Daily Papers

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.

Pretrained contextualized embeddings are powerful word representations for structured prediction tasks. Recent work found that better word representations can be obtained by concatenating different types of embeddings. However, the selection of embeddings to form the best concatenated representation usually varies depending on the task and the collection of candidate embeddings, and the ever-increasing number of embedding types makes it a more difficult problem. In this paper, we propose Automated Concatenation of Embeddings (ACE) to automate the process of finding better concatenations of embeddings for structured prediction tasks, based on a formulation inspired by recent progress on neural architecture search. Specifically, a controller alternately samples a concatenation of embeddings, according to its current belief of the effectiveness of individual embedding types in consideration for a task, and updates the belief based on a reward. We follow strategies in reinforcement learning to optimize the parameters of the controller and compute the reward based on the accuracy of a task model, which is fed with the sampled concatenation as input and trained on a task dataset. Empirical results on 6 tasks and 21 datasets show that our approach outperforms strong baselines and achieves state-of-the-art performance with fine-tuned embeddings in all the evaluations.

In this paper, we study the problem of inference in high-order structured prediction tasks. In the context of Markov random fields, the goal of a high-order inference task is to maximize a score function on the space of labels, and the score function can be decomposed into sum of unary and high-order potentials. We apply a generative model approach to study the problem of high-order inference, and provide a two-stage convex optimization algorithm for exact label recovery. We also provide a new class of hypergraph structural properties related to hyperedge expansion that drives the success in general high-order inference problems. Finally, we connect the performance of our algorithm and the hyperedge expansion property using a novel hypergraph Cheeger-type inequality.

Recently, binary representation has been proposed as a novel representation that lies between continuous and discrete representations. It exhibits considerable information-preserving capability when being used to replace continuous input vectors. In this paper, we investigate the feasibility of further introducing it to the output side, aiming to allow models to output binary labels instead. To preserve the structural information on the output side along with label information, we extend the previous contrastive hashing method as structured contrastive hashing. More specifically, we upgrade CKY from label-level to bit-level, define a new similarity function with span marginal probabilities, and introduce a novel contrastive loss function with a carefully designed instance selection strategy. Our model achieves competitive performance on various structured prediction tasks, and demonstrates that binary representation can be considered a novel representation that further bridges the gap between the continuous nature of deep learning and the discrete intrinsic property of natural languages.

Large language models (LLMs) effectively generate fluent text when the target output follows natural language patterns. However, structured prediction tasks confine the output format to a limited ontology, causing even very large models to struggle since they were never trained with such restrictions in mind. The difficulty of using LLMs for direct prediction is exacerbated in few-shot learning scenarios, which commonly arise due to domain shift and resource limitations. We flip the problem on its head by leveraging the LLM as a tool for data augmentation rather than direct prediction. Our proposed Mixture of Soft Prompts (MSP) serves as a parameter-efficient procedure for generating data in a controlled manner. Denoising mechanisms are further applied to improve the quality of synthesized data. Automatic metrics show our method is capable of producing diverse and natural text, while preserving label semantics. Moreover, MSP achieves state-of-the-art results on three benchmarks when compared against strong baselines. Our method offers an alternate data-centric approach for applying LLMs to complex prediction tasks.

Pose Machines provide a sequential prediction framework for learning rich implicit spatial models. In this work we show a systematic design for how convolutional networks can be incorporated into the pose machine framework for learning image features and image-dependent spatial models for the task of pose estimation. The contribution of this paper is to implicitly model long-range dependencies between variables in structured prediction tasks such as articulated pose estimation. We achieve this by designing a sequential architecture composed of convolutional networks that directly operate on belief maps from previous stages, producing increasingly refined estimates for part locations, without the need for explicit graphical model-style inference. Our approach addresses the characteristic difficulty of vanishing gradients during training by providing a natural learning objective function that enforces intermediate supervision, thereby replenishing back-propagated gradients and conditioning the learning procedure. We demonstrate state-of-the-art performance and outperform competing methods on standard benchmarks including the MPII, LSP, and FLIC datasets.

A major challenge in structured prediction is to represent the interdependencies within output structures. When outputs are structured as sequences, linear-chain conditional random fields (CRFs) are a widely used model class which can learn local dependencies in the output. However, the CRF's Markov assumption makes it impossible for CRFs to represent distributions with nonlocal dependencies, and standard CRFs are unable to respect nonlocal constraints of the data (such as global arity constraints on output labels). We present a generalization of CRFs that can enforce a broad class of constraints, including nonlocal ones, by specifying the space of possible output structures as a regular language L. The resulting regular-constrained CRF (RegCCRF) has the same formal properties as a standard CRF, but assigns zero probability to all label sequences not in L. Notably, RegCCRFs can incorporate their constraints during training, while related models only enforce constraints during decoding. We prove that constrained training is never worse than constrained decoding, and show empirically that it can be substantially better in practice. Additionally, we demonstrate a practical benefit on downstream tasks by incorporating a RegCCRF into a deep neural model for semantic role labeling, exceeding state-of-the-art results on a standard dataset.

Large Language Models (LLMs) stand at the forefront of a number of Natural Language Processing (NLP) tasks. Despite the widespread adoption of LLMs in NLP, much of their potential in broader fields remains largely unexplored, and significant limitations persist in their design and implementation. Notably, LLMs struggle with structured data, such as graphs, and often falter when tasked with answering domain-specific questions requiring deep expertise, such as those in biology and chemistry. In this paper, we explore a fundamental question: Can LLMs effectively handle molecule prediction tasks? Rather than pursuing top-tier performance, our goal is to assess how LLMs can contribute to diverse molecule tasks. We identify several classification and regression prediction tasks across six standard molecule datasets. Subsequently, we carefully design a set of prompts to query LLMs on these tasks and compare their performance with existing Machine Learning (ML) models, which include text-based models and those specifically designed for analysing the geometric structure of molecules. Our investigation reveals several key insights: Firstly, LLMs generally lag behind ML models in achieving competitive performance on molecule tasks, particularly when compared to models adept at capturing the geometric structure of molecules, highlighting the constrained ability of LLMs to comprehend graph data. Secondly, LLMs show promise in enhancing the performance of ML models when used collaboratively. Lastly, we engage in a discourse regarding the challenges and promising avenues to harness LLMs for molecule prediction tasks. The code and models are available at https://github.com/zhiqiangzhongddu/LLMaMol.

This paper introduces Graph Convolutional Recurrent Network (GCRN), a deep learning model able to predict structured sequences of data. Precisely, GCRN is a generalization of classical recurrent neural networks (RNN) to data structured by an arbitrary graph. Such structured sequences can represent series of frames in videos, spatio-temporal measurements on a network of sensors, or random walks on a vocabulary graph for natural language modeling. The proposed model combines convolutional neural networks (CNN) on graphs to identify spatial structures and RNN to find dynamic patterns. We study two possible architectures of GCRN, and apply the models to two practical problems: predicting moving MNIST data, and modeling natural language with the Penn Treebank dataset. Experiments show that exploiting simultaneously graph spatial and dynamic information about data can improve both precision and learning speed.

We present a self-supervised, time-to-event (TTE) foundation model called MOTOR (Many Outcome Time Oriented Representations) which is pretrained on timestamped sequences of events in electronic health records (EHR) and health insurance claims. TTE models are used for estimating the probability distribution of the time until a specific event occurs, which is an important task in medical settings. TTE models provide many advantages over classification using fixed time horizons, including naturally handling censored observations, but are challenging to train with limited labeled data. MOTOR addresses this challenge by pretraining on up to 55M patient records (9B clinical events). We evaluate MOTOR's transfer learning performance on 19 tasks, across 3 patient databases (a private EHR system, MIMIC-IV, and Merative claims data). Task-specific models adapted from MOTOR improve time-dependent C statistics by 4.6% over state-of-the-art, improve label efficiency by up to 95% ,and are more robust to temporal distributional shifts. We further evaluate cross-site portability by adapting our MOTOR foundation model for six prediction tasks on the MIMIC-IV dataset, where it outperforms all baselines. MOTOR is the first foundation model for medical TTE predictions and we release a 143M parameter pretrained model for research use at [redacted URL].

Structured variational autoencoders (SVAEs) combine probabilistic graphical model priors on latent variables, deep neural networks to link latent variables to observed data, and structure-exploiting algorithms for approximate posterior inference. These models are particularly appealing for sequential data, where the prior can capture temporal dependencies. However, despite their conceptual elegance, SVAEs have proven difficult to implement, and more general approaches have been favored in practice. Here, we revisit SVAEs using modern machine learning tools and demonstrate their advantages over more general alternatives in terms of both accuracy and efficiency. First, we develop a modern implementation for hardware acceleration, parallelization, and automatic differentiation of the message passing algorithms at the core of the SVAE. Second, we show that by exploiting structure in the prior, the SVAE learns more accurate models and posterior distributions, which translate into improved performance on prediction tasks. Third, we show how the SVAE can naturally handle missing data, and we leverage this ability to develop a novel, self-supervised training approach. Altogether, these results show that the time is ripe to revisit structured variational autoencoders.

Expressing confidence is challenging for embodied agents navigating dynamic multimodal environments, where uncertainty arises from both perception and decision-making processes. We present the first work investigating embodied confidence elicitation in open-ended multimodal environments. We introduce Elicitation Policies, which structure confidence assessment across inductive, deductive, and abductive reasoning, along with Execution Policies, which enhance confidence calibration through scenario reinterpretation, action sampling, and hypothetical reasoning. Evaluating agents in calibration and failure prediction tasks within the Minecraft environment, we show that structured reasoning approaches, such as Chain-of-Thoughts, improve confidence calibration. However, our findings also reveal persistent challenges in distinguishing uncertainty, particularly under abductive settings, underscoring the need for more sophisticated embodied confidence elicitation methods.

Improving large language models (LLMs) for electronic health record (EHR) reasoning is essential for enabling accurate and generalizable clinical predictions. While LLMs excel at medical text understanding, they underperform on EHR-based prediction tasks due to challenges in modeling temporally structured, high-dimensional data. Existing approaches often rely on hybrid paradigms, where LLMs serve merely as frozen prior retrievers while downstream deep learning (DL) models handle prediction, failing to improve the LLM's intrinsic reasoning capacity and inheriting the generalization limitations of DL models. To this end, we propose EAG-RL, a novel two-stage training framework designed to intrinsically enhance LLMs' EHR reasoning ability through expert attention guidance, where expert EHR models refer to task-specific DL models trained on EHR data. Concretely, EAG-RL first constructs high-quality, stepwise reasoning trajectories using expert-guided Monte Carlo Tree Search to effectively initialize the LLM's policy. Then, EAG-RL further optimizes the policy via reinforcement learning by aligning the LLM's attention with clinically salient features identified by expert EHR models. Extensive experiments on two real-world EHR datasets show that EAG-RL improves the intrinsic EHR reasoning ability of LLMs by an average of 14.62%, while also enhancing robustness to feature perturbations and generalization to unseen clinical domains. These results demonstrate the practical potential of EAG-RL for real-world deployment in clinical prediction tasks. Our code have been available at https://github.com/devilran6/EAG-RL.

Despite recent advances in large language models (LLMs), most QA benchmarks are still confined to single-paragraph or single-document settings, failing to capture the complexity of real-world information-seeking tasks. Practical QA often requires multi-hop reasoning over information distributed across multiple documents, modalities, and structural formats. Although prior datasets made progress in this area, they rely heavily on Wikipedia-based content and unimodal plain text, with shallow reasoning paths that typically produce brief phrase-level or single-sentence answers, thus limiting their realism and generalizability. We propose DocHop-QA, a large-scale benchmark comprising 11,379 QA instances for multimodal, multi-document, multi-hop question answering. Constructed from publicly available scientific documents sourced from PubMed, DocHop-QA is domain-agnostic and incorporates diverse information formats, including textual passages, tables, and structural layout cues. Unlike existing datasets, DocHop-QA does not rely on explicitly hyperlinked documents; instead, it supports open-ended reasoning through semantic similarity and layout-aware evidence synthesis. To scale realistic QA construction, we designed an LLM-driven pipeline grounded in 11 high-frequency scientific question concepts. We evaluated DocHop-QA through four tasks spanning structured index prediction, generative answering, and multimodal integration, reflecting both discriminative and generative paradigms. These tasks demonstrate DocHop-QA's capacity to support complex, multimodal reasoning across multiple documents.

Categorical variables are a natural choice for representing discrete structure in the world. However, stochastic neural networks rarely use categorical latent variables due to the inability to backpropagate through samples. In this work, we present an efficient gradient estimator that replaces the non-differentiable sample from a categorical distribution with a differentiable sample from a novel Gumbel-Softmax distribution. This distribution has the essential property that it can be smoothly annealed into a categorical distribution. We show that our Gumbel-Softmax estimator outperforms state-of-the-art gradient estimators on structured output prediction and unsupervised generative modeling tasks with categorical latent variables, and enables large speedups on semi-supervised classification.

Visual Planning for Assistance (VPA) aims to predict a sequence of user actions required to achieve a specified goal based on a video showing the user's progress. Although recent advances in multimodal large language models (MLLMs) have shown promising results in video understanding, long-horizon visual planning remains a challenging problem. We identify two challenges in training large MLLMs for video-based planning tasks: (1) scarcity of procedural annotations, limiting the model's ability to learn procedural task dynamics effectively, and (2) inefficiency of next-token prediction objective to explicitly capture the structured action space for visual planning when compared to free-form, natural language. To tackle data scarcity, we introduce Auxiliary Task Augmentation. We design and train our model on auxiliary tasks relevant to long-horizon video-based planning (e.g., goal prediction) to augment the model's planning ability. To more explicitly model the structured action space unique to visual planning tasks, we leverage Multi-token Prediction, extending traditional next-token prediction by using multiple heads to predict multiple future tokens during training. Our approach, VideoPlan, achieves state-of-the-art VPA performance on the COIN and CrossTask datasets, surpassing prior methods by 7.3% and 3.4%, respectively, when predicting 3 future actions. We further extend our method to the challenging Ego4D Long-term Action Anticipation task, and show that it is on par with the state-of-the-art approaches despite not using specialized egocentric features. Code will be made available.

Automating legal document drafting can significantly enhance efficiency, reduce manual effort, and streamline legal workflows. While prior research has explored tasks such as judgment prediction and case summarization, the structured generation of private legal documents in the Indian legal domain remains largely unaddressed. To bridge this gap, we introduce VidhikDastaavej, a novel, anonymized dataset of private legal documents, and develop NyayaShilp, a fine-tuned legal document generation model specifically adapted to Indian legal texts. We propose a Model-Agnostic Wrapper (MAW), a two-step framework that first generates structured section titles and then iteratively produces content while leveraging retrieval-based mechanisms to ensure coherence and factual accuracy. We benchmark multiple open-source LLMs, including instruction-tuned and domain-adapted versions, alongside proprietary models for comparison. Our findings indicate that while direct fine-tuning on small datasets does not always yield improvements, our structured wrapper significantly enhances coherence, factual adherence, and overall document quality while mitigating hallucinations. To ensure real-world applicability, we developed a Human-in-the-Loop (HITL) Document Generation System, an interactive user interface that enables users to specify document types, refine section details, and generate structured legal drafts. This tool allows legal professionals and researchers to generate, validate, and refine AI-generated legal documents efficiently. Extensive evaluations, including expert assessments, confirm that our framework achieves high reliability in structured legal drafting. This research establishes a scalable and adaptable foundation for AI-assisted legal drafting in India, offering an effective approach to structured legal document generation.

The complexity and variability inherent in high-resolution pathological images present significant challenges in computational pathology. While pathology foundation models leveraging AI have catalyzed transformative advancements, their development demands large-scale datasets, considerable storage capacity, and substantial computational resources. Furthermore, ensuring their clinical applicability and generalizability requires rigorous validation across a broad spectrum of clinical tasks. Here, we present PathOrchestra, a versatile pathology foundation model trained via self-supervised learning on a dataset comprising 300K pathological slides from 20 tissue and organ types across multiple centers. The model was rigorously evaluated on 112 clinical tasks using a combination of 61 private and 51 public datasets. These tasks encompass digital slide preprocessing, pan-cancer classification, lesion identification, multi-cancer subtype classification, biomarker assessment, gene expression prediction, and the generation of structured reports. PathOrchestra demonstrated exceptional performance across 27,755 WSIs and 9,415,729 ROIs, achieving over 0.950 accuracy in 47 tasks, including pan-cancer classification across various organs, lymphoma subtype diagnosis, and bladder cancer screening. Notably, it is the first model to generate structured reports for high-incidence colorectal cancer and diagnostically complex lymphoma-areas that are infrequently addressed by foundational models but hold immense clinical potential. Overall, PathOrchestra exemplifies the feasibility and efficacy of a large-scale, self-supervised pathology foundation model, validated across a broad range of clinical-grade tasks. Its high accuracy and reduced reliance on extensive data annotation underline its potential for clinical integration, offering a pathway toward more efficient and high-quality medical services.

We argue that progress toward general intelligence requires complementary foundation models grounded in language, the physical world, and structured data. This report presents LimiX, the first installment of our large structured-data models (LDMs). LimiX treats structured data as a joint distribution over variables and missingness, thus capable of addressing a wide range of tabular tasks through query-based conditional prediction via a single model. LimiX is pretrained using masked joint-distribution modeling with an episodic, context-conditional objective, where the model predicts for query subsets conditioned on dataset-specific contexts, supporting rapid, training-free adaptation at inference. We evaluate LimiX across 10 large structured-data benchmarks with broad regimes of sample size, feature dimensionality, class number, categorical-to-numerical feature ratio, missingness, and sample-to-feature ratios. With a single model and a unified interface, LimiX consistently surpasses strong baselines including gradient-boosting trees, deep tabular networks, recent tabular foundation models, and automated ensembles, as shown in Figure 1 and Figure 2. The superiority holds across a wide range of tasks, such as classification, regression, missing value imputation, and data generation, often by substantial margins, while avoiding task-specific architectures or bespoke training per task. All LimiX models are publicly accessible under Apache 2.0.

Despite constituting 65% of all internet traffic in 2023, video content is underrepresented in generative AI research. Meanwhile, recent large language models (LLMs) have become increasingly integrated with capabilities in the visual modality. Integrating video with LLMs is a natural next step, so how can this gap be bridged? To advance video reasoning, we propose a new research direction of VideoCOT on video keyframes, which leverages the multimodal generative abilities of vision-language models to enhance video reasoning while reducing the computational complexity of processing hundreds or thousands of frames. We introduce VIP, an inference-time dataset that can be used to evaluate VideoCOT, containing 1) a variety of real-life videos with keyframes and corresponding unstructured and structured scene descriptions, and 2) two new video reasoning tasks: video infilling and scene prediction. We benchmark various vision-language models on VIP, demonstrating the potential to use vision-language models and LLMs to enhance video chain of thought reasoning.

Integration of Vision-Language Models (VLMs) in surgical intelligence is hindered by hallucinations, domain knowledge gaps, and limited understanding of task interdependencies within surgical scenes, undermining clinical reliability. While recent VLMs demonstrate strong general reasoning and thinking capabilities, they still lack the domain expertise and task-awareness required for precise surgical scene interpretation. Although Chain-of-Thought (CoT) can structure reasoning more effectively, current approaches rely on self-generated CoT steps, which often exacerbate inherent domain gaps and hallucinations. To overcome this, we present SurgRAW, a CoT-driven multi-agent framework that delivers transparent, interpretable insights for most tasks in robotic-assisted surgery. By employing specialized CoT prompts across five tasks: instrument recognition, action recognition, action prediction, patient data extraction, and outcome assessment, SurgRAW mitigates hallucinations through structured, domain-aware reasoning. Retrieval-Augmented Generation (RAG) is also integrated to external medical knowledge to bridge domain gaps and improve response reliability. Most importantly, a hierarchical agentic system ensures that CoT-embedded VLM agents collaborate effectively while understanding task interdependencies, with a panel discussion mechanism promotes logical consistency. To evaluate our method, we introduce SurgCoTBench, the first reasoning-based dataset with structured frame-level annotations. With comprehensive experiments, we demonstrate the effectiveness of proposed SurgRAW with 29.32% accuracy improvement over baseline VLMs on 12 robotic procedures, achieving the state-of-the-art performance and advancing explainable, trustworthy, and autonomous surgical assistance.

Recent advances in vision-language-action (VLA) models have shown promise in integrating image generation with action prediction to improve generalization and reasoning in robot manipulation. However, existing methods are limited to challenging image-based forecasting, which suffers from redundant information and lacks comprehensive and critical world knowledge, including dynamic, spatial and semantic information. To address these limitations, we propose DreamVLA, a novel VLA framework that integrates comprehensive world knowledge forecasting to enable inverse dynamics modeling, thereby establishing a perception-prediction-action loop for manipulation tasks. Specifically, DreamVLA introduces a dynamic-region-guided world knowledge prediction, integrated with the spatial and semantic cues, which provide compact yet comprehensive representations for action planning. This design aligns with how humans interact with the world by first forming abstract multimodal reasoning chains before acting. To mitigate interference among the dynamic, spatial and semantic information during training, we adopt a block-wise structured attention mechanism that masks their mutual attention, preventing information leakage and keeping each representation clean and disentangled. Moreover, to model the conditional distribution over future actions, we employ a diffusion-based transformer that disentangles action representations from shared latent features. Extensive experiments on both real-world and simulation environments demonstrate that DreamVLA achieves 76.7% success rate on real robot tasks and 4.44 average length on the CALVIN ABC-D benchmarks.

This work investigates the integration of spatially aligned aerial imagery into perception tasks for automated vehicles (AVs). As a central contribution, we present AID4AD, a publicly available dataset that augments the nuScenes dataset with high-resolution aerial imagery precisely aligned to its local coordinate system. The alignment is performed using SLAM-based point cloud maps provided by nuScenes, establishing a direct link between aerial data and nuScenes local coordinate system. To ensure spatial fidelity, we propose an alignment workflow that corrects for localization and projection distortions. A manual quality control process further refines the dataset by identifying a set of high-quality alignments, which we publish as ground truth to support future research on automated registration. We demonstrate the practical value of AID4AD in two representative tasks: in online map construction, aerial imagery serves as a complementary input that improves the mapping process; in motion prediction, it functions as a structured environmental representation that replaces high-definition maps. Experiments show that aerial imagery leads to a 15-23% improvement in map construction accuracy and a 2% gain in trajectory prediction performance. These results highlight the potential of aerial imagery as a scalable and adaptable source of environmental context in automated vehicle systems, particularly in scenarios where high-definition maps are unavailable, outdated, or costly to maintain. AID4AD, along with evaluation code and pretrained models, is publicly released to foster further research in this direction: https://github.com/DriverlessMobility/AID4AD.

Artificial intelligence-assisted imaging analysis has made substantial strides in tumor diagnosis and management. Here we present PASTA, a pan-tumor CT foundation model that achieves state-of-the-art performance on 45 of 46 representative oncology tasks -- including lesion segmentation, tumor detection in plain CT, tumor staging, survival prediction, structured report generation, and cross-modality transfer learning, significantly outperforming the second-best models on 35 tasks. This remarkable advancement is driven by our development of PASTA-Gen, an innovative synthetic tumor generation framework that produces a comprehensive dataset of 30,000 CT scans with pixel-level annotated lesions and paired structured reports, encompassing malignancies across ten organs and five benign lesion types. By leveraging this rich, high-quality synthetic data, we overcome a longstanding bottleneck in the development of CT foundation models -- specifically, the scarcity of publicly available, high-quality annotated datasets due to privacy constraints and the substantial labor required for scaling precise data annotation. Encouragingly, PASTA demonstrates exceptional data efficiency with promising practical value, markedly improving performance on various tasks with only a small amount of real-world data. The open release of both the synthetic dataset and PASTA foundation model effectively addresses the challenge of data scarcity, thereby advancing oncological research and clinical translation.

Biomedical data is inherently multimodal, consisting of electronic health records, medical imaging, digital pathology, genome sequencing, wearable sensors, and more. The application of artificial intelligence tools to these multifaceted sensing technologies has the potential to revolutionize the prognosis, diagnosis, and management of human health and disease. However, current approaches to biomedical AI typically only train and evaluate with one or a small set of medical modalities and tasks. This limitation hampers the development of comprehensive tools that can leverage the rich interconnected information across many heterogeneous biomedical sensors. To address this challenge, we present MultiMed, a benchmark designed to evaluate and enable large-scale learning across a wide spectrum of medical modalities and tasks. MultiMed consists of 2.56 million samples across ten medical modalities such as medical reports, pathology, genomics, and protein data, and is structured into eleven challenging tasks, including disease prognosis, protein structure prediction, and medical question answering. Using MultiMed, we conduct comprehensive experiments benchmarking state-of-the-art unimodal, multimodal, and multitask models. Our analysis highlights the advantages of training large-scale medical models across many related modalities and tasks. Moreover, MultiMed enables studies of generalization across related medical concepts, robustness to real-world noisy data and distribution shifts, and novel modality combinations to improve prediction performance. MultiMed will be publicly available and regularly updated and welcomes inputs from the community.

Ribonucleic acid (RNA) plays a variety of crucial roles in fundamental biological processes. Recently, RNA has become an interesting drug target, emphasizing the need to improve our understanding of its structures and functions. Over the years, sequencing technologies have produced an enormous amount of unlabeled RNA data, which hides important knowledge and potential. Motivated by the successes of protein language models, we introduce RiboNucleic Acid Language Model (RiNALMo) to help unveil the hidden code of RNA. RiNALMo is the largest RNA language model to date with 650 million parameters pre-trained on 36 million non-coding RNA sequences from several available databases. RiNALMo is able to extract hidden knowledge and capture the underlying structure information implicitly embedded within the RNA sequences. RiNALMo achieves state-of-the-art results on several downstream tasks. Notably, we show that its generalization capabilities can overcome the inability of other deep learning methods for secondary structure prediction to generalize on unseen RNA families. The code has been made publicly available on https://github.com/lbcb-sci/RiNALMo.

In biological research, fluorescence staining is a key technique to reveal the locations and morphology of subcellular structures. However, it is slow, expensive, and harmful to cells. In this paper, we model it as a deep learning task termed subcellular structure prediction (SSP), aiming to predict the 3D fluorescent images of multiple subcellular structures from a 3D transmitted-light image. Unfortunately, due to the limitations of current biotechnology, each image is partially labeled in SSP. Besides, naturally, subcellular structures vary considerably in size, which causes the multi-scale issue of SSP. To overcome these challenges, we propose Re-parameterizing Mixture-of-Diverse-Experts (RepMode), a network that dynamically organizes its parameters with task-aware priors to handle specified single-label prediction tasks. In RepMode, the Mixture-of-Diverse-Experts (MoDE) block is designed to learn the generalized parameters for all tasks, and gating re-parameterization (GatRep) is performed to generate the specialized parameters for each task, by which RepMode can maintain a compact practical topology exactly like a plain network, and meanwhile achieves a powerful theoretical topology. Comprehensive experiments show that RepMode can achieve state-of-the-art overall performance in SSP.

Generative modeling of crystal data distribution is an important yet challenging task due to the unique periodic physical symmetry of crystals. Diffusion-based methods have shown early promise in modeling crystal distribution. More recently, Bayesian Flow Networks were introduced to aggregate noisy latent variables, resulting in a variance-reduced parameter space that has been shown to be advantageous for modeling Euclidean data distributions with structural constraints (Song et al., 2023). Inspired by this, we seek to unlock its potential for modeling variables located in non-Euclidean manifolds e.g. those within crystal structures, by overcoming challenging theoretical issues. We introduce CrysBFN, a novel crystal generation method by proposing a periodic Bayesian flow, which essentially differs from the original Gaussian-based BFN by exhibiting non-monotonic entropy dynamics. To successfully realize the concept of periodic Bayesian flow, CrysBFN integrates a new entropy conditioning mechanism and empirically demonstrates its significance compared to time-conditioning. Extensive experiments over both crystal ab initio generation and crystal structure prediction tasks demonstrate the superiority of CrysBFN, which consistently achieves new state-of-the-art on all benchmarks. Surprisingly, we found that CrysBFN enjoys a significant improvement in sampling efficiency, e.g., ~100x speedup 10 v.s. 2000 steps network forwards) compared with previous diffusion-based methods on MP-20 dataset. Code is available at https://github.com/wu-han-lin/CrysBFN.

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

We address 2D floorplan reconstruction from 3D scans. Existing approaches typically employ heuristically designed multi-stage pipelines. Instead, we formulate floorplan reconstruction as a single-stage structured prediction task: find a variable-size set of polygons, which in turn are variable-length sequences of ordered vertices. To solve it we develop a novel Transformer architecture that generates polygons of multiple rooms in parallel, in a holistic manner without hand-crafted intermediate stages. The model features two-level queries for polygons and corners, and includes polygon matching to make the network end-to-end trainable. Our method achieves a new state-of-the-art for two challenging datasets, Structured3D and SceneCAD, along with significantly faster inference than previous methods. Moreover, it can readily be extended to predict additional information, i.e., semantic room types and architectural elements like doors and windows. Our code and models are available at: https://github.com/ywyue/RoomFormer.

Entity linking is a prominent thread of research focused on structured data creation by linking spans of text to an ontology or knowledge source. We revisit the use of structured prediction for entity linking which classifies each individual input token as an entity, and aggregates the token predictions. Our system, called SpEL (Structured prediction for Entity Linking) is a state-of-the-art entity linking system that uses some new ideas to apply structured prediction to the task of entity linking including: two refined fine-tuning steps; a context sensitive prediction aggregation strategy; reduction of the size of the model's output vocabulary, and; we address a common problem in entity-linking systems where there is a training vs. inference tokenization mismatch. Our experiments show that we can outperform the state-of-the-art on the commonly used AIDA benchmark dataset for entity linking to Wikipedia. Our method is also very compute efficient in terms of number of parameters and speed of inference.

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

Recent years have witnessed a surge in the development of protein foundation models, significantly improving performance in protein prediction and generative tasks ranging from 3D structure prediction and protein design to conformational dynamics. However, the capabilities and limitations associated with these models remain poorly understood due to the absence of a unified evaluation framework. To fill this gap, we introduce ProteinBench, a holistic evaluation framework designed to enhance the transparency of protein foundation models. Our approach consists of three key components: (i) A taxonomic classification of tasks that broadly encompass the main challenges in the protein domain, based on the relationships between different protein modalities; (ii) A multi-metric evaluation approach that assesses performance across four key dimensions: quality, novelty, diversity, and robustness; and (iii) In-depth analyses from various user objectives, providing a holistic view of model performance. Our comprehensive evaluation of protein foundation models reveals several key findings that shed light on their current capabilities and limitations. To promote transparency and facilitate further research, we release the evaluation dataset, code, and a public leaderboard publicly for further analysis and a general modular toolkit. We intend for ProteinBench to be a living benchmark for establishing a standardized, in-depth evaluation framework for protein foundation models, driving their development and application while fostering collaboration within the field.

Understanding the 3D structures of protein multimers is crucial, as they play a vital role in regulating various cellular processes. It has been empirically confirmed that the multimer structure prediction~(MSP) can be well handled in a step-wise assembly fashion using provided dimer structures and predicted protein-protein interactions~(PPIs). However, due to the biological gap in the formation of dimers and larger multimers, directly applying PPI prediction techniques can often cause a poor generalization to the MSP task. To address this challenge, we aim to extend the PPI knowledge to multimers of different scales~(i.e., chain numbers). Specifically, we propose \textsc{PromptMSP}, a pre-training and Prompt tuning framework for Multimer Structure Prediction. First, we tailor the source and target tasks for effective PPI knowledge learning and efficient inference, respectively. We design PPI-inspired prompt learning to narrow the gaps of two task formats and generalize the PPI knowledge to multimers of different scales. We provide a meta-learning strategy to learn a reliable initialization of the prompt model, enabling our prompting framework to effectively adapt to limited data for large-scale multimers. Empirically, we achieve both significant accuracy (RMSD and TM-Score) and efficiency improvements compared to advanced MSP models. The code, data and checkpoints are released at https://github.com/zqgao22/PromptMSP.

Multiple Sequence Alignment (MSA) plays a pivotal role in unveiling the evolutionary trajectories of protein families. The accuracy of protein structure predictions is often compromised for protein sequences that lack sufficient homologous information to construct high quality MSA. Although various methods have been proposed to generate virtual MSA under these conditions, they fall short in comprehensively capturing the intricate coevolutionary patterns within MSA or require guidance from external oracle models. Here we introduce MSAGPT, a novel approach to prompt protein structure predictions via MSA generative pretraining in the low MSA regime. MSAGPT employs a simple yet effective 2D evolutionary positional encoding scheme to model complex evolutionary patterns. Endowed by this, its flexible 1D MSA decoding framework facilitates zero or few shot learning. Moreover, we demonstrate that leveraging the feedback from AlphaFold2 can further enhance the model capacity via Rejective Fine tuning (RFT) and Reinforcement Learning from AF2 Feedback (RLAF). Extensive experiments confirm the efficacy of MSAGPT in generating faithful virtual MSA to enhance the structure prediction accuracy. The transfer learning capabilities also highlight its great potential for facilitating other protein tasks.

Recently, the community has made tremendous progress in developing effective methods for point cloud video understanding that learn from massive amounts of labeled data. However, annotating point cloud videos is usually notoriously expensive. Moreover, training via one or only a few traditional tasks (e.g., classification) may be insufficient to learn subtle details of the spatio-temporal structure existing in point cloud videos. In this paper, we propose a Masked Spatio-Temporal Structure Prediction (MaST-Pre) method to capture the structure of point cloud videos without human annotations. MaST-Pre is based on spatio-temporal point-tube masking and consists of two self-supervised learning tasks. First, by reconstructing masked point tubes, our method is able to capture the appearance information of point cloud videos. Second, to learn motion, we propose a temporal cardinality difference prediction task that estimates the change in the number of points within a point tube. In this way, MaST-Pre is forced to model the spatial and temporal structure in point cloud videos. Extensive experiments on MSRAction-3D, NTU-RGBD, NvGesture, and SHREC'17 demonstrate the effectiveness of the proposed method.

Recent advances in protein structure prediction have achieved near-atomic accuracy for well-folded proteins. However, current benchmarks inadequately assess model performance in biologically challenging contexts, especially those involving intrinsically disordered regions (IDRs), limiting their utility in applications such as drug discovery, disease variant interpretation, and protein interface design. We introduce DisProtBench, a comprehensive benchmark for evaluating protein structure prediction models (PSPMs) under structural disorder and complex biological conditions. DisProtBench spans three key axes: (1) Data complexity, covering disordered regions, G protein-coupled receptor (GPCR) ligand pairs, and multimeric complexes; (2) Task diversity, benchmarking twelve leading PSPMs across structure-based tasks with unified classification, regression, and interface metrics; and (3) Interpretability, via the DisProtBench Portal, which provides precomputed 3D structures and visual error analyses. Our results reveal significant variability in model robustness under disorder, with low-confidence regions linked to functional prediction failures. Notably, global accuracy metrics often fail to predict task performance in disordered settings, emphasizing the need for function-aware evaluation. DisProtBench establishes a reproducible, extensible, and biologically grounded framework for assessing next-generation PSPMs in realistic biomedical scenarios.

Learning to capture text-table alignment is essential for tasks like text-to-SQL. A model needs to correctly recognize natural language references to columns and values and to ground them in the given database schema. In this paper, we present a novel weakly supervised Structure-Grounded pretraining framework (StruG) for text-to-SQL that can effectively learn to capture text-table alignment based on a parallel text-table corpus. We identify a set of novel prediction tasks: column grounding, value grounding and column-value mapping, and leverage them to pretrain a text-table encoder. Additionally, to evaluate different methods under more realistic text-table alignment settings, we create a new evaluation set Spider-Realistic based on Spider dev set with explicit mentions of column names removed, and adopt eight existing text-to-SQL datasets for cross-database evaluation. STRUG brings significant improvement over BERT-LARGE in all settings. Compared with existing pretraining methods such as GRAPPA, STRUG achieves similar performance on Spider, and outperforms all baselines on more realistic sets. The Spider-Realistic dataset is available at https://doi.org/10.5281/zenodo.5205322.

Lightweight inference is critical for biomolecular structure prediction and other downstream tasks, enabling efficient real-world deployment and inference-time scaling for large-scale applications. In this work, we address the challenge of balancing model efficiency and prediction accuracy by making several key modifications, 1) Multi-step AF3 sampler is replaced by a few-step ODE sampler, significantly reducing computational overhead for the diffusion module part during inference; 2) In the open-source Protenix framework, a subset of pairformer or diffusion transformer blocks doesn't make contributions to the final structure prediction, presenting opportunities for architectural pruning and lightweight redesign; 3) A model incorporating an ESM module is trained to substitute the conventional MSA module, reducing MSA preprocessing time. Building on these key insights, we present Protenix-Mini, a compact and optimized model designed for efficient protein structure prediction. This streamlined version incorporates a more efficient architectural design with a two-step Ordinary Differential Equation (ODE) sampling strategy. By eliminating redundant Transformer components and refining the sampling process, Protenix-Mini significantly reduces model complexity with slight accuracy drop. Evaluations on benchmark datasets demonstrate that it achieves high-fidelity predictions, with only a negligible 1 to 5 percent decrease in performance on benchmark datasets compared to its full-scale counterpart. This makes Protenix-Mini an ideal choice for applications where computational resources are limited but accurate structure prediction remains crucial.

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.

The goal of knowledge graph completion (KGC) is to predict missing links in a KG using trained facts that are already known. In recent, pre-trained language model (PLM) based methods that utilize both textual and structural information are emerging, but their performances lag behind state-of-the-art (SOTA) structure-based methods or some methods lose their inductive inference capabilities in the process of fusing structure embedding to text encoder. In this paper, we propose a novel method to effectively unify structure information and language semantics without losing the power of inductive reasoning. We adopt entity anchors and these anchors and textual description of KG elements are fed together into the PLM-based encoder to learn unified representations. In addition, the proposed method utilizes additional random negative samples which can be reused in the each mini-batch during contrastive learning to learn a generalized entity representations. We verify the effectiveness of the our proposed method through various experiments and analysis. The experimental results on standard benchmark widely used in link prediction task show that the proposed model outperforms existing the SOTA KGC models. Especially, our method show the largest performance improvement on FB15K-237, which is competitive to the SOTA of structure-based KGC 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.

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.

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

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.

Despite being self-supervised, protein language models have shown remarkable performance in fundamental biological tasks such as predicting impact of genetic variation on protein structure and function. The effectiveness of these models on diverse set of tasks suggests that they learn meaningful representations of fitness landscape that can be useful for downstream clinical applications. Here, we interrogate the use of these language models in characterizing known pathogenic mutations in curated, medically actionable genes through an exhaustive search of putative compensatory mutations on each variant's genetic background. Systematic analysis of the predicted effects of these compensatory mutations reveal unappreciated structural features of proteins that are missed by other structure predictors like AlphaFold. While deep mutational scan experiments provide an unbiased estimate of the mutational landscape, we encourage the community to generate and curate rescue mutation experiments to inform the design of more sophisticated co-masking strategies and leverage large language models more effectively for downstream clinical prediction tasks.

Protein language models (PLMs) have emerged as powerful tools to detect complex patterns of protein sequences. However, the capability of PLMs to fully capture information on protein sequences might be limited by focusing on single pre-training tasks. Although adding data modalities or supervised objectives can improve the performance of PLMs, pre-training often remains focused on denoising corrupted sequences. To push the boundaries of PLMs, our research investigated a multi-task pre-training strategy. We developed Ankh3, a model jointly optimized on two objectives: masked language modeling with multiple masking probabilities and protein sequence completion relying only on protein sequences as input. This multi-task pre-training demonstrated that PLMs can learn richer and more generalizable representations solely from protein sequences. The results demonstrated improved performance in downstream tasks, such as secondary structure prediction, fluorescence, GB1 fitness, and contact prediction. The integration of multiple tasks gave the model a more comprehensive understanding of protein properties, leading to more robust and accurate predictions.

The multi-modal nature of many vision problems calls for neural network architectures that can perform multiple tasks concurrently. Typically, such architectures have been handcrafted in the literature. However, given the size and complexity of the problem, this manual architecture exploration likely exceeds human design abilities. In this paper, we propose a principled approach, rooted in differentiable neural architecture search, to automatically define branching (tree-like) structures in the encoding stage of a multi-task neural network. To allow flexibility within resource-constrained environments, we introduce a proxyless, resource-aware loss that dynamically controls the model size. Evaluations across a variety of dense prediction tasks show that our approach consistently finds high-performing branching structures within limited resource budgets.

We are now witnessing significant progress of deep learning methods in a variety of tasks (or datasets) of proteins. However, there is a lack of a standard benchmark to evaluate the performance of different methods, which hinders the progress of deep learning in this field. In this paper, we propose such a benchmark called PEER, a comprehensive and multi-task benchmark for Protein sEquence undERstanding. PEER provides a set of diverse protein understanding tasks including protein function prediction, protein localization prediction, protein structure prediction, protein-protein interaction prediction, and protein-ligand interaction prediction. We evaluate different types of sequence-based methods for each task including traditional feature engineering approaches, different sequence encoding methods as well as large-scale pre-trained protein language models. In addition, we also investigate the performance of these methods under the multi-task learning setting. Experimental results show that large-scale pre-trained protein language models achieve the best performance for most individual tasks, and jointly training multiple tasks further boosts the performance. The datasets and source codes of this benchmark are all available at https://github.com/DeepGraphLearning/PEER_Benchmark

Scene synthesis and editing has emerged as a promising direction in computer graphics. Current trained approaches for 3D indoor scenes either oversimplify object semantics through one-hot class encodings (e.g., 'chair' or 'table'), require masked diffusion for editing, ignore room boundaries, or rely on floor plan renderings that fail to capture complex layouts. In contrast, LLM-based methods enable richer semantics via natural language (e.g., 'modern studio with light wood furniture') but do not support editing, remain limited to rectangular layouts or rely on weak spatial reasoning from implicit world models. We introduce ReSpace, a generative framework for text-driven 3D indoor scene synthesis and editing using autoregressive language models. Our approach features a compact structured scene representation with explicit room boundaries that frames scene editing as a next-token prediction task. We leverage a dual-stage training approach combining supervised fine-tuning and preference alignment, enabling a specially trained language model for object addition that accounts for user instructions, spatial geometry, object semantics, and scene-level composition. For scene editing, we employ a zero-shot LLM to handle object removal and prompts for addition. We further introduce a novel voxelization-based evaluation that captures fine-grained geometry beyond 3D bounding boxes. Experimental results surpass state-of-the-art on object addition while maintaining competitive results on full scene synthesis.

Many machine learning tasks can be expressed as the transformation---or transduction---of input sequences into output sequences: speech recognition, machine translation, protein secondary structure prediction and text-to-speech to name but a few. One of the key challenges in sequence transduction is learning to represent both the input and output sequences in a way that is invariant to sequential distortions such as shrinking, stretching and translating. Recurrent neural networks (RNNs) are a powerful sequence learning architecture that has proven capable of learning such representations. However RNNs traditionally require a pre-defined alignment between the input and output sequences to perform transduction. This is a severe limitation since finding the alignment is the most difficult aspect of many sequence transduction problems. Indeed, even determining the length of the output sequence is often challenging. This paper introduces an end-to-end, probabilistic sequence transduction system, based entirely on RNNs, that is in principle able to transform any input sequence into any finite, discrete output sequence. Experimental results for phoneme recognition are provided on the TIMIT speech corpus.

With the increase in availability of large pre-trained language models (LMs) in Natural Language Processing (NLP), it becomes critical to assess their fit for a specific target task a priori - as fine-tuning the entire space of available LMs is computationally prohibitive and unsustainable. However, encoder transferability estimation has received little to no attention in NLP. In this paper, we propose to generate quantitative evidence to predict which LM, out of a pool of models, will perform best on a target task without having to fine-tune all candidates. We provide a comprehensive study on LM ranking for 10 NLP tasks spanning the two fundamental problem types of classification and structured prediction. We adopt the state-of-the-art Logarithm of Maximum Evidence (LogME) measure from Computer Vision (CV) and find that it positively correlates with final LM performance in 94% of the setups. In the first study of its kind, we further compare transferability measures with the de facto standard of human practitioner ranking, finding that evidence from quantitative metrics is more robust than pure intuition and can help identify unexpected LM candidates.

End-to-end relation extraction aims to identify named entities and extract relations between them. Most recent work models these two subtasks jointly, either by casting them in one structured prediction framework, or performing multi-task learning through shared representations. In this work, we present a simple pipelined approach for entity and relation extraction, and establish the new state-of-the-art on standard benchmarks (ACE04, ACE05 and SciERC), obtaining a 1.7%-2.8% absolute improvement in relation F1 over previous joint models with the same pre-trained encoders. Our approach essentially builds on two independent encoders and merely uses the entity model to construct the input for the relation model. Through a series of careful examinations, we validate the importance of learning distinct contextual representations for entities and relations, fusing entity information early in the relation model, and incorporating global context. Finally, we also present an efficient approximation to our approach which requires only one pass of both entity and relation encoders at inference time, achieving an 8-16times speedup with a slight reduction in accuracy.

The convolutional neural network-based methods have become more and more popular for medical image segmentation due to their outstanding performance. However, they struggle with capturing long-range dependencies, which are essential for accurately modeling global contextual correlations. Thanks to the ability to model long-range dependencies by expanding the receptive field, the transformer-based methods have gained prominence. Inspired by this, we propose an advanced 2D feature extraction method by combining the convolutional neural network and Transformer architectures. More specifically, we introduce a parallelized encoder structure, where one branch uses ResNet to extract local information from images, while the other branch uses Transformer to extract global information. Furthermore, we integrate pyramid structures into the Transformer to extract global information at varying resolutions, especially in intensive prediction tasks. To efficiently utilize the different information in the parallelized encoder at the decoder stage, we use a channel attention module to merge the features of the encoder and propagate them through skip connections and bottlenecks. Intensive numerical experiments are performed on both aortic vessel tree, cardiac, and multi-organ datasets. By comparing with state-of-the-art medical image segmentation methods, our method is shown with better segmentation accuracy, especially on small organs. The code is publicly available on https://github.com/HongkunSun/ParaTransCNN.

Multiple sequence alignments (MSAs) of proteins encode rich biological information and have been workhorses in bioinformatic methods for tasks like protein design and protein structure prediction for decades. Recent breakthroughs like AlphaFold2 that use transformers to attend directly over large quantities of raw MSAs have reaffirmed their importance. Generation of MSAs is highly computationally intensive, however, and no datasets comparable to those used to train AlphaFold2 have been made available to the research community, hindering progress in machine learning for proteins. To remedy this problem, we introduce OpenProteinSet, an open-source corpus of more than 16 million MSAs, associated structural homologs from the Protein Data Bank, and AlphaFold2 protein structure predictions. We have previously demonstrated the utility of OpenProteinSet by successfully retraining AlphaFold2 on it. We expect OpenProteinSet to be broadly useful as training and validation data for 1) diverse tasks focused on protein structure, function, and design and 2) large-scale multimodal machine learning research.

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.

In recent years, large language models (LLMs) have achieved state-of-the-art results in various biological sequence analysis tasks, such as sequence classification, structure prediction, and function prediction. Similar to advancements in AI for other scientific fields, deeper research into biological LLMs has begun to focus on using these models to rediscover important existing biological laws or uncover entirely new patterns in biological sequences.This study leverages GPT-like LLMs to utilize language transfer capabilities to rediscover the genetic code rules of the central dogma. In our experimental design, we transformed the central dogma into a binary classification problem of aligning DNA sequences with protein sequences, where positive examples are matching DNA and protein sequences, and negative examples are non-matching pairs.We first trained a GPT-2 model from scratch using a dataset comprising protein sequences, DNA sequences, and sequences from languages such as English and Chinese. Subsequently, we fine-tuned the model using the English similarity judgment dataset from PAWS-X. When tested on a dataset for DNA and protein sequence alignment judgment, the fine-tuned model achieved a classification accuracy of 76%. The study also analyzed factors contributing to this zero-shot capability, including model training stability and types of training data.This research demonstrates that LLMs can, through the transfer of natural language capabilities and solely relying on the analysis of sequences themselves, rediscover the central dogma without prior knowledge of it. This study opens a new door for AI-driven biological research.

The cross-lingual language models are typically pretrained with masked language modeling on multilingual text or parallel sentences. In this paper, we introduce denoising word alignment as a new cross-lingual pre-training task. Specifically, the model first self-labels word alignments for parallel sentences. Then we randomly mask tokens in a bitext pair. Given a masked token, the model uses a pointer network to predict the aligned token in the other language. We alternately perform the above two steps in an expectation-maximization manner. Experimental results show that our method improves cross-lingual transferability on various datasets, especially on the token-level tasks, such as question answering, and structured prediction. Moreover, the model can serve as a pretrained word aligner, which achieves reasonably low error rates on the alignment benchmarks. The code and pretrained parameters are available at https://github.com/CZWin32768/XLM-Align.

The complementarity-determining regions of antibodies are loop structures that are key to their interactions with antigens, and of high importance to the design of novel biologics. Since the 1980s, categorizing the diversity of CDR structures into canonical clusters has enabled the identification of key structural motifs of antibodies. However, existing approaches have limited coverage and cannot be readily incorporated into protein foundation models. Here we introduce ImmunoGlobulin LOOp Tokenizer, Igloo, a multimodal antibody loop tokenizer that encodes backbone dihedral angles and sequence. Igloo is trained using a contrastive learning objective to map loops with similar backbone dihedral angles closer together in latent space. Igloo can efficiently retrieve the closest matching loop structures from a structural antibody database, outperforming existing methods on identifying similar H3 loops by 5.9\%. Igloo assigns tokens to all loops, addressing the limited coverage issue of canonical clusters, while retaining the ability to recover canonical loop conformations. To demonstrate the versatility of Igloo tokens, we show that they can be incorporated into protein language models with IglooLM and IglooALM. On predicting binding affinity of heavy chain variants, IglooLM outperforms the base protein language model on 8 out of 10 antibody-antigen targets. Additionally, it is on par with existing state-of-the-art sequence-based and multimodal protein language models, performing comparably to models with 7times more parameters. IglooALM samples antibody loops which are diverse in sequence and more consistent in structure than state-of-the-art antibody inverse folding models. Igloo demonstrates the benefit of introducing multimodal tokens for antibody loops for encoding the diverse landscape of antibody loops, improving protein foundation models, and for antibody CDR design.

The Information Bottleneck (IB) principle has emerged as a promising approach for enhancing the generalization, robustness, and interpretability of deep neural networks, demonstrating efficacy across image segmentation, document clustering, and semantic communication. Among IB implementations, the IB Lagrangian method, employing Lagrangian multipliers, is widely adopted. While numerous methods for the optimizations of IB Lagrangian based on variational bounds and neural estimators are feasible, their performance is highly dependent on the quality of their design, which is inherently prone to errors. To address this limitation, we introduce Structured IB, a framework for investigating potential structured features. By incorporating auxiliary encoders to extract missing informative features, we generate more informative representations. Our experiments demonstrate superior prediction accuracy and task-relevant information preservation compared to the original IB Lagrangian method, even with reduced network size.

Small molecules are essential to drug discovery, and graph-language models hold promise for learning molecular properties and functions from text. However, existing molecule-text datasets are limited in scale and informativeness, restricting the training of generalizable multimodal models. We present MolTextNet, a dataset of 2.5 million high-quality molecule-text pairs designed to overcome these limitations. To construct it, we propose a synthetic text generation pipeline that integrates structural features, computed properties, bioactivity data, and synthetic complexity. Using GPT-4o-mini, we create structured descriptions for 2.5 million molecules from ChEMBL35, with text over 10 times longer than prior datasets. MolTextNet supports diverse downstream tasks, including property prediction and structure retrieval. Pretraining CLIP-style models with Graph Neural Networks and ModernBERT on MolTextNet yields improved performance, highlighting its potential for advancing foundational multimodal modeling in molecular science. Our dataset is available at https://huggingface.co/datasets/liuganghuggingface/moltextnet.

Exploring spatial-temporal dependencies from observed motions is one of the core challenges of human motion prediction. Previous methods mainly focus on dedicated network structures to model the spatial and temporal dependencies. This paper considers a new direction by introducing a model learning framework with auxiliary tasks. In our auxiliary tasks, partial body joints' coordinates are corrupted by either masking or adding noise and the goal is to recover corrupted coordinates depending on the rest coordinates. To work with auxiliary tasks, we propose a novel auxiliary-adapted transformer, which can handle incomplete, corrupted motion data and achieve coordinate recovery via capturing spatial-temporal dependencies. Through auxiliary tasks, the auxiliary-adapted transformer is promoted to capture more comprehensive spatial-temporal dependencies among body joints' coordinates, leading to better feature learning. Extensive experimental results have shown that our method outperforms state-of-the-art methods by remarkable margins of 7.2%, 3.7%, and 9.4% in terms of 3D mean per joint position error (MPJPE) on the Human3.6M, CMU Mocap, and 3DPW datasets, respectively. We also demonstrate that our method is more robust under data missing cases and noisy data cases. Code is available at https://github.com/MediaBrain-SJTU/AuxFormer.

Document structure analysis, aka document layout analysis, is crucial for understanding both the physical layout and logical structure of documents, serving information retrieval, document summarization, knowledge extraction, etc. Hierarchical Document Structure Analysis (HDSA) specifically aims to restore the hierarchical structure of documents created using authoring software with hierarchical schemas. Previous research has primarily followed two approaches: one focuses on tackling specific subtasks of HDSA in isolation, such as table detection or reading order prediction, while the other adopts a unified framework that uses multiple branches or modules, each designed to address a distinct task. In this work, we propose a unified relation prediction approach for HDSA, called UniHDSA, which treats various HDSA sub-tasks as relation prediction problems and consolidates relation prediction labels into a unified label space. This allows a single relation prediction module to handle multiple tasks simultaneously, whether at a page-level or document-level structure analysis. To validate the effectiveness of UniHDSA, we develop a multimodal end-to-end system based on Transformer architectures. Extensive experimental results demonstrate that our approach achieves state-of-the-art performance on a hierarchical document structure analysis benchmark, Comp-HRDoc, and competitive results on a large-scale document layout analysis dataset, DocLayNet, effectively illustrating the superiority of our method across all sub-tasks. The Comp-HRDoc benchmark and UniHDSA's configurations are publicly available at https://github.com/microsoft/CompHRDoc.

We introduce a pattern mining framework that operates on semi-structured datasets and exploits the dichotomy between outcomes. Our approach takes advantage of constraint reasoning to find sequential patterns that occur frequently and exhibit desired properties. This allows the creation of novel pattern embeddings that are useful for knowledge extraction and predictive modeling. Finally, we present an application on customer intent prediction from digital clickstream data. Overall, we show that pattern embeddings play an integrator role between semi-structured data and machine learning models, improve the performance of the downstream task and retain interpretability.

Drug discovery is a complex and time-intensive process that requires identifying and validating new therapeutic candidates. Computational approaches using large-scale biomedical knowledge graphs (KGs) offer a promising solution to accelerate this process. However, extracting meaningful insights from large-scale KGs remains challenging due to the complexity of graph traversal. Existing subgraph-based methods are tailored to graph neural networks (GNNs), making them incompatible with other models, such as large language models (LLMs). We introduce K-Paths, a retrieval framework that extracts structured, diverse, and biologically meaningful paths from KGs. Integrating these paths enables LLMs and GNNs to effectively predict unobserved drug-drug and drug-disease interactions. Unlike traditional path-ranking approaches, K-Paths retrieves and transforms paths into a structured format that LLMs can directly process, facilitating explainable reasoning. K-Paths employs a diversity-aware adaptation of Yen's algorithm to retrieve the K shortest loopless paths between entities in an interaction query, prioritizing biologically relevant and diverse relationships. Our experiments on benchmark datasets show that K-Paths improves the zero-shot performance of Llama 8.1B's F1-score by 12.45 points on drug repurposing and 13.42 points on interaction severity prediction. We also show that Llama 70B achieves F1-score gains of 6.18 and 8.46 points, respectively. K-Paths also improves the supervised training efficiency of EmerGNN, a state-of-the-art GNN, by reducing KG size by 90% while maintaining strong predictive performance. Beyond its scalability and efficiency, K-Paths uniquely bridges the gap between KGs and LLMs, providing explainable rationales for predicted interactions. These capabilities show that K-Paths is a valuable tool for efficient data-driven drug discovery.

Singing-driven 3D head animation is a challenging yet promising task with applications in virtual avatars, entertainment, and education. Unlike speech, singing involves richer emotional nuance, dynamic prosody, and lyric-based semantics, requiring the synthesis of fine-grained, temporally coherent facial motion. Existing speech-driven approaches often produce oversimplified, emotionally flat, and semantically inconsistent results, which are insufficient for singing animation. To address this, we propose Think2Sing, a diffusion-based framework that leverages pretrained large language models to generate semantically coherent and temporally consistent 3D head animations, conditioned on both lyrics and acoustics. A key innovation is the introduction of motion subtitles, an auxiliary semantic representation derived through a novel Singing Chain-of-Thought reasoning process combined with acoustic-guided retrieval. These subtitles contain precise timestamps and region-specific motion descriptions, serving as interpretable motion priors. We frame the task as a motion intensity prediction problem, enabling finer control over facial regions and improving the modeling of expressive motion. To support this, we create a multimodal singing dataset with synchronized video, acoustic descriptors, and motion subtitles, enabling diverse and expressive motion learning. Extensive experiments show that Think2Sing outperforms state-of-the-art methods in realism, expressiveness, and emotional fidelity, while also offering flexible, user-controllable animation editing.

Recently, Large Language Models (LLMs) have achieved remarkable success using in-context learning (ICL) in the language domain. However, leveraging the ICL capabilities within LLMs to directly predict robot actions remains largely unexplored. In this paper, we introduce RoboPrompt, a framework that enables off-the-shelf text-only LLMs to directly predict robot actions through ICL without training. Our approach first heuristically identifies keyframes that capture important moments from an episode. Next, we extract end-effector actions from these keyframes as well as the estimated initial object poses, and both are converted into textual descriptions. Finally, we construct a structured template to form ICL demonstrations from these textual descriptions and a task instruction. This enables an LLM to directly predict robot actions at test time. Through extensive experiments and analysis, RoboPrompt shows stronger performance over zero-shot and ICL baselines in simulated and real-world settings.

Motion prediction is crucial for autonomous vehicles to operate safely in complex traffic environments. Extracting effective spatiotemporal relationships among traffic elements is key to accurate forecasting. Inspired by the successful practice of pretrained large language models, this paper presents SEPT, a modeling framework that leverages self-supervised learning to develop powerful spatiotemporal understanding for complex traffic scenes. Specifically, our approach involves three masking-reconstruction modeling tasks on scene inputs including agents' trajectories and road network, pretraining the scene encoder to capture kinematics within trajectory, spatial structure of road network, and interactions among roads and agents. The pretrained encoder is then finetuned on the downstream forecasting task. Extensive experiments demonstrate that SEPT, without elaborate architectural design or manual feature engineering, achieves state-of-the-art performance on the Argoverse 1 and Argoverse 2 motion forecasting benchmarks, outperforming previous methods on all main metrics by a large margin.

Machine learning frameworks such as graph neural networks typically rely on a given, fixed graph to exploit relational inductive biases and thus effectively learn from network data. However, when said graphs are (partially) unobserved, noisy, or dynamic, the problem of inferring graph structure from data becomes relevant. In this paper, we postulate a graph convolutional relationship between the observed and latent graphs, and formulate the graph learning task as a network inverse (deconvolution) problem. In lieu of eigendecomposition-based spectral methods or iterative optimization solutions, we unroll and truncate proximal gradient iterations to arrive at a parameterized neural network architecture that we call a Graph Deconvolution Network (GDN). GDNs can learn a distribution of graphs in a supervised fashion, perform link prediction or edge-weight regression tasks by adapting the loss function, and they are inherently inductive. We corroborate GDN's superior graph recovery performance and its generalization to larger graphs using synthetic data in supervised settings. Furthermore, we demonstrate the robustness and representation power of GDNs on real world neuroimaging and social network datasets.

Masked autoencoders (MAE) have recently been introduced to 3D self-supervised pretraining for point clouds due to their great success in NLP and computer vision. Unlike MAEs used in the image domain, where the pretext task is to restore features at the masked pixels, such as colors, the existing 3D MAE works reconstruct the missing geometry only, i.e, the location of the masked points. In contrast to previous studies, we advocate that point location recovery is inessential and restoring intrinsic point features is much superior. To this end, we propose to ignore point position reconstruction and recover high-order features at masked points including surface normals and surface variations, through a novel attention-based decoder which is independent of the encoder design. We validate the effectiveness of our pretext task and decoder design using different encoder structures for 3D training and demonstrate the advantages of our pretrained networks on various point cloud analysis tasks.

Channel prediction permits to acquire channel state information (CSI) without signaling overhead. However, almost all existing channel prediction methods necessitate the deployment of a dedicated model to accommodate a specific configuration. Leveraging the powerful modeling and multi-task learning capabilities of foundation models, we propose the first space-time-frequency (STF) wireless foundation model (WiFo) to address time-frequency channel prediction tasks in a one-for-all manner. Specifically, WiFo is initially pre-trained over massive and extensive diverse CSI datasets. Then, the model will be instantly used for channel prediction under various CSI configurations without any fine-tuning. We propose a masked autoencoder (MAE)-based network structure for WiFo to handle heterogeneous STF CSI data, and design several mask reconstruction tasks for self-supervised pre-training to capture the inherent 3D variations of CSI. To fully unleash its predictive power, we build a large-scale heterogeneous simulated CSI dataset consisting of 160K CSI samples for pre-training. Simulations validate its superior unified learning performance across multiple datasets and demonstrate its state-of-the-art (SOTA) zero-shot generalization performance via comparisons with other full-shot baselines.

In this paper, we present StrucTexTv2, an effective document image pre-training framework, by performing masked visual-textual prediction. It consists of two self-supervised pre-training tasks: masked image modeling and masked language modeling, based on text region-level image masking. The proposed method randomly masks some image regions according to the bounding box coordinates of text words. The objectives of our pre-training tasks are reconstructing the pixels of masked image regions and the corresponding masked tokens simultaneously. Hence the pre-trained encoder can capture more textual semantics in comparison to the masked image modeling that usually predicts the masked image patches. Compared to the masked multi-modal modeling methods for document image understanding that rely on both the image and text modalities, StrucTexTv2 models image-only input and potentially deals with more application scenarios free from OCR pre-processing. Extensive experiments on mainstream benchmarks of document image understanding demonstrate the effectiveness of StrucTexTv2. It achieves competitive or even new state-of-the-art performance in various downstream tasks such as image classification, layout analysis, table structure recognition, document OCR, and information extraction under the end-to-end scenario.

Information extraction (IE) is an important task in Natural Language Processing (NLP), involving the extraction of named entities and their relationships from unstructured text. In this paper, we propose a novel approach to this task by formulating it as graph structure learning (GSL). By formulating IE as GSL, we enhance the model's ability to dynamically refine and optimize the graph structure during the extraction process. This formulation allows for better interaction and structure-informed decisions for entity and relation prediction, in contrast to previous models that have separate or untied predictions for these tasks. When compared against state-of-the-art baselines on joint entity and relation extraction benchmarks, our model, GraphER, achieves competitive results.

Protein language models (pLMs) pre-trained on vast protein sequence databases excel at various downstream tasks but lack the structural knowledge essential for many biological applications. To address this, we integrate structural insights from pre-trained protein graph neural networks (pGNNs) into pLMs through a latent-level contrastive learning task. This task aligns residue representations from pLMs with those from pGNNs across multiple proteins, enriching pLMs with inter-protein structural knowledge. Additionally, we incorporate a physical-level task that infuses intra-protein structural knowledge by optimizing pLMs to predict structural tokens. The proposed dual-task framework effectively incorporates both inter-protein and intra-protein structural knowledge into pLMs. Given the variability in the quality of protein structures in PDB, we further introduce a residue loss selection module, which uses a small model trained on high-quality structures to select reliable yet challenging residue losses for the pLM to learn. Applying our structure alignment method to the state-of-the-art ESM2 and AMPLIFY results in notable performance gains across a wide range of tasks, including a 12.7% increase in ESM2 contact prediction. The data, code, and resulting SaESM2 and SaAMPLIFY models will be released on Hugging Face.

Nanobodies, single-domain antibody fragments derived from camelid heavy-chain-only antibodies, exhibit unique advantages such as compact size, high stability, and strong binding affinity, making them valuable tools in therapeutics and diagnostics. While recent advances in pretrained protein and antibody language models (PPLMs and PALMs) have greatly enhanced biomolecular understanding, nanobody-specific modeling remains underexplored and lacks a unified benchmark. To address this gap, we introduce NbBench, the first comprehensive benchmark suite for nanobody representation learning. Spanning eight biologically meaningful tasks across nine curated datasets, NbBench encompasses structure annotation, binding prediction, and developability assessment. We systematically evaluate eleven representative models--including general-purpose protein LMs, antibody-specific LMs, and nanobody-specific LMs--in a frozen setting. Our analysis reveals that antibody language models excel in antigen-related tasks, while performance on regression tasks such as thermostability and affinity remains challenging across all models. Notably, no single model consistently outperforms others across all tasks. By standardizing datasets, task definitions, and evaluation protocols, NbBench offers a reproducible foundation for assessing and advancing nanobody modeling.

Most graph neural network models learn embeddings of nodes in static attributed graphs for predictive analysis. Recent attempts have been made to learn temporal proximity of the nodes. We find that real dynamic attributed graphs exhibit complex co-evolution of node attributes and graph structure. Learning node embeddings for forecasting change of node attributes and birth and death of links over time remains an open problem. In this work, we present a novel framework called CoEvoGNN for modeling dynamic attributed graph sequence. It preserves the impact of earlier graphs on the current graph by embedding generation through the sequence. It has a temporal self-attention mechanism to model long-range dependencies in the evolution. Moreover, CoEvoGNN optimizes model parameters jointly on two dynamic tasks, attribute inference and link prediction over time. So the model can capture the co-evolutionary patterns of attribute change and link formation. This framework can adapt to any graph neural algorithms so we implemented and investigated three methods based on it: CoEvoGCN, CoEvoGAT, and CoEvoSAGE. Experiments demonstrate the framework (and its methods) outperform strong baselines on predicting an entire unseen graph snapshot of personal attributes and interpersonal links in dynamic social graphs and financial graphs.

Large language models have evolved data-efficient generalists, benefiting from the universal language interface and large-scale pre-training. However, constructing a data-efficient generalist for dense visual prediction presents a distinct challenge due to the variation in label structures across different tasks. Consequently, generalization to unseen dense prediction tasks in the low-data regime is not straightforward and has received less attention from previous vision generalists. In this study, we explore a universal model that can flexibly adapt to unseen dense label structures with a few examples, enabling it to serve as a data-efficient vision generalist in diverse real-world scenarios. To this end, we base our method on a powerful meta-learning framework and explore several axes to improve its performance and versatility for real-world problems, such as flexible adaptation mechanisms and scalability. We evaluate our model across a spectrum of unseen real-world scenarios where low-shot learning is desirable, including video, 3D, medical, biological, and user-interactive tasks. Equipped with a generic architecture and an effective adaptation mechanism, our model flexibly adapts to all of these tasks with at most 50 labeled images, showcasing a significant advancement over existing data-efficient generalist approaches. Codes are available at https://github.com/GitGyun/chameleon.

Camera traps are valuable tools in animal ecology for biodiversity monitoring and conservation. However, challenges like poor generalization to deployment at new unseen locations limit their practical application. Images are naturally associated with heterogeneous forms of context possibly in different modalities. In this work, we leverage the structured context associated with the camera trap images to improve out-of-distribution generalization for the task of species identification in camera traps. For example, a photo of a wild animal may be associated with information about where and when it was taken, as well as structured biology knowledge about the animal species. While typically overlooked by existing work, bringing back such context offers several potential benefits for better image understanding, such as addressing data scarcity and enhancing generalization. However, effectively integrating such heterogeneous context into the visual domain is a challenging problem. To address this, we propose a novel framework that reformulates species classification as link prediction in a multimodal knowledge graph (KG). This framework seamlessly integrates various forms of multimodal context for visual recognition. We apply this framework for out-of-distribution species classification on the iWildCam2020-WILDS and Snapshot Mountain Zebra datasets and achieve competitive performance with state-of-the-art approaches. Furthermore, our framework successfully incorporates biological taxonomy for improved generalization and enhances sample efficiency for recognizing under-represented species.

Next Location Prediction is a fundamental task in the study of human mobility, with wide-ranging applications in transportation planning, urban governance, and epidemic forecasting. In practice, when humans attempt to predict the next location in a trajectory, they often visualize the trajectory on a map and reason based on road connectivity and movement trends. However, the vast majority of existing next-location prediction models do not reason over maps in the way that humans do. Fortunately, the recent development of Vision-Language Models (VLMs) has demonstrated strong capabilities in visual perception and even visual reasoning. This opens up a new possibility: by rendering both the road network and trajectory onto an image and leveraging the reasoning abilities of VLMs, we can enable models to perform trajectory inference in a human-like manner. To explore this idea, we first propose a method called Vision-Guided Location Search (VGLS), which evaluates whether a general-purpose VLM is capable of trajectory-based reasoning without modifying any of its internal parameters. Based on insights from the VGLS results, we further propose our main approach: VLMLocPredictor, which is composed of two stages: In the first stage, we design two Supervised Fine-Tuning (SFT) tasks that help the VLM understand road network and trajectory structures and acquire basic reasoning ability on such visual inputs. In the second stage, we introduce Reinforcement Learning from Visual Map Feedback, enabling the model to self-improve its next-location prediction ability through interaction with the environment. Experiments conducted on datasets from four different cities show that our method achieves state-of-the-art (SOTA) performance and exhibits superior cross-city generalization compared to other LLM-based approaches.

Prevalent models based on artificial neural network (ANN) for sentence classification often classify sentences in isolation without considering the context in which sentences appear. This hampers the traditional sentence classification approaches to the problem of sequential sentence classification, where structured prediction is needed for better overall classification performance. In this work, we present a hierarchical sequential labeling network to make use of the contextual information within surrounding sentences to help classify the current sentence. Our model outperforms the state-of-the-art results by 2%-3% on two benchmarking datasets for sequential sentence classification in medical scientific abstracts.

Large language models (LLMs) have shown remarkable ability in various language tasks, especially with their emergent in-context learning capability. Extending LLMs to incorporate visual inputs, large vision-language models (LVLMs) have shown impressive performance in tasks such as recognition and visual question answering (VQA). Despite increasing interest in the utility of LLMs in causal reasoning tasks such as causal discovery and counterfactual reasoning, there has been relatively little work showcasing the abilities of LVLMs on visual causal reasoning tasks. We take this opportunity to formally introduce a comprehensive causal reasoning benchmark for multi-modal in-context learning from LVLMs. Our CausalVLBench encompasses three representative tasks: causal structure inference, intervention target prediction, and counterfactual prediction. We evaluate the ability of state-of-the-art open-source LVLMs on our causal reasoning tasks across three causal representation learning datasets and demonstrate their fundamental strengths and weaknesses. We hope that our benchmark elucidates the drawbacks of existing vision-language models and motivates new directions and paradigms in improving the visual causal reasoning abilities of LVLMs.

Self-supervised pre-training based on next-token prediction has enabled large language models to capture the underlying structure of text, and has led to unprecedented performance on a large array of tasks when applied at scale. Similarly, autonomous driving generates vast amounts of spatiotemporal data, alluding to the possibility of harnessing scale to learn the underlying geometric and semantic structure of the environment and its evolution over time. In this direction, we propose a geometric and semantic self-supervised pre-training method, GASP, that learns a unified representation by predicting, at any queried future point in spacetime, (1) general occupancy, capturing the evolving structure of the 3D scene; (2) ego occupancy, modeling the ego vehicle path through the environment; and (3) distilled high-level features from a vision foundation model. By modeling geometric and semantic 4D occupancy fields instead of raw sensor measurements, the model learns a structured, generalizable representation of the environment and its evolution through time. We validate GASP on multiple autonomous driving benchmarks, demonstrating significant improvements in semantic occupancy forecasting, online mapping, and ego trajectory prediction. Our results demonstrate that continuous 4D geometric and semantic occupancy prediction provides a scalable and effective pre-training paradigm for autonomous driving. For code and additional visualizations, see \href{https://research.zenseact.com/publications/gasp/.

Existing solutions to zero-shot text classification either conduct prompting with pre-trained language models, which is sensitive to the choices of templates, or rely on large-scale annotated data of relevant tasks for meta-tuning. In this work, we propose a new paradigm based on self-supervised learning to solve zero-shot text classification tasks by tuning the language models with unlabeled data, called self-supervised tuning. By exploring the inherent structure of free texts, we propose a new learning objective called first sentence prediction to bridge the gap between unlabeled data and text classification tasks. After tuning the model to learn to predict the first sentence in a paragraph based on the rest, the model is able to conduct zero-shot inference on unseen tasks such as topic classification and sentiment analysis. Experimental results show that our model outperforms the state-of-the-art baselines on 7 out of 10 tasks. Moreover, the analysis reveals that our model is less sensitive to the prompt design. Our code and pre-trained models are publicly available at https://github.com/DAMO-NLP-SG/SSTuning .

We study how vision-language models (VLMs) trained on web-scale data can be integrated into end-to-end driving systems to boost generalization and enable interactivity with human users. While recent approaches adapt VLMs to driving via single-round visual question answering (VQA), human drivers reason about decisions in multiple steps. Starting from the localization of key objects, humans estimate object interactions before taking actions. The key insight is that with our proposed task, Graph VQA, where we model graph-structured reasoning through perception, prediction and planning question-answer pairs, we obtain a suitable proxy task to mimic the human reasoning process. We instantiate datasets (DriveLM-Data) built upon nuScenes and CARLA, and propose a VLM-based baseline approach (DriveLM-Agent) for jointly performing Graph VQA and end-to-end driving. The experiments demonstrate that Graph VQA provides a simple, principled framework for reasoning about a driving scene, and DriveLM-Data provides a challenging benchmark for this task. Our DriveLM-Agent baseline performs end-to-end autonomous driving competitively in comparison to state-of-the-art driving-specific architectures. Notably, its benefits are pronounced when it is evaluated zero-shot on unseen objects or sensor configurations. We hope this work can be the starting point to shed new light on how to apply VLMs for autonomous driving. To facilitate future research, all code, data, and models are available to the public.

Graph learning has become indispensable for interpreting and harnessing relational data in diverse fields, ranging from recommendation systems to social network analysis. In this context, a variety of GNNs have emerged as promising methodologies for encoding the structural information of graphs. By effectively capturing the graph's underlying structure, these GNNs have shown great potential in enhancing performance in graph learning tasks, such as link prediction and node classification. However, despite their successes, a significant challenge persists: these advanced methods often face difficulties in generalizing to unseen graph data that significantly differs from the training instances. In this work, our aim is to advance the graph learning paradigm by developing a general graph foundation model. This model is designed to understand the complex topological patterns present in diverse graph data, enabling it to excel in zero-shot graph learning tasks across different downstream datasets. To achieve this goal, we address several key technical challenges in our OpenGraph model. Firstly, we propose a unified graph tokenizer to adapt our graph model to generalize well on unseen graph data, even when the underlying graph properties differ significantly from those encountered during training. Secondly, we develop a scalable graph transformer as the foundational encoder, which effectively captures node-wise dependencies within the global topological context. Thirdly, we introduce a data augmentation mechanism enhanced by a LLM to alleviate the limitations of data scarcity in real-world scenarios. Extensive experiments validate the effectiveness of our framework. By adapting our OpenGraph to new graph characteristics and comprehending the nuances of diverse graphs, our approach achieves remarkable zero-shot graph learning performance across various settings and domains.

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 binding between proteins and ligands plays a crucial role in the realm of drug discovery. Previous deep learning approaches have shown promising results over traditional computationally intensive methods, but resulting in poor generalization due to limited supervised data. In this paper, we propose to learn protein-ligand binding representation in a self-supervised learning manner. Different from existing pre-training approaches which treat proteins and ligands individually, we emphasize to discern the intricate binding patterns from fine-grained interactions. Specifically, this self-supervised learning problem is formulated as a prediction of the conclusive binding complex structure given a pocket and ligand with a Transformer based interaction module, which naturally emulates the binding process. To ensure the representation of rich binding information, we introduce two pre-training tasks, i.e.~atomic pairwise distance map prediction and mask ligand reconstruction, which comprehensively model the fine-grained interactions from both structure and feature space. Extensive experiments have demonstrated the superiority of our method across various binding tasks, including protein-ligand affinity prediction, virtual screening and protein-ligand docking.

Self-supervised learning (SSL) achieves great success in speech recognition, while limited exploration has been attempted for other speech processing tasks. As speech signal contains multi-faceted information including speaker identity, paralinguistics, spoken content, etc., learning universal representations for all speech tasks is challenging. To tackle the problem, we propose a new pre-trained model, WavLM, to solve full-stack downstream speech tasks. WavLM jointly learns masked speech prediction and denoising in pre-training. By this means, WavLM does not only keep the speech content modeling capability by the masked speech prediction, but also improves the potential to non-ASR tasks by the speech denoising. In addition, WavLM employs gated relative position bias for the Transformer structure to better capture the sequence ordering of input speech. We also scale up the training dataset from 60k hours to 94k hours. WavLM Large achieves state-of-the-art performance on the SUPERB benchmark, and brings significant improvements for various speech processing tasks on their representative benchmarks. The code and pre-trained models are available at https://aka.ms/wavlm.

Deep learning has deeply influenced protein science, enabling breakthroughs in predicting protein properties, higher-order structures, and molecular interactions. This paper introduces DeepProtein, a comprehensive and user-friendly deep learning library tailored for protein-related tasks. It enables researchers to seamlessly address protein data with cutting-edge deep learning models. To assess model performance, we establish a benchmark evaluating different deep learning architectures across multiple protein-related tasks, including protein function prediction, subcellular localization prediction, protein-protein interaction prediction, and protein structure prediction. Furthermore, we introduce DeepProt-T5, a series of fine-tuned Prot-T5-based models that achieve state-of-the-art performance on four benchmark tasks, while demonstrating competitive results on six of others. Comprehensive documentation and tutorials are available which could ensure accessibility and support reproducibility. Built upon the widely used drug discovery library DeepPurpose, DeepProtein is publicly available at https://github.com/jiaqingxie/DeepProtein.

Graph Neural Networks (GNNs) have displayed considerable promise in graph representation learning across various applications. The core learning process requires the initialization of model weight matrices within each GNN layer, which is typically accomplished via classic initialization methods such as Xavier initialization. However, these methods were originally motivated to stabilize the variance of hidden embeddings and gradients across layers of Feedforward Neural Networks (FNNs) and Convolutional Neural Networks (CNNs) to avoid vanishing gradients and maintain steady information flow. In contrast, within the GNN context classical initializations disregard the impact of the input graph structure and message passing on variance. In this paper, we analyze the variance of forward and backward propagation across GNN layers and show that the variance instability of GNN initializations comes from the combined effect of the activation function, hidden dimension, graph structure and message passing. To better account for these influence factors, we propose a new initialization method for Variance Instability Reduction within GNN Optimization (Virgo), which naturally tends to equate forward and backward variances across successive layers. We conduct comprehensive experiments on 15 datasets to show that Virgo can lead to superior model performance and more stable variance at initialization on node classification, link prediction and graph classification tasks. Codes are in https://github.com/LspongebobJH/virgo_icml2023.

In this work, we aim to connect two research areas: instruction models and retrieval-based models. While instruction-tuned Large Language Models (LLMs) excel at extracting information from text, they are not suitable for semantic retrieval. Similarity search over embedding vectors allows to index and query vectors, but the similarity reflected in the embedding is sub-optimal for many use cases. We identify the task of retrieving sentences based on abstract descriptions of their content. We demonstrate the inadequacy of current text embeddings and propose an alternative model that significantly improves when used in standard nearest neighbor search. The model is trained using positive and negative pairs sourced through prompting an a large language model (LLM). While it is easy to source the training material from an LLM, the retrieval task cannot be performed by the LLM directly. This demonstrates that data from LLMs can be used not only for distilling more efficient specialized models than the original LLM, but also for creating new capabilities not immediately possible using the original model.

There have been many successful applications of sentence embedding methods. However, it has not been well understood what properties are captured in the resulting sentence embeddings depending on the supervision signals. In this paper, we focus on two types of sentence embedding methods with similar architectures and tasks: one fine-tunes pre-trained language models on the natural language inference task, and the other fine-tunes pre-trained language models on word prediction task from its definition sentence, and investigate their properties. Specifically, we compare their performances on semantic textual similarity (STS) tasks using STS datasets partitioned from two perspectives: 1) sentence source and 2) superficial similarity of the sentence pairs, and compare their performances on the downstream and probing tasks. Furthermore, we attempt to combine the two methods and demonstrate that combining the two methods yields substantially better performance than the respective methods on unsupervised STS tasks and downstream tasks.

Taking inspiration from Set Theory, we introduce SetCSE, an innovative information retrieval framework. SetCSE employs sets to represent complex semantics and incorporates well-defined operations for structured information querying under the provided context. Within this framework, we introduce an inter-set contrastive learning objective to enhance comprehension of sentence embedding models concerning the given semantics. Furthermore, we present a suite of operations, including SetCSE intersection, difference, and operation series, that leverage sentence embeddings of the enhanced model for complex sentence retrieval tasks. Throughout this paper, we demonstrate that SetCSE adheres to the conventions of human language expressions regarding compounded semantics, provides a significant enhancement in the discriminatory capability of underlying sentence embedding models, and enables numerous information retrieval tasks involving convoluted and intricate prompts which cannot be achieved using existing querying methods.

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.

Spoken language understanding (SLU) is a structure prediction task in the field of speech. Recently, many works on SLU that treat it as a sequence-to-sequence task have achieved great success. However, This method is not suitable for simultaneous speech recognition and understanding. In this paper, we propose a joint speech recognition and structure learning framework (JSRSL), an end-to-end SLU model based on span, which can accurately transcribe speech and extract structured content simultaneously. We conduct experiments on name entity recognition and intent classification using the Chinese dataset AISHELL-NER and the English dataset SLURP. The results show that our proposed method not only outperforms the traditional sequence-to-sequence method in both transcription and extraction capabilities but also achieves state-of-the-art performance on the two datasets.

Generative models for materials, especially inorganic crystals, hold potential to transform the theoretical prediction of novel compounds and structures. Advancement in this field depends critically on robust benchmarks and minimal, information-rich datasets that enable meaningful model evaluation. This paper critically examines common datasets and reported metrics for a crystal structure prediction taskx2014generating the most likely structures given the chemical composition of a material. We focus on three key issues: First, materials datasets should contain unique crystal structures; for example, we show that the widely-utilized carbon-24 dataset only contains approx40% unique structures. Second, materials datasets should not be split randomly if polymorphs of many different compositions are numerous, which we find to be the case for the perov-5 dataset. Third, benchmarks can mislead if used uncritically, e.g., reporting a match rate metric without considering the structural variety exhibited by identical building blocks. To address these oft-overlooked issues, we introduce several fixes. We provide revised versions of the carbon-24 dataset: one with duplicates removed, one deduplicated and split by number of atoms N, and two containing only identical structures but with different unit cells. We also propose a new split for the perov-5 dataset which ensures polymorphs are grouped within each split subset, setting a more sensible standard for benchmarking model performance. Finally, we present METRe and cRMSE, new model evaluation metrics that can correct existing issues with the match rate metric.

We propose a cascade of neural models that performs sentence classification, phrase recognition, and triple extraction to automatically structure the scholarly contributions of NLP publications. To identify the most important contribution sentences in a paper, we used a BERT-based classifier with positional features (Subtask 1). A BERT-CRF model was used to recognize and characterize relevant phrases in contribution sentences (Subtask 2). We categorized the triples into several types based on whether and how their elements were expressed in text, and addressed each type using separate BERT-based classifiers as well as rules (Subtask 3). Our system was officially ranked second in Phase 1 evaluation and first in both parts of Phase 2 evaluation. After fixing a submission error in Pharse 1, our approach yields the best results overall. In this paper, in addition to a system description, we also provide further analysis of our results, highlighting its strengths and limitations. We make our code publicly available at https://github.com/Liu-Hy/nlp-contrib-graph.

In populous countries, pending legal cases have been growing exponentially. There is a need for developing NLP-based techniques for processing and automatically understanding legal documents. To promote research in the area of Legal NLP we organized the shared task LegalEval - Understanding Legal Texts at SemEval 2023. LegalEval task has three sub-tasks: Task-A (Rhetorical Roles Labeling) is about automatically structuring legal documents into semantically coherent units, Task-B (Legal Named Entity Recognition) deals with identifying relevant entities in a legal document and Task-C (Court Judgement Prediction with Explanation) explores the possibility of automatically predicting the outcome of a legal case along with providing an explanation for the prediction. In total 26 teams (approx. 100 participants spread across the world) submitted systems paper. In each of the sub-tasks, the proposed systems outperformed the baselines; however, there is a lot of scope for improvement. This paper describes the tasks, and analyzes techniques proposed by various teams.

Existing models based on artificial neural networks (ANNs) for sentence classification often do not incorporate the context in which sentences appear, and classify sentences individually. However, traditional sentence classification approaches have been shown to greatly benefit from jointly classifying subsequent sentences, such as with conditional random fields. In this work, we present an ANN architecture that combines the effectiveness of typical ANN models to classify sentences in isolation, with the strength of structured prediction. Our model achieves state-of-the-art results on two different datasets for sequential sentence classification in medical abstracts.

We present our submission to the Task 5 of SemEval-2025 that aims to aid librarians in assigning subject tags to the library records by producing a list of likely relevant tags for a given document. We frame the task as an information retrieval problem, where the document content is used to retrieve subject tags from a large subject taxonomy. We leverage two types of encoder models to build a two-stage information retrieval system -- a bi-encoder for coarse-grained candidate extraction at the first stage, and a cross-encoder for fine-grained re-ranking at the second stage. This approach proved effective, demonstrating significant improvements in recall compared to single-stage methods and showing competitive results according to qualitative evaluation.

Decoder transformers have continued increasing in scale reaching hundreds of billions of parameters. Due to their scale the same decoder sets state-of-the-art results on various language tasks via prompting or fine-tuning. Yet, these large foundation models remain unusable for the related fields of semantic search and sentence embeddings. This prevents possibly new state-of-the-art results and forces organizations to train and maintain separate models. To this end, we propose SGPT to use decoders for sentence embeddings and semantic search via prompting or fine-tuning. At 5.8 billion parameters SGPT improves on the previously best sentence embeddings by a margin of 7% and outperforms a concurrent method with 175 billion parameters as measured on the BEIR search benchmark. Code, models and result files are freely available at https://github.com/Muennighoff/sgpt.

As a step toward better document-level understanding, we explore classification of a sequence of sentences into their corresponding categories, a task that requires understanding sentences in context of the document. Recent successful models for this task have used hierarchical models to contextualize sentence representations, and Conditional Random Fields (CRFs) to incorporate dependencies between subsequent labels. In this work, we show that pretrained language models, BERT (Devlin et al., 2018) in particular, can be used for this task to capture contextual dependencies without the need for hierarchical encoding nor a CRF. Specifically, we construct a joint sentence representation that allows BERT Transformer layers to directly utilize contextual information from all words in all sentences. Our approach achieves state-of-the-art results on four datasets, including a new dataset of structured scientific abstracts.

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.

Web search is an essential way for humans to obtain information, but it's still a great challenge for machines to understand the contents of web pages. In this paper, we introduce the task of structural reading comprehension (SRC) on web. Given a web page and a question about it, the task is to find the answer from the web page. This task requires a system not only to understand the semantics of texts but also the structure of the web page. Moreover, we proposed WebSRC, a novel Web-based Structural Reading Comprehension dataset. WebSRC consists of 400K question-answer pairs, which are collected from 6.4K web pages. Along with the QA pairs, corresponding HTML source code, screenshots, and metadata are also provided in our dataset. Each question in WebSRC requires a certain structural understanding of a web page to answer, and the answer is either a text span on the web page or yes/no. We evaluate various baselines on our dataset to show the difficulty of our task. We also investigate the usefulness of structural information and visual features. Our dataset and baselines have been publicly available at https://x-lance.github.io/WebSRC/.

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.

Neural networks -- especially those that use large, pre-trained language models -- have improved search engines in various ways. Most prominently, they can estimate the relevance of a passage or document to a user's query. In this work, we depart from this direction by exploring whether neural networks can effectively predict which of a document's passages are unlikely to be relevant to any query submitted to the search engine. We refer to this query-agnostic estimation of passage relevance as a passage's quality. We find that our novel methods for estimating passage quality allow passage corpora to be pruned considerably while maintaining statistically equivalent effectiveness; our best methods can consistently prune >25% of passages in a corpora, across various retrieval pipelines. Such substantial pruning reduces the operating costs of neural search engines in terms of computing resources, power usage, and carbon footprint -- both when processing queries (thanks to a smaller index size) and when indexing (lightweight models can prune low-quality passages prior to the costly dense or learned sparse encoding step). This work sets the stage for developing more advanced neural "learning-what-to-index" methods.

This report presents a unified instruction-based framework for learning generalized text embeddings optimized for both information retrieval (IR) and non-IR tasks. Built upon a decoder-only large language model (Mistral-7B), our approach combines in-context learning, soft supervision, and adaptive hard-negative mining to generate context-aware embeddings without task-specific fine-tuning. Structured instructions and few-shot examples are used to guide the model across diverse tasks, enabling strong performance on classification, semantic similarity, clustering, and reranking benchmarks. To improve semantic discrimination, we employ a soft labeling framework where continuous relevance scores, distilled from a high-performance dense retriever and reranker, serve as fine-grained supervision signals. In addition, we introduce adaptive margin-based hard-negative mining, which filters out semantically ambiguous negatives based on their similarity to positive examples, thereby enhancing training stability and retrieval robustness. Our model is evaluated on the newly introduced MTEB (English, v2) benchmark, covering 41 tasks across seven categories. Results show that our method achieves strong generalization and ranks among the top-performing models by Borda score, outperforming several larger or fully fine-tuned baselines. These findings highlight the effectiveness of combining in-context prompting, soft supervision, and adaptive sampling for scalable, high-quality embedding generation.

Typically, machine learning systems solve new tasks by training on thousands of examples. In contrast, humans can solve new tasks by reading some instructions, with perhaps an example or two. To take a step toward closing this gap, we introduce a framework for developing NLP systems that solve new tasks after reading their descriptions, synthesizing prior work in this area. We instantiate this framework with a new English language dataset, ZEST, structured for task-oriented evaluation on unseen tasks. Formulating task descriptions as questions, we ensure each is general enough to apply to many possible inputs, thus comprehensively evaluating a model's ability to solve each task. Moreover, the dataset's structure tests specific types of systematic generalization. We find that the state-of-the-art T5 model achieves a score of 12% on ZEST, leaving a significant challenge for NLP researchers.

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.

This paper summarizes our work on the first track of the ninth Dialog System Technology Challenge (DSTC 9), "Beyond Domain APIs: Task-oriented Conversational Modeling with Unstructured Knowledge Access". The goal of the task is to generate responses to user turns in a task-oriented dialog that require knowledge from unstructured documents. The task is divided into three subtasks: detection, selection and generation. In order to be compute efficient, we formulate the selection problem in terms of hierarchical classification steps. We achieve our best results with this model. Alternatively, we employ siamese sequence embedding models, referred to as Dense Knowledge Retrieval, to retrieve relevant documents. This method further reduces the computation time by a factor of more than 100x at the cost of degradation in R@1 of 5-6% compared to the first model. Then for either approach, we use Retrieval Augmented Generation to generate responses based on multiple selected snippets and we show how the method can be used to fine-tune trained embeddings.

Large language models (LLMs) have shown impressive performance in following natural language instructions to solve unseen tasks. However, it remains unclear whether models truly understand task definitions and whether the human-written definitions are optimal. In this paper, we systematically study the role of task definitions in instruction learning. We first conduct an ablation analysis informed by human annotations to understand which parts of a task definition are most important, and find that model performance only drops substantially when removing contents describing the task output, in particular label information. Next, we propose an automatic algorithm to compress task definitions to a minimal supporting set of tokens, and find that 60\% of tokens can be removed while maintaining or even improving model performance. Based on these results, we propose two strategies to help models better leverage task instructions: (1) providing only key information for tasks in a common structured format, and (2) adding a meta-tuning stage to help the model better understand the definitions. With these two strategies, we achieve a 4.2 Rouge-L improvement over 119 unseen test tasks.

Playlists have become a significant part of our listening experience because of the digital cloud-based services such as Spotify, Pandora, Apple Music. Owing to the meteoric rise in the usage of playlists, recommending playlists is crucial to music services today. Although there has been a lot of work done in playlist prediction, the area of playlist representation hasn't received that level of attention. Over the last few years, sequence-to-sequence models, especially in the field of natural language processing, have shown the effectiveness of learned embeddings in capturing the semantic characteristics of sequences. We can apply similar concepts to music to learn fixed length representations for playlists and use those representations for downstream tasks such as playlist discovery, browsing, and recommendation. In this work, we formulate the problem of learning a fixed-length playlist representation in an unsupervised manner, using Sequence-to-sequence (Seq2seq) models, interpreting playlists as sentences and songs as words. We compare our model with two other encoding architectures for baseline comparison. We evaluate our work using the suite of tasks commonly used for assessing sentence embeddings, along with a few additional tasks pertaining to music, and a recommendation task to study the traits captured by the playlist embeddings and their effectiveness for the purpose of music recommendation.

We consider the large-scale query-document retrieval problem: given a query (e.g., a question), return the set of relevant documents (e.g., paragraphs containing the answer) from a large document corpus. This problem is often solved in two steps. The retrieval phase first reduces the solution space, returning a subset of candidate documents. The scoring phase then re-ranks the documents. Critically, the retrieval algorithm not only desires high recall but also requires to be highly efficient, returning candidates in time sublinear to the number of documents. Unlike the scoring phase witnessing significant advances recently due to the BERT-style pre-training tasks on cross-attention models, the retrieval phase remains less well studied. Most previous works rely on classic Information Retrieval (IR) methods such as BM-25 (token matching + TF-IDF weights). These models only accept sparse handcrafted features and can not be optimized for different downstream tasks of interest. In this paper, we conduct a comprehensive study on the embedding-based retrieval models. We show that the key ingredient of learning a strong embedding-based Transformer model is the set of pre-training tasks. With adequately designed paragraph-level pre-training tasks, the Transformer models can remarkably improve over the widely-used BM-25 as well as embedding models without Transformers. The paragraph-level pre-training tasks we studied are Inverse Cloze Task (ICT), Body First Selection (BFS), Wiki Link Prediction (WLP), and the combination of all three.

BERT (Devlin et al., 2018) and RoBERTa (Liu et al., 2019) has set a new state-of-the-art performance on sentence-pair regression tasks like semantic textual similarity (STS). However, it requires that both sentences are fed into the network, which causes a massive computational overhead: Finding the most similar pair in a collection of 10,000 sentences requires about 50 million inference computations (~65 hours) with BERT. The construction of BERT makes it unsuitable for semantic similarity search as well as for unsupervised tasks like clustering. In this publication, we present Sentence-BERT (SBERT), a modification of the pretrained BERT network that use siamese and triplet network structures to derive semantically meaningful sentence embeddings that can be compared using cosine-similarity. This reduces the effort for finding the most similar pair from 65 hours with BERT / RoBERTa to about 5 seconds with SBERT, while maintaining the accuracy from BERT. We evaluate SBERT and SRoBERTa on common STS tasks and transfer learning tasks, where it outperforms other state-of-the-art sentence embeddings methods.

This article focuses on the development and evaluation of Small-sized Czech sentence embedding models. Small models are important components for real-time industry applications in resource-constrained environments. Given the limited availability of labeled Czech data, alternative approaches, including pre-training, knowledge distillation, and unsupervised contrastive fine-tuning, are investigated. Comprehensive intrinsic and extrinsic analyses are conducted, showcasing the competitive performance of our models compared to significantly larger counterparts, with approximately 8 times smaller size and 5 times faster speed than conventional Base-sized models. To promote cooperation and reproducibility, both the models and the evaluation pipeline are made publicly accessible. Ultimately, this article presents practical applications of the developed sentence embedding models in Seznam.cz, the Czech search engine. These models have effectively replaced previous counterparts, enhancing the overall search experience for instance, in organic search, featured snippets, and image search. This transition has yielded improved performance.

Over the past decade, machine learning has revolutionized computers' ability to analyze text through flexible computational models. Due to their structural similarity to written language, transformer-based architectures have also shown promise as tools to make sense of a range of multi-variate sequences from protein-structures, music, electronic health records to weather-forecasts. We can also represent human lives in a way that shares this structural similarity to language. From one perspective, lives are simply sequences of events: People are born, visit the pediatrician, start school, move to a new location, get married, and so on. Here, we exploit this similarity to adapt innovations from natural language processing to examine the evolution and predictability of human lives based on detailed event sequences. We do this by drawing on arguably the most comprehensive registry data in existence, available for an entire nation of more than six million individuals across decades. Our data include information about life-events related to health, education, occupation, income, address, and working hours, recorded with day-to-day resolution. We create embeddings of life-events in a single vector space showing that this embedding space is robust and highly structured. Our models allow us to predict diverse outcomes ranging from early mortality to personality nuances, outperforming state-of-the-art models by a wide margin. Using methods for interpreting deep learning models, we probe the algorithm to understand the factors that enable our predictions. Our framework allows researchers to identify new potential mechanisms that impact life outcomes and associated possibilities for personalized interventions.

Recent state-of-the-art natural language understanding models, such as BERT and XLNet, score a pair of sentences (A and B) using multiple cross-attention operations - a process in which each word in sentence A attends to all words in sentence B and vice versa. As a result, computing the similarity between a query sentence and a set of candidate sentences, requires the propagation of all query-candidate sentence-pairs throughout a stack of cross-attention layers. This exhaustive process becomes computationally prohibitive when the number of candidate sentences is large. In contrast, sentence embedding techniques learn a sentence-to-vector mapping and compute the similarity between the sentence vectors via simple elementary operations. In this paper, we introduce Distilled Sentence Embedding (DSE) - a model that is based on knowledge distillation from cross-attentive models, focusing on sentence-pair tasks. The outline of DSE is as follows: Given a cross-attentive teacher model (e.g. a fine-tuned BERT), we train a sentence embedding based student model to reconstruct the sentence-pair scores obtained by the teacher model. We empirically demonstrate the effectiveness of DSE on five GLUE sentence-pair tasks. DSE significantly outperforms several ELMO variants and other sentence embedding methods, while accelerating computation of the query-candidate sentence-pairs similarities by several orders of magnitude, with an average relative degradation of 4.6% compared to BERT. Furthermore, we show that DSE produces sentence embeddings that reach state-of-the-art performance on universal sentence representation benchmarks. Our code is made publicly available at https://github.com/microsoft/Distilled-Sentence-Embedding.

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.

The principal goal of the TREC Neural Cross-Language Information Retrieval (NeuCLIR) track is to study the impact of neural approaches to cross-language information retrieval. The track has created four collections, large collections of Chinese, Persian, and Russian newswire and a smaller collection of Chinese scientific abstracts. The principal tasks are ranked retrieval of news in one of the three languages, using English topics. Results for a multilingual task, also with English topics but with documents from all three newswire collections, are also reported. New in this second year of the track is a pilot technical documents CLIR task for ranked retrieval of Chinese technical documents using English topics. A total of 220 runs across all tasks were submitted by six participating teams and, as baselines, by track coordinators. Task descriptions and results are presented.

We consider the problem of Recognizing Textual Entailment within an Information Retrieval context, where we must simultaneously determine the relevancy as well as degree of entailment for individual pieces of evidence to determine a yes/no answer to a binary natural language question. We compare several variants of neural networks for sentence embeddings in a setting of decision-making based on evidence of varying relevance. We propose a basic model to integrate evidence for entailment, show that joint training of the sentence embeddings to model relevance and entailment is feasible even with no explicit per-evidence supervision, and show the importance of evaluating strong baselines. We also demonstrate the benefit of carrying over text comprehension model trained on an unrelated task for our small datasets. Our research is motivated primarily by a new open dataset we introduce, consisting of binary questions and news-based evidence snippets. We also apply the proposed relevance-entailment model on a similar task of ranking multiple-choice test answers, evaluating it on a preliminary dataset of school test questions as well as the standard MCTest dataset, where we improve the neural model state-of-art.