. However, there are many difficult design decisions to represent structures (e.g. tagged text, coreference chains) in a way such that they can be captured by PLMs. Prior work on structured prediction with PLMs typically flattens the structured output into a sequence, which limits the quality of structural information being learned and leads to inferior performance compared to classic discriminative models. In this work, we describe an approach to model structures as sequences of actions in an autoregressive manner with PLMs, allowing in-structure dependencies to be learned without any loss. Our approach achieves the new state-of-the-art on all the structured prediction tasks we looked at, namely, named entity recognition, end-to-end relation extraction, and coreference resolution.

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

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

Pretrained Transformer encoders are the dominant approach to sequence labeling. While some alternative architectures-such as xLSTMs, structured state-space models, diffusion models, and adversarial learning-have shown promise in language modeling, few have been applied to sequence labeling, and mostly on flat or simplified tasks. We study how these architectures adapt across tagging tasks that vary in structural complexity, label space, and token dependencies, with evaluation spanning multiple languages. We find that the strong performance previously observed in simpler settings does not always generalize well across languages or datasets, nor does it extend to more complex structured tasks.

Despite the power of Large Language Models (LLMs) like GPT-4, they still struggle with tasks that require generating complex, structured outputs. In this study, we assess the capability of Current LLMs in generating complex structured data and propose a structure-aware fine-tuning approach as a solution to improve this ability. To perform a comprehensive evaluation, we propose Struc-Bench, include five representative LLMs (i.e., GPT-NeoX 20B, GPT-3.5, GPT-4, and Vicuna) and evaluate them on our carefully constructed datasets spanning raw text, HTML, and LaTeX tables. Based on our analysis of current model performance, we identify specific common formatting errors and areas of potential improvement. To address complex formatting requirements, we utilize FormatCoT (Chain-of-Thought) to generate format instructions from target outputs. Our experiments show that our structure-aware fine-tuning method, when applied to LLaMA-7B, significantly improves adherence to natural language constraints, outperforming other evaluated LLMs. Based on these results, we present an ability map of model capabilities from six dimensions (i.e., coverage, formatting, reasoning, comprehension, pragmatics, and hallucination). This map highlights the weaknesses of LLMs in handling complex structured outputs and suggests promising directions for future work. Our code and models can be found at https://github.com/gersteinlab/Struc-Bench.

Decoder-based transformers, while revolutionizing language modeling and scaling to immense sizes, have not completely overtaken encoder-heavy architectures in natural language processing. Specifically, encoder-only models remain dominant in tasks like classification, regression, and ranking. This is primarily due to the inherent structure of decoder-based models, which limits their direct applicability to these tasks. In this paper, we introduce Gemma Encoder, adapting the powerful Gemma decoder model to an encoder architecture, thereby unlocking its potential for a wider range of non-generative applications. To optimize the adaptation from decoder to encoder, we systematically analyze various pooling strategies, attention mechanisms, and hyperparameters (e.g., dropout rate). Furthermore, we benchmark Gemma Encoder against established approaches on the GLUE benchmarks, and MS MARCO ranking benchmark, demonstrating its effectiveness and versatility.

Proteins are essential macromolecules defined by their amino acid sequences, which determine their three-dimensional structures and, consequently, their functions in all living organisms. Therefore, generative protein modeling necessitates a multimodal approach to simultaneously model, understand, and generate both sequences and structures. However, existing methods typically use separate models for each modality, limiting their ability to capture the intricate relationships between sequence and structure. This results in suboptimal performance in tasks that requires joint understanding and generation of both modalities. In this paper, we introduce DPLM-2, a multimodal protein foundation model that extends discrete diffusion protein language model (DPLM) to accommodate both sequences and structures. To enable structural learning with the language model, 3D coordinates are converted to discrete tokens using a lookup-free quantization-based tokenizer. By training on both experimental and high-quality synthetic structures, DPLM-2 learns the joint distribution of sequence and structure, as well as their marginals and conditionals. We also implement an efficient warm-up strategy to exploit the connection between large-scale evolutionary data and structural inductive biases from pre-trained sequence-based protein language models. Empirical evaluation shows that DPLM-2 can simultaneously generate highly compatible amino acid sequences and their corresponding 3D structures eliminating the need for a two-stage generation approach. Moreover, DPLM-2 demonstrates competitive performance in various conditional generation tasks, including folding, inverse folding, and scaffolding with multimodal motif inputs, as well as providing structure-aware representations for predictive tasks.

Pre-trained encoders are widely employed in dense prediction tasks for their capability to effectively extract visual features from images. The decoder subsequently processes these features to generate pixel-level predictions. However, due to structural differences and variations in input data, only encoders benefit from pre-learned representations from vision benchmarks such as image classification and self-supervised learning, while decoders are typically trained from scratch. In this paper, we introduce timesNet, which facilitates a "pre-trained encoder times pre-trained decoder" collaboration through three innovative designs. timesNet enables the direct utilization of pre-trained models within the decoder, integrating pre-learned representations into the decoding process to enhance performance in dense prediction tasks. By simply coupling the pre-trained encoder and pre-trained decoder, timesNet distinguishes itself as a highly promising approach. Remarkably, it achieves this without relying on decoding-specific structures or task-specific algorithms. Despite its streamlined design, timesNet outperforms advanced methods in tasks such as monocular depth estimation and semantic segmentation, achieving state-of-the-art performance particularly in monocular depth estimation. and semantic segmentation, achieving state-of-the-art results, especially in monocular depth estimation. embedding algorithms. Despite its streamlined design, timesNet outperforms advanced methods in tasks such as monocular depth estimation and semantic segmentation, achieving state-of-the-art performance particularly in monocular depth estimation.

Pre-trained encoder-decoder transformer architectures have become increasingly popular recently with the advent of T5 models. T5 has also become more favorable over other architectures like BERT due to the amount of data that it is pre-trained on, increased scale of model parameter sizes and easy applicability to a diverse set of tasks due to the generative nature of the model. While being able to generalize to a wide variety of tasks, it is not clear that encoder-decoder architectures are the most efficient for fine-tuning tasks that don't require auto-regressive decoding. In this work, we study fine-tuning pre-trained encoder-decoder models for tasks such as classification, multi-label classification, and structured prediction. We propose EncT5, a framework for these problems, and illustrate instantiations for these tasks. Our experiment results show that EncT5 has advantages over T5 such as efficiency and usability out performs BERT when evaluated on publicly available pre-trained checkpoints.

The world of language models is going through turbulent times, better and ever larger models are coming out at an unprecedented speed. However, we argue that, especially for the scientific community, encoder models of up to 1 billion parameters are still very much needed, their primary usage being in enriching large collections of data with metadata necessary for downstream research. We investigate the best way to ensure the existence of such encoder models on the set of very closely related languages - Croatian, Serbian, Bosnian and Montenegrin, by setting up a diverse benchmark for these languages, and comparing the trained-from-scratch models with the new models constructed via additional pretraining of existing multilingual models. We show that comparable performance to dedicated from-scratch models can be obtained by additionally pretraining available multilingual models even with a limited amount of computation. We also show that neighboring languages, in our case Slovenian, can be included in the additional pretraining with little to no loss in the performance of the final model.

Sentence encoder encode the semantics of their input, enabling key downstream applications such as classification, clustering, or retrieval. In this paper, we present Serafim PT*, a family of open-source sentence encoders for Portuguese with various sizes, suited to different hardware/compute budgets. Each model exhibits state-of-the-art performance and is made openly available under a permissive license, allowing its use for both commercial and research purposes. Besides the sentence encoders, this paper contributes a systematic study and lessons learned concerning the selection criteria of learning objectives and parameters that support top-performing encoders.

While decoder-only large language models (LLMs) have shown impressive results, encoder-decoder models are still widely adopted in real-world applications for their inference efficiency and richer encoder representation. In this paper, we study a novel problem: adapting pretrained decoder-only LLMs to encoder-decoder, with the goal of leveraging the strengths of both approaches to achieve a more favorable quality-efficiency trade-off. We argue that adaptation not only enables inheriting the capability of decoder-only LLMs but also reduces the demand for computation compared to pretraining from scratch. We rigorously explore different pretraining objectives and parameter initialization/optimization techniques. Through extensive experiments based on Gemma 2 (2B and 9B) and a suite of newly pretrained mT5-sized models (up to 1.6B), we demonstrate the effectiveness of adaptation and the advantage of encoder-decoder LLMs. Under similar inference budget, encoder-decoder LLMs achieve comparable (often better) pretraining performance but substantially better finetuning performance than their decoder-only counterpart. For example, Gemma 2B-2B outperforms Gemma 2B by sim7\% after instruction tuning. Encoder-decoder adaptation also allows for flexible combination of different-sized models, where Gemma 9B-2B significantly surpasses Gemma 2B-2B by >3\%. The adapted encoder representation also yields better results on SuperGLUE. We will release our checkpoints to facilitate future research.

Compact models often lose the structure of their embedding space. The issue shows up when the capacity is tight or the data spans several languages. Such collapse makes it difficult for downstream tasks to build on the resulting representation. Existing compression methods focus on aligning model outputs at a superficial level but fail to preserve the underlying manifold structure. This mismatch often leads to semantic drift in the compact model, causing both task behavior and linguistic properties to deviate from the reference model. To address those issues, we provide a new framework called Embedding Consistency Regulation (ECR). This framework first derives a set of semantic anchors from teacher embeddings (computed once offline). Then, the compact model learns to maintain consistent geometry around these anchors, without relying on matching logits or internal features. ECR adds only a small projection step at inference, without altering the decoding architecture or its runtime behavior. In experiments on a 100K multilingual corpus, ECR consistently stabilizes training and preserves semantic structure across tasks and languages. It also produces a more compact and task-aligned representation space, enabling low-capacity models to learn cleaner manifolds than conventional baselines. ECR works without teacher outputs and is compatible with, but independent of, distillation. Taken together, our results show that ECR helps compact models better follow task requirements and makes them easier to deploy under strict efficiency or privacy limits.

Large-scale vision-language pre-training has achieved significant performance in multi-modal understanding and generation tasks. However, existing methods often perform poorly on image-text matching tasks that require structured representations, i.e., representations of objects, attributes, and relations. As illustrated in Fig.~reffig:case (a), the models cannot make a distinction between ``An astronaut rides a horse" and ``A horse rides an astronaut". This is because they fail to fully leverage structured knowledge when learning representations in multi-modal scenarios. In this paper, we present an end-to-end framework Structure-CLIP, which integrates Scene Graph Knowledge (SGK) to enhance multi-modal structured representations. Firstly, we use scene graphs to guide the construction of semantic negative examples, which results in an increased emphasis on learning structured representations. Moreover, a Knowledge-Enhance Encoder (KEE) is proposed to leverage SGK as input to further enhance structured representations. To verify the effectiveness of the proposed framework, we pre-train our model with the aforementioned approaches and conduct experiments on downstream tasks. Experimental results demonstrate that Structure-CLIP achieves state-of-the-art (SOTA) performance on VG-Attribution and VG-Relation datasets, with 12.5% and 4.1% ahead of the multi-modal SOTA model respectively. Meanwhile, the results on MSCOCO indicate that Structure-CLIP significantly enhances the structured representations while maintaining the ability of general representations. Our code is available at https://github.com/zjukg/Structure-CLIP.

Interpreting hierarchical structures latent in language is a key limitation of current language models (LMs). While previous research has implicitly leveraged these hierarchies to enhance LMs, approaches for their explicit encoding are yet to be explored. To address this, we introduce a novel approach to re-train transformer encoder-based LMs as Hierarchy Transformer encoders (HiTs), harnessing the expansive nature of hyperbolic space. Our method situates the output embedding space of pre-trained LMs within a Poincar\'e ball with a curvature that adapts to the embedding dimension, followed by re-training on hyperbolic cluster and centripetal losses. These losses are designed to effectively cluster related entities (input as texts) and organise them hierarchically. We evaluate HiTs against pre-trained and fine-tuned LMs, focusing on their capabilities in simulating transitive inference, predicting subsumptions, and transferring knowledge across hierarchies. The results demonstrate that HiTs consistently outperform both pre-trained and fine-tuned LMs in these tasks, underscoring the effectiveness and transferability of our re-trained hierarchy encoders.

The large language model (LLM) community focuses almost exclusively on decoder-only language models, since they are easier to use for text generation. However, a large subset of the community still uses encoder-only models for tasks such as classification or retrieval. Previous work has attempted to compare these architectures, but is forced to make comparisons with models that have different numbers of parameters, training techniques, and datasets. We introduce the SOTA open-data Ettin suite of models: paired encoder-only and decoder-only models ranging from 17 million parameters to 1 billion, trained on up to 2 trillion tokens. Using the same recipe for both encoder-only and decoder-only models produces SOTA recipes in both categories for their respective sizes, beating ModernBERT as an encoder and Llama 3.2 and SmolLM2 as decoders. Like previous work, we find that encoder-only models excel at classification and retrieval tasks while decoders excel at generative tasks. However, we show that adapting a decoder model to encoder tasks (and vice versa) through continued training is subpar compared to using only the reverse objective (i.e. a 400M encoder outperforms a 1B decoder on MNLI, and vice versa for generative tasks). We open-source all artifacts of this study including training data, training order segmented by checkpoint, and 200+ checkpoints to allow future work to analyze or extend all aspects of training.

Large language models record impressive performance on many natural language processing tasks. However, their knowledge capacity is limited to the pretraining corpus. Retrieval augmentation offers an effective solution by retrieving context from external knowledge sources to complement the language model. However, existing retrieval augmentation techniques ignore the structural relationships between these documents. Furthermore, retrieval models are not explored much in scientific tasks, especially in regard to the faithfulness of retrieved documents. In this paper, we propose a novel structure-aware retrieval augmented language model that accommodates document structure during retrieval augmentation. We create a heterogeneous document graph capturing multiple types of relationships (e.g., citation, co-authorship, etc.) that connect documents from more than 15 scientific disciplines (e.g., Physics, Medicine, Chemistry, etc.). We train a graph neural network on the curated document graph to act as a structural encoder for the corresponding passages retrieved during the model pretraining. Particularly, along with text embeddings of the retrieved passages, we obtain structural embeddings of the documents (passages) and fuse them together before feeding them to the language model. We evaluate our model extensively on various scientific benchmarks that include science question-answering and scientific document classification tasks. Experimental results demonstrate that structure-aware retrieval improves retrieving more coherent, faithful and contextually relevant passages, while showing a comparable performance in the overall accuracy.

Large language models (LLMs) have demonstrated remarkable abilities in representation learning for program synthesis and understanding tasks. The quality of the learned representations appears to be dictated by the neural scaling laws as a function of the number of model parameters and observations, while imposing upper bounds on the model performance by the amount of available data and compute, which is costly. In this study, we attempt to render the training of LLMs for program synthesis more efficient by unifying four key components: (1) model architectures, (2) learning methods, (3) infill sampling, and, (4) data distributions. Specifically, for the model architecture, we attempt to unify encoder and decoder-based models into a single prefix-LM. For learning methods, (i) causal language modeling, (ii) span corruption, (iii) infilling are unified into a simple learning algorithm. For infill sampling, we explore the claim of a "free lunch" hypothesis. For data distributions, the effect of a mixture distribution of programming and natural languages on model performance is explored. We conduct a comprehensive series of empirical experiments on 1B LLMs, for which failures and successes of this exploration are distilled into four lessons. We will provide a final recipe for training and release CodeGen2 models in size 1B, 3.7B, 7B, and, 16B parameters, along with the training framework as open-source: https://github.com/salesforce/CodeGen2.

The Transformer architecture has become a dominant choice in many domains, such as natural language processing and computer vision. Yet, it has not achieved competitive performance on popular leaderboards of graph-level prediction compared to mainstream GNN variants. Therefore, it remains a mystery how Transformers could perform well for graph representation learning. In this paper, we solve this mystery by presenting Graphormer, which is built upon the standard Transformer architecture, and could attain excellent results on a broad range of graph representation learning tasks, especially on the recent OGB Large-Scale Challenge. Our key insight to utilizing Transformer in the graph is the necessity of effectively encoding the structural information of a graph into the model. To this end, we propose several simple yet effective structural encoding methods to help Graphormer better model graph-structured data. Besides, we mathematically characterize the expressive power of Graphormer and exhibit that with our ways of encoding the structural information of graphs, many popular GNN variants could be covered as the special cases of Graphormer.

Abstractive summarization of scientific papers has always been a research focus, yet existing methods face two main challenges. First, most summarization models rely on Encoder-Decoder architectures that treat papers as sequences of words, thus fail to fully capture the structured information inherent in scientific papers. Second, existing research often use keyword mapping or feature engineering to identify the structural information, but these methods struggle with the structural flexibility of scientific papers and lack robustness across different disciplines. To address these challenges, we propose a two-stage abstractive summarization framework that leverages automatic recognition of structural functions within scientific papers. In the first stage, we standardize chapter titles from numerous scientific papers and construct a large-scale dataset for structural function recognition. A classifier is then trained to automatically identify the key structural components (e.g., Background, Methods, Results, Discussion), which provides a foundation for generating more balanced summaries. In the second stage, we employ Longformer to capture rich contextual relationships across sections and generating context-aware summaries. Experiments conducted on two domain-specific scientific paper summarization datasets demonstrate that our method outperforms advanced baselines, and generates more comprehensive summaries. The code and dataset can be accessed at https://github.com/tongbao96/code-for-SFR-AS.

Handwritten mathematical expression recognition (HMER) is a challenging task that has many potential applications. Recent methods for HMER have achieved outstanding performance with an encoder-decoder architecture. However, these methods adhere to the paradigm that the prediction is made "from one character to another", which inevitably yields prediction errors due to the complicated structures of mathematical expressions or crabbed handwritings. In this paper, we propose a simple and efficient method for HMER, which is the first to incorporate syntax information into an encoder-decoder network. Specifically, we present a set of grammar rules for converting the LaTeX markup sequence of each expression into a parsing tree; then, we model the markup sequence prediction as a tree traverse process with a deep neural network. In this way, the proposed method can effectively describe the syntax context of expressions, alleviating the structure prediction errors of HMER. Experiments on three benchmark datasets demonstrate that our method achieves better recognition performance than prior arts. To further validate the effectiveness of our method, we create a large-scale dataset consisting of 100k handwritten mathematical expression images acquired from ten thousand writers. The source code, new dataset, and pre-trained models of this work will be publicly available.

While learning models are typically studied for inputs in the form of a fixed dimensional feature vector, real world data is rarely found in this form. In order to meet the basic requirement of traditional learning models, structural data generally have to be converted into fix-length vectors in a handcrafted manner, which is tedious and may even incur information loss. A common form of structured data is what we term "semantic tree-structures", corresponding to data where rich semantic information is encoded in a compositional manner, such as those expressed in JavaScript Object Notation (JSON) and eXtensible Markup Language (XML). For tree-structured data, several learning models have been studied to allow for working directly on raw tree-structure data, However such learning models are limited to either a specific tree-topology or a specific tree-structured data format, e.g., synthetic parse trees. In this paper, we propose a novel framework for end-to-end learning on generic semantic tree-structured data of arbitrary topology and heterogeneous data types, such as data expressed in JSON, XML and so on. Motivated by the works in recursive and recurrent neural networks, we develop exemplar neural implementations of our framework for the JSON format. We evaluate our approach on several UCI benchmark datasets, including ablation and data-efficiency studies, and on a toy reinforcement learning task. Experimental results suggest that our framework yields comparable performance to use of standard models with dedicated feature-vectors in general, and even exceeds baseline performance in cases where compositional nature of the data is particularly important. The source code for a JSON-based implementation of our framework along with experiments can be downloaded at https://github.com/EndingCredits/json2vec.

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

Recent studies on AMR-to-text generation often formalize the task as a sequence-to-sequence (seq2seq) learning problem by converting an Abstract Meaning Representation (AMR) graph into a word sequence. Graph structures are further modeled into the seq2seq framework in order to utilize the structural information in the AMR graphs. However, previous approaches only consider the relations between directly connected concepts while ignoring the rich structure in AMR graphs. In this paper we eliminate such a strong limitation and propose a novel structure-aware self-attention approach to better modeling the relations between indirectly connected concepts in the state-of-the-art seq2seq model, i.e., the Transformer. In particular, a few different methods are explored to learn structural representations between two concepts. Experimental results on English AMR benchmark datasets show that our approach significantly outperforms the state of the art with 29.66 and 31.82 BLEU scores on LDC2015E86 and LDC2017T10, respectively. To the best of our knowledge, these are the best results achieved so far by supervised models on the benchmarks.

BERT (Bidirectional Encoder Representations from Transformers) has revolutionized the field of natural language processing through its exceptional performance on numerous tasks. Yet, the majority of researchers have mainly concentrated on enhancements related to the model structure, such as relative position embedding and more efficient attention mechanisms. Others have delved into pretraining tricks associated with Masked Language Modeling, including whole word masking. DeBERTa introduced an enhanced decoder adapted for BERT's encoder model for pretraining, proving to be highly effective. We argue that the design and research around enhanced masked language modeling decoders have been underappreciated. In this paper, we propose several designs of enhanced decoders and introduce DrBERT (Decoder-refined BERT), a novel method for modeling training. Typically, a pretrained BERT model is fine-tuned for specific Natural Language Understanding (NLU) tasks. In our approach, we utilize the original BERT model as the encoder, making only changes to the decoder without altering the encoder. This approach does not necessitate extensive modifications to the model's architecture and can be seamlessly integrated into existing fine-tuning pipelines and services, offering an efficient and effective enhancement strategy. Compared to other methods, while we also incur a moderate training cost for the decoder during the pretraining process, our approach does not introduce additional training costs during the fine-tuning phase. We test multiple enhanced decoder structures after pretraining and evaluate their performance on the GLUE benchmark. Our results demonstrate that DrBERT, having only undergone subtle refinements to the model structure during pretraining, significantly enhances model performance without escalating the inference time and serving budget.

In this paper, we describe our submission to the BabyLM Challenge 2023 shared task on data-efficient language model (LM) pretraining (Warstadt et al., 2023). We train transformer-based masked language models that incorporate unsupervised predictions about hierarchical sentence structure into the model architecture. Concretely, we use the Structformer architecture (Shen et al., 2021) and variants thereof. StructFormer models have been shown to perform well on unsupervised syntactic induction based on limited pretraining data, and to yield performance improvements over a vanilla transformer architecture (Shen et al., 2021). Evaluation of our models on 39 tasks provided by the BabyLM challenge shows promising improvements of models that integrate a hierarchical bias into the architecture at some particular tasks, even though they fail to consistently outperform the RoBERTa baseline model provided by the shared task organizers on all tasks.

With hundreds of thousands of language models available on Huggingface today, efficiently evaluating and utilizing these models across various downstream, tasks has become increasingly critical. Many existing methods repeatedly learn task-specific representations of Large Language Models (LLMs), which leads to inefficiencies in both time and computational resources. To address this, we propose EmbedLLM, a framework designed to learn compact vector representations, of LLMs that facilitate downstream applications involving many models, such as model routing. We introduce an encoder-decoder approach for learning such embeddings, along with a systematic framework to evaluate their effectiveness. Empirical results show that EmbedLLM outperforms prior methods in model routing both in accuracy and latency. Additionally, we demonstrate that our method can forecast a model's performance on multiple benchmarks, without incurring additional inference cost. Extensive probing experiments validate that the learned embeddings capture key model characteristics, e.g. whether the model is specialized for coding tasks, even without being explicitly trained on them. We open source our dataset, code and embedder to facilitate further research and application.

State-of-the-art vision-language models (VLMs) still have limited performance in structural knowledge extraction, such as relations between objects. In this work, we present ViStruct, a training framework to learn VLMs for effective visual structural knowledge extraction. Two novel designs are incorporated. First, we propose to leverage the inherent structure of programming language to depict visual structural information. This approach enables explicit and consistent representation of visual structural information of multiple granularities, such as concepts, relations, and events, in a well-organized structured format. Second, we introduce curriculum-based learning for VLMs to progressively comprehend visual structures, from fundamental visual concepts to intricate event structures. Our intuition is that lower-level knowledge may contribute to complex visual structure understanding. Furthermore, we compile and release a collection of datasets tailored for visual structural knowledge extraction. We adopt a weakly-supervised approach to directly generate visual event structures from captions for ViStruct training, capitalizing on abundant image-caption pairs from the web. In experiments, we evaluate ViStruct on visual structure prediction tasks, demonstrating its effectiveness in improving the understanding of visual structures. The code is public at https://github.com/Yangyi-Chen/vi-struct.

Transformer encoders are widely deployed in large-scale web services for natural language understanding tasks such as text classification, semantic retrieval, and content ranking. However, their high inference latency and memory consumption pose significant challenges for real-time serving and scalability. These limitations stem largely from architectural redundancy, particularly in the attention module. The inherent parameter redundancy of the attention mechanism, coupled with the fact that its attention heads operate with a degree of independence, makes it particularly amenable to structured model compression. In this paper, we propose SHRP (Specialized Head Routing and Pruning), a novel structured pruning framework that automatically identifies and removes redundant attention heads while preserving most of the model's accuracy and compatibility. SHRP introduces Expert Attention, a modular design that treats each attention head as an independent expert, followed by a lightweight shared expander feed-forward network that refines their outputs. The framework employs a unified Top-1 usage-driven mechanism to jointly perform dynamic routing during training and deterministic pruning at deployment. Experimental results on the GLUE benchmark using a BERT-base encoder show that SHRP achieves 93% of the original model accuracy while reducing parameters by 48 percent. Under an extreme compression scenario where 11/12 of the layers are pruned, the model still maintains 84% accuracy and delivers a 4.2x throughput gain while reducing computation to as low as 11.5 percent of the original FLOPs, demonstrating its practical utility for large-scale and latency-sensitive web deployments.

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

Strong inductive biases enable learning from little data and help generalization outside of the training distribution. Popular neural architectures such as Transformers lack strong structural inductive biases for seq2seq NLP tasks on their own. Consequently, they struggle with systematic generalization beyond the training distribution, e.g. with extrapolating to longer inputs, even when pre-trained on large amounts of text. We show how a structural inductive bias can be efficiently injected into a seq2seq model by pre-training it to simulate structural transformations on synthetic data. Specifically, we inject an inductive bias towards Finite State Transducers (FSTs) into a Transformer by pre-training it to simulate FSTs given their descriptions. Our experiments show that our method imparts the desired inductive bias, resulting in improved systematic generalization and better few-shot learning for FST-like tasks. Our analysis shows that fine-tuned models accurately capture the state dynamics of the unseen underlying FSTs, suggesting that the simulation process is internalized by the fine-tuned model.

Understanding the locus of semantic representation in large language models (LLMs) is crucial for interpretability and architectural innovation. The dominant paradigm posits that trainable input embeddings serve as foundational "meaning vectors." This paper challenges that view. We construct Transformer models where the embedding layer is entirely frozen, with vectors derived not from data, but from the visual structure of Unicode glyphs. These non-semantic, precomputed visual embeddings are fixed throughout training. Our method is compatible with any tokenizer, including a novel Unicode-centric tokenizer we introduce to ensure universal text coverage. Despite the absence of trainable, semantically initialized embeddings, our models converge, generate coherent text, and, critically, outperform architecturally identical models with trainable embeddings on the MMLU reasoning benchmark. We attribute this to "representational interference" in conventional models, where the embedding layer is burdened with learning both structural and semantic features. Our results indicate that high-level semantics are not inherent to input embeddings but are an emergent property of the Transformer's compositional architecture and data scale. This reframes the role of embeddings from meaning containers to structural primitives. We release all code and models to foster further research.

Relational tables on the Web store a vast amount of knowledge. Owing to the wealth of such tables, there has been tremendous progress on a variety of tasks in the area of table understanding. However, existing work generally relies on heavily-engineered task-specific features and model architectures. In this paper, we present TURL, a novel framework that introduces the pre-training/fine-tuning paradigm to relational Web tables. During pre-training, our framework learns deep contextualized representations on relational tables in an unsupervised manner. Its universal model design with pre-trained representations can be applied to a wide range of tasks with minimal task-specific fine-tuning. Specifically, we propose a structure-aware Transformer encoder to model the row-column structure of relational tables, and present a new Masked Entity Recovery (MER) objective for pre-training to capture the semantics and knowledge in large-scale unlabeled data. We systematically evaluate TURL with a benchmark consisting of 6 different tasks for table understanding (e.g., relation extraction, cell filling). We show that TURL generalizes well to all tasks and substantially outperforms existing methods in almost all instances.

We present models for encoding sentences into embedding vectors that specifically target transfer learning to other NLP tasks. The models are efficient and result in accurate performance on diverse transfer tasks. Two variants of the encoding models allow for trade-offs between accuracy and compute resources. For both variants, we investigate and report the relationship between model complexity, resource consumption, the availability of transfer task training data, and task performance. Comparisons are made with baselines that use word level transfer learning via pretrained word embeddings as well as baselines do not use any transfer learning. We find that transfer learning using sentence embeddings tends to outperform word level transfer. With transfer learning via sentence embeddings, we observe surprisingly good performance with minimal amounts of supervised training data for a transfer task. We obtain encouraging results on Word Embedding Association Tests (WEAT) targeted at detecting model bias. Our pre-trained sentence encoding models are made freely available for download and on TF Hub.

Despite the fast developmental pace of new sentence embedding methods, it is still challenging to find comprehensive evaluations of these different techniques. In the past years, we saw significant improvements in the field of sentence embeddings and especially towards the development of universal sentence encoders that could provide inductive transfer to a wide variety of downstream tasks. In this work, we perform a comprehensive evaluation of recent methods using a wide variety of downstream and linguistic feature probing tasks. We show that a simple approach using bag-of-words with a recently introduced language model for deep context-dependent word embeddings proved to yield better results in many tasks when compared to sentence encoders trained on entailment datasets. We also show, however, that we are still far away from a universal encoder that can perform consistently across several downstream tasks.

Automatic bundle construction is a crucial prerequisite step in various bundle-aware online services. Previous approaches are mostly designed to model the bundling strategy of existing bundles. However, it is hard to acquire large-scale well-curated bundle dataset, especially for those platforms that have not offered bundle services before. Even for platforms with mature bundle services, there are still many items that are included in few or even zero bundles, which give rise to sparsity and cold-start challenges in the bundle construction models. To tackle these issues, we target at leveraging multimodal features, item-level user feedback signals, and the bundle composition information, to achieve a comprehensive formulation of bundle construction. Nevertheless, such formulation poses two new technical challenges: 1) how to learn effective representations by optimally unifying multiple features, and 2) how to address the problems of modality missing, noise, and sparsity problems induced by the incomplete query bundles. In this work, to address these technical challenges, we propose a Contrastive Learning-enhanced Hierarchical Encoder method (CLHE). Specifically, we use self-attention modules to combine the multimodal and multi-item features, and then leverage both item- and bundle-level contrastive learning to enhance the representation learning, thus to counter the modality missing, noise, and sparsity problems. Extensive experiments on four datasets in two application domains demonstrate that our method outperforms a list of SOTA methods. The code and dataset are available at https://github.com/Xiaohao-Liu/CLHE.

Spatial pyramid pooling module or encode-decoder structure are used in deep neural networks for semantic segmentation task. The former networks are able to encode multi-scale contextual information by probing the incoming features with filters or pooling operations at multiple rates and multiple effective fields-of-view, while the latter networks can capture sharper object boundaries by gradually recovering the spatial information. In this work, we propose to combine the advantages from both methods. Specifically, our proposed model, DeepLabv3+, extends DeepLabv3 by adding a simple yet effective decoder module to refine the segmentation results especially along object boundaries. We further explore the Xception model and apply the depthwise separable convolution to both Atrous Spatial Pyramid Pooling and decoder modules, resulting in a faster and stronger encoder-decoder network. We demonstrate the effectiveness of the proposed model on PASCAL VOC 2012 and Cityscapes datasets, achieving the test set performance of 89.0\% and 82.1\% without any post-processing. Our paper is accompanied with a publicly available reference implementation of the proposed models in Tensorflow at https://github.com/tensorflow/models/tree/master/research/deeplab.

Large language models (LLMs) excel in language tasks, especially with supervised fine-tuning after pre-training. However, their substantial memory and computational requirements hinder practical applications. Structural pruning, which reduces less significant weight dimensions, is one solution. Yet, traditional post-hoc pruning often leads to significant performance loss, with limited recovery from further fine-tuning due to reduced capacity. Since the model fine-tuning refines the general and chaotic knowledge in pre-trained models, we aim to incorporate structural pruning with the fine-tuning, and propose the Pruning-Aware Tuning (PAT) paradigm to eliminate model redundancy while preserving the model performance to the maximum extend. Specifically, we insert the innovative Hybrid Sparsification Modules (HSMs) between the Attention and FFN components to accordingly sparsify the upstream and downstream linear modules. The HSM comprises a lightweight operator and a globally shared trainable mask. The lightweight operator maintains a training overhead comparable to that of LoRA, while the trainable mask unifies the channels to be sparsified, ensuring structural pruning. Additionally, we propose the Identity Loss which decouples the transformation and scaling properties of the HSMs to enhance training robustness. Extensive experiments demonstrate that PAT excels in both performance and efficiency. For example, our Llama2-7b model with a 25\% pruning ratio achieves 1.33times speedup while outperforming the LoRA-finetuned model by up to 1.26\% in accuracy with a similar training cost. Code: https://github.com/kriskrisliu/PAT_Pruning-Aware-Tuning

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.

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

Transformers generalize to novel compositions of structures and entities after being trained on a complex dataset, but easily overfit on datasets of insufficient complexity. We observe that when the training set is sufficiently complex, the model encodes sentences that have a common syntactic structure using a systematic attention pattern. Inspired by this observation, we propose SQ-Transformer (Structurally Quantized) that explicitly encourages systematicity in the embeddings and attention layers, even with a training set of low complexity. At the embedding level, we introduce Structure-oriented Vector Quantization (SoVQ) to cluster word embeddings into several classes of structurally equivalent entities. At the attention level, we devise the Systematic Attention Layer (SAL) and an alternative, Systematically Regularized Layer (SRL) that operate on the quantized word embeddings so that sentences of the same structure are encoded with invariant or similar attention patterns. Empirically, we show that SQ-Transformer achieves stronger compositional generalization than the vanilla Transformer on multiple low-complexity semantic parsing and machine translation datasets. In our analysis, we show that SoVQ indeed learns a syntactically clustered embedding space and SAL/SRL induces generalizable attention patterns, which lead to improved systematicity.

We study speech intent classification and slot filling (SICSF) by proposing to use an encoder pretrained on speech recognition (ASR) to initialize an end-to-end (E2E) Conformer-Transformer model, which achieves the new state-of-the-art results on the SLURP dataset, with 90.14% intent accuracy and 82.27% SLURP-F1. We compare our model with encoders pretrained on self-supervised learning (SSL), and show that ASR pretraining is much more effective than SSL for SICSF. To explore parameter efficiency, we freeze the encoder and add Adapter modules, and show that parameter efficiency is only achievable with an ASR-pretrained encoder, while the SSL encoder needs full finetuning to achieve comparable results. In addition, we provide an in-depth comparison on end-to-end models versus cascading models (ASR+NLU), and show that E2E models are better than cascaded models unless an oracle ASR model is provided. Last but not least, our model is the first E2E model that achieves the same performance as cascading models with oracle ASR. Code, checkpoints and configs are available.

Although graph-based learning has attracted a lot of attention, graph representation learning is still a challenging task whose resolution may impact key application fields such as chemistry or biology. To this end, we introduce GRALE, a novel graph autoencoder that encodes and decodes graphs of varying sizes into a shared embedding space. GRALE is trained using an Optimal Transport-inspired loss that compares the original and reconstructed graphs and leverages a differentiable node matching module, which is trained jointly with the encoder and decoder. The proposed attention-based architecture relies on Evoformer, the core component of AlphaFold, which we extend to support both graph encoding and decoding. We show, in numerical experiments on simulated and molecular data, that GRALE enables a highly general form of pre-training, applicable to a wide range of downstream tasks, from classification and regression to more complex tasks such as graph interpolation, editing, matching, and prediction.

Language models have the ability to perform in-context learning (ICL), allowing them to flexibly adapt their behavior based on context. This contrasts with in-weights learning, where information is statically encoded in model parameters from iterated observations of the data. Despite this apparent ability to learn in-context, language models are known to struggle when faced with unseen or rarely seen tokens. Hence, we study structural in-context learning, which we define as the ability of a model to execute in-context learning on arbitrary tokens -- so called because the model must generalize on the basis of e.g. sentence structure or task structure, rather than semantic content encoded in token embeddings. An ideal model would be able to do both: flexibly deploy in-weights operations (in order to robustly accommodate ambiguous or unknown contexts using encoded semantic information) and structural in-context operations (in order to accommodate novel tokens). We study structural in-context algorithms in a simple part-of-speech setting using both practical and toy models. We find that active forgetting, a technique that was recently introduced to help models generalize to new languages, forces models to adopt structural in-context learning solutions. Finally, we introduce temporary forgetting, a straightforward extension of active forgetting that enables one to control how much a model relies on in-weights vs. in-context solutions. Importantly, temporary forgetting allows us to induce a dual process strategy where in-context and in-weights solutions coexist within a single model.

General-purpose multilingual vector representations, used in retrieval, regression and classification, are traditionally obtained from bidirectional encoder models. Despite their wide applicability, encoders have been recently overshadowed by advances in generative decoder-only models. However, many innovations driving this progress are not inherently tied to decoders. In this paper, we revisit the development of multilingual encoders through the lens of these advances, and introduce EuroBERT, a family of multilingual encoders covering European and widely spoken global languages. Our models outperform existing alternatives across a diverse range of tasks, spanning multilingual capabilities, mathematics, and coding, and natively supporting sequences of up to 8,192 tokens. We also examine the design decisions behind EuroBERT, offering insights into our dataset composition and training pipeline. We publicly release the EuroBERT models, including intermediate training checkpoints, together with our training framework.

Deploying language models often requires handling model size vs. performance trade-offs to satisfy downstream latency constraints while preserving the model's usefulness. Model distillation is commonly employed to reduce model size while maintaining acceptable performance. However, distillation can be inefficient since it involves multiple training steps. In this work, we introduce MODULARSTARENCODER, a modular multi-exit encoder with 1B parameters, useful for multiple tasks within the scope of code retrieval. MODULARSTARENCODER is trained with a novel self-distillation mechanism that significantly improves lower-layer representations-allowing different portions of the model to be used while still maintaining a good trade-off in terms of performance. Our architecture focuses on enhancing text-to-code and code-to-code search by systematically capturing syntactic and semantic structures across multiple levels of representation. Specific encoder layers are targeted as exit heads, allowing higher layers to guide earlier layers during training. This self-distillation effect improves intermediate representations, increasing retrieval recall at no extra training cost. In addition to the multi-exit scheme, our approach integrates a repository-level contextual loss that maximally utilizes the training context window, further enhancing the learned representations. We also release a new dataset constructed via code translation, seamlessly expanding traditional text-to-code benchmarks with code-to-code pairs across diverse programming languages. Experimental results highlight the benefits of self-distillation through multi-exit supervision.

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.

Hypothesis. Artificial general intelligence is, at its core, a compression problem. Effective compression demands resonance: deep learning scales best when its architecture aligns with the fundamental structure of the data. These are the fundamental principles. Yet, modern vision architectures have strayed from these truths: visual signals are highly redundant, while discriminative information, the surprise, is sparse. Current models process dense pixel grids uniformly, wasting vast compute on static background rather than focusing on the predictive residuals that define motion and meaning. We argue that to solve visual understanding, we must align our architectures with the information-theoretic principles of video, i.e., Codecs. Method. OneVision-Encoder encodes video by compressing predictive visual structure into semantic meaning. By adopting Codec Patchification, OV-Encoder abandons uniform computation to focus exclusively on the 3.1%-25% of regions rich in signal entropy. To unify spatial and temporal reasoning under irregular token layouts, OneVision-Encoder employs a shared 3D RoPE and is trained with a large-scale cluster discrimination objective over more than one million semantic concepts, jointly capturing object permanence and motion dynamics. Evidence. The results validate our core hypothesis: efficiency and accuracy are not a trade-off; they are positively correlated. When integrated into LLM, it consistently outperforms strong vision backbones such as Qwen3-ViT and SigLIP2 across 16 image, video, and document understanding benchmarks, despite using substantially fewer visual tokens and pretraining data. Notably, on video understanding tasks, OV-Encoder achieves an average improvement of 4.1% over Qwen3-ViT. Codec-aligned, patch-level sparsity is a foundational principle, enabling OV-Encoder as a scalable engine for next-generation visual generalists.

Modern learning frameworks often train deep neural networks with massive amounts of unlabeled data to learn representations by solving simple pretext tasks, then use the representations as foundations for downstream tasks. These networks are empirically designed; as such, they are usually not interpretable, their representations are not structured, and their designs are potentially redundant. White-box deep networks, in which each layer explicitly identifies and transforms structures in the data, present a promising alternative. However, existing white-box architectures have only been shown to work at scale in supervised settings with labeled data, such as classification. In this work, we provide the first instantiation of the white-box design paradigm that can be applied to large-scale unsupervised representation learning. We do this by exploiting a fundamental connection between diffusion, compression, and (masked) completion, deriving a deep transformer-like masked autoencoder architecture, called CRATE-MAE, in which the role of each layer is mathematically fully interpretable: they transform the data distribution to and from a structured representation. Extensive empirical evaluations confirm our analytical insights. CRATE-MAE demonstrates highly promising performance on large-scale imagery datasets while using only ~30% of the parameters compared to the standard masked autoencoder with the same model configuration. The representations learned by CRATE-MAE have explicit structure and also contain semantic meaning. Code is available at https://github.com/Ma-Lab-Berkeley/CRATE .

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

We introduce Image2Struct, a benchmark to evaluate vision-language models (VLMs) on extracting structure from images. Our benchmark 1) captures real-world use cases, 2) is fully automatic and does not require human judgment, and 3) is based on a renewable stream of fresh data. In Image2Struct, VLMs are prompted to generate the underlying structure (e.g., LaTeX code or HTML) from an input image (e.g., webpage screenshot). The structure is then rendered to produce an output image (e.g., rendered webpage), which is compared against the input image to produce a similarity score. This round-trip evaluation allows us to quantitatively evaluate VLMs on tasks with multiple valid structures. We create a pipeline that downloads fresh data from active online communities upon execution and evaluates the VLMs without human intervention. We introduce three domains (Webpages, LaTeX, and Musical Scores) and use five image metrics (pixel similarity, cosine similarity between the Inception vectors, learned perceptual image patch similarity, structural similarity index measure, and earth mover similarity) that allow efficient and automatic comparison between pairs of images. We evaluate Image2Struct on 14 prominent VLMs and find that scores vary widely, indicating that Image2Struct can differentiate between the performances of different VLMs. Additionally, the best score varies considerably across domains (e.g., 0.402 on sheet music vs. 0.830 on LaTeX equations), indicating that Image2Struct contains tasks of varying difficulty. For transparency, we release the full results at https://crfm.stanford.edu/helm/image2struct/v1.0.1/.

GNN-to-MLP distillation aims to utilize knowledge distillation (KD) to learn computationally-efficient multi-layer perceptron (student MLP) on graph data by mimicking the output representations of teacher GNN. Existing methods mainly make the MLP to mimic the GNN predictions over a few class labels. However, the class space may not be expressive enough for covering numerous diverse local graph structures, thus limiting the performance of knowledge transfer from GNN to MLP. To address this issue, we propose to learn a new powerful graph representation space by directly labeling nodes' diverse local structures for GNN-to-MLP distillation. Specifically, we propose a variant of VQ-VAE to learn a structure-aware tokenizer on graph data that can encode each node's local substructure as a discrete code. The discrete codes constitute a codebook as a new graph representation space that is able to identify different local graph structures of nodes with the corresponding code indices. Then, based on the learned codebook, we propose a new distillation target, namely soft code assignments, to directly transfer the structural knowledge of each node from GNN to MLP. The resulting framework VQGraph achieves new state-of-the-art performance on GNN-to-MLP distillation in both transductive and inductive settings across seven graph datasets. We show that VQGraph with better performance infers faster than GNNs by 828x, and also achieves accuracy improvement over GNNs and stand-alone MLPs by 3.90% and 28.05% on average, respectively. Code: https://github.com/YangLing0818/VQGraph.

Code retrieval is a crucial component in modern software development, particularly in large-scale projects. However, existing approaches relying on sequence-based models often fail to fully exploit the structural dependencies inherent in code, leading to suboptimal retrieval performance, particularly with structurally complex code fragments. In this paper, we introduce GNN-Coder, a novel framework based on Graph Neural Network (GNN) to utilize Abstract Syntax Tree (AST). We make the first attempt to study how GNN-integrated Transformer can promote the development of semantic retrieval tasks by capturing the structural and semantic features of code. We further propose an innovative graph pooling method tailored for AST, utilizing the number of child nodes as a key feature to highlight the intrinsic topological relationships within the AST. This design effectively integrates both sequential and hierarchical representations, enhancing the model's ability to capture code structure and semantics. Additionally, we introduce the Mean Angular Margin (MAM), a novel metric for quantifying the uniformity of code embedding distributions, providing a standardized measure of feature separability. The proposed method achieves a lower MAM, indicating a more discriminative feature representation. This underscores GNN-Coder's superior ability to distinguish between code snippets, thereby enhancing retrieval accuracy. Experimental results show that GNN-Coder significantly boosts retrieval performance, with a 1\%-10\% improvement in MRR on the CSN dataset, and a notable 20\% gain in zero-shot performance on the CosQA dataset.