Daily Papers

As the large language model (LLM) ecosystem expands, individual models exhibit varying capabilities across queries, benchmarks, and domains, motivating the development of LLM routing. While prior work has largely focused on router mechanism design, LLM profiles, which capture model capabilities, remain underexplored. In this work, we ask: How does LLM profile design affect routing performance across different routers? Addressing this question helps clarify the role of profiles in routing, disentangle profile design from router design, and enable fairer comparison and more principled development of routing systems. To this end, we view LLM profiling as a structured information integration problem over heterogeneous interaction histories. We develop a general design space of LLM profiles, named RouteProfile, along four key dimensions: organizational form, representation type, aggregation depth, and learning configuration. Through systematic evaluation across three representative routers under both standard and new-LLM generalization settings, we show that: (1) structured profiles consistently outperform flat ones; (2) query-level signals are more reliable than coarse domain-level signals; and (3) generalization to newly introduced models benefits most from structured profiles under trainable configurations. Overall, our work highlights LLM profile design as an important direction for future routing research.

Text-to-image (T2I) generation has advanced rapidly, yet faithfully capturing spatial relationships described in natural language prompts remains a major challenge. Prior efforts have addressed this issue through prompt optimization, spatially grounded generation, and semantic refinement. This work introduces a lightweight approach that augments prompts with tuple-based structured information, using a fine-tuned language model for automatic conversion and seamless integration into T2I pipelines. Experimental results demonstrate substantial improvements in spatial accuracy, without compromising overall image quality as measured by Inception Score. Furthermore, the automatically generated tuples exhibit quality comparable to human-crafted tuples. This structured information provides a practical and portable solution to enhance spatial relationships in T2I generation, addressing a key limitation of current large-scale generative systems.

The task of condensing large chunks of textual information into concise and structured tables has gained attention recently due to the emergence of Large Language Models (LLMs) and their potential benefit for downstream tasks, such as text summarization and text mining. Previous approaches often generate tables that directly replicate information from the text, limiting their applicability in broader contexts, as text-to-table generation in real-life scenarios necessitates information extraction, reasoning, and integration. However, there is a lack of both datasets and methodologies towards this task. In this paper, we introduce LiveSum, a new benchmark dataset created for generating summary tables of competitions based on real-time commentary texts. We evaluate the performances of state-of-the-art LLMs on this task in both fine-tuning and zero-shot settings, and additionally propose a novel pipeline called T^3(Text-Tuple-Table) to improve their performances. Extensive experimental results demonstrate that LLMs still struggle with this task even after fine-tuning, while our approach can offer substantial performance gains without explicit training. Further analyses demonstrate that our method exhibits strong generalization abilities, surpassing previous approaches on several other text-to-table datasets. Our code and data can be found at https://github.com/HKUST-KnowComp/LiveSum-TTT.

Scientific research involves complex information-seeking and reasoning workflows across heterogeneous sources. However, existing benchmarks primarily emphasize general-domain retrieval or static scientific question answering, and therefore fail to assess key capabilities required in realistic scientific research workflows. We introduce SciExplore, a benchmark designed to evaluate scientific information-seeking and reasoning capabilities of LLMs and agents. SciExplore comprises four task types covering 103 expert-curated tasks across more than ten scientific disciplines: scientific database navigation, ambiguous literature retrieval, missing reference completion, and cross-source structured knowledge synthesis, which probe progressively higher-level abilities from entity-level reasoning and document-level identification to evidence-level grounding and domain-level synthesis. We evaluate over ten state-of-the-art LLMs and autonomous agents on SciExplore, revealing substantial performance gaps with performance degrading sharply as task complexity increases and extremely low accuracy on the most challenging structured synthesis tasks. These results highlight significant limitations of current models and agents in realistic scientific information-seeking scenarios.

Document parsing is essential for converting unstructured and semi-structured documents-such as contracts, academic papers, and invoices-into structured, machine-readable data. Document parsing extract reliable structured data from unstructured inputs, providing huge convenience for numerous applications. Especially with recent achievements in Large Language Models, document parsing plays an indispensable role in both knowledge base construction and training data generation. This survey presents a comprehensive review of the current state of document parsing, covering key methodologies, from modular pipeline systems to end-to-end models driven by large vision-language models. Core components such as layout detection, content extraction (including text, tables, and mathematical expressions), and multi-modal data integration are examined in detail. Additionally, this paper discusses the challenges faced by modular document parsing systems and vision-language models in handling complex layouts, integrating multiple modules, and recognizing high-density text. It emphasizes the importance of developing larger and more diverse datasets and outlines future research directions.

Pre-trained transformer language models (LMs) have in recent years become the dominant paradigm in applied NLP. These models have achieved state-of-the-art performance on tasks such as information extraction, question answering, sentiment analysis, document classification and many others. In the biomedical domain, significant progress has been made in adapting this paradigm to NLP tasks that require the integration of domain-specific knowledge as well as statistical modelling of language. In particular, research in this area has focused on the question of how best to construct LMs that take into account not only the patterns of token distribution in medical text, but also the wealth of structured information contained in terminology resources such as the UMLS. This work contributes a data-centric paradigm for enriching the language representations of biomedical transformer-encoder LMs by extracting text sequences from the UMLS. This allows for graph-based learning objectives to be combined with masked-language pre-training. Preliminary results from experiments in the extension of pre-trained LMs as well as training from scratch show that this framework improves downstream performance on multiple biomedical and clinical Named Entity Recognition (NER) tasks.

Although large language models (LLMs) have made significant progress in understanding Structured Knowledge (SK) like KG and Table, existing evaluations for SK understanding are non-rigorous (i.e., lacking evaluations of specific capabilities) and focus on a single type of SK. Therefore, we aim to propose a more comprehensive and rigorous structured knowledge understanding benchmark to diagnose the shortcomings of LLMs. In this paper, we introduce SKA-Bench, a Structured Knowledge Augmented QA Benchmark that encompasses four widely used structured knowledge forms: KG, Table, KG+Text, and Table+Text. We utilize a three-stage pipeline to construct SKA-Bench instances, which includes a question, an answer, positive knowledge units, and noisy knowledge units. To evaluate the SK understanding capabilities of LLMs in a fine-grained manner, we expand the instances into four fundamental ability testbeds: Noise Robustness, Order Insensitivity, Information Integration, and Negative Rejection. Empirical evaluations on 8 representative LLMs, including the advanced DeepSeek-R1, indicate that existing LLMs still face significant challenges in understanding structured knowledge, and their performance is influenced by factors such as the amount of noise, the order of knowledge units, and hallucination phenomenon. Our dataset and code are available at https://github.com/Lza12a/SKA-Bench.

As an embodiment of intelligence evolution toward interconnected architectures, Deep Research Agents (DRAs) systematically exhibit the capabilities in task decomposition, cross-source retrieval, multi-stage reasoning, information integration, and structured output, which markedly enhance performance on complex and open-ended tasks. However, existing benchmarks remain deficient in evaluation dimensions, response format, and scoring mechanisms, limiting their effectiveness in assessing such agents. This paper introduces Dr. Bench, a multidimensional evaluation framework tailored to DRAs and long-form report-style responses. The benchmark comprises 214 expert-curated challenging tasks across 10 broad domains, each accompanied by manually constructed reference bundles to support composite evaluation. This framework incorporates metrics for semantic quality, topical focus, and retrieval trustworthiness, enabling a comprehensive evaluation of long reports generated by DRAs. Extensive experimentation confirms the superior performance of mainstream DRAs over web-search-tool-augmented reasoning models, yet reveals considerable scope for further improvement. This study provides a robust foundation for capability assessment, architectural refinement, and paradigm advancement of DRAs.

Breast cancer is a major global health concern, and mammography screening plays a central role in early detection. The large volume of screening examinations creates a substantial workload for radiologists, making accurate and consistent report generation a critical clinical challenge. Existing automated mammography report generation methods primarily focus on direct visual-to-text mapping, while overlooking the structured clinical reasoning process followed by radiologists in real-world practice. To address this limitation, we propose MammoRG, a mammography report generation framework that explicitly simulates the clinical reporting workflow by following the BI-RADS guideline and incorporating prior clinical knowledge to produce diagnostic reports. Specifically, MammoRG adopts a two-stage training framework. In the first stage, the model learns to integrate clinically relevant prior knowledge from a patient's four-view mammograms through classification-based supervision. In the second stage, a terminology-aware supervised fine-tuning strategy is introduced to model mammography-specific clinical terms as atomic semantic units, enabling the generation of high-quality reports with improved clinical consistency. To facilitate clinical efficacy evaluation of generated reports, we further develop MammoRGTool, a dedicated mammography report parsing tool that extracts structured clinical information from free-text reports. Extensive experiments demonstrate that MammoRG consistently outperforms existing methods across multiple clinical efficacy metrics, particularly in diagnosis-related BI-RADS F1, where it surpasses the second-best model by 2.73%, 2.04%, 1.90%, and 3.27% on the internal, external 1, external 2, and VinDr-Mammo datasets, respectively.

Recent advancements in large language models have significantly improved their context windows, yet challenges in effective long-term memory management remain. We introduce MemTree, an algorithm that leverages a dynamic, tree-structured memory representation to optimize the organization, retrieval, and integration of information, akin to human cognitive schemas. MemTree organizes memory hierarchically, with each node encapsulating aggregated textual content, corresponding semantic embeddings, and varying abstraction levels across the tree's depths. Our algorithm dynamically adapts this memory structure by computing and comparing semantic embeddings of new and existing information to enrich the model's context-awareness. This approach allows MemTree to handle complex reasoning and extended interactions more effectively than traditional memory augmentation methods, which often rely on flat lookup tables. Evaluations on benchmarks for multi-turn dialogue understanding and document question answering show that MemTree significantly enhances performance in scenarios that demand structured memory management.

Recent advancements in biological research leverage the integration of molecules, proteins, and natural language to enhance drug discovery. However, current models exhibit several limitations, such as the generation of invalid molecular SMILES, underutilization of contextual information, and equal treatment of structured and unstructured knowledge. To address these issues, we propose BioT5, a comprehensive pre-training framework that enriches cross-modal integration in biology with chemical knowledge and natural language associations. BioT5 utilizes SELFIES for 100% robust molecular representations and extracts knowledge from the surrounding context of bio-entities in unstructured biological literature. Furthermore, BioT5 distinguishes between structured and unstructured knowledge, leading to more effective utilization of information. After fine-tuning, BioT5 shows superior performance across a wide range of tasks, demonstrating its strong capability of capturing underlying relations and properties of bio-entities. Our code is available at https://github.com/QizhiPei/BioT5{Github}.

Deep research agents aim to solve complex knowledge-intensive tasks through long-horizon planning, evidence gathering, reasoning, and report generation. While recent progress in search agents has demonstrated strong capabilities in information retrieval and answer verification, most existing training datasets remain search-centric, focusing primarily on closed-ended question answering and information localization. As a result, they mainly train information-seeking behavior while providing limited coverage of key deep research capabilities, including evidence integration, knowledge synthesis, planning, file understanding, and structured report generation. In this work, we propose a unified trajectory construction paradigm for deep research agents that combines closed-ended QA and open-ended exploration. The proposed framework consists of graph-grounded task formulation, agentic trajectory rollout, and multi-dimensional trajectory verification, enabling scalable synthesis of high-quality agentic trajectories spanning long-chain complex reasoning, deep research instruction following, report writing, file understanding and generation, and skills usage. Compared with existing search-oriented datasets, our synthesized trajectories place greater emphasis on knowledge synthesis, complex reasoning, and planning. S1-DeepResearch-32B achieves state-of-the-art performance among open-source models of comparable scale across 20 benchmarks spanning five capability dimensions, including complex reasoning, instruction following, report generation, file understanding, and skills usage. On several challenging deep research benchmarks, it approaches the performance of leading proprietary frontier models. These results highlight the importance of jointly modeling information acquisition, knowledge synthesis, and planning-oriented agent behaviors for building effective deep research agents.

Automatic open-domain dialogue evaluation has attracted increasing attention. Trainable evaluation metrics, typically trained with true positive and randomly selected negative responses, tend to assign higher scores to responses that share greater content similarity with a given context. However, adversarial negative responses, despite possessing high content similarity with the contexts, are semantically different. Consequently, existing evaluation metrics are not robust enough to evaluate such responses, resulting in low correlations with human judgments. While recent studies have demonstrated the effectiveness of Large Language Models (LLMs) for open-domain dialogue evaluation, they still face challenges in effectively handling adversarial negative examples. In this paper, we propose an effective framework for open-domain dialogue evaluation, which combines domain-specific language models (SLMs) enhanced with Abstract Meaning Representation (AMR) knowledge with LLMs. The SLMs can explicitly incorporate AMR graph information of the dialogue through a gating mechanism for enhanced dialogue semantic representation learning. Both the evaluation result from the SLMs and the AMR graph information are incorporated into the LLM's prompt for enhanced evaluation performance. Experimental results on open-domain dialogue evaluation tasks demonstrate the superiority of our method compared to a wide range of state-of-the-art baselines, especially in discriminating adversarial negative responses. Our code and data are publicly available at https://github.com/Bernard-Yang/SIMAMR.

This paper introduces VisuCraft, a novel framework designed to significantly enhance the capabilities of Large Vision-Language Models (LVLMs) in complex visual-guided creative content generation. Existing LVLMs often exhibit limitations in maintaining high visual fidelity, genuine creativity, and precise adherence to nuanced user instructions when generating long-form texts. VisuCraft addresses these challenges by integrating a multimodal structured information extractor (E) and a dynamic prompt generation module (G). The extractor distills fine-grained visual attributes from input images into a rich, structured representation, which the dynamic prompt module then combines with user instructions to create highly optimized prompts for underlying LVLMs (e.g., LLaVA, InstructBLIP). Evaluated on the self-constructed ImageStoryGen-500K dataset using VisuGen Metrics (Visual Grounding, Creativity, and Instruction Adherence), VisuCraft consistently outperforms baseline LVLMs across tasks like story generation and poetry composition. Our results demonstrate remarkable improvements, particularly in creativity and instruction adherence, validating VisuCraft's effectiveness in producing imaginative, visually grounded, and user-aligned long-form creative text. This work unlocks new potential for LVLMs in sophisticated creative AI applications.

Introduction: The scientific publishing landscape is expanding rapidly, creating challenges for researchers to stay up-to-date with the evolution of the literature. Natural Language Processing (NLP) has emerged as a potent approach to automating knowledge extraction from this vast amount of publications and preprints. Tasks such as Named-Entity Recognition (NER) and Named-Entity Linking (NEL), in conjunction with context-dependent semantic interpretation, offer promising and complementary approaches to extracting structured information and revealing key concepts. Results: We present the SourceData-NLP dataset produced through the routine curation of papers during the publication process. A unique feature of this dataset is its emphasis on the annotation of bioentities in figure legends. We annotate eight classes of biomedical entities (small molecules, gene products, subcellular components, cell lines, cell types, tissues, organisms, and diseases), their role in the experimental design, and the nature of the experimental method as an additional class. SourceData-NLP contains more than 620,000 annotated biomedical entities, curated from 18,689 figures in 3,223 papers in molecular and cell biology. We illustrate the dataset's usefulness by assessing BioLinkBERT and PubmedBERT, two transformers-based models, fine-tuned on the SourceData-NLP dataset for NER. We also introduce a novel context-dependent semantic task that infers whether an entity is the target of a controlled intervention or the object of measurement. Conclusions: SourceData-NLP's scale highlights the value of integrating curation into publishing. Models trained with SourceData-NLP will furthermore enable the development of tools able to extract causal hypotheses from the literature and assemble them into knowledge graphs.

In customer service technical support, swiftly and accurately retrieving relevant past issues is critical for efficiently resolving customer inquiries. The conventional retrieval methods in retrieval-augmented generation (RAG) for large language models (LLMs) treat a large corpus of past issue tracking tickets as plain text, ignoring the crucial intra-issue structure and inter-issue relations, which limits performance. We introduce a novel customer service question-answering method that amalgamates RAG with a knowledge graph (KG). Our method constructs a KG from historical issues for use in retrieval, retaining the intra-issue structure and inter-issue relations. During the question-answering phase, our method parses consumer queries and retrieves related sub-graphs from the KG to generate answers. This integration of a KG not only improves retrieval accuracy by preserving customer service structure information but also enhances answering quality by mitigating the effects of text segmentation. Empirical assessments on our benchmark datasets, utilizing key retrieval (MRR, Recall@K, NDCG@K) and text generation (BLEU, ROUGE, METEOR) metrics, reveal that our method outperforms the baseline by 77.6% in MRR and by 0.32 in BLEU. Our method has been deployed within LinkedIn's customer service team for approximately six months and has reduced the median per-issue resolution time by 28.6%.

In software maintenance, bug reproduction is essential for effective fault localization and repair. Manually writing reproduction scripts is a time-consuming task with high requirements for developers. Hence, automation of bug reproduction has increasingly attracted attention from researchers and practitioners. However, the existing studies on bug reproduction are generally limited to specific bug types such as program crashes, and hard to be applied to general bug reproduction. In this paper, considering the superior performance of agent-based methods in code intelligence tasks, we focus on designing an agent-based framework for the task. Directly employing agents would lead to limited bug reproduction performance, due to entangled subtasks, lengthy retrieved context, and unregulated actions. To mitigate the challenges, we propose an Automated gEneral buG reproductIon Scripts generation framework, named AEGIS, which is the first agent-based framework for the task. AEGIS mainly contains two modules: (1) A concise context construction module, which aims to guide the code agent in extracting structured information from issue descriptions, identifying issue-related code with detailed explanations, and integrating these elements to construct the concise context; (2) A FSM-based multi-feedback optimization module to further regulate the behavior of the code agent within the finite state machine (FSM), ensuring a controlled and efficient script generation process based on multi-dimensional feedback. Extensive experiments on the public benchmark dataset show that AEGIS outperforms the state-of-the-art baseline by 23.0% in F->P metric. In addition, the bug reproduction scripts generated by AEGIS can improve the relative resolved rate of Agentless by 12.5%.

Large language models (LLMs) have achieved remarkable success in text-based tasks but often struggle to provide actionable guidance in real-world physical environments. This is because of their inability to recognize their limited understanding of the user's physical context. We present SituationalLLM, a novel approach that integrates structured scene information into an LLM to deliver proactive, context-aware assistance. By encoding objects, attributes, and relationships in a custom Scene Graph Language, SituationalLLM actively identifies gaps in environmental context and seeks clarifications during user interactions. This behavior emerges from training on the Situational Awareness Database for Instruct-Tuning (SAD-Instruct), which combines diverse, scenario-specific scene graphs with iterative, dialogue-based refinements. Experimental results indicate that SituationalLLM outperforms generic LLM baselines in task specificity, reliability, and adaptability, paving the way for environment-aware AI assistants capable of delivering robust, user-centric guidance under real-world constraints.

Acute poly-substance intoxication requires rapid, life-saving decisions under substantial uncertainty, as clinicians must rely on incomplete ingestion details and nonspecific symptoms. Effective diagnostic reasoning in this chaotic environment requires fusing unstructured, non-medical narratives (e.g. paramedic scene descriptions and unreliable patient self-reports or known histories), with structured medical data like vital signs. While Large Language Models (LLMs) show potential for processing such heterogeneous inputs, they struggle in this setting, often underperforming simple baselines that rely solely on patient histories. To address this, we present DeToxR (Decision-support for Toxicology with Reasoning), the first adaptation of Reinforcement Learning (RL) to emergency toxicology. We design a robust data-fusion engine for multi-label prediction across 14 substance classes based on an LLM finetuned with Group Relative Policy Optimization (GRPO). We optimize the model's reasoning directly using a clinical performance reward. By formulating a multi-label agreement metric as the reward signal, the model is explicitly penalized for missing co-ingested substances and hallucinating absent poisons. Our model significantly outperforms its unadapted base LLM counterpart and supervised baselines. Furthermore, in a clinical validation study, the model indicates a clinical advantage by outperforming an expert toxicologist in identifying the correct poisons (Micro-F1: 0.644 vs. 0.473). These results demonstrate the potential of RL-aligned LLMs to synthesize unstructured pre-clinical narratives and structured medical data for decision support in high-stakes environments.

Large Language Models (LLMs) present massive inherent knowledge and superior semantic comprehension capability, which have revolutionized various tasks in natural language processing. Despite their success, a critical gap remains in enabling LLMs to perform knowledge graph completion (KGC). Empirical evidence suggests that LLMs consistently perform worse than conventional KGC approaches, even through sophisticated prompt design or tailored instruction-tuning. Fundamentally, applying LLMs on KGC introduces several critical challenges, including a vast set of entity candidates, hallucination issue of LLMs, and under-exploitation of the graph structure. To address these challenges, we propose a novel instruction-tuning-based method, namely FtG. Specifically, we present a filter-then-generate paradigm and formulate the KGC task into a multiple-choice question format. In this way, we can harness the capability of LLMs while mitigating the issue casused by hallucinations. Moreover, we devise a flexible ego-graph serialization prompt and employ a structure-text adapter to couple structure and text information in a contextualized manner. Experimental results demonstrate that FtG achieves substantial performance gain compared to existing state-of-the-art methods. The instruction dataset and code are available at https://github.com/LB0828/FtG.

Large Language Models (LLMs) often suffer from hallucination and struggle with complex reasoning tasks requiring multi-hop domain knowledge. While integrating Knowledge Graphs (KGs) provides a structured and verifiable information source, current KG-enhanced LLM paradigms usually rely on single-agent path extraction and fixed prompting, lacking adaptability and facing huge search spaces. To address these challenges, we propose RACER, a Reinforced Agent Collaboration framework for Explainable Reasoning on knowledge graphs. RACER employs a semantic-aware action pruning and teacher-guided reinforcement learning mechanism to efficiently extract high-quality reasoning pathways from large-scale KGs. Furthermore, to mitigate single-path generation pitfalls, we introduce a cross-task accumulated shared memory graph paired with an attention-driven multi-path knowledge refinement module. Finally, RACER orchestrates these components through a four-role multi-agent collaboration system (GraphAgent, TemplateAgent, AnswerAgent, and CriticAgent) to dynamically refine prompts and evaluate answers. Extensive experiments on CommonsenseQA and OpenBookQA datasets demonstrate that RACER significantly outperforms state-of-the-art KG-enhanced LLM baselines with an average improvement of 5\%, offering robust and highly interpretable reasoning capabilities.

Histopathologic diagnosis relies on simultaneous integration of information from a broad range of scales, ranging from nuclear aberrations (approx O(0.1{μm})) through cellular structures (approx O(10{μm})) to the global tissue architecture (gtrapprox O(1{mm})). To explicitly mimic how human pathologists combine multi-scale information, we introduce a family of multi-encoder FCNs with deep fusion. We present a simple block for merging model paths with differing spatial scales in a spatial relationship-preserving fashion, which can readily be included in standard encoder-decoder networks. Additionally, a context classification gate block is proposed as an alternative for the incorporation of global context. Our experiments were performed on three publicly available whole-slide images of recent challenges (PAIP 2019, BACH 2020, CAMELYON 2016). The multi-scale architectures consistently outperformed the baseline single-scale U-Nets by a large margin. They benefit from local as well as global context and particularly a combination of both. If feature maps from different scales are fused, doing so in a manner preserving spatial relationships was found to be beneficial. Deep guidance by a context classification loss appeared to improve model training at low computational costs. All multi-scale models had a reduced GPU memory footprint compared to ensembles of individual U-Nets trained on different image scales. Additional path fusions were shown to be possible at low computational cost, opening up possibilities for further, systematic and task-specific architecture optimization. The findings demonstrate the potential of the presented family of human-inspired, end-to-end trainable, multi-scale multi-encoder FCNs to improve deep histopathologic diagnosis by extensive integration of largely different spatial scales.

CoT has significantly enhanced the reasoning ability of LLMs while it faces challenges when extended to multimodal domains, particularly in mathematical tasks. Existing MLLMs typically perform textual reasoning solely from a single static mathematical image, overlooking dynamic visual acquisition during reasoning. In contrast, humans repeatedly examine visual image and employ step-by-step reasoning to prove intermediate propositions. This strategy of decomposing the problem-solving process into key logical nodes adheres to Miller's Law in cognitive science. Inspired by this insight, we propose a ViRC framework for multimodal mathematical tasks, introducing a Reason Chunking mechanism that structures multimodal mathematical CoT into consecutive Critical Reasoning Units (CRUs) to simulate human expert problem-solving patterns. CRUs ensure intra-unit textual coherence for intermediate proposition verification while integrating visual information across units to generate subsequent propositions and support structured reasoning. To this end, we present CRUX dataset by using three visual tools and four reasoning patterns to provide explicitly annotated CRUs across multiple reasoning paths for each mathematical problem. Leveraging the CRUX dataset, we propose a progressive training strategy inspired by human cognitive learning, which includes Instructional SFT, Practice SFT, and Strategic RL, aimed at further strengthening the Reason Chunking ability of the model. The resulting ViRC-7B model achieves a 18.8% average improvement over baselines across multiple mathematical benchmarks. Code is available at https://github.com/Leon-LihongWang/ViRC.

Augmenting Large Language Models (LLMs) for Question Answering (QA) with domain specific data has attracted wide attention. However, domain data often exists in a hybrid format, including text and semi-structured tables, posing challenges for the seamless integration of information. Table-to-Text Generation is a promising solution by facilitating the transformation of hybrid data into a uniformly text-formatted corpus. Although this technique has been widely studied by the NLP community, there is currently no comparative analysis on how corpora generated by different table-to-text methods affect the performance of QA systems. In this paper, we address this research gap in two steps. First, we innovatively integrate table-to-text generation into the framework of enhancing LLM-based QA systems with domain hybrid data. Then, we utilize this framework in real-world industrial data to conduct extensive experiments on two types of QA systems (DSFT and RAG frameworks) with four representative methods: Markdown format, Template serialization, TPLM-based method, and LLM-based method. Based on the experimental results, we draw some empirical findings and explore the underlying reasons behind the success of some methods. We hope the findings of this work will provide a valuable reference for the academic and industrial communities in developing robust QA systems.

This research presents a comprehensive methodology for utilizing an ontology-driven structured prompts system in interplay with ChatGPT, a widely used large language model (LLM). The study develops formal models, both information and functional, and establishes the methodological foundations for integrating ontology-driven prompts with ChatGPT's meta-learning capabilities. The resulting productive triad comprises the methodological foundations, advanced information technology, and the OntoChatGPT system, which collectively enhance the effectiveness and performance of chatbot systems. The implementation of this technology is demonstrated using the Ukrainian language within the domain of rehabilitation. By applying the proposed methodology, the OntoChatGPT system effectively extracts entities from contexts, classifies them, and generates relevant responses. The study highlights the versatility of the methodology, emphasizing its applicability not only to ChatGPT but also to other chatbot systems based on LLMs, such as Google's Bard utilizing the PaLM 2 LLM. The underlying principles of meta-learning, structured prompts, and ontology-driven information retrieval form the core of the proposed methodology, enabling their adaptation and utilization in various LLM-based systems. This versatile approach opens up new possibilities for NLP and dialogue systems, empowering developers to enhance the performance and functionality of chatbot systems across different domains and languages.

We identify the free half shuffle algebra of Schützenberger (1958) with an algebra of real-valued functionals on paths, where the half shuffle emulates integration of a functional against another. We then provide two, to our knowledge, new identities in arity 3 involving its commutator (area), and show that these are sufficient to recover the Zinbiel and Tortkara identities of Dzhumadil'daev (2007). We use these identities to prove that any element of the free half shuffle algebra can be expressed as a polynomial over iterated areas. Moreover, we consider minimal sets of iterated integrals defined through the recursive application of the half shuffle on Hall trees. Leveraging the duality between this set of Hall integrals and classical Hall bases of the free Lie algebra, we prove using combinatorial arguments that any element of the free half shuffle algebra can be written uniquely as a polynomial over Hall integrals. We interpret this result as a structure theorem for streamed information, loosely analogous to the unique prime factorisation of integers, allowing to split any real valued function on streamed data into two parts: a first that extracts and packages the streamed information into recursively defined atomic objects (Hall integrals), and a second that evaluates a polynomial function in these objects without further reference to the original stream. The question of whether a similar result holds if Hall integrals are replaced by Hall areas is left as an open conjecture. Finally, we construct a canonical, but to our knowledge, new decomposition of the free half shuffle algebra as shuffle power series in the greatest letter of the original alphabet with coefficients in a sub-algebra freely generated by a new alphabet with an infinite number of letters. We use this construction to provide a second proof of our structure theorem.

Machine Reading Comprehension (MRC) holds a pivotal role in shaping Medical Question Answering Systems (QAS) and transforming the landscape of accessing and applying medical information. However, the inherent challenges in the medical field, such as complex terminology and question ambiguity, necessitate innovative solutions. One key solution involves integrating specialized medical datasets and creating dedicated datasets. This strategic approach enhances the accuracy of QAS, contributing to advancements in clinical decision-making and medical research. To address the intricacies of medical terminology, a specialized dataset was integrated, exemplified by a novel Span extraction dataset derived from emrQA but restructured into 163,695 questions and 4,136 manually obtained answers, this new dataset was called emrQA-msquad dataset. Additionally, for ambiguous questions, a dedicated medical dataset for the Span extraction task was introduced, reinforcing the system's robustness. The fine-tuning of models such as BERT, RoBERTa, and Tiny RoBERTa for medical contexts significantly improved response accuracy within the F1-score range of 0.75 to 1.00 from 10.1% to 37.4%, 18.7% to 44.7% and 16.0% to 46.8%, respectively. Finally, emrQA-msquad dataset is publicy available at https://huggingface.co/datasets/Eladio/emrqa-msquad.

To address the limitations of Transformer decoders in capturing edge details, recognizing local textures and modeling spatial continuity, this paper proposes a novel decoder framework specifically designed for medical image segmentation, comprising three core modules. First, the Adaptive Cross-Fusion Attention (ACFA) module integrates channel feature enhancement with spatial attention mechanisms and introduces learnable guidance in three directions (planar, horizontal, and vertical) to enhance responsiveness to key regions and structural orientations. Second, the Triple Feature Fusion Attention (TFFA) module fuses features from Spatial, Fourier and Wavelet domains, achieving joint frequency-spatial representation that strengthens global dependency and structural modeling while preserving local information such as edges and textures, making it particularly effective in complex and blurred boundary scenarios. Finally, the Structural-aware Multi-scale Masking Module (SMMM) optimizes the skip connections between encoder and decoder by leveraging multi-scale context and structural saliency filtering, effectively reducing feature redundancy and improving semantic interaction quality. Working synergistically, these modules not only address the shortcomings of traditional decoders but also significantly enhance performance in high-precision tasks such as tumor segmentation and organ boundary extraction, improving both segmentation accuracy and model generalization. Experimental results demonstrate that this framework provides an efficient and practical solution for medical image segmentation.

Large Language Models (LLMs) have shown strong promise for mining Electronic Health Records (EHRs) by reasoning over longitudinal clinical information to capture context-rich patient trajectories. However, leveraging LLMs for structured EHRs (e.g., standardized diagnosis and medication codes) presents two key challenges. First, translating time-stamped EHR sequences into plain text can obscure both temporal structure and code identities, weakening the ability to capture code co-occurrence and longitudinal regularities. Second, unlike cohort-trained predictive models that learn a shared, task-aligned representation space across patients, LLMs are often applied in a case-isolated inference setting where each patient is processed independently without leveraging population-level patterns. To address these challenges, we introduce RePrompT, a time-aware LLM framework that integrates structured EHR encoders through prompt tuning, without modifying underlying architectures. Specifically, RePrompT recurrently incorporates latent states from prior visits to preserve longitudinal information, and injects population-level information through trainable prompt tokens derived from a cohort-trained, task-aligned EHR encoder. Experiments on MIMIC-III and MIMIC-IV demonstrate that RePrompT consistently outperforms both EHR-based and LLM-based baselines across multiple clinical prediction tasks.

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.

We introduce a novel 3D generation method for versatile and high-quality 3D asset creation. The cornerstone is a unified Structured LATent (SLAT) representation which allows decoding to different output formats, such as Radiance Fields, 3D Gaussians, and meshes. This is achieved by integrating a sparsely-populated 3D grid with dense multiview visual features extracted from a powerful vision foundation model, comprehensively capturing both structural (geometry) and textural (appearance) information while maintaining flexibility during decoding. We employ rectified flow transformers tailored for SLAT as our 3D generation models and train models with up to 2 billion parameters on a large 3D asset dataset of 500K diverse objects. Our model generates high-quality results with text or image conditions, significantly surpassing existing methods, including recent ones at similar scales. We showcase flexible output format selection and local 3D editing capabilities which were not offered by previous models. Code, model, and data will be released.

Predicting disease trajectories from electronic health records (EHRs) is a complex task due to major challenges such as data non-stationarity, high granularity of medical codes, and integration of multimodal data. EHRs contain both structured data, such as diagnostic codes, and unstructured data, such as clinical notes, which hold essential information often overlooked. Current models, primarily based on structured data, struggle to capture the complete medical context of patients, resulting in a loss of valuable information. To address this issue, we propose an approach that integrates unstructured clinical notes into transformer-based deep learning models for sequential disease prediction. This integration enriches the representation of patients' medical histories, thereby improving the accuracy of diagnosis predictions. Experiments on MIMIC-IV datasets demonstrate that the proposed approach outperforms traditional models relying solely on structured data.

The increasing complexity and scale of modern telecommunications networks demand intelligent automation to enhance efficiency, adaptability, and resilience. Agentic AI has emerged as a key paradigm for intelligent communications and networking, enabling AI-driven agents to perceive, reason, decide, and act within dynamic networking environments. However, effective decision-making in telecom applications, such as network planning, management, and resource allocation, requires integrating retrieval mechanisms that support multi-hop reasoning, historical cross-referencing, and compliance with evolving 3GPP standards. This article presents a forward-looking perspective on generative information retrieval-inspired intelligent communications and networking, emphasizing the role of knowledge acquisition, processing, and retrieval in agentic AI for telecom systems. We first provide a comprehensive review of generative information retrieval strategies, including traditional retrieval, hybrid retrieval, semantic retrieval, knowledge-based retrieval, and agentic contextual retrieval. We then analyze their advantages, limitations, and suitability for various networking scenarios. Next, we present a survey about their applications in communications and networking. Additionally, we introduce an agentic contextual retrieval framework to enhance telecom-specific planning by integrating multi-source retrieval, structured reasoning, and self-reflective validation. Experimental results demonstrate that our framework significantly improves answer accuracy, explanation consistency, and retrieval efficiency compared to traditional and semantic retrieval methods. Finally, we outline future research directions.

Electronic band structure (BS) and crystal structure are the two complementary identifiers of solid state materials. While convenient instruments and reconstruction algorithms have made large, empirical, crystal structure databases possible, extracting quasiparticle dispersion (closely related to BS) from photoemission band mapping data is currently limited by the available computational methods. To cope with the growing size and scale of photoemission data, we develop a pipeline including probabilistic machine learning and the associated data processing, optimization and evaluation methods for band structure reconstruction, leveraging theoretical calculations. The pipeline reconstructs all 14 valence bands of a semiconductor and shows excellent performance on benchmarks and other materials datasets. The reconstruction uncovers previously inaccessible momentum-space structural information on both global and local scales, while realizing a path towards integration with materials science databases. Our approach illustrates the potential of combining machine learning and domain knowledge for scalable feature extraction in multidimensional data.

Recent advancements in Large Language Models (LLMs) have demonstrated significant promise in clinical diagnosis. However, current models struggle to emulate the iterative, diagnostic hypothesis-driven reasoning of real clinical scenarios. Specifically, current LLMs suffer from three critical limitations: (1) generating hallucinated medical content due to weak grounding in verified knowledge, (2) asking redundant or inefficient questions rather than discriminative ones that hinder diagnostic progress, and (3) losing coherence over multi-turn dialogues, leading to contradictory or inconsistent conclusions. To address these challenges, we propose MedKGI, a diagnostic framework grounded in clinical practices. MedKGI integrates a medical knowledge graph (KG) to constrain reasoning to validated medical ontologies, selects questions based on information gain to maximize diagnostic efficiency, and adopts an OSCE-format structured state to maintain consistent evidence tracking across turns. Experiments on clinical benchmarks show that MedKGI outperforms strong LLM baselines in both diagnostic accuracy and inquiry efficiency, improving dialogue efficiency by 30% on average while maintaining state-of-the-art accuracy.

Monitoring of reforestation is currently being considerably streamlined through the use of drones and image recognition algorithms, which have already proven to be effective on colour imagery. In addition to colour imagery, elevation data is often also available. The primary aim of this work was to improve the performance of the faster-RCNN object detection algorithm by integrating this height information, which showed itself to notably improve performance. Interestingly, the structure of the network played a key role, with direct addition of the height information as a fourth image channel showing no improvement, while integration after the backbone network and before the region proposal network led to marked improvements. This effect persisted with very long training regimes. Increasing the resolution of this height information also showed little effect.

Despite advancements in Large Language Models (LLMs) and Retrieval-Augmented Generation (RAG) systems, their effectiveness is often hindered by a lack of integration with entity relationships and community structures, limiting their ability to provide contextually rich and accurate information retrieval for fact-checking. We introduce CommunityKG-RAG (Community Knowledge Graph-Retrieval Augmented Generation), a novel zero-shot framework that integrates community structures within Knowledge Graphs (KGs) with RAG systems to enhance the fact-checking process. Capable of adapting to new domains and queries without additional training, CommunityKG-RAG utilizes the multi-hop nature of community structures within KGs to significantly improve the accuracy and relevance of information retrieval. Our experimental results demonstrate that CommunityKG-RAG outperforms traditional methods, representing a significant advancement in fact-checking by offering a robust, scalable, and efficient solution.

Motivation: Proteins are of great significance in living organisms. However, understanding their functions encounters numerous challenges, such as insufficient integration of multimodal information, a large number of training parameters, limited flexibility of classification-based methods, and the lack of systematic evaluation metrics for protein Q&A systems. To tackle these issues, we propose the Prot2Chat framework. Results: We modified ProteinMPNN to encode protein sequence and structural information in a unified way. We used a large language model (LLM) to encode questions into vectors and developed a protein-text adapter to compress protein information into virtual tokens based on these vectors, achieving the early fusion of text and protein information. Finally, the same LLM reads the virtual tokens and the questions to generate answers. To optimize training efficiency, we froze the encoder and employed Low-Rank Adaptation (LoRA) techniques for the LLM. Experiments on two datasets show that both automated metrics and expert evaluations demonstrate the superior performance of our model, and zero-shot prediction results highlight its generalization ability. The models and codes are available at https://github.com/ wangzc1233/Prot2Chat. Contact: zqcao@suda.edu.cn or wangzc025@163.com Key words: Protein Q&A, Early-Fusion, LLM

Foundation models for single-cell RNA sequencing (scRNA-seq) have shown promising capabilities in capturing gene expression patterns. However, current approaches face critical limitations: they ignore biological prior knowledge encoded in gene regulatory relationships and fail to leverage multi-omics signals that could provide complementary regulatory insights. In this paper, we propose GRNFormer, a new framework that systematically integrates multi-scale Gene Regulatory Networks (GRNs) inferred from multi-omics data into RNA foundation model training. Our framework introduces two key innovations. First, we introduce a pipeline for constructing hierarchical GRNs that capture regulatory relationships at both cell-type-specific and cell-specific resolutions. Second, we design a structure-aware integration framework that addresses the information asymmetry in GRNs through two technical advances: (1) A graph topological adapter using multi-head cross-attention to weight regulatory relationships dynamically, and (2) a novel edge perturbation strategy that perturb GRNs with biologically-informed co-expression links to augment graph neural network training. Comprehensive experiments have been conducted on three representative downstream tasks across multiple model architectures to demonstrate the effectiveness of GRNFormer. It achieves consistent improvements over state-of-the-art (SoTA) baselines: 3.6% increase in drug response prediction correlation, 9.6% improvement in single-cell drug classification AUC, and 1.1% average gain in gene perturbation prediction accuracy.

Recent end-to-end autonomous driving approaches have leveraged Vision-Language Models (VLMs) to enhance planning capabilities in complex driving scenarios. However, VLMs are inherently trained as generalist models, lacking specialized understanding of driving-specific reasoning in 3D space and time. When applied to autonomous driving, these models struggle to establish structured spatial-temporal representations that capture geometric relationships, scene context, and motion patterns critical for safe trajectory planning. To address these limitations, we propose SGDrive, a novel framework that explicitly structures the VLM's representation learning around driving-specific knowledge hierarchies. Built upon a pre-trained VLM backbone, SGDrive decomposes driving understanding into a scene-agent-goal hierarchy that mirrors human driving cognition: drivers first perceive the overall environment (scene context), then attend to safety-critical agents and their behaviors, and finally formulate short-term goals before executing actions. This hierarchical decomposition provides the structured spatial-temporal representation that generalist VLMs lack, integrating multi-level information into a compact yet comprehensive format for trajectory planning. Extensive experiments on the NAVSIM benchmark demonstrate that SGDrive achieves state-of-the-art performance among camera-only methods on both PDMS and EPDMS, validating the effectiveness of hierarchical knowledge structuring for adapting generalist VLMs to autonomous driving.

Generative Sequential Recommendation (GSR) has emerged as a promising paradigm, reframing recommendation as an autoregressive sequence generation task over discrete Semantic IDs (SIDs), typically derived via codebook-based quantization. Despite its great potential in unifying retrieval and ranking, existing GSR frameworks still face two critical limitations: (1) impure and unstable semantic tokenization, where quantization methods struggle with interaction noise and codebook collapse, resulting in SIDs with ambiguous discrimination; and (2) lossy and weakly structured generation, where reliance solely on coarse-grained discrete tokens inevitably introduces information loss and neglects items' hierarchical logic. To address these issues, we propose a novel generative recommendation framework, PRISM, with Purified Representation and Integrated Semantic Modeling. Specifically, to ensure high-quality tokenization, we design a Purified Semantic Quantizer that constructs a robust codebook via adaptive collaborative denoising and hierarchical semantic anchoring mechanisms. To compensate for information loss during quantization, we further propose an Integrated Semantic Recommender, which incorporates a dynamic semantic integration mechanism to integrate fine-grained semantics and enforces logical validity through a semantic structure alignment objective. PRISM consistently outperforms state-of-the-art baselines across four real-world datasets, demonstrating substantial performance gains, particularly in high-sparsity scenarios.

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

Explainable recommendation has demonstrated significant advantages in informing users about the logic behind recommendations, thereby increasing system transparency, effectiveness, and trustworthiness. To provide personalized and interpretable explanations, existing works often combine the generation capabilities of large language models (LLMs) with collaborative filtering (CF) information. CF information extracted from the user-item interaction graph captures the user behaviors and preferences, which is crucial for providing informative explanations. However, due to the complexity of graph structure, effectively extracting the CF information from graphs still remains a challenge. Moreover, existing methods often struggle with the integration of extracted CF information with LLMs due to its implicit representation and the modality gap between graph structures and natural language explanations. To address these challenges, we propose G-Refer, a framework using graph retrieval-augmented large language models (LLMs) for explainable recommendation. Specifically, we first employ a hybrid graph retrieval mechanism to retrieve explicit CF signals from both structural and semantic perspectives. The retrieved CF information is explicitly formulated as human-understandable text by the proposed graph translation and accounts for the explanations generated by LLMs. To bridge the modality gap, we introduce knowledge pruning and retrieval-augmented fine-tuning to enhance the ability of LLMs to process and utilize the retrieved CF information to generate explanations. Extensive experiments show that G-Refer achieves superior performance compared with existing methods in both explainability and stability. Codes and data are available at https://github.com/Yuhan1i/G-Refer.

Due to the presence of the natural gap between Knowledge Graph (KG) structures and the natural language, the effective integration of holistic structural information of KGs with Large Language Models (LLMs) has emerged as a significant question. To this end, we propose a two-stage framework to learn and apply quantized codes for each entity, aiming for the seamless integration of KGs with LLMs. Firstly, a self-supervised quantized representation (SSQR) method is proposed to compress both KG structural and semantic knowledge into discrete codes (\ie, tokens) that align the format of language sentences. We further design KG instruction-following data by viewing these learned codes as features to directly input to LLMs, thereby achieving seamless integration. The experiment results demonstrate that SSQR outperforms existing unsupervised quantized methods, producing more distinguishable codes. Further, the fine-tuned LLaMA2 and LLaMA3.1 also have superior performance on KG link prediction and triple classification tasks, utilizing only 16 tokens per entity instead of thousands in conventional prompting methods.

Recent research on integrating Large Language Models (LLMs) with Graph Neural Networks (GNNs) typically follows two approaches: LLM-centered models, which convert graph data into tokens for LLM processing, and GNN-centered models, which use LLMs to encode text features into node and edge representations for GNN input. LLM-centered models often struggle to capture graph structures effectively, while GNN-centered models compress variable-length textual data into fixed-size vectors, limiting their ability to understand complex semantics. Additionally, GNN-centered approaches require converting tasks into a uniform, manually-designed format, restricting them to classification tasks and preventing language output. To address these limitations, we introduce a new architecture that deeply integrates GNN with LLM, featuring three key innovations: (1) Structure-Aware Transformers, which incorporate GNN's message-passing capabilities directly into LLM's transformer layers, allowing simultaneous processing of textual and structural information and generating outputs from both GNN and LLM; (2) Graph-Text Cross-Attention, which processes full, uncompressed text from graph nodes and edges, ensuring complete semantic integration; and (3) GNN-LLM Twin Predictor, enabling LLM's flexible autoregressive generation alongside GNN's scalable one-pass prediction. GL-Fusion achieves outstand performance on various tasks. Notably, it achieves state-of-the-art performance on OGBN-Arxiv and OGBG-Code2.

Conversational semantic role labeling (CSRL) is a newly proposed task that uncovers the shallow semantic structures in a dialogue text. Unfortunately several important characteristics of the CSRL task have been overlooked by the existing works, such as the structural information integration, near-neighbor influence. In this work, we investigate the integration of a latent graph for CSRL. We propose to automatically induce a predicate-oriented latent graph (POLar) with a predicate-centered Gaussian mechanism, by which the nearer and informative words to the predicate will be allocated with more attention. The POLar structure is then dynamically pruned and refined so as to best fit the task need. We additionally introduce an effective dialogue-level pre-trained language model, CoDiaBERT, for better supporting multiple utterance sentences and handling the speaker coreference issue in CSRL. Our system outperforms best-performing baselines on three benchmark CSRL datasets with big margins, especially achieving over 4% F1 score improvements on the cross-utterance argument detection. Further analyses are presented to better understand the effectiveness of our proposed methods.

Data comes in many forms. From a shallow perspective, they can be viewed as being either in structured (e.g., as a relation, as key-value pairs) or unstructured (e.g., text, image) formats. So far, machines have been fairly good at processing and reasoning over structured data that follows a precise schema. However, the heterogeneity of data poses a significant challenge on how well diverse categories of data can be meaningfully stored and processed. Data Integration, a crucial part of the data engineering pipeline, addresses this by combining disparate data sources and providing unified data access to end-users. Until now, most data integration systems have leaned on only combining structured data sources. Nevertheless, unstructured data (a.k.a. free text) also contains a plethora of knowledge waiting to be utilized. Thus, in this chapter, we firstly make the case for the integration of textual data, to later present its challenges, state of the art and open problems.

Learning to represent free text is a core task in many clinical machine learning (ML) applications, as clinical text contains observations and plans not otherwise available for inference. State-of-the-art methods use large language models developed with immense computational resources and training data; however, applying these models is challenging because of the highly varying syntax and vocabulary in clinical free text. Structured information such as International Classification of Disease (ICD) codes often succinctly abstracts the most important facts of a clinical encounter and yields good performance, but is often not as available as clinical text in real-world scenarios. We propose a multi-view learning framework that jointly learns from codes and text to combine the availability and forward-looking nature of text and better performance of ICD codes. The learned text embeddings can be used as inputs to predictive algorithms independent of the ICD codes during inference. Our approach uses a Graph Neural Network (GNN) to process ICD codes, and Bi-LSTM to process text. We apply Deep Canonical Correlation Analysis (DCCA) to enforce the two views to learn a similar representation of each patient. In experiments using planned surgical procedure text, our model outperforms BERT models fine-tuned to clinical data, and in experiments using diverse text in MIMIC-III, our model is competitive to a fine-tuned BERT at a tiny fraction of its computational effort.

Protein biology focuses on the intricate relationships among sequences, structures, and functions. Deciphering protein functions is crucial for understanding biological processes, advancing drug discovery, and enabling synthetic biology applications. Since protein sequences determine tertiary structures, which in turn govern functions, integrating sequence and structure information is essential for accurate prediction of protein functions. Traditional protein language models (pLMs) have advanced protein-related tasks by learning representations from large-scale sequence and structure data. However, pLMs are limited in integrating broader contextual knowledge, particularly regarding functional modalities that are fundamental to protein biology. In contrast, large language models (LLMs) have exhibited outstanding performance in contextual understanding, reasoning, and generation across diverse domains. Leveraging these capabilities, STELLA is proposed as a multimodal LLM integrating protein sequence-structure representations with general knowledge to address protein function prediction. Through multimodal instruction tuning (MMIT) using the proposed OPI-Struc dataset, STELLA achieves state-of-the-art performance in two function-related tasks-functional description prediction (FP) and enzyme-catalyzed reaction prediction (EP). This study highlights the potential of multimodal LLMs as an alternative paradigm to pLMs to advance protein biology research.

The extraction of pharmacological knowledge from regulatory documents has become a key focus in biomedical natural language processing, with applications ranging from adverse event monitoring to AI-assisted clinical decision support. However, research in this field has predominantly relied on English-language corpora such as DrugBank, leaving a significant gap in resources tailored to other healthcare systems. To address this limitation, we introduce DART (Drug Annotation from Regulatory Texts), the first structured corpus of Italian Summaries of Product Characteristics derived from the official repository of the Italian Medicines Agency (AIFA). The dataset was built through a reproducible pipeline encompassing web-scale document retrieval, semantic segmentation of regulatory sections, and clinical summarization using a few-shot-tuned large language model with low-temperature decoding. DART provides structured information on key pharmacological domains such as indications, adverse drug reactions, and drug-drug interactions. To validate its utility, we implemented an LLM-based drug interaction checker that leverages the dataset to infer clinically meaningful interactions. Experimental results show that instruction-tuned LLMs can accurately infer potential interactions and their clinical implications when grounded in the structured textual fields of DART. We publicly release our code on GitHub: https://github.com/PRAISELab-PicusLab/DART.

Large language model (LLM) agents often struggle in long-context interactions. As the agent accumulates more interaction history, context management approaches such as sliding window and prompt compression may omit earlier structured information that later steps rely on. Recent retrieval-based memory systems surface relevant content but still overlook the causal and logical structure needed for multi-step reasoning. We introduce ContextWeaver, a selective and dependency-structured memory framework that organizes an agent's interaction trace into a graph of reasoning steps and selects the relevant context for future actions. Unlike prior context management approaches, ContextWeaver supports: (1) dependency-based construction and traversal that link each step to the earlier steps it relies on; (2) compact dependency summarization that condenses root-to-step reasoning paths into reusable units; and (3) a lightweight validation layer that incorporates execution feedback. On the SWE-Bench Verified and Lite benchmarks, ContextWeaver improves performance over a sliding-window baseline in pass@1, while reducing reasoning steps and token usage. Our observations suggest that modeling logical dependencies provides a stable and scalable memory mechanism for LLM agents that use tools.

Diffusion-based super-resolution (SR) models have recently garnered significant attention due to their potent restoration capabilities. But conventional diffusion models perform noise sampling from a single distribution, constraining their ability to handle real-world scenes and complex textures across semantic regions. With the success of segment anything model (SAM), generating sufficiently fine-grained region masks can enhance the detail recovery of diffusion-based SR model. However, directly integrating SAM into SR models will result in much higher computational cost. In this paper, we propose the SAM-DiffSR model, which can utilize the fine-grained structure information from SAM in the process of sampling noise to improve the image quality without additional computational cost during inference. In the process of training, we encode structural position information into the segmentation mask from SAM. Then the encoded mask is integrated into the forward diffusion process by modulating it to the sampled noise. This adjustment allows us to independently adapt the noise mean within each corresponding segmentation area. The diffusion model is trained to estimate this modulated noise. Crucially, our proposed framework does NOT change the reverse diffusion process and does NOT require SAM at inference. Experimental results demonstrate the effectiveness of our proposed method, showcasing superior performance in suppressing artifacts, and surpassing existing diffusion-based methods by 0.74 dB at the maximum in terms of PSNR on DIV2K dataset. The code and dataset are available at https://github.com/lose4578/SAM-DiffSR.

Image compression techniques typically focus on compressing rectangular images for human consumption, however, resulting in transmitting redundant content for downstream applications. To overcome this limitation, some previous works propose to semantically structure the bitstream, which can meet specific application requirements by selective transmission and reconstruction. Nevertheless, they divide the input image into multiple rectangular regions according to semantics and ignore avoiding information interaction among them, causing waste of bitrate and distorted reconstruction of region boundaries. In this paper, we propose to decouple an image into multiple groups with irregular shapes based on a customized group mask and compress them independently. Our group mask describes the image at a finer granularity, enabling significant bitrate saving by reducing the transmission of redundant content. Moreover, to ensure the fidelity of selective reconstruction, this paper proposes the concept of group-independent transform that maintain the independence among distinct groups. And we instantiate it by the proposed Group-Independent Swin-Block (GI Swin-Block). Experimental results demonstrate that our framework structures the bitstream with negligible cost, and exhibits superior performance on both visual quality and intelligent task supporting.

This paper studies learning on text-attributed graphs (TAGs), where each node is associated with a text description. An ideal solution for such a problem would be integrating both the text and graph structure information with large language models and graph neural networks (GNNs). However, the problem becomes very challenging when graphs are large due to the high computational complexity brought by training large language models and GNNs together. In this paper, we propose an efficient and effective solution to learning on large text-attributed graphs by fusing graph structure and language learning with a variational Expectation-Maximization (EM) framework, called GLEM. Instead of simultaneously training large language models and GNNs on big graphs, GLEM proposes to alternatively update the two modules in the E-step and M-step. Such a procedure allows training the two modules separately while simultaneously allowing the two modules to interact and mutually enhance each other. Extensive experiments on multiple data sets demonstrate the efficiency and effectiveness of the proposed approach.

Despite initial successes and a variety of architectures, retrieval-augmented generation (RAG) systems still struggle to reliably retrieve and connect the multi-step evidence required for complicated reasoning tasks. Most of the standard RAG frameworks regard all retrieved information as equally reliable, overlooking the varying credibility and interconnected nature of large textual corpora. GraphRAG approaches offer potential improvement to RAG systems by integrating knowledge graphs, which structure information into nodes and edges, capture entity relationships, and enable multi-step logical traversal. However, GraphRAG is not always an ideal solution as it depends on high-quality graph representations of the corpus, which requires either pre-existing knowledge graphs that are expensive to build and update, or automated graph construction pipelines that are often unreliable. Moreover, systems following this paradigm typically use large language models to guide graph traversal and evidence retrieval, leading to challenges similar to those encountered with standard RAG. In this paper, we propose a novel RAG framework that employs the spreading activation algorithm to retrieve information from a corpus of documents interconnected by automatically constructed knowledge graphs, thereby enhancing the performance of large language models on complex tasks such as multi-hop question answering. Experiments show that our method achieves better or comparable performance to iterative RAG methodologies, while also being easily integrable as a plug-and-play module with a wide range of RAG-based approaches. Combining our method with chain-of-thought iterative retrieval yields up to a 39\% absolute gain in answer correctness compared to naive RAG, achieving these results with small open-weight language models and highlighting its effectiveness in resource-constrained settings.

Test-time scaling has become an effective paradigm for improving the reasoning ability of large language models by allocating additional computation during inference. Recent structured approaches have further advanced this paradigm by organizing inference across multiple trajectories, refinement rounds, and verification-based feedback. However, existing structured test-time scaling methods either weakly coordinate parallel reasoning trajectories or rely on noisy historical information without explicitly deciding what should be retained and reused, limiting their ability to balance exploration and exploitation. In this work, we propose TMAS, a framework for scaling test-time compute via multi-agent synergy. TMAS organizes inference as a collaborative process among specialized agents, enabling structured information flow across agents, trajectories, and refinement iterations. To support effective cross-trajectory collaboration, TMAS introduces hierarchical memories: the experience bank reuses low-level reliable intermediate conclusions and local feedback, while the guideline bank records previously explored high-level strategies to steer subsequent rollouts away from redundant reasoning patterns. Furthermore, we design a hybrid reward reinforcement learning scheme tailored to TMAS, which jointly preserves basic reasoning capability, enhances experience utilization, and encourages exploration beyond previously attempted solution strategies. Extensive experiments on challenging reasoning benchmarks demonstrate that TMAS achieves stronger iterative scaling than existing test-time scaling baselines, while hybrid reward training further improves scaling effectiveness and stability across iterations. Code and data are available at https://github.com/george-QF/TMAS-code.

Text embeddings have attracted growing interest due to their effectiveness across a wide range of natural language processing (NLP) tasks, such as retrieval, classification, clustering, bitext mining, and summarization. With the emergence of pretrained language models (PLMs), general-purpose text embeddings (GPTE) have gained significant traction for their ability to produce rich, transferable representations. The general architecture of GPTE typically leverages PLMs to derive dense text representations, which are then optimized through contrastive learning on large-scale pairwise datasets. In this survey, we provide a comprehensive overview of GPTE in the era of PLMs, focusing on the roles PLMs play in driving its development. We first examine the fundamental architecture and describe the basic roles of PLMs in GPTE, i.e., embedding extraction, expressivity enhancement, training strategies, learning objectives, and data construction. Then, we describe advanced roles enabled by PLMs, such as multilingual support, multimodal integration, code understanding, and scenario-specific adaptation. Finally, we highlight potential future research directions that move beyond traditional improvement goals, including ranking integration, safety considerations, bias mitigation, structural information incorporation, and the cognitive extension of embeddings. This survey aims to serve as a valuable reference for both newcomers and established researchers seeking to understand the current state and future potential of GPTE.

Many organizations rely on data from government and third-party sources, and those sources rarely follow the same data formatting. This introduces challenges in integrating data from multiple sources or aligning external sources with internal databases. Commercial database systems do not offer adequate support for integrating data from heterogeneous sources, and manual integration is both time-consuming and inefficient. State-of-the-art data integration approaches that rely on similarity functions and textual transformations often fail to handle challenging cases where multiple mappings are required, or the mappings go beyond simple textual transformations. In this paper, we study the potentials of deep neural models for transforming tables for joinability. In particular, we cast the problem as a prediction task and develop a framework that leverages large deep-learning language models to transform tabular data from a source formatting to a desired target representation. Our framework can efficiently learn the patterns for mapping a source formatting into an expected target using just a few examples, which can then be used for tasks such as table joining, filling in missing values, and error detection. Compared to state-of-the-art mapping and joining approaches, our framework delivers noticeably more accurate and scalable performance on both real-world and synthetic datasets. Our experimental evaluation also shows that the performance of the proposed framework using our fine-tuned model is at par or better than large language models such as GPT-3, despite the significant difference in size, and that using large language models within our framework improves their performance.

E-commerce search and recommendation usually operate on structured data such as product catalogs and taxonomies. However, creating better search and recommendation systems often requires a large variety of unstructured data including customer reviews and articles on the web. Traditionally, the solution has always been converting unstructured data into structured data through information extraction, and conducting search over the structured data. However, this is a costly approach that often has low quality. In this paper, we envision a solution that does entirely the opposite. Instead of converting unstructured data (web pages, customer reviews, etc) to structured data, we instead convert structured data (product inventory, catalogs, taxonomies, etc) into textual data, which can be easily integrated into the text corpus that trains LLMs. Then, search and recommendation can be performed through a Q/A mechanism through an LLM instead of using traditional information retrieval methods over structured data.

We present lambda layers -- an alternative framework to self-attention -- for capturing long-range interactions between an input and structured contextual information (e.g. a pixel surrounded by other pixels). Lambda layers capture such interactions by transforming available contexts into linear functions, termed lambdas, and applying these linear functions to each input separately. Similar to linear attention, lambda layers bypass expensive attention maps, but in contrast, they model both content and position-based interactions which enables their application to large structured inputs such as images. The resulting neural network architectures, LambdaNetworks, significantly outperform their convolutional and attentional counterparts on ImageNet classification, COCO object detection and COCO instance segmentation, while being more computationally efficient. Additionally, we design LambdaResNets, a family of hybrid architectures across different scales, that considerably improves the speed-accuracy tradeoff of image classification models. LambdaResNets reach excellent accuracies on ImageNet while being 3.2 - 4.4x faster than the popular EfficientNets on modern machine learning accelerators. When training with an additional 130M pseudo-labeled images, LambdaResNets achieve up to a 9.5x speed-up over the corresponding EfficientNet checkpoints.

Integrating information from different reference data sources is a major challenge for Retrieval-Augmented Generation (RAG) systems because each knowledge source adopts a unique data structure and follows different conventions. Retrieving from multiple knowledge sources with one fixed strategy usually leads to under-exploitation of information. To mitigate this drawback, inspired by Mix-of-Expert, we introduce Mix-of-Granularity (MoG), a method that dynamically determines the optimal granularity of a knowledge database based on input queries using a router. The router is efficiently trained with a newly proposed loss function employing soft labels. We further extend MoG to Mix-of-Granularity-Graph (MoGG), where reference documents are pre-processed into graphs, enabling the retrieval of relevant information from distantly situated chunks. Extensive experiments demonstrate that both MoG and MoGG effectively predict optimal granularity levels, significantly enhancing the performance of the RAG system in downstream tasks. The code of both MoG and MoGG will be made public.

Most Large Language Model (LLM) agent memory systems rely on a small set of static, hand-designed operations for extracting memory. These fixed procedures hard-code human priors about what to store and how to revise memory, making them rigid under diverse interaction patterns and inefficient on long histories. To this end, we present MemSkill, which reframes these operations as learnable and evolvable memory skills, structured and reusable routines for extracting, consolidating, and pruning information from interaction traces. Inspired by the design philosophy of agent skills, MemSkill employs a controller that learns to select a small set of relevant skills, paired with an LLM-based executor that produces skill-guided memories. Beyond learning skill selection, MemSkill introduces a designer that periodically reviews hard cases where selected skills yield incorrect or incomplete memories, and evolves the skill set by proposing refinements and new skills. Together, MemSkill forms a closed-loop procedure that improves both the skill-selection policy and the skill set itself. Experiments on LoCoMo, LongMemEval, HotpotQA, and ALFWorld demonstrate that MemSkill improves task performance over strong baselines and generalizes well across settings. Further analyses shed light on how skills evolve, offering insights toward more adaptive, self-evolving memory management for LLM agents.

Understanding the relationships between protein sequence, structure and function is a long-standing biological challenge with manifold implications from drug design to our understanding of evolution. Recently, protein language models have emerged as the preferred method for this challenge, thanks to their ability to harness large sequence databases. Yet, their reliance on expansive sequence data and parameter sets limits their flexibility and practicality in real-world scenarios. Concurrently, the recent surge in computationally predicted protein structures unlocks new opportunities in protein representation learning. While promising, the computational burden carried by such complex data still hinders widely-adopted practical applications. To address these limitations, we introduce a novel framework that enhances protein language models by integrating protein structural data. Drawing from recent advances in graph transformers, our approach refines the self-attention mechanisms of pretrained language transformers by integrating structural information with structure extractor modules. This refined model, termed Protein Structure Transformer (PST), is further pretrained on a small protein structure database, using the same masked language modeling objective as traditional protein language models. Empirical evaluations of PST demonstrate its superior parameter efficiency relative to protein language models, despite being pretrained on a dataset comprising only 542K structures. Notably, PST consistently outperforms the state-of-the-art foundation model for protein sequences, ESM-2, setting a new benchmark in protein function prediction. Our findings underscore the potential of integrating structural information into protein language models, paving the way for more effective and efficient protein modeling Code and pretrained models are available at https://github.com/BorgwardtLab/PST.

Information seeking and integration is a complex cognitive task that consumes enormous time and effort. Inspired by the remarkable progress of Large Language Models, recent works attempt to solve this task by combining LLMs and search engines. However, these methods still obtain unsatisfying performance due to three challenges: (1) complex requests often cannot be accurately and completely retrieved by the search engine once (2) corresponding information to be integrated is spread over multiple web pages along with massive noise, and (3) a large number of web pages with long contents may quickly exceed the maximum context length of LLMs. Inspired by the cognitive process when humans solve these problems, we introduce MindSearch to mimic the human minds in web information seeking and integration, which can be instantiated by a simple yet effective LLM-based multi-agent framework. The WebPlanner models the human mind of multi-step information seeking as a dynamic graph construction process: it decomposes the user query into atomic sub-questions as nodes in the graph and progressively extends the graph based on the search result from WebSearcher. Tasked with each sub-question, WebSearcher performs hierarchical information retrieval with search engines and collects valuable information for WebPlanner. The multi-agent design of MindSearch enables the whole framework to seek and integrate information parallelly from larger-scale (e.g., more than 300) web pages in 3 minutes, which is worth 3 hours of human effort. MindSearch demonstrates significant improvement in the response quality in terms of depth and breadth, on both close-set and open-set QA problems. Besides, responses from MindSearch based on InternLM2.5-7B are preferable by humans to ChatGPT-Web and Perplexity.ai applications, which implies that MindSearch can already deliver a competitive solution to the proprietary AI search engine.

One of the limitations of large language models is that they do not have access to up-to-date, proprietary or personal data. As a result, there are multiple efforts to extend language models with techniques for accessing external data. In that sense, LLMs share the vision of data integration systems whose goal is to provide seamless access to a large collection of heterogeneous data sources. While the details and the techniques of LLMs differ greatly from those of data integration, this paper shows that some of the lessons learned from research on data integration can elucidate the research path we are conducting today on language models.

Semi-structured documents integrate diverse interleaved data elements (e.g., tables, charts, hierarchical paragraphs) arranged in various and often irregular layouts. These documents are widely observed across domains and account for a large portion of real-world data. However, existing methods struggle to support natural language question answering over these documents due to three main technical challenges: (1) The elements extracted by techniques like OCR are often fragmented and stripped of their original semantic context, making them inadequate for analysis. (2) Existing approaches lack effective representations to capture hierarchical structures within documents (e.g., associating tables with nested chapter titles) and to preserve layout-specific distinctions (e.g., differentiating sidebars from main content). (3) Answering questions often requires retrieving and aligning relevant information scattered across multiple regions or pages, such as linking a descriptive paragraph to table cells located elsewhere in the document. To address these issues, we propose MoDora, an LLM-powered system for semi-structured document analysis. First, we adopt a local-alignment aggregation strategy to convert OCR-parsed elements into layout-aware components, and conduct type-specific information extraction for components with hierarchical titles or non-text elements. Second, we design the Component-Correlation Tree (CCTree) to hierarchically organize components, explicitly modeling inter-component relations and layout distinctions through a bottom-up cascade summarization process. Finally, we propose a question-type-aware retrieval strategy that supports (1) layout-based grid partitioning for location-based retrieval and (2) LLM-guided pruning for semantic-based retrieval. Experiments show MoDora outperforms baselines by 5.97%-61.07% in accuracy. The code is at https://github.com/weAIDB/MoDora.

Retrieval-Augmented Generation systems depend on retrieving semantically relevant document chunks to support accurate, grounded outputs from large language models. In structured and repetitive corpora such as regulatory filings, chunk similarity alone often fails to distinguish between documents with overlapping language. Practitioners often flatten metadata into input text as a heuristic, but the impact and trade-offs of this practice remain poorly understood. We present a systematic study of metadata-aware retrieval strategies, comparing plain-text baselines with approaches that embed metadata directly. Our evaluation spans metadata-as-text (prefix and suffix), a dual-encoder unified embedding that fuses metadata and content in a single index, dual-encoder late-fusion retrieval, and metadata-aware query reformulation. Across multiple retrieval metrics and question types, we find that prefixing and unified embeddings consistently outperform plain-text baselines, with the unified at times exceeding prefixing while being easier to maintain. Beyond empirical comparisons, we analyze embedding space, showing that metadata integration improves effectiveness by increasing intra-document cohesion, reducing inter-document confusion, and widening the separation between relevant and irrelevant chunks. Field-level ablations show that structural cues provide strong disambiguating signals. Our code, evaluation framework, and the RAGMATE-10K dataset are publicly hosted.

Dungeons & Dragons (D&D) is a tabletop roleplaying game with complex natural language interactions between players and hidden state information. Recent work has shown that large language models (LLMs) that have access to state information can generate higher quality game turns than LLMs that use dialog history alone. However, previous work used game state information that was heuristically created and was not a true gold standard game state. We present FIREBALL, a large dataset containing nearly 25,000 unique sessions from real D&D gameplay on Discord with true game state info. We recorded game play sessions of players who used the Avrae bot, which was developed to aid people in playing D&D online, capturing language, game commands and underlying game state information. We demonstrate that FIREBALL can improve natural language generation (NLG) by using Avrae state information, improving both automated metrics and human judgments of quality. Additionally, we show that LLMs can generate executable Avrae commands, particularly after finetuning.

Integrating structured knowledge from tabular formats poses significant challenges within natural language processing (NLP), mainly when dealing with complex, semi-structured tables like those found in the FeTaQA dataset. These tables require advanced methods to interpret and generate meaningful responses accurately. Traditional approaches, such as SQL and SPARQL, often fail to fully capture the semantics of such data, especially in the presence of irregular table structures like web tables. This paper addresses these challenges by proposing a novel approach that extracts triples straightforward from tabular data and integrates it with a retrieval-augmented generation (RAG) model to enhance the accuracy, coherence, and contextual richness of responses generated by a fine-tuned GPT-3.5-turbo-0125 model. Our approach significantly outperforms existing baselines on the FeTaQA dataset, particularly excelling in Sacre-BLEU and ROUGE metrics. It effectively generates contextually accurate and detailed long-form answers from tables, showcasing its strength in complex data interpretation.

Real-world information needs require access to structurally diverse knowledge sources, from unstructured text and relational tables to knowledge graphs and property graphs. Existing retrievers, however, operate over one source at a time under a fixed query language, leaving the broader landscape of available knowledge fragmented behind incompatible interfaces. A natural attempt at unification would collapse these sources into a shared space, but this erases the structural affordances (such as schemas, ontologies, compositional operators) that give each source its expressive power. Effective retrieval over diverse knowledge, therefore, requires not homogenization but an overarching layer that meets each source on its own terms. To achieve this, we present OmniRetrieval, a framework that takes any natural-language query, identifies appropriate knowledge sources, and dispatches source-native queries to their native execution engines. Across an extensive benchmark spanning 13 datasets and 309 distinct knowledge bases over text, relational, and graph-structured sources, OmniRetrieval exceeds single-source baselines, demonstrating that it can serve as a general-purpose interface to the heterogeneous sources while preserving the structural distinctions that make each source valuable.

Large Language Models (LLMs) often struggle with requests related to information retrieval and data manipulation that frequently arise in real-world scenarios under multiple conditions. In this paper, we demonstrate that leveraging tabular structures in LLM interactions, is more effective than utilizing other structures for handling prevalent requests that operate over factual data. Through comprehensive evaluations across various scenarios and request types, we show that providing tabular structures yields a 40.29\% average performance gain along with better robustness and token efficiency. Through attention-value analysis, we discover that tables help LLMs better locate relevant information, explaining these improvements. Beyond tables and text, we evaluate whether (1) blending structuredness within text, such as providing templates or fixing the order of attributes, and (2) other representative structures, such as knowledge graphs and JSON are helpful. We observe that utilizing tables offers the best balance between efficiency and effectiveness. The method remains robust to task complexity and adapts to unstructured sources through text-to-table conversion. Overall, we highlight the untapped potential of tabular representations for future LLM applications.

Recent progress in using recurrent neural networks (RNNs) for image description has motivated the exploration of their application for video description. However, while images are static, working with videos requires modeling their dynamic temporal structure and then properly integrating that information into a natural language description. In this context, we propose an approach that successfully takes into account both the local and global temporal structure of videos to produce descriptions. First, our approach incorporates a spatial temporal 3-D convolutional neural network (3-D CNN) representation of the short temporal dynamics. The 3-D CNN representation is trained on video action recognition tasks, so as to produce a representation that is tuned to human motion and behavior. Second we propose a temporal attention mechanism that allows to go beyond local temporal modeling and learns to automatically select the most relevant temporal segments given the text-generating RNN. Our approach exceeds the current state-of-art for both BLEU and METEOR metrics on the Youtube2Text dataset. We also present results on a new, larger and more challenging dataset of paired video and natural language descriptions.

Traditional systems designed for task oriented dialog utilize knowledge present only in structured knowledge sources to generate responses. However, relevant information required to generate responses may also reside in unstructured sources, such as documents. Recent state of the art models such as HyKnow and SeKnow aimed at overcoming these challenges make limiting assumptions about the knowledge sources. For instance, these systems assume that certain types of information, such as a phone number, is always present in a structured knowledge base (KB) while information about aspects such as entrance ticket prices, would always be available in documents. In this paper, we create a modified version of the MutliWOZ-based dataset prepared by SeKnow to demonstrate how current methods have significant degradation in performance when strict assumptions about the source of information are removed. Then, in line with recent work exploiting pre-trained language models, we fine-tune a BART based model using prompts for the tasks of querying knowledge sources, as well as, for response generation, without making assumptions about the information present in each knowledge source. Through a series of experiments, we demonstrate that our model is robust to perturbations to knowledge modality (source of information), and that it can fuse information from structured as well as unstructured knowledge to generate responses.

Existing Open-Ended Deep Research (OEDR) systems primarily generate reports from scratch, making them inefficient for scenarios where research reports need to be continuously maintained as new information emerges. We introduce Incremental Open-Ended Deep Research (Incremental-OEDR), a research setting that treats a report as an evolving research state and incrementally updates it by preserving valid knowledge, revising outdated or incomplete content, and incorporating newly available information. To support this setting, we propose Structured Harness, which represents reports as structured collections of outlines, sections, and supporting evidence, and provides structured retrieval, a persistent structured evidence pool, and structured generation for selective report updating and evidence reuse. We further establish a temporal evaluation framework spanning ten years, with Single-Step Task and Long-Chain Task to evaluate incremental updates over both individual transitions and long-term update chains. Extensive Experiments on DeepResearch Bench and DeepConsult under both the Open-source Configuration (OC) and Proprietary Configuration (PC) show that Incremental-OEDR maintains competitive report quality while substantially improving report continuity and reducing research costs. As shown in Figure~fig:profile, it achieves up to 0.51 higher content-level ROUGE-L F1, 0.63 higher outline-level EM F1, 33\% lower token consumption, and 61\% fewer search calls than OEDR on DeepResearch Bench. For more details, please refer to our project page: https://ioedr-project.github.io/.

Extracting meaningful insights from large and complex datasets poses significant challenges, particularly in ensuring the accuracy and relevance of retrieved information. Traditional data retrieval methods such as sequential search and index-based retrieval often fail when handling intricate and interconnected data structures, resulting in incomplete or misleading outputs. To overcome these limitations, we introduce Structured-GraphRAG, a versatile framework designed to enhance information retrieval across structured datasets in natural language queries. Structured-GraphRAG utilizes multiple knowledge graphs, which represent data in a structured format and capture complex relationships between entities, enabling a more nuanced and comprehensive retrieval of information. This graph-based approach reduces the risk of errors in language model outputs by grounding responses in a structured format, thereby enhancing the reliability of results. We demonstrate the effectiveness of Structured-GraphRAG by comparing its performance with that of a recently published method using traditional retrieval-augmented generation. Our findings show that Structured-GraphRAG significantly improves query processing efficiency and reduces response times. While our case study focuses on soccer data, the framework's design is broadly applicable, offering a powerful tool for data analysis and enhancing language model applications across various structured domains.

The integration of Large Language Models (LLM) with Knowledge Representation Learning (KRL) signifies a significant advancement in the field of artificial intelligence (AI), enhancing the ability to capture and utilize both structure and textual information. Despite the increasing research on enhancing KRL with LLMs, a thorough survey that analyse processes of these enhanced models is conspicuously absent. Our survey addresses this by categorizing these models based on three distinct Transformer architectures, and by analyzing experimental data from various KRL downstream tasks to evaluate the strengths and weaknesses of each approach. Finally, we identify and explore potential future research directions in this emerging yet underexplored domain.

Intelligent document processing (IDP) encompasses a broad range of tasks, including optical character recognition (OCR), document question answering (DocQA), and key information extraction (KIE). Despite their distinct objectives, these tasks share a common need to perceive document content, acquire task-relevant information, and progressively refine intermediate results. However, they are typically formulated as separate prediction problems and addressed by task-specific models or processing pipelines. We introduce DocClaw, a unified agentic system that formulates diverse intelligent document processing tasks as a shared process of interaction between an agent and a document. Given a document and a task-specific query, DocClaw follows an appropriate document skill to iteratively identify the information required, invoke relevant tools, and integrate the resulting observations into the desired output. Throughout this process, a structured document state organizes reusable document knowledge and task-specific interaction context, allowing the agent to accumulate, revisit, and progressively refine information as the interaction proceeds. Under this formulation, task-specific requirements are captured by the agent's interpretation of the query objective and the corresponding document skill, while the underlying interaction loop, tool space, and document state are shared across tasks. Extensive experiments across multiple intelligent document processing benchmarks demonstrate that DocClaw effectively handles diverse tasks within a single agentic framework and achieves competitive performance compared with both general-purpose VLMs and task-specific methods.

In many use-cases, information is stored in text but not available in structured data. However, extracting data from natural language text to precisely fit a schema, and thus enable querying, is a challenging task. With the rise of pre-trained Large Language Models (LLMs), there is now an effective solution to store and use information extracted from massive corpora of text documents. Thus, we envision the use of SQL queries to cover a broad range of data that is not captured by traditional databases by tapping the information in LLMs. To ground this vision, we present Galois, a prototype based on a traditional database architecture, but with new physical operators for querying the underlying LLM. The main idea is to execute some operators of the the query plan with prompts that retrieve data from the LLM. For a large class of SQL queries, querying LLMs returns well structured relations, with encouraging qualitative results. Preliminary experimental results make pre-trained LLMs a promising addition to the field of database systems, introducing a new direction for hybrid query processing. However, we pinpoint several research challenges that must be addressed to build a DBMS that exploits LLMs. While some of these challenges necessitate integrating concepts from the NLP literature, others offer novel research avenues for the DB community.

Even for a conservative estimate, 80% of enterprise data reside in unstructured files, stored in data lakes that accommodate heterogeneous formats. Classical search engines can no longer meet information seeking needs, especially when the task is to browse and explore for insight formulation. In other words, there are no obvious search keywords to use. Knowledge graphs, due to their natural visual appeals that reduce the human cognitive load, become the winning candidate for heterogeneous data integration and knowledge representation. In this paper, we introduce Docs2KG, a novel framework designed to extract multimodal information from diverse and heterogeneous unstructured documents, including emails, web pages, PDF files, and Excel files. Dynamically generates a unified knowledge graph that represents the extracted key information, Docs2KG enables efficient querying and exploration of document data lakes. Unlike existing approaches that focus on domain-specific data sources or pre-designed schemas, Docs2KG offers a flexible and extensible solution that can adapt to various document structures and content types. The proposed framework unifies data processing supporting a multitude of downstream tasks with improved domain interpretability. Docs2KG is publicly accessible at https://docs2kg.ai4wa.com, and a demonstration video is available at https://docs2kg.ai4wa.com/Video.

Large language models (LLMs) and agent techniques have brought a fundamental shift in the functionality and development paradigm of data analysis tasks (a.k.a LLM/Agent-as-Data-Analyst), demonstrating substantial impact across both academia and industry. In comparison with traditional rule or small-model based approaches, (agentic) LLMs enable complex data understanding, natural language interfaces, semantic analysis functions, and autonomous pipeline orchestration. From a modality perspective, we review LLM-based techniques for (i) structured data (e.g., NL2SQL, NL2GQL, ModelQA), (ii) semi-structured data (e.g., markup languages understanding, semi-structured table question answering), (iii) unstructured data (e.g., chart understanding, text/image document understanding), and (iv) heterogeneous data (e.g., data retrieval and modality alignment in data lakes). The technical evolution further distills four key design goals for intelligent data analysis agents, namely semantic-aware design, autonomous pipelines, tool-augmented workflows, and support for open-world tasks. Finally, we outline the remaining challenges and propose several insights and practical directions for advancing LLM/Agent-powered data analysis.

Enterprises often own large collections of structured data in the form of large databases or an enterprise data lake. Such data collections come with limited metadata and strict access policies that could limit access to the data contents and, therefore, limit the application of classic retrieval and analysis solutions. As a result, there is a need for solutions that can effectively utilize the available metadata. In this paper, we study the problem of matching table metadata to a business glossary containing data labels and descriptions. The resulting matching enables the use of an available or curated business glossary for retrieval and analysis without or before requesting access to the data contents. One solution to this problem is to use manually-defined rules or similarity measures on column names and glossary descriptions (or their vector embeddings) to find the closest match. However, such approaches need to be tuned through manual labeling and cannot handle many business glossaries that contain a combination of simple as well as complex and long descriptions. In this work, we leverage the power of large language models (LLMs) to design generic matching methods that do not require manual tuning and can identify complex relations between column names and glossaries. We propose methods that utilize LLMs in two ways: a) by generating additional context for column names that can aid with matching b) by using LLMs to directly infer if there is a relation between column names and glossary descriptions. Our preliminary experimental results show the effectiveness of our proposed methods.

Large language models (LLMs) such as GPT-4 have emerged as frontrunners, showcasing unparalleled prowess in diverse applications, including answering queries, code generation, and more. Parallelly, graph-structured data, an intrinsic data type, is pervasive in real-world scenarios. Merging the capabilities of LLMs with graph-structured data has been a topic of keen interest. This paper bifurcates such integrations into two predominant categories. The first leverages LLMs for graph learning, where LLMs can not only augment existing graph algorithms but also stand as prediction models for various graph tasks. Conversely, the second category underscores the pivotal role of graphs in advancing LLMs. Mirroring human cognition, we solve complex tasks by adopting graphs in either reasoning or collaboration. Integrating with such structures can significantly boost the performance of LLMs in various complicated tasks. We also discuss and propose open questions for integrating LLMs with graph-structured data for the future direction of the field.

Answering real-world user queries, such as product search, often requires accurate retrieval of information from semi-structured knowledge bases or databases that involve blend of unstructured (e.g., textual descriptions of products) and structured (e.g., entity relations of products) information. However, previous works have mostly studied textual and relational retrieval tasks as separate topics. To address the gap, we develop STARK, a large-scale Semi-structure retrieval benchmark on Textual and Relational Knowledge Bases. We design a novel pipeline to synthesize natural and realistic user queries that integrate diverse relational information and complex textual properties, as well as their ground-truth answers. Moreover, we rigorously conduct human evaluation to validate the quality of our benchmark, which covers a variety of practical applications, including product recommendations, academic paper searches, and precision medicine inquiries. Our benchmark serves as a comprehensive testbed for evaluating the performance of retrieval systems, with an emphasis on retrieval approaches driven by large language models (LLMs). Our experiments suggest that the STARK datasets present significant challenges to the current retrieval and LLM systems, indicating the demand for building more capable retrieval systems that can handle both textual and relational aspects.

Despite advances in large language model (LLM)-based natural language interfaces for databases, scaling to enterprise-level data catalogs remains an under-explored challenge. Prior works addressing this challenge rely on domain-specific fine-tuning - complicating deployment - and fail to leverage important semantic context contained within database metadata. To address these limitations, we introduce a component-based retrieval architecture that decomposes database schemas and metadata into discrete semantic units, each separately indexed for targeted retrieval. Our approach prioritizes effective table identification while leveraging column-level information, ensuring the total number of retrieved tables remains within a manageable context budget. Experiments demonstrate that our method maintains high recall and accuracy, with our system outperforming baselines over massive databases with varying structure and available metadata. Our solution enables practical text-to-SQL systems deployable across diverse enterprise settings without specialized fine-tuning, addressing a critical scalability gap in natural language database interfaces.

Predictive process monitoring is a process mining task aimed at forecasting information about a running process trace, such as the most correct next activity to be executed. In medical domains, predictive process monitoring can provide valuable decision support in atypical and nontrivial situations. Decision support and quality assessment in medicine cannot ignore domain knowledge, in order to be grounded on all the available information (which is not limited to data) and to be really acceptable by end users. In this paper, we propose a predictive process monitoring approach relying on the use of a {\em transformer}, a deep learning architecture based on the attention mechanism. A major contribution of our work lies in the incorporation of ontological domain-specific knowledge, carried out through a graph positional encoding technique. The paper presents and discusses the encouraging experimental result we are collecting in the domain of stroke management.

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.

Model cards describe model behavior through a mixture of textual descriptions and structured artifacts, including performance, configuration, and dataset tables. Existing model search systems rely predominantly on semantic similarity over text, which can produce homogeneous result sets and limit exploration of alternatives. We argue that model search is inherently comparative: users want models that are task-aligned yet differentiated in measurable ways. We hypothesize that this balance requires retrieval over condensed, high-quality evidence rather than verbose descriptions, and much of that evidence is concentrated in structured tables. We present StructuredSemanticSearch, a table-driven model search framework built on the ModelTables benchmark. Given a query, StructuredSemanticSearch combines a semantic baseline for task alignment with a structure-aware pipeline that discovers query-related model-card tables using table discovery operators such as unionability, joinability, and keyword search. Retrieved tables are mapped back to model cards under a controlled top-k budget, enabling fair comparison between text-based and table-based retrieval. Beyond retrieval, StructuredSemanticSearch adapts table integration to the model-table domain through orientation-aware integration, producing compact integrated views of tables from partially overlapping and sometimes transposed evidence tables. For evaluation, we introduce a nugget-based, auditable protocol that extracts compact evidence items from model cards, matches queries to condition- or intent-specific nuggets, and measures evidence coverage and diversity over retrieved model-card candidate sets. This protocol also provides a scalable path toward approximate, evidence-based labeling in dynamic model lakes. Experiments on 597 model-recommendation queries show improved nugget coverage for the structure-aware pipeline than semantic baseline

Graphs are a fundamental data structure for representing relationships in real-world scenarios. With the success of Large Language Models (LLMs) across various natural language processing (NLP) tasks, there has been growing interest in integrating LLMs for graph learning. However, applying LLMs to graph-related tasks poses significant challenges, as these models are not inherently designed to capture the complex structural information present in graphs. Existing approaches address this challenge through two strategies: the chain of tasks approach, which uses Graph Neural Networks (GNNs) to encode the graph structure so that LLMs are relieved from understanding spatial positions; and Graph-to-Text Conversion, which translates graph structures into semantic text representations that LLMs can process. Despite their progress, these methods often struggle to fully preserve the topological information of graphs or require extensive computational resources, limiting their practical applicability. In this work, we introduce Node Tokenizer for Large Language Models (NT-LLM), a novel framework that efficiently encodes graph structures by selecting key nodes as anchors and representing each node based on its relative distance to these anchors. This position-anchored encoding effectively captures the graph topology, enabling enhanced reasoning capabilities in LLMs over graph data. Additionally, we implement a task-specific tuning procedure to further improve structural understanding within LLMs. Through extensive empirical evaluations, NT-LLM demonstrates significant performance improvements across a variety of graph-related tasks.

Entity resolution is a widely studied problem with several proposals to match records across relations. Matching textual content is a widespread task in many applications, such as question answering and search. While recent methods achieve promising results for these two tasks, there is no clear solution for the more general problem of matching textual content and structured data. We introduce a framework that supports this new task in an unsupervised setting for any pair of corpora, being relational tables or text documents. Our method builds a fine-grained graph over the content of the corpora and derives word embeddings to represent the objects to match in a low dimensional space. The learned representation enables effective and efficient matching at different granularity, from relational tuples to text sentences and paragraphs. Our flexible framework can exploit pre-trained resources, but it does not depends on their existence and achieves better quality performance in matching content when the vocabulary is domain specific. We also introduce optimizations in the graph creation process with an "expand and compress" approach that first identifies new valid relationships across elements, to improve matching, and then prunes nodes and edges, to reduce the graph size. Experiments on real use cases and public datasets show that our framework produces embeddings that outperform word embeddings and fine-tuned language models both in results' quality and in execution times.

For clinical data integration and healthcare services, the HL7 FHIR standard has established itself as a desirable format for interoperability between complex health data. Previous attempts at automating the translation from free-form clinical notes into structured FHIR resources rely on modular, rule-based systems or LLMs with instruction tuning and constrained decoding. Since they frequently suffer from limited generalizability and structural inconformity, we propose an end-to-end framework powered by LLM agents, code execution, and healthcare terminology database tools to address these issues. Our solution, called Infherno, is designed to adhere to the FHIR document schema and competes well with a human baseline in predicting FHIR resources from unstructured text. The implementation features a front end for custom and synthetic data and both local and proprietary models, supporting clinical data integration processes and interoperability across institutions.

In this paper we introduce the olog, or ontology log, a category-theoretic model for knowledge representation (KR). Grounded in formal mathematics, ologs can be rigorously formulated and cross-compared in ways that other KR models (such as semantic networks) cannot. An olog is similar to a relational database schema; in fact an olog can serve as a data repository if desired. Unlike database schemas, which are generally difficult to create or modify, ologs are designed to be user-friendly enough that authoring or reconfiguring an olog is a matter of course rather than a difficult chore. It is hoped that learning to author ologs is much simpler than learning a database definition language, despite their similarity. We describe ologs carefully and illustrate with many examples. As an application we show that any primitive recursive function can be described by an olog. We also show that ologs can be aligned or connected together into a larger network using functors. The various methods of information flow and institutions can then be used to integrate local and global world-views. We finish by providing several different avenues for future research.

The data landscape is rich with structured data, often of high value to organizations, driving important applications in data analysis and machine learning. Recent progress in representation learning and generative models for such data has led to the development of natural language interfaces to structured data, including those leveraging text-to-SQL. Contextualizing interactions, either through conversational interfaces or agentic components, in structured data through retrieval-augmented generation can provide substantial benefits in the form of freshness, accuracy, and comprehensiveness of answers. The key question is: how do we retrieve the right table(s) for the analytical query or task at hand? To this end, we introduce TARGET: a benchmark for evaluating TAble Retrieval for GEnerative Tasks. With TARGET we analyze the retrieval performance of different retrievers in isolation, as well as their impact on downstream tasks. We find that dense embedding-based retrievers far outperform a BM25 baseline which is less effective than it is for retrieval over unstructured text. We also surface the sensitivity of retrievers across various metadata (e.g., missing table titles), and demonstrate a stark variation of retrieval performance across datasets and tasks. TARGET is available at https://target-benchmark.github.io.

Structured data sources, such as tables, graphs, and databases, are ubiquitous knowledge sources. Despite the demonstrated capabilities of large language models (LLMs) on plain text, their proficiency in interpreting and utilizing structured data remains limited. Our investigation reveals a notable deficiency in LLMs' ability to process structured data, e.g., ChatGPT lags behind state-of-the-art (SoTA) model by an average of 35%. To augment the Structured Knowledge Grounding (SKG) capabilities in LLMs, we have developed a comprehensive instruction tuning dataset comprising 1.1 million examples. Utilizing this dataset, we train a series of models, referred to as StructLM, based on the Code-LLaMA architecture, ranging from 7B to 34B parameters. Our StructLM series surpasses task-specific models on 14 out of 18 evaluated datasets and establishes new SoTA achievements on 7 SKG tasks. Furthermore, StructLM demonstrates exceptional generalization across 6 novel SKG tasks. Contrary to expectations, we observe that scaling model size offers marginal benefits, with StructLM-34B showing only slight improvements over StructLM-7B. This suggests that structured knowledge grounding is still a challenging task and requires more innovative design to push to a new level.

The effective utilization of structured data, integral to corporate data strategies, has been challenged by the rise of large language models (LLMs) capable of processing unstructured information. This shift prompts the question: can LLMs interpret structured data directly in its unstructured form? We propose an automatic evaluation data generation method for assessing LLMs' reasoning capabilities on structure-rich text to explore this. Our approach supports 8 structured languages and 29 tasks, generating data with adjustable complexity through controllable nesting and structural width. We introduce StrucText-Eval, a benchmark containing 5,800 pre-generated and annotated samples designed to evaluate how well LLMs understand and reason through structured text. StrucText-Eval is divided into two suites: a regular Test suite (3,712 samples) and a Test-Hard suite (2,088 samples), the latter emphasizing the gap between human and model performance on more complex tasks. Experimental results show that while open-source LLMs achieve a maximum accuracy of 74.9\% on the standard dataset, their performance drops significantly to 45.8\% on the harder dataset. In contrast, human participants reach an accuracy of 92.6\% on StrucText-Eval-Hard, highlighting LLMs' current limitations in handling intricate structural information. The benchmark and generation codes are open sourced in https://github.com/MikeGu721/StrucText-Eval

Multi-document Multi-entity Question Answering inherently demands models to track implicit logic between multiple entities across scattered documents. However, existing Large Language Models (LLMs) and Retrieval-Augmented Generation (RAG) frameworks suffer from critical limitations: standard RAG's vector similarity-based coarse-grained retrieval often omits critical facts, graph-based RAG fails to efficiently integrate fragmented complex relationship networks, and both lack schema awareness, leading to inadequate cross-document evidence chain construction and inaccurate entity relationship deduction. To address these challenges, we propose DocSage, an end-to-end agentic framework that integrates dynamic schema discovery, structured information extraction, and schema-aware relational reasoning with error guarantees. DocSage operates through three core modules: (1) A schema discovery module dynamically infers query-specific minimal joinable schemas to capture essential entities and relationships; (2) An extraction module transforms unstructured text into semantically coherent relational tables, enhanced by error-aware correction mechanisms to reduce extraction errors; (3) A reasoning module performs multi-hop relational reasoning over structured tables, leveraging schema awareness to efficiently align cross-document entities and aggregate evidence. This agentic design offers three key advantages: precise fact localization via SQL-powered indexing, natural support for cross-document entity joins through relational tables, and mitigated LLM attention diffusion via structured representation. Evaluations on two MDMEQA benchmarks demonstrate that DocSage significantly outperforms state-of-the-art long-context LLMs and RAG systems, achieving more than 27% accuracy improvements respectively.

Structured access is an emerging paradigm for the safe deployment of artificial intelligence (AI). Instead of openly disseminating AI systems, developers facilitate controlled, arm's length interactions with their AI systems. The aim is to prevent dangerous AI capabilities from being widely accessible, whilst preserving access to AI capabilities that can be used safely. The developer must both restrict how the AI system can be used, and prevent the user from circumventing these restrictions through modification or reverse engineering of the AI system. Structured access is most effective when implemented through cloud-based AI services, rather than disseminating AI software that runs locally on users' hardware. Cloud-based interfaces provide the AI developer greater scope for controlling how the AI system is used, and for protecting against unauthorized modifications to the system's design. This chapter expands the discussion of "publication norms" in the AI community, which to date has focused on the question of how the informational content of AI research projects should be disseminated (e.g., code and models). Although this is an important question, there are limits to what can be achieved through the control of information flows. Structured access views AI software not only as information that can be shared but also as a tool with which users can have arm's length interactions. There are early examples of structured access being practiced by AI developers, but there is much room for further development, both in the functionality of cloud-based interfaces and in the wider institutional framework.

Parody is an emerging phenomenon on social media, where individuals imitate a role or position opposite to their own, often for humor, provocation, or controversy. Detecting and analyzing parody can be challenging and is often reliant on context, yet it plays a crucial role in understanding cultural values, promoting subcultures, and enhancing self-expression. However, the study of parody is hindered by limited available data and deficient diversity in current datasets. To bridge this gap, we built seven parody datasets from both English and Chinese corpora, with 14,755 annotated users and 21,210 annotated comments in total. To provide sufficient context information, we also collect replies and construct user-interaction graphs to provide richer contextual information, which is lacking in existing datasets. With these datasets, we test traditional methods and Large Language Models (LLMs) on three key tasks: (1) parody detection, (2) comment sentiment analysis with parody, and (3) user sentiment analysis with parody. Our extensive experiments reveal that parody-related tasks still remain challenging for all models, and contextual information plays a critical role. Interestingly, we find that, in certain scenarios, traditional sentence embedding methods combined with simple classifiers can outperform advanced LLMs, i.e. DeepSeek-R1 and GPT-o3, highlighting parody as a significant challenge for LLMs.

Large language models still struggle with reliable long-term conversational memory: simply enlarging context windows or applying naive retrieval often introduces noise and destabilizes responses. We present APEX-MEM, a conversational memory system that combines three key innovations: (1) a property graph which uses domain-agnostic ontology to structure conversations as temporally grounded events in an entity-centric framework, (2) append-only storage that preserves the full temporal evolution of information, and (3) a multi-tool retrieval agent that understands and resolves conflicting or evolving information at query time, producing a compact and contextually relevant memory summary. This retrieval-time resolution preserves the full interaction history while suppressing irrelevant details. APEX-MEM achieves 88.88% accuracy on LOCOMO's Question Answering task and 86.2% on LongMemEval, outperforming state-of-the-art session-aware approaches and demonstrating that structured property graphs enable more temporally coherent long-term conversational reasoning.

Reasoning over heterogeneous artifacts (PDFs, spreadsheets, slide decks, etc.) increasingly occurs within structured agent workflows that iteratively extract, transform, and reference external information. In these workflows, uncertainty is not merely an input-quality issue: it can redirect decomposition and routing decisions, reshape intermediate state, and produce qualitatively different execution trajectories. We study this phenomenon by treating uncertainty as a controlled variable: we inject structured perturbations into artifact-derived representations, execute fixed workflows under comprehensive logging, and quantify contamination via trace divergence in plans, tool invocations, and intermediate state. Across 614 paired runs on 32 GAIA tasks with three different language models, we find a decoupling: workflows may diverge substantially yet recover correct answers, or remain structurally similar while producing incorrect outputs. We characterize three manifestation types: silent semantic corruption, behavioral detours with recovery, and combined structural disruption and their control-flow signatures (rerouting, extended execution, early termination). We measure operational costs and characterize why commonly used verification guardrails fail to intercept contamination. We contribute (i) a formal taxonomy of contamination manifestations in structured workflows, (ii) a trace-based measurement framework for detecting and localizing contamination across agent interactions, and (iii) empirical evidence with implications for targeted verification, defensive design, and cost control.

As a prototypical latent world model, Joint-Embedding Predictive Architectures (JEPAs) provide strong semantic representations. However, dense patch representations expose a redundant interface to downstream predictors, which must implicitly infer spatial organization and temporal correspondence, presenting three challenges. First, object information is distributed across patches, forcing each downstream predictor to redundantly recover object structure that could otherwise be reused across tasks before modeling interactions. Second, the lack of explicit entity correspondence across time makes historical transitions expensive, restricting the predictor's flexibility in utilizing context. Third, without explicit transport structure, existing JEPA models typically use pointwise l1/l2 distances, which are insensitive to spatial displacement when predicted and goal supports are largely disjoint. We propose the Slot-based Joint-Embedding Predictive Architecture (Slot-JEPA), which decomposes dense representations into stable semantic slots and time-varying spatial masks. Pretrained once and frozen downstream, this decomposition exposes a reusable object-structured interface. Building on it, our Transition Memory Predictor (TMP) stores visual transitions as compact masks and retrieves useful context using statistics of corresponding slots. Its two branches separate slot-specific dynamics from shared cross-slot dynamics. We further use Unbalanced Optimal Transport (UOT) to supervise mask prediction and evaluate candidate plans by transporting mass between aligned predicted and goal masks, providing a signal better aligned with spatial progress. Across seven visual-understanding benchmarks, the slot-reconstructed features remain transferable. Slot-JEPA also improves goal-conditioned planning across six planar environments and four robotic arm planning tasks on the REALM-JEPA benchmark.

Deep learning has been widely used for protein engineering. However, it is limited by the lack of sufficient experimental data to train an accurate model for predicting the functional fitness of high-order mutants. Here, we develop SESNet, a supervised deep-learning model to predict the fitness for protein mutants by leveraging both sequence and structure information, and exploiting attention mechanism. Our model integrates local evolutionary context from homologous sequences, the global evolutionary context encoding rich semantic from the universal protein sequence space and the structure information accounting for the microenvironment around each residue in a protein. We show that SESNet outperforms state-of-the-art models for predicting the sequence-function relationship on 26 deep mutational scanning datasets. More importantly, we propose a data augmentation strategy by leveraging the data from unsupervised models to pre-train our model. After that, our model can achieve strikingly high accuracy in prediction of the fitness of protein mutants, especially for the higher order variants (> 4 mutation sites), when finetuned by using only a small number of experimental mutation data (<50). The strategy proposed is of great practical value as the required experimental effort, i.e., producing a few tens of experimental mutation data on a given protein, is generally affordable by an ordinary biochemical group and can be applied on almost any protein.

The growing sophistication of drug discovery calls for new advances in artificial intelligence (AI). Transformers have underpinned recent breakthroughs in AI, yet their conventional source-target attention mechanism can become a bottleneck for modeling complex interactions. Here, we introduce TopoLIA, a topology-inspired latent interaction attention mechanism that learns not only how much information should be exchanged between interaction partners, but also how that information should be transformed. Source-target-dependent attention is mediated through a compact latent interaction space, providing a structured representation of complex interactions. We further incorporate topological spectral representations to capture multiscale data geometry and extract algebraic relationships. TopoLIA thus incorporates topological principles into both data representation and neural network architecture. We demonstrate TopoLIA on protein-ligand binding, where persistent spectra encode multiscale topological and geometric patterns in 3D protein-ligand complexes, while latent interaction attention (LIA) enables structured, source-target-dependent information exchange. We pretrain TopoLIA by reconstructing masked multiscale spectral tokens from unlabeled molecular structures, yielding transferable structural representations without task-specific annotations. Across multiple scoring and docking benchmarks, TopoLIA achieves state-of-the-art performance and consistently outperforms its standard-attention counterpart. Rank analyses show that compact latent dimensions yield the best performance, supporting compact interaction spaces as an effective inductive bias for biomolecular learning. More broadly, LIA provides a general framework for structured, source-target-dependent information exchange that is applicable to diverse scientific and AI problems involving complex heterogeneous interactions.

Establishing dense correspondence between two images is a fundamental computer vision problem, which is typically tackled by matching local feature descriptors. However, without global awareness, such local features are often insufficient for disambiguating similar regions. And computing the pairwise feature correlation across images is both computation-expensive and memory-intensive. To make the local features aware of the global context and improve their matching accuracy, we introduce DenseGAP, a new solution for efficient Dense correspondence learning with a Graph-structured neural network conditioned on Anchor Points. Specifically, we first propose a graph structure that utilizes anchor points to provide sparse but reliable prior on inter- and intra-image context and propagates them to all image points via directed edges. We also design a graph-structured network to broadcast multi-level contexts via light-weighted message-passing layers and generate high-resolution feature maps at low memory cost. Finally, based on the predicted feature maps, we introduce a coarse-to-fine framework for accurate correspondence prediction using cycle consistency. Our feature descriptors capture both local and global information, thus enabling a continuous feature field for querying arbitrary points at high resolution. Through comprehensive ablative experiments and evaluations on large-scale indoor and outdoor datasets, we demonstrate that our method advances the state-of-the-art of correspondence learning on most benchmarks.

Text-attributed graphs (TAGs) present unique challenges in representation learning by requiring models to capture both the semantic richness of node-associated texts and the structural dependencies of the graph. While graph neural networks (GNNs) excel at modeling topological information, they lack the capacity to process unstructured text. Conversely, large language models (LLMs) are proficient in text understanding but are typically unaware of graph structure. In this work, we propose BiGTex (Bidirectional Graph Text), a novel architecture that tightly integrates GNNs and LLMs through stacked Graph-Text Fusion Units. Each unit allows for mutual attention between textual and structural representations, enabling information to flow in both directions, text influencing structure and structure guiding textual interpretation. The proposed architecture is trained using parameter-efficient fine-tuning (LoRA), keeping the LLM frozen while adapting to task-specific signals. Extensive experiments on five benchmark datasets demonstrate that BiGTex achieves state-of-the-art performance in node classification and generalizes effectively to link prediction. An ablation study further highlights the importance of soft prompting and bi-directional attention in the model's success.

Schema matching is a crucial task in data integration, involving the alignment of a source schema with a target schema to establish correspondence between their elements. This task is challenging due to textual and semantic heterogeneity, as well as differences in schema sizes. Although machine-learning-based solutions have been explored in numerous studies, they often suffer from low accuracy, require manual mapping of the schemas for model training, or need access to source schema data which might be unavailable due to privacy concerns. In this paper we present a novel method, named ReMatch, for matching schemas using retrieval-enhanced Large Language Models (LLMs). Our method avoids the need for predefined mapping, any model training, or access to data in the source database. Our experimental results on large real-world schemas demonstrate that ReMatch is an effective matcher. By eliminating the requirement for training data, ReMatch becomes a viable solution for real-world scenarios.

The rapid evolution of artificial intelligence in drug discovery encounters challenges with generalization and extensive training, yet Large Language Models (LLMs) offer promise in reshaping interactions with complex molecular data. Our novel contribution, InstructMol, a multi-modal LLM, effectively aligns molecular structures with natural language via an instruction-tuning approach, utilizing a two-stage training strategy that adeptly combines limited domain-specific data with molecular and textual information. InstructMol showcases substantial performance improvements in drug discovery-related molecular tasks, surpassing leading LLMs and significantly reducing the gap with specialized models, thereby establishing a robust foundation for a versatile and dependable drug discovery assistant.

Rapid progress in deep learning has spurred its application to bioinformatics problems including protein structure prediction and design. In classic machine learning problems like computer vision, progress has been driven by standardized data sets that facilitate fair assessment of new methods and lower the barrier to entry for non-domain experts. While data sets of protein sequence and structure exist, they lack certain components critical for machine learning, including high-quality multiple sequence alignments and insulated training / validation splits that account for deep but only weakly detectable homology across protein space. We have created the ProteinNet series of data sets to provide a standardized mechanism for training and assessing data-driven models of protein sequence-structure relationships. ProteinNet integrates sequence, structure, and evolutionary information in programmatically accessible file formats tailored for machine learning frameworks. Multiple sequence alignments of all structurally characterized proteins were created using substantial high-performance computing resources. Standardized data splits were also generated to emulate the difficulty of past CASP (Critical Assessment of protein Structure Prediction) experiments by resetting protein sequence and structure space to the historical states that preceded six prior CASPs. Utilizing sensitive evolution-based distance metrics to segregate distantly related proteins, we have additionally created validation sets distinct from the official CASP sets that faithfully mimic their difficulty. ProteinNet thus represents a comprehensive and accessible resource for training and assessing machine-learned models of protein structure.

Taxonomy is a hierarchically structured knowledge graph that plays a crucial role in machine intelligence. The taxonomy expansion task aims to find a position for a new term in an existing taxonomy to capture the emerging knowledge in the world and keep the taxonomy dynamically updated. Previous taxonomy expansion solutions neglect valuable information brought by the hierarchical structure and evaluate the correctness of merely an added edge, which downgrade the problem to node-pair scoring or mini-path classification. In this paper, we propose the Hierarchy Expansion Framework (HEF), which fully exploits the hierarchical structure's properties to maximize the coherence of expanded taxonomy. HEF makes use of taxonomy's hierarchical structure in multiple aspects: i) HEF utilizes subtrees containing most relevant nodes as self-supervision data for a complete comparison of parental and sibling relations; ii) HEF adopts a coherence modeling module to evaluate the coherence of a taxonomy's subtree by integrating hypernymy relation detection and several tree-exclusive features; iii) HEF introduces the Fitting Score for position selection, which explicitly evaluates both path and level selections and takes full advantage of parental relations to interchange information for disambiguation and self-correction. Extensive experiments show that by better exploiting the hierarchical structure and optimizing taxonomy's coherence, HEF vastly surpasses the prior state-of-the-art on three benchmark datasets by an average improvement of 46.7% in accuracy and 32.3% in mean reciprocal rank.

Information seeking is a fundamental requirement for humans. However, existing LLM agents rely heavily on open-web search, which exposes two fundamental weaknesses: online content is noisy and unreliable, and many real-world tasks require precise, domain-specific knowledge unavailable from the web. The emergence of the Model Context Protocol (MCP) now allows agents to interface with thousands of specialized tools, seemingly resolving this limitation. Yet it remains unclear whether agents can effectively leverage such tools -- and more importantly, whether they can integrate them with general-purpose search to solve complex tasks. Therefore, we introduce InfoMosaic-Bench, the first benchmark dedicated to multi-source information seeking in tool-augmented agents. Covering six representative domains (medicine, finance, maps, video, web, and multi-domain integration), InfoMosaic-Bench requires agents to combine general-purpose search with domain-specific tools. Tasks are synthesized with InfoMosaic-Flow, a scalable pipeline that grounds task conditions in verified tool outputs, enforces cross-source dependencies, and filters out shortcut cases solvable by trivial lookup. This design guarantees both reliability and non-triviality. Experiments with 14 state-of-the-art LLM agents reveal three findings: (i) web information alone is insufficient, with GPT-5 achieving only 38.2% accuracy and 67.5% pass rate; (ii) domain tools provide selective but inconsistent benefits, improving some domains while degrading others; and (iii) 22.4% of failures arise from incorrect tool usage or selection, highlighting that current LLMs still struggle with even basic tool handling.

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.

Retrieval-Augmented Generation (RAG) systems enhance large language models (LLMs) by integrating external knowledge sources, enabling more accurate and contextually relevant responses tailored to user needs. However, existing RAG systems have significant limitations, including reliance on flat data representations and inadequate contextual awareness, which can lead to fragmented answers that fail to capture complex inter-dependencies. To address these challenges, we propose LightRAG, which incorporates graph structures into text indexing and retrieval processes. This innovative framework employs a dual-level retrieval system that enhances comprehensive information retrieval from both low-level and high-level knowledge discovery. Additionally, the integration of graph structures with vector representations facilitates efficient retrieval of related entities and their relationships, significantly improving response times while maintaining contextual relevance. This capability is further enhanced by an incremental update algorithm that ensures the timely integration of new data, allowing the system to remain effective and responsive in rapidly changing data environments. Extensive experimental validation demonstrates considerable improvements in retrieval accuracy and efficiency compared to existing approaches. We have made our LightRAG open-source and available at the link: https://github.com/HKUDS/LightRAG.

Accurate breast cancer classification from mammography requires effective integration of complementary information from craniocaudal (CC) and mediolateral oblique (MLO) views, which provide a more complete characterization of breast abnormalities. However, existing multi-view learning approaches typically rely on feature-level aggregation or single-stage cross-attention, which can entangle view-specific and shared representations and restrict interaction to limited network depths. To address these limitations, we propose a token-centric dual-view learning framework that unifies prompt-based adaptation and cross-view fusion within a frozen vision transformer backbone. The framework reformulates inter-view interaction as structured token-level communication, where dedicated fusion tokens explicitly encode bidirectional information exchange between CC and MLO views via cross-attention, serving as intermediate carriers of cross-view dependencies rather than relying on direct feature fusion. Unlike conventional methods that apply fusion at a single layer, fusion modules are inserted at multiple transformer depths, enabling progressive and repeated interaction across the encoder hierarchy. Fusion tokens are reintegrated into the token sequence and refined by subsequent transformer layers, facilitating hierarchical propagation of complementary information while preserving view-specific structure. Experiments on VinDr-Mammo and CMMD datasets demonstrate consistent improvements over linear probing, prompt-only adaptation, and conventional fusion baselines. On the VinDr-Mammo BI-RADS classification task, the framework achieves 50.40% F1-score and 0.8090 AUC, including a 0.10 AUC improvement over a dual-view fusion baseline in the binary setting. Ablation studies further validate the effectiveness of token-based fusion and multi-depth interaction design.

Recently, the emergence of the large-scale vision-language model (VLM), such as CLIP, has opened the way towards open-world object perception. Many works have explored the utilization of pre-trained VLM for the challenging open-vocabulary dense prediction task that requires perceiving diverse objects with novel classes at inference time. Existing methods construct experiments based on the public datasets of related tasks, which are not tailored for open vocabulary and rarely involve imperceptible objects camouflaged in complex scenes due to data collection bias and annotation costs. To fill in the gaps, we introduce a new task, open-vocabulary camouflaged object segmentation (OVCOS), and construct a large-scale complex scene dataset (OVCamo) containing 11,483 hand-selected images with fine annotations and corresponding object classes. Further, we build a strong single-stage open-vocabulary camouflaged object segmentation transformer baseline OVCoser attached to the parameter-fixed CLIP with iterative semantic guidance and structure enhancement. By integrating the guidance of class semantic knowledge and the supplement of visual structure cues from the edge and depth information, the proposed method can efficiently capture camouflaged objects. Moreover, this effective framework also surpasses previous state-of-the-arts of open-vocabulary semantic image segmentation by a large margin on our OVCamo dataset. With the proposed dataset and baseline, we hope that this new task with more practical value can further expand the research on open-vocabulary dense prediction tasks. Our code and data can be found in the https://github.com/lartpang/OVCamo{link}.

Recent advancements in large multimodal models (LMMs) have showcased impressive code generation capabilities, primarily evaluated through image-to-code benchmarks. However, these benchmarks are limited to specific visual programming scenarios where the logic reasoning and the multimodal understanding capacities are split apart. To fill this gap, we propose ScratchEval, a novel benchmark designed to evaluate the visual programming reasoning ability of LMMs. ScratchEval is based on Scratch, a block-based visual programming language widely used in children's programming education. By integrating visual elements and embedded programming logic, ScratchEval requires the model to process both visual information and code structure, thereby comprehensively evaluating its programming intent understanding ability. Our evaluation approach goes beyond the traditional image-to-code mapping and focuses on unified logical thinking and problem-solving abilities, providing a more comprehensive and challenging framework for evaluating the visual programming ability of LMMs. ScratchEval not only fills the gap in existing evaluation methods, but also provides new insights for the future development of LMMs in the field of visual programming. Our benchmark can be accessed at https://github.com/HKBUNLP/ScratchEval .

To support reliable long-term interaction in complex environments, LLM agents require memory systems that efficiently manage historical experiences. Existing approaches either retain full interaction histories via passive context extension, leading to substantial redundancy, or rely on iterative reasoning to filter noise, incurring high token costs. To address this challenge, we introduce SimpleMem, an efficient memory framework based on semantic lossless compression. We propose a three-stage pipeline designed to maximize information density and token utilization: (1) Semantic Structured Compression, which applies entropy-aware filtering to distill unstructured interactions into compact, multi-view indexed memory units; (2) Recursive Memory Consolidation, an asynchronous process that integrates related units into higher-level abstract representations to reduce redundancy; and (3) Adaptive Query-Aware Retrieval, which dynamically adjusts retrieval scope based on query complexity to construct precise context efficiently. Experiments on benchmark datasets show that our method consistently outperforms baseline approaches in accuracy, retrieval efficiency, and inference cost, achieving an average F1 improvement of 26.4% while reducing inference-time token consumption by up to 30-fold, demonstrating a superior balance between performance and efficiency. Code is available at https://github.com/aiming-lab/SimpleMem.

Recent studies have revealed the vulnerability of Deep Neural Networks (DNNs) to adversarial examples, which can easily fool DNNs into making incorrect predictions. To mitigate this deficiency, we propose a novel adversarial defense method called "Immunity" (Innovative MoE with MUtual information \& positioN stabilITY) based on a modified Mixture-of-Experts (MoE) architecture in this work. The key enhancements to the standard MoE are two-fold: 1) integrating of Random Switch Gates (RSGs) to obtain diverse network structures via random permutation of RSG parameters at evaluation time, despite of RSGs being determined after one-time training; 2) devising innovative Mutual Information (MI)-based and Position Stability-based loss functions by capitalizing on Grad-CAM's explanatory power to increase the diversity and the causality of expert networks. Notably, our MI-based loss operates directly on the heatmaps, thereby inducing subtler negative impacts on the classification performance when compared to other losses of the same type, theoretically. Extensive evaluation validates the efficacy of the proposed approach in improving adversarial robustness against a wide range of attacks.

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.

Learning dexterous humanoid loco-manipulation from human demonstrations requires transferring not only human motion, but also the coordinated interaction structure underlying the demonstrated behavior. This is challenging because embodiment differences distort the coupling among body motion, wrist placement, finger articulation, and object interaction, while kinematically accurate references may still be difficult to realize under robot dynamics. We present DexWeave, a unified framework that connects interaction-consistent motion retargeting with anatomy-aware whole-body policy learning. DexWeave first employs a two-stage retargeting procedure that initializes body and hand motions with specialized solvers and subsequently performs coupled refinement over the upper-body interaction chain while preserving lower-body support. The resulting references are tracked by an anatomy-aware Transformer policy that represents anatomical regions as structured tokens and uses directed masked attention to model their dependencies, with object information selectively conditioning the upper-body pathway for dexterous interaction. The policy jointly outputs body and dexterous-hand actions and is trained directly with reinforcement learning, without pretrained tracking policies, teacher-student distillation, or subsequent residual refinement. DexWeave improves retargeting fidelity and interaction consistency while achieving higher manipulation performance and faster policy convergence than MLP baselines. We further deploy the learned policies on a physical Unitree G1 humanoid equipped with Inspire dexterous hands, demonstrating dexterous whole-body loco-manipulation in the real world. See our project page (https://dexweave.github.io) for videos.

Recent structured RAG methods leverage tree- or graph-based reasoning structures to improve multi-hop QA. However, they face key limitations in evidence-intensive QA, where answering a question requires synthesizing information scattered across dozens or even hundreds of documents: structural rigidity, which limits adaptive reasoning expansion, and topology-ignorant evidence gathering, which prevents effective integration of evidence across different reasoning nodes. To address these issues, we propose APT-RAG, an Adaptive Planning and Topology-aware evidence gathering RAG framework. Adaptive planning dynamically expands the reasoning structure based on question dependencies and evidence requirements, while topology-aware evidence gathering improves evidence coverage through sibling evidence reuse, direct retrieval, and evidence aggregation from child nodes. We further introduce evidence-guided batched answer generation to reduce significant generation overhead in evidence-intensive QA. In the experiments on evidence-intensive QA benchmarks, APT-RAG outperforms existing structured RAG methods. Our code is available at https://github.com/hyudsl/APT-RAG.

The ability to extract structured information from unstructured sources-such as free-text documents and scientific literature-is critical for accelerating scientific discovery and knowledge synthesis. Large Language Models (LLMs) have demonstrated remarkable capabilities in various natural language processing tasks, including structured information extraction. However, their effectiveness often diminishes in specialized, domain-specific contexts that require nuanced understanding and expert-level domain knowledge. In addition, existing LLM-based approaches frequently exhibit poor transferability across tasks and domains, limiting their scalability and adaptability. To address these challenges, we introduce StructSense, a modular, task-agnostic, open-source framework for structured information extraction built on LLMs. StructSense is guided by domain-specific symbolic knowledge encoded in ontologies, enabling it to navigate complex domain content more effectively. It further incorporates agentic capabilities through self-evaluative judges that form a feedback loop for iterative refinement, and includes human-in-the-loop mechanisms to ensure quality and validation. We demonstrate that StructSense can overcome both the limitations of domain sensitivity and the lack of cross-task generalizability, as shown through its application to diverse neuroscience information extraction tasks.