Daily Papers

We introduce Generalized Instruction Tuning (called GLAN), a general and scalable method for instruction tuning of Large Language Models (LLMs). Unlike prior work that relies on seed examples or existing datasets to construct instruction tuning data, GLAN exclusively utilizes a pre-curated taxonomy of human knowledge and capabilities as input and generates large-scale synthetic instruction data across all disciplines. Specifically, inspired by the systematic structure in human education system, we build the taxonomy by decomposing human knowledge and capabilities to various fields, sub-fields and ultimately, distinct disciplines semi-automatically, facilitated by LLMs. Subsequently, we generate a comprehensive list of subjects for every discipline and proceed to design a syllabus tailored to each subject, again utilizing LLMs. With the fine-grained key concepts detailed in every class session of the syllabus, we are able to generate diverse instructions with a broad coverage across the entire spectrum of human knowledge and skills. Extensive experiments on large language models (e.g., Mistral) demonstrate that GLAN excels in multiple dimensions from mathematical reasoning, coding, academic exams, logical reasoning to general instruction following without using task-specific training data of these tasks. In addition, GLAN allows for easy customization and new fields or skills can be added by simply incorporating a new node into our taxonomy.

The performance of unified multimodal models for image generation and editing is fundamentally constrained by the quality and comprehensiveness of their training data. While existing datasets have covered basic tasks like style transfer and simple object manipulation, they often lack the systematic structure and challenging scenarios required for real-world applications. To address this bottleneck, we introduce OpenGPT-4o-Image, a large-scale dataset constructed using a novel methodology that combines hierarchical task taxonomy with automated data generation. Our taxonomy not only includes fundamental capabilities such as text rendering and style control but also introduces highly practical yet challenging categories like scientific imagery for chemistry illustrations and complex instruction editing requiring simultaneous execution of multiple operations. Through an automated pipeline leveraging structured resource pools and GPT-4o, we generate 80k high-quality instruction-image pairs with controlled diversity, covering 11 major domains and 51 subtasks. Extensive experiments show that fine-tuning leading models on our dataset achieves significant performance gains across multiple benchmarks, with improvements of up to 18\% on editing tasks (UniWorld-V1 on ImgEdit-Bench) and 13% on generation tasks (Harmon on GenEval). Our work demonstrates that systematic data construction is key to advancing multimodal AI capabilities.

Large language models have demonstrated substantial advancements in reasoning capabilities, particularly through inference-time scaling, as illustrated by models such as OpenAI's o1. However, current Vision-Language Models (VLMs) often struggle to perform systematic and structured reasoning, especially when handling complex visual question-answering tasks. In this work, we introduce LLaVA-o1, a novel VLM designed to conduct autonomous multistage reasoning. Unlike chain-of-thought prompting, LLaVA-o1 independently engages in sequential stages of summarization, visual interpretation, logical reasoning, and conclusion generation. This structured approach enables LLaVA-o1 to achieve marked improvements in precision on reasoning-intensive tasks. To accomplish this, we compile the LLaVA-o1-100k dataset, integrating samples from various visual question answering sources and providing structured reasoning annotations. Besides, we propose an inference-time stage-level beam search method, which enables effective inference-time scaling. Remarkably, with only 100k training samples and a simple yet effective inference time scaling method, LLaVA-o1 not only outperforms its base model by 8.9% on a wide range of multimodal reasoning benchmarks, but also surpasses the performance of larger and even closed-source models, such as Gemini-1.5-pro, GPT-4o-mini, and Llama-3.2-90B-Vision-Instruct.

Phone call transcript labeling is prohibitively expensive (approximately 2 USD per minute) due to privacy regulations, consent requirements, and manual annotation costs requiring 3 hours of expert time per hour of audio. Existing extraction methods fail on conversational speech containing disfluencies, interruptions, and speaker overlap. We introduce LingVarBench, a synthetic data generation pipeline that addresses these constraints through automated validation. First, we prompt an LLM to generate realistic structured field values across multiple use cases. Second, we recursively prompt the model to transform these values into thousands of natural conversational utterances containing typical phone call characteristics. Third, we validate each synthetic utterance by testing whether a separate LLM-based extractor can recover the original structured information. We employ DSPy's SIMBA optimizer to automatically synthesize extraction prompts from validated synthetic transcripts, eliminating manual prompt engineering. Our optimized prompts achieve up to 95 percent accuracy for numeric fields (vs. 88-89 percent zero-shot), 90 percent for names (vs. 47-79 percent), and over 80 percent for dates (vs. 72-77 percent) on real customer transcripts, demonstrating substantial gains over zero-shot prompting. The synthetic-to-real transfer demonstrates that conversational patterns learned from generated data generalize effectively to authentic phone calls containing background noise and domain-specific terminology. LingVarBench provides the first systematic benchmark for structured extraction from synthetic conversational data, demonstrating that automated prompt optimization overcomes cost and privacy barriers preventing large-scale phone call analysis in commercial settings.

In Large Language Models (LLMs), there have been consistent advancements in task-specific performance, largely influenced by effective prompt design. While recent research on prompting has enhanced the reasoning capabilities of LLMs, a gap remains in further improving their understanding abilities. In this study, we introduce Metacognitive Prompting (MP), a strategy inspired by human introspective reasoning processes. Using MP, LLMs undergo a systematic series of structured, self-aware evaluations, drawing on both their vast inherent knowledge and new insights. Our experiments involve five prevalent LLMs: Llama2, Vicuna, PaLM, GPT-3.5, and GPT-4, all of which span various general natural language understanding (NLU) tasks from the GLUE and SuperGLUE benchmarks. Results indicate that, although GPT-4 consistently excels in most tasks, PaLM, when equipped with MP, approaches its performance level. Furthermore, across models and datasets, MP consistently outperforms existing prompting methods, including standard and chain-of-thought prompting. This study underscores the potential to amplify the understanding abilities of LLMs and highlights the benefits of mirroring human introspective reasoning in NLU tasks.

Legal practitioners, particularly those early in their careers, face complex, high-stakes tasks that require adaptive, context-sensitive reasoning. While AI holds promise in supporting legal work, current datasets and models are narrowly focused on isolated subtasks and fail to capture the end-to-end decision-making required in real-world practice. To address this gap, we introduce LawFlow, a dataset of complete end-to-end legal workflows collected from trained law students, grounded in real-world business entity formation scenarios. Unlike prior datasets focused on input-output pairs or linear chains of thought, LawFlow captures dynamic, modular, and iterative reasoning processes that reflect the ambiguity, revision, and client-adaptive strategies of legal practice. Using LawFlow, we compare human and LLM-generated workflows, revealing systematic differences in structure, reasoning flexibility, and plan execution. Human workflows tend to be modular and adaptive, while LLM workflows are more sequential, exhaustive, and less sensitive to downstream implications. Our findings also suggest that legal professionals prefer AI to carry out supportive roles, such as brainstorming, identifying blind spots, and surfacing alternatives, rather than executing complex workflows end-to-end. Building on these findings, we propose a set of design suggestions, rooted in empirical observations, that align AI assistance with human goals of clarity, completeness, creativity, and efficiency, through hybrid planning, adaptive execution, and decision-point support. Our results highlight both the current limitations of LLMs in supporting complex legal workflows and opportunities for developing more collaborative, reasoning-aware legal AI systems. All data and code are available on our project page (https://minnesotanlp.github.io/LawFlow-website/).

Without proper safeguards, large language models will readily follow malicious instructions and generate toxic content. This motivates safety efforts such as red-teaming and large-scale feedback learning, which aim to make models both helpful and harmless. However, there is a tension between these two objectives, since harmlessness requires models to refuse complying with unsafe prompts, and thus not be helpful. Recent anecdotal evidence suggests that some models may have struck a poor balance, so that even clearly safe prompts are refused if they use similar language to unsafe prompts or mention sensitive topics. In this paper, we introduce a new test suite called XSTest to identify such eXaggerated Safety behaviours in a structured and systematic way. In its current form, XSTest comprises 200 safe prompts across ten prompt types that well-calibrated models should not refuse to comply with. We describe XSTest's creation and composition, and use the test suite to highlight systematic failure modes in a recently-released state-of-the-art language model.

We investigate the relationship between the Lyman-alpha (Lya) forest transmission in the intergalactic medium (IGM) and the environmental density of galaxies, focusing on its implications for the measurement of ionizing radiation escape fractions. Using a sample of 268 spectroscopically confirmed background galaxies at 2.7<z<3.0 and a galaxy density map at z~2.5 within the COSMOS field, we measure the Lya transmission photometrically, leveraging the multiwavelength data available from the COSMOS2020 catalog. Our results reveal a weak but statistically significant positive correlation between Lya optical depth and galaxy density contrast, suggesting that overdense regions are enriched in neutral gas, which could bias escape fraction measurements. This emphasizes the need to account for the large-scale structure of the IGM in analyses of ionizing radiation escape fractions, and highlights the advantages of a photometric approach for increasing the number of sampled lines of sight across large fields. The photometric redshifts provided by upcoming all-sky surveys, such as Euclid, will make it possible to account for this effect across widely separated fields.

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

Pre-trained multilingual language models underpin a large portion of modern NLP tools outside of English. A strong baseline for specializing these models for specific languages is Language-Adaptive Pre-Training (LAPT). However, retaining a large cross-lingual vocabulary and embedding matrix comes at considerable excess computational cost during adaptation. In this study, we propose several simple techniques to replace a cross-lingual vocabulary with a compact, language-specific one. Namely, we address strategies for re-initializing the token embedding matrix after vocabulary specialization. We then provide a systematic experimental comparison of our techniques, in addition to the recently-proposed Focus method. We demonstrate that: 1) Embedding-replacement techniques in the monolingual transfer literature are inadequate for adapting multilingual models. 2) Replacing cross-lingual vocabularies with smaller specialized ones provides an efficient method to improve performance in low-resource languages. 3) Simple embedding re-initialization techniques based on script-wise sub-distributions rival techniques such as Focus, which rely on similarity scores obtained from an auxiliary model.

A central question in artificial intelligence is the extent to which machine learning models comprehend mathematics. To address this, we propose a novel framework for measuring mathematical reasoning that moves beyond standard benchmarks to diagnose specific failure points. Our method first generates structured, step-by-step reasoning from gpt-3.5-turbo on the GSM8K dataset. We then use a more capable analyst model, gpt-4o-mini, to categorize errors and, crucially, perform an unsupervised clustering of every reasoning sentence to identify emergent "reasoning modes." This analysis reveals a cognitive profile with a stark, nonhuman-like brittleness: while the model achieves near-perfect accuracy on procedural modes like sequential calculation, its performance on modes requiring combinatorial reasoning with restrictions plummets. By identifying and quantifying the reliability of these distinct reasoning skills, our work provides a more granular method to evaluate mathematical comprehension and offers a precise roadmap for developing new capabilities and more reliable future applications.

We propose cognitive prompting as a novel approach to guide problem-solving in large language models (LLMs) through structured, human-like cognitive operations such as goal clarification, decomposition, filtering, abstraction, and pattern recognition. By employing systematic, step-by-step reasoning, cognitive prompting enables LLMs to efficiently tackle complex, multi-step tasks. We evaluate the effectiveness of cognitive prompting on Meta's LLaMA models, comparing performance on arithmetic reasoning tasks using the GSM8K dataset and on commonsense reasoning benchmarks. Our analysis includes comparisons between models without cognitive prompting, models with a static sequence of cognitive operations, and models using reflective cognitive prompting, where the LLM dynamically self-selects the sequence of cognitive operations. The results show that cognitive prompting, particularly when dynamically adapted, significantly improves the performance of larger models, such as LLaMA3.1 70B, and enhances their ability to handle multi-step reasoning tasks. This approach also improves interpretability and flexibility, highlighting cognitive prompting as a promising strategy for general-purpose AI reasoning.

Prompt engineering has emerged as an indispensable technique for extending the capabilities of large language models (LLMs) and vision-language models (VLMs). This approach leverages task-specific instructions, known as prompts, to enhance model efficacy without modifying the core model parameters. Rather than updating the model parameters, prompts allow seamless integration of pre-trained models into downstream tasks by eliciting desired model behaviors solely based on the given prompt. Prompts can be natural language instructions that provide context to guide the model or learned vector representations that activate relevant knowledge. This burgeoning field has enabled success across various applications, from question-answering to commonsense reasoning. However, there remains a lack of systematic organization and understanding of the diverse prompt engineering methods and techniques. This survey paper addresses the gap by providing a structured overview of recent advancements in prompt engineering, categorized by application area. For each prompting approach, we provide a summary detailing the prompting methodology, its applications, the models involved, and the datasets utilized. We also delve into the strengths and limitations of each approach and include a taxonomy diagram and table summarizing datasets, models, and critical points of each prompting technique. This systematic analysis enables a better understanding of this rapidly developing field and facilitates future research by illuminating open challenges and opportunities for prompt engineering.

Developing artificial intelligence (AI) for vertical domains requires a solid data foundation for both training and evaluation. In this work, we introduce TrialPanorama, a large-scale, structured database comprising 1,657,476 clinical trial records aggregated from 15 global sources. The database captures key aspects of trial design and execution, including trial setups, interventions, conditions, biomarkers, and outcomes, and links them to standard biomedical ontologies such as DrugBank and MedDRA. This structured and ontology-grounded design enables TrialPanorama to serve as a unified, extensible resource for a wide range of clinical trial tasks, including trial planning, design, and summarization. To demonstrate its utility, we derive a suite of benchmark tasks directly from the TrialPanorama database. The benchmark spans eight tasks across two categories: three for systematic review (study search, study screening, and evidence summarization) and five for trial design (arm design, eligibility criteria, endpoint selection, sample size estimation, and trial completion assessment). The experiments using five state-of-the-art large language models (LLMs) show that while general-purpose LLMs exhibit some zero-shot capability, their performance is still inadequate for high-stakes clinical trial workflows. We release TrialPanorama database and the benchmark to facilitate further research on AI for clinical trials.

Natural Language Processing (NLP) research has traditionally been predominantly focused on English, driven by the availability of resources, the size of the research community, and market demands. Recently, there has been a noticeable shift towards multilingualism in NLP, recognizing the need for inclusivity and effectiveness across diverse languages and cultures. Monolingual surveys have the potential to complement the broader trend towards multilingualism in NLP by providing foundational insights and resources, necessary for effectively addressing the linguistic diversity of global communication. However, monolingual NLP surveys are extremely rare in the literature. This study introduces a generalizable methodology for creating systematic and comprehensive monolingual NLP surveys, aimed at optimizing the process of constructing such surveys and thoroughly addressing a language's NLP support. Our approach integrates a structured search protocol to avoid selection bias and ensure reproducibility, an NLP task taxonomy to organize the surveyed material coherently, and language resources (LRs) taxonomies to identify potential benchmarks and highlight opportunities for improving resource availability (e.g., through better maintenance or licensing). We apply this methodology to Greek NLP (2012-2023), providing a comprehensive overview of its current state and challenges. We discuss the progress of Greek NLP and outline the Greek LRs found, classified by availability and usability, assessing language support per NLP task. The presented systematic literature review of Greek NLP serves as an application of our method that showcases the benefits of monolingual NLP surveys more broadly. Similar applications could be considered for the myriads of languages whose progress in NLP lags behind that of well-supported languages.

The complexity of the Generally Accepted Accounting Principles (GAAP) and the hierarchical structure of eXtensible Business Reporting Language (XBRL) filings make financial auditing increasingly difficult to automate and verify. While large language models (LLMs) have demonstrated strong capabilities in unstructured text understanding, their ability to reason over structured, interdependent, and taxonomy-driven financial documents remains largely unexplored. To fill this gap, we introduce FinAuditing, the first taxonomy-aligned, structure-aware, multi-document benchmark for evaluating LLMs on financial auditing tasks. Built from real US-GAAP-compliant XBRL filings, FinAuditing defines three complementary subtasks, FinSM for semantic consistency, FinRE for relational consistency, and FinMR for numerical consistency, each targeting a distinct aspect of structured auditing reasoning. We further propose a unified evaluation framework integrating retrieval, classification, and reasoning metrics across these subtasks. Extensive zero-shot experiments on 13 state-of-the-art LLMs reveal that current models perform inconsistently across semantic, relational, and mathematical dimensions, with accuracy drops of up to 60-90% when reasoning over hierarchical multi-document structures. Our findings expose the systematic limitations of modern LLMs in taxonomy-grounded financial reasoning and establish FinAuditing as a foundation for developing trustworthy, structure-aware, and regulation-aligned financial intelligence systems. The benchmark dataset is available at Hugging Face.

Large language models (LLMs) have achieved remarkable success across various domains, driving significant technological advancements and innovations. Despite the rapid growth in model scale and capability, systematic, data-driven research on how structural configurations affect performance remains scarce. To address this gap, we present a large-scale dataset encompassing diverse open-source LLM structures and their performance across multiple benchmarks. Leveraging this dataset, we conduct a systematic, data mining-driven analysis to validate and quantify the relationship between structural configurations and performance. Our study begins with a review of the historical development of LLMs and an exploration of potential future trends. We then analyze how various structural choices impact performance across benchmarks and further corroborate our findings using mechanistic interpretability techniques. By providing data-driven insights into LLM optimization, our work aims to guide the targeted development and application of future models. We will release our dataset at https://huggingface.co/datasets/DX0369/LLM-Structure-Performance-Dataset

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

Generative Artificial Intelligence (GenAI) systems are being increasingly deployed across all parts of industry and research settings. Developers and end users interact with these systems through the use of prompting or prompt engineering. While prompting is a widespread and highly researched concept, there exists conflicting terminology and a poor ontological understanding of what constitutes a prompt due to the area's nascency. This paper establishes a structured understanding of prompts, by assembling a taxonomy of prompting techniques and analyzing their use. We present a comprehensive vocabulary of 33 vocabulary terms, a taxonomy of 58 text-only prompting techniques, and 40 techniques for other modalities. We further present a meta-analysis of the entire literature on natural language prefix-prompting.

Recent advances in diffusion large language models (dLLMs) have introduced a promising alternative to autoregressive (AR) LLMs for natural language generation tasks, leveraging full attention and denoising-based decoding strategies. However, the deployment of these models on edge devices remains challenging due to their massive parameter scale and high resource demands. While post-training quantization (PTQ) has emerged as a widely adopted technique for compressing AR LLMs, its applicability to dLLMs remains largely unexplored. In this work, we present the first systematic study on quantizing diffusion-based language models. We begin by identifying the presence of activation outliers, characterized by abnormally large activation values that dominate the dynamic range. These outliers pose a key challenge to low-bit quantization, as they make it difficult to preserve precision for the majority of values. More importantly, we implement state-of-the-art PTQ methods and conduct a comprehensive evaluation across multiple task types and model variants. Our analysis is structured along four key dimensions: bit-width, quantization method, task category, and model type. Through this multi-perspective evaluation, we offer practical insights into the quantization behavior of dLLMs under different configurations. We hope our findings provide a foundation for future research in efficient dLLM deployment. All codes and experimental setups will be released to support the community.

Retrieval-Augmented Generation (RAG) enhances the performance of LLMs across various tasks by retrieving relevant information from external sources, particularly on text-based data. For structured data, such as knowledge graphs, GraphRAG has been widely used to retrieve relevant information. However, recent studies have revealed that structuring implicit knowledge from text into graphs can benefit certain tasks, extending the application of GraphRAG from graph data to general text-based data. Despite their successful extensions, most applications of GraphRAG for text data have been designed for specific tasks and datasets, lacking a systematic evaluation and comparison between RAG and GraphRAG on widely used text-based benchmarks. In this paper, we systematically evaluate RAG and GraphRAG on well-established benchmark tasks, such as Question Answering and Query-based Summarization. Our results highlight the distinct strengths of RAG and GraphRAG across different tasks and evaluation perspectives. Inspired by these observations, we investigate strategies to integrate their strengths to improve downstream tasks. Additionally, we provide an in-depth discussion of the shortcomings of current GraphRAG approaches and outline directions for future research.

We present DART, an open domain structured DAta Record to Text generation dataset with over 82k instances (DARTs). Data-to-Text annotations can be a costly process, especially when dealing with tables which are the major source of structured data and contain nontrivial structures. To this end, we propose a procedure of extracting semantic triples from tables that encodes their structures by exploiting the semantic dependencies among table headers and the table title. Our dataset construction framework effectively merged heterogeneous sources from open domain semantic parsing and dialogue-act-based meaning representation tasks by utilizing techniques such as: tree ontology annotation, question-answer pair to declarative sentence conversion, and predicate unification, all with minimum post-editing. We present systematic evaluation on DART as well as new state-of-the-art results on WebNLG 2017 to show that DART (1) poses new challenges to existing data-to-text datasets and (2) facilitates out-of-domain generalization. Our data and code can be found at https://github.com/Yale-LILY/dart.

Multi-turn instruction following capability constitutes a core competency of large language models (LLMs) in real-world applications. Existing evaluation benchmarks predominantly focus on fine-grained constraint satisfaction and domain-specific capability assessment, yet overlook the crucial structural dependency between dialogue turns that distinguishes multi-turn from single-turn interactions. This structural dependency not only reflects user intent but also establishes a second dimension for instruction following evaluation beyond constraint satisfaction. To address this gap, we propose StructFlowBench, a multi-turn instruction following benchmark with structural flow modeling. The benchmark innovatively defines a structural flow framework comprising six fundamental inter-turn relationships, which not only introduces novel structural constraints for model evaluation but also serves as generation parameters for creating customized dialogue flows tailored to specific scenarios. Adopting established LLM-based automatic evaluation methodologies, we conduct systematic evaluations of 13 leading open-source and closed-source LLMs. Experimental results reveal significant deficiencies in current models' comprehension of multi-turn dialogue structures. The code is available at https://github.com/MLGroupJLU/StructFlowBench.

Despite their impressive capabilities, Multimodal Large Language Models (MLLMs) face challenges with fine-grained perception and complex reasoning. Prevalent multimodal pre-training approaches focus on enhancing perception by training on high-quality image captions due to the extremely high cost of collecting chain-of-thought (CoT) reasoning data for improving reasoning. While leveraging advanced MLLMs for caption generation enhances scalability, the outputs often lack comprehensiveness and accuracy. In this paper, we introduce Self-Improving cognition (SIcog), a self-learning framework designed to construct next-generation foundation MLLMs by enhancing their systematic cognitive capabilities through multimodal pre-training with self-generated data. Specifically, we propose Chain-of-Description, an approach that improves an MLLM's systematic perception by enabling step-by-step visual understanding, ensuring greater comprehensiveness and accuracy. Additionally, we adopt a structured CoT reasoning technique to enable MLLMs to integrate in-depth multimodal reasoning. To construct a next-generation foundation MLLM with self-improved cognition, SIcog first equips an MLLM with systematic perception and reasoning abilities using minimal external annotations. The enhanced models then generate detailed captions and CoT reasoning data, which are further curated through self-consistency. This curated data is ultimately used for multimodal pre-training to develop next-generation foundation models. Extensive experiments on both low- and high-resolution MLLMs across diverse benchmarks demonstrate that, with merely 213K self-generated pre-training samples, SIcog produces next-generation foundation MLLMs with significantly improved cognition, achieving benchmark-leading performance compared to prevalent pre-training approaches.

Knowledge bases (KBs) and text often contain complementary knowledge: KBs store structured knowledge that can support long range reasoning, while text stores more comprehensive and timely knowledge in an unstructured way. Separately embedding the individual knowledge sources into vector spaces has demonstrated tremendous successes in encoding the respective knowledge, but how to jointly embed and reason with both knowledge sources to fully leverage the complementary information is still largely an open problem. We conduct a large-scale, systematic investigation of aligning KB and text embeddings for joint reasoning. We set up a novel evaluation framework with two evaluation tasks, few-shot link prediction and analogical reasoning, and evaluate an array of KB-text embedding alignment methods. We also demonstrate how such alignment can infuse textual information into KB embeddings for more accurate link prediction on emerging entities and events, using COVID-19 as a case study.

Large language models (LLMs) have demonstrated enhanced performance through the Thinking then Responding paradigm, where models generate internal thoughts before final responses (aka, System 2 thinking). However, existing research lacks a systematic understanding of the mechanisms underlying how thinking patterns affect performance across model sizes. In this work, we conduct a comprehensive analysis of the impact of various thinking types on model performance and introduce ThinkPatterns-21k, a curated dataset comprising 21k instruction-response pairs (QA) collected from existing instruction-following datasets with five thinking types. For each pair, we augment it with five distinct internal thinking patterns: one unstructured thinking (monologue) and four structured variants (decomposition, self-ask, self-debate and self-critic), while maintaining the same instruction and response. Through extensive evaluation across different model sizes (3B-32B parameters), we have two key findings: (1) smaller models (<30B parameters) can benefit from most of structured thinking patterns, while larger models (32B) with structured thinking like decomposition would degrade performance and (2) unstructured monologue demonstrates broad effectiveness across different model sizes. Finally, we released all of our datasets, checkpoints, training logs of diverse thinking patterns to reproducibility, aiming to facilitate further research in this direction.

Existing methods for vision-language task planning excel in short-horizon tasks but often fall short in complex, long-horizon planning within dynamic environments. These challenges primarily arise from the difficulty of effectively training models to produce high-quality reasoning processes for long-horizon tasks. To address this, we propose Structured Preference Optimization (SPO), which aims to enhance reasoning and action selection in long-horizon task planning through structured preference evaluation and optimized training strategies. Specifically, SPO introduces: 1) Preference-Based Scoring and Optimization, which systematically evaluates reasoning chains based on task relevance, visual grounding, and historical consistency; and 2) Curriculum-Guided Training, where the model progressively adapts from simple to complex tasks, improving its generalization ability in long-horizon scenarios and enhancing reasoning robustness. To advance research in vision-language long-horizon task planning, we introduce ExtendaBench, a comprehensive benchmark covering 1,509 tasks across VirtualHome and Habitat 2.0, categorized into ultra-short, short, medium, and long tasks. Experimental results demonstrate that SPO significantly improves reasoning quality and final decision accuracy, outperforming prior methods on long-horizon tasks and underscoring the effectiveness of preference-driven optimization in vision-language task planning. Specifically, SPO achieves a +5.98% GCR and +4.68% SR improvement in VirtualHome and a +3.30% GCR and +2.11% SR improvement in Habitat over the best-performing baselines.

Text generation under constraints have seen increasing interests in natural language processing, especially with the rapidly improving capabilities of large language models. However, existing benchmarks for constrained generation usually focus on fixed constraint types (e.g.,generate a sentence containing certain words) that have proved to be easy for state-of-the-art models like GPT-4. We present COLLIE, a grammar-based framework that allows the specification of rich, compositional constraints with diverse generation levels (word, sentence, paragraph, passage) and modeling challenges (e.g.,language understanding, logical reasoning, counting, semantic planning). We also develop tools for automatic extraction of task instances given a constraint structure and a raw text corpus. Using COLLIE, we compile the COLLIE-v1 dataset with 2080 instances comprising 13 constraint structures. We perform systematic experiments across five state-of-the-art instruction-tuned language models and analyze their performances to reveal shortcomings. COLLIE is designed to be extensible and lightweight, and we hope the community finds it useful to develop more complex constraints and evaluations in the future.

Reliably generating structured outputs has become a critical capability for modern language model (LM) applications. Constrained decoding has emerged as the dominant technology across sectors for enforcing structured outputs during generation. Despite its growing adoption, little has been done with the systematic evaluation of the behaviors and performance of constrained decoding. Constrained decoding frameworks have standardized around JSON Schema as a structured data format, with most uses guaranteeing constraint compliance given a schema. However, there is poor understanding of the effectiveness of the methods in practice. We present an evaluation framework to assess constrained decoding approaches across three critical dimensions: efficiency in generating constraint-compliant outputs, coverage of diverse constraint types, and quality of the generated outputs. To facilitate this evaluation, we introduce JSONSchemaBench, a benchmark for constrained decoding comprising 10K real-world JSON schemas that encompass a wide range of constraints with varying complexity. We pair the benchmark with the existing official JSON Schema Test Suite and evaluate six state-of-the-art constrained decoding frameworks, including Guidance, Outlines, Llamacpp, XGrammar, OpenAI, and Gemini. Through extensive experiments, we gain insights into the capabilities and limitations of constrained decoding on structured generation with real-world JSON schemas. Our work provides actionable insights for improving constrained decoding frameworks and structured generation tasks, setting a new standard for evaluating constrained decoding and structured generation. We release JSONSchemaBench at https://github.com/guidance-ai/jsonschemabench

The rapid advancement of large language models (LLMs) has accelerated their application in reasoning, with strategic reasoning drawing increasing attention. To evaluate LLMs' strategic reasoning capabilities, game theory, with its concise structure, has become a preferred approach. However, current research focuses on a limited selection of games, resulting in low coverage. Classic game scenarios risk data leakage, and existing benchmarks often lack extensibility, making them inadequate for evaluating state-of-the-art models. To address these challenges, we propose TMGBench, a benchmark with comprehensive game type coverage, novel scenarios, and flexible organization. Specifically, we incorporate all 144 game types summarized by the Robinson-Goforth topology of 2x2 games, constructed as classic games. We also employ synthetic data generation to create diverse, higher-quality scenarios through topic guidance and human inspection, referred to as story-based games. Lastly, we provide a sustainable framework for increasingly powerful LLMs by treating these games as atomic units and organizing them into more complex forms via sequential, parallel, and nested structures. Our comprehensive evaluation of mainstream LLMs covers tests on rational reasoning, robustness, Theory-of-Mind (ToM), and reasoning in complex forms. Results reveal flaws in accuracy, consistency, and varying mastery of ToM. Additionally, o1-mini, OpenAI's latest reasoning model, achieved accuracy rates of 66.6%, 60.0%, and 70.0% on sequential, parallel, and nested games, highlighting TMGBench's challenges.

Large Language Models (LLMs) are widely used for tasks such as natural language and code generation. Still, their outputs often suffer from issues like privacy violations, and semantically inaccurate code generation. Current libraries for LLM generation rely on left-to-right decoding without systematic support for backtracking, limiting the ability to correct or refine outputs mid-generation. To address this issue, we introduce IterGen, an intuitive framework for iterative, grammar-guided LLM generation that enables users to move both forward and backward within the generated output based on grammar symbols. By leveraging a symbol-to-position mapping, IterGen ensures efficient and structured generation while allowing for corrections during the process. We demonstrate IterGen's effectiveness in two important applications: reducing privacy leakage in LLM outputs and improving the accuracy of LLM-generated SQL queries. Our code is available at https://github.com/uiuc-arc/itergen

The rapid evolution of modern malware presents significant challenges to the development of effective defense mechanisms. Traditional cyber deception techniques often rely on static or manually configured parameters, limiting their adaptability to dynamic and sophisticated threats. This study leverages Generative AI (GenAI) models to automate the creation of adaptive cyber deception ploys, focusing on structured prompt engineering (PE) to enhance relevance, actionability, and deployability. We introduce a systematic framework (SPADE) to address inherent challenges large language models (LLMs) pose to adaptive deceptions, including generalized outputs, ambiguity, under-utilization of contextual information, and scalability constraints. Evaluations across diverse malware scenarios using metrics such as Recall, Exact Match (EM), BLEU Score, and expert quality assessments identified ChatGPT-4o as the top performer. Additionally, it achieved high engagement (93%) and accuracy (96%) with minimal refinements. Gemini and ChatGPT-4o Mini demonstrated competitive performance, with Llama3.2 showing promise despite requiring further optimization. These findings highlight the transformative potential of GenAI in automating scalable, adaptive deception strategies and underscore the critical role of structured PE in advancing real-world cybersecurity applications.

Non-coding RNA structure and function are essential to understanding various biological processes, such as cell signaling, gene expression, and post-transcriptional regulations. These are all among the core problems in the RNA field. With the rapid growth of sequencing technology, we have accumulated a massive amount of unannotated RNA sequences. On the other hand, expensive experimental observatory results in only limited numbers of annotated data and 3D structures. Hence, it is still challenging to design computational methods for predicting their structures and functions. The lack of annotated data and systematic study causes inferior performance. To resolve the issue, we propose a novel RNA foundation model (RNA-FM) to take advantage of all the 23 million non-coding RNA sequences through self-supervised learning. Within this approach, we discover that the pre-trained RNA-FM could infer sequential and evolutionary information of non-coding RNAs without using any labels. Furthermore, we demonstrate RNA-FM's effectiveness by applying it to the downstream secondary/3D structure prediction, SARS-CoV-2 genome structure and evolution prediction, protein-RNA binding preference modeling, and gene expression regulation modeling. The comprehensive experiments show that the proposed method improves the RNA structural and functional modelling results significantly and consistently. Despite only being trained with unlabelled data, RNA-FM can serve as the foundational model for the field.

Recent progress in large language models demonstrates that hybrid architectures--combining self-attention mechanisms with structured state space models like Mamba--can achieve a compelling balance between modeling quality and computational efficiency, particularly for long-context tasks. While these hybrid models show promising performance, systematic comparisons of hybridization strategies and analyses on the key factors behind their effectiveness have not been clearly shared to the community. In this work, we present a holistic evaluation of hybrid architectures based on inter-layer (sequential) or intra-layer (parallel) fusion. We evaluate these designs from a variety of perspectives: language modeling performance, long-context capabilities, scaling analysis, and training and inference efficiency. By investigating the core characteristics of their computational primitive, we identify the most critical elements for each hybridization strategy and further propose optimal design recipes for both hybrid models. Our comprehensive analysis provides practical guidance and valuable insights for developing hybrid language models, facilitating the optimization of architectural configurations.

We present RAG Playground, an open-source framework for systematic evaluation of Retrieval-Augmented Generation (RAG) systems. The framework implements and compares three retrieval approaches: naive vector search, reranking, and hybrid vector-keyword search, combined with ReAct agents using different prompting strategies. We introduce a comprehensive evaluation framework with novel metrics and provide empirical results comparing different language models (Llama 3.1 and Qwen 2.5) across various retrieval configurations. Our experiments demonstrate significant performance improvements through hybrid search methods and structured self-evaluation prompting, achieving up to 72.7% pass rate on our multi-metric evaluation framework. The results also highlight the importance of prompt engineering in RAG systems, with our custom-prompted agents showing consistent improvements in retrieval accuracy and response quality.

Complex networks can be used for modeling street meshes and urban agglomerates. With such a model, many aspects of a city can be investigated to promote a better quality of life to its citizens. Along these lines, this paper proposes a set of distance-based pattern-discovery algorithmic instruments to improve urban structures modeled as complex networks, detecting nodes that lack access from/to points of interest in a given city. Furthermore, we introduce a greedy algorithm that is able to recommend improvements to the structure of a city by suggesting where points of interest are to be placed. We contribute to a thorough process to deal with complex networks, including mathematical modeling and algorithmic innovation. The set of our contributions introduces a systematic manner to treat a recurrent problem of broad interest in cities.

Multilingual large language models (LLMs) often demonstrate a performance gap between English and non-English languages, particularly in low-resource settings. Aligning these models to low-resource languages is essential yet challenging due to limited high-quality data. While English alignment datasets are readily available, curating equivalent data in other languages is expensive and time-consuming. A common workaround is to translate existing English alignment data; however, standard translation techniques often fail to preserve critical elements such as code, mathematical expressions, and structured formats like JSON. In this work, we investigate LLM-based selective translation, a technique that selectively translates only the translatable parts of a text while preserving non-translatable content and sentence structure. We conduct a systematic study to explore key questions around this approach, including its effectiveness compared to vanilla translation, the importance of filtering noisy outputs, and the benefits of mixing translated samples with original English data during alignment. Our experiments focus on the low-resource Indic language Hindi and compare translations generated by Google Cloud Translation (GCP) and Llama-3.1-405B. The results highlight the promise of selective translation as a practical and effective method for improving multilingual alignment in LLMs.

Large vision-language models (VLMs) are increasingly deployed for optical character recognition (OCR) in healthcare settings, raising critical concerns about protected health information (PHI) exposure during document processing. This work presents the first systematic evaluation of inference-time vision token masking as a privacy-preserving mechanism for medical document OCR using DeepSeek-OCR. We introduce seven masking strategies (V3-V9) targeting different architectural layers (SAM encoder blocks, compression layers, dual vision encoders, projector fusion) and evaluate PHI reduction across HIPAA-defined categories using 100 synthetic medical billing statements (drawn from a corpus of 38,517 annotated documents) with perfect ground-truth annotations. All masking strategies converge to 42.9% PHI reduction, successfully suppressing long-form spatially-distributed identifiers (patient names, dates of birth, physical addresses at 100% effectiveness) while failing to prevent short structured identifiers (medical record numbers, social security numbers, email addresses, account numbers at 0% effectiveness). Ablation studies varying mask expansion radius (r=1,2,3) demonstrate that increased spatial coverage does not improve reduction beyond this ceiling, indicating that language model contextual inference - not insufficient visual masking - drives structured identifier leakage. A simulated hybrid architecture combining vision masking with NLP post-processing achieves 88.6% total PHI reduction (assuming 80% NLP accuracy on remaining identifiers). This negative result establishes boundaries for vision-only privacy interventions in VLMs, provides guidance distinguishing PHI types amenable to vision-level versus language-level redaction, and redirects future research toward decoder-level fine-tuning and hybrid defense-in-depth architectures for HIPAA-compliant medical document processing.

Generating novel and creative scientific hypotheses is a cornerstone in achieving Artificial General Intelligence. Large language and reasoning models have the potential to aid in the systematic creation, selection, and validation of scientifically informed hypotheses. However, current foundation models often struggle to produce scientific ideas that are both novel and feasible. One reason is the lack of a dedicated dataset that frames Scientific Hypothesis Generation (SHG) as a Natural Language Generation (NLG) task. In this paper, we introduce HypoGen, the first dataset of approximately 5500 structured problem-hypothesis pairs extracted from top-tier computer science conferences structured with a Bit-Flip-Spark schema, where the Bit is the conventional assumption, the Spark is the key insight or conceptual leap, and the Flip is the resulting counterproposal. HypoGen uniquely integrates an explicit Chain-of-Reasoning component that reflects the intellectual process from Bit to Flip. We demonstrate that framing hypothesis generation as conditional language modelling, with the model fine-tuned on Bit-Flip-Spark and the Chain-of-Reasoning (and where, at inference, we only provide the Bit), leads to improvements in the overall quality of the hypotheses. Our evaluation employs automated metrics and LLM judge rankings for overall quality assessment. We show that by fine-tuning on our HypoGen dataset we improve the novelty, feasibility, and overall quality of the generated hypotheses. The HypoGen dataset is publicly available at huggingface.co/datasets/UniverseTBD/hypogen-dr1.

The increasing capability of large language models (LLMs) to generate synthetic content has heightened concerns about their misuse, driving the development of Machine-Generated Text (MGT) detection models. However, these detectors face significant challenges due to the lack of systematically generated, high-quality datasets for training. To address this issue, we propose five novel data augmentation frameworks for synthetic user dialogue generation through a structured prompting approach, reducing the costs associated with traditional data collection methods. Our proposed method yields 14 new dialogue datasets, which we benchmark against seven MGT detection models. The results demonstrate improved generalization performance when utilizing a mixed dataset produced by our proposed augmentation framework. Furthermore, considering that real-world agents lack knowledge of future opponent utterances, we simulate online dialogue detection and examine the relationship between chat history length and detection accuracy. We also benchmark online detection performance with limited chat history on our frameworks. Our open-source datasets can be downloaded from https://github.com/AngieYYF/SPADE-customer-service-dialogue.

We introduce the first metric for evaluating disentanglement at individual hierarchy levels of a structured latent representation. Applied to object-centric generative models, this offers a systematic, unified approach to evaluating (i) object separation between latent slots (ii) disentanglement of object properties inside individual slots (iii) disentanglement of intrinsic and extrinsic object properties. We theoretically show that for structured representations, our framework gives stronger guarantees of selecting a good model than previous disentanglement metrics. Experimentally, we demonstrate that viewing object compositionality as a disentanglement problem addresses several issues with prior visual metrics of object separation. As a core technical component, we present the first representation probing algorithm handling slot permutation invariance.

Large reasoning models (LRMs) spend substantial test-time compute on long chain-of-thought (CoT) traces, but what *characterizes* an effective CoT remains unclear. While prior work reports gains from lengthening CoTs and increasing review (revisiting earlier steps) via appended *wait* tokens, recent studies suggest that shorter thinking can outperform longer traces. We therefore conduct a systematic evaluation across ten LRMs on math and scientific reasoning. Contrary to the "longer-is-better" narrative, we find that both naive CoT lengthening and increased review are associated with *lower* accuracy. As CoT unfolds step by step, token-level metrics can conflate verbosity with process quality. We introduce a graph view of CoT to extract structure and identify a single statistic-the *Failed-Step Fraction (FSF)*, the fraction of steps in abandoned branches-that consistently outpredicts length and review ratio for correctness across models. To probe causality, we design two interventions. First, we rank candidate CoTs by each metric at test time, where FSF yields the largest pass@1 gains; second, we edit CoTs to remove failed branches, which significantly improves accuracy, indicating that failed branches bias subsequent reasoning. Taken together, these results characterize effective CoTs as those that *fail less* and support *structure-aware* test-time scaling over indiscriminately generating long CoT.

While modern visual generation models excel at creating aesthetically pleasing natural images, they struggle with producing or editing structured visuals like charts, diagrams, and mathematical figures, which demand composition planning, text rendering, and multimodal reasoning for factual fidelity. To address this, we present the first comprehensive, systematic investigation of this domain, encompassing data construction, model training, and an evaluation benchmark. First, we construct a large-scale dataset of 1.3 million high-quality structured image pairs derived from executable drawing programs and augmented with chain-of-thought reasoning annotations. Building on it, we train a unified model that integrates a VLM with FLUX.1 Kontext via a lightweight connector for enhanced multimodal understanding. A three-stage training curriculum enables progressive feature alignment, knowledge infusion, and reasoning-augmented generation, further boosted by an external reasoner at inference time. Finally, we introduce StructBench, a novel benchmark for generation and editing with over 1,700 challenging instances, and an accompanying evaluation metric, StructScore, which employs a multi-round Q\&A protocol to assess fine-grained factual accuracy. Evaluations of 15 models reveal that even leading closed-source systems remain far from satisfactory. Our model attains strong editing performance, and inference-time reasoning yields consistent gains across diverse architectures. By releasing the dataset, model, and benchmark, we aim to advance unified multimodal foundations for structured visuals.

State-of-the-art vision-language models (VLMs) suffer from a critical failure in understanding negation, often referred to as affirmative bias. This limitation is particularly severe in described object detection (DOD) tasks. To address this, we propose two primary contributions: (1) a new dataset pipeline and (2) a novel, lightweight adaptation recipe. First, we introduce CoVAND, a dataset constructed with a systematic chain-of-thought (CoT) and VQA-based pipeline to generate high-quality, instance-grounded negation data. Second, we propose NegToMe, a novel text token merging module that directly tackles the architectural cause of affirmative bias. NegToMe fundamentally addresses the structural loss of negation cues in tokenization, grouping them with attributes into coherent semantic phrases. It maintains correct polarity at the input level, enabling robust negation understanding even with limited data. For instance, to prevent a model from treating the fragmented tokens "not" and "girl" as simply "girl", NegToMe binds them into a single token whose meaning is correctly distinguished from that of "girl" alone. This module is integrated with a parameter-efficient and strategic LoRA fine-tuning approach. Our method significantly improves performance on challenging negation benchmarks with a lowered false positive rate, boosting NMS-AP by up to +10.8 points on OVDEval and demonstrating generalization to SoTA VLMs. This work marks a crucial step forward in addressing negation understanding for real-world detection applications.

The use of large language models (LLMs) for automated code generation has emerged as a significant focus within AI research. As these pretrained models continue to evolve, their ability to understand and generate complex code structures has opened new possibilities for automating intricate programming tasks for the sake of accurate code generation. Although contemporary foundational models demonstrate promoting results, researchers continue to explore optimal post-training strategies to enhance code quality. These include supervised fine-tuning, retrieval-augmented generation (RAG), debugging, and many others. In this paper, we combine two widely used approaches namely multi-agent collaboration and runtime execution information-based debugging, for improving code generation functionality, reliability, and practical applicability. We perform an empirical study in order to extend the evaluation of the individual strategies as well as the proposed composition of the activities of both strategies. Our study use 19 LLMs to examines the performance of individual and the proposed strategies, offering comprehensive insights into how different programming activities compositions and training paradigms influence code generation effectiveness. In particular, we implement a chained system that combines both strategies to assess their combined impact on functional accuracy, code reliability, and generation latency using two benchmark datasets commonly used for code generation. Our findings provide valuable insights for organizations seeking robust AI-driven coding solutions by guiding them in selecting models that can better adapt to complex post-training strategies, ultimately fostering the adoption of more effective and reliable code generation technologies.

Structured knowledge grounding (SKG) leverages structured knowledge to complete user requests, such as semantic parsing over databases and question answering over knowledge bases. Since the inputs and outputs of SKG tasks are heterogeneous, they have been studied separately by different communities, which limits systematic and compatible research on SKG. In this paper, we overcome this limitation by proposing the UnifiedSKG framework, which unifies 21 SKG tasks into a text-to-text format, aiming to promote systematic SKG research, instead of being exclusive to a single task, domain, or dataset. We use UnifiedSKG to benchmark T5 with different sizes and show that T5, with simple modifications when necessary, achieves state-of-the-art performance on almost all of the 21 tasks. We further demonstrate that multi-task prefix-tuning improves the performance on most tasks, largely improving the overall performance. UnifiedSKG also facilitates the investigation of zero-shot and few-shot learning, and we show that T0, GPT-3, and Codex struggle in zero-shot and few-shot learning for SKG. We also use UnifiedSKG to conduct a series of controlled experiments on structured knowledge encoding variants across SKG tasks. UnifiedSKG is easily extensible to more tasks, and it is open-sourced at https://github.com/hkunlp/unifiedskg.

The accelerating development of general medical artificial intelligence (GMAI), powered by multimodal large language models (MLLMs), offers transformative potential for addressing persistent healthcare challenges, including workforce deficits and escalating costs. The parallel development of systematic evaluation benchmarks emerges as a critical imperative to enable performance assessment and provide technological guidance. Meanwhile, as an invaluable knowledge source, the potential of medical textbooks for benchmark development remains underexploited. Here, we present MedBookVQA, a systematic and comprehensive multimodal benchmark derived from open-access medical textbooks. To curate this benchmark, we propose a standardized pipeline for automated extraction of medical figures while contextually aligning them with corresponding medical narratives. Based on this curated data, we generate 5,000 clinically relevant questions spanning modality recognition, disease classification, anatomical identification, symptom diagnosis, and surgical procedures. A multi-tier annotation system categorizes queries through hierarchical taxonomies encompassing medical imaging modalities (42 categories), body anatomies (125 structures), and clinical specialties (31 departments), enabling nuanced analysis across medical subdomains. We evaluate a wide array of MLLMs, including proprietary, open-sourced, medical, and reasoning models, revealing significant performance disparities across task types and model categories. Our findings highlight critical capability gaps in current GMAI systems while establishing textbook-derived multimodal benchmarks as essential evaluation tools. MedBookVQA establishes textbook-derived benchmarking as a critical paradigm for advancing clinical AI, exposing limitations in GMAI systems while providing anatomically structured performance metrics across specialties.

Solving complex reasoning tasks is a key real-world application of agents. Thanks to the pretraining of Large Language Models (LLMs) on code data, recent approaches like CodeAct successfully use code as LLM agents' action, achieving good results. However, CodeAct greedily generates the next action's code block by relying on fragmented thoughts, resulting in inconsistency and instability. Moreover, CodeAct lacks action-related ground-truth (GT), making its supervision signals and termination conditions questionable in multi-turn interactions. To address these issues, we first introduce a simple yet effective end-to-end code generation paradigm, CodeProgram, which leverages code's systematic logic to align with global reasoning and enable cohesive problem-solving. Then, we propose Tree-of-Code (ToC), which self-grows CodeProgram nodes based on the executable nature of the code and enables self-supervision in a GT-free scenario. Experimental results on two datasets using ten popular zero-shot LLMs show ToC remarkably boosts accuracy by nearly 20% over CodeAct with less than 1/4 turns. Several LLMs even perform better on one-turn CodeProgram than on multi-turn CodeAct. To further investigate the trade-off between efficacy and efficiency, we test different ToC tree sizes and exploration mechanisms. We also highlight the potential of ToC's end-to-end data generation for supervised and reinforced fine-tuning.

Trustworthy interpretation of deep learning models is critical for neuroimaging applications, yet commonly used Explainable AI (XAI) methods lack rigorous validation, risking misinterpretation. We performed the first large-scale, systematic comparison of XAI methods on ~45,000 structural brain MRIs using a novel XAI validation framework. This framework establishes verifiable ground truth by constructing prediction tasks with known signal sources - from localized anatomical features to subject-specific clinical lesions - without artificially altering input images. Our analysis reveals systematic failures in two of the most widely used methods: GradCAM consistently failed to localize predictive features, while Layer-wise Relevance Propagation generated extensive, artifactual explanations that suggest incompatibility with neuroimaging data characteristics. Our results indicate that these failures stem from a domain mismatch, where methods with design principles tailored to natural images require substantial adaptation for neuroimaging data. In contrast, the simpler, gradient-based method SmoothGrad, which makes fewer assumptions about data structure, proved consistently accurate, suggesting its conceptual simplicity makes it more robust to this domain shift. These findings highlight the need for domain-specific adaptation and validation of XAI methods, suggest that interpretations from prior neuroimaging studies using standard XAI methodology warrant re-evaluation, and provide urgent guidance for practical application of XAI in neuroimaging.

The rapid progress of Large Language Models (LLMs) has given rise to a new category of autonomous AI systems, referred to as Deep Research (DR) agents. These agents are designed to tackle complex, multi-turn informational research tasks by leveraging a combination of dynamic reasoning, adaptive long-horizon planning, multi-hop information retrieval, iterative tool use, and the generation of structured analytical reports. In this paper, we conduct a detailed analysis of the foundational technologies and architectural components that constitute Deep Research agents. We begin by reviewing information acquisition strategies, contrasting API-based retrieval methods with browser-based exploration. We then examine modular tool-use frameworks, including code execution, multimodal input processing, and the integration of Model Context Protocols (MCPs) to support extensibility and ecosystem development. To systematize existing approaches, we propose a taxonomy that differentiates between static and dynamic workflows, and we classify agent architectures based on planning strategies and agent composition, including single-agent and multi-agent configurations. We also provide a critical evaluation of current benchmarks, highlighting key limitations such as restricted access to external knowledge, sequential execution inefficiencies, and misalignment between evaluation metrics and the practical objectives of DR agents. Finally, we outline open challenges and promising directions for future research. A curated and continuously updated repository of DR agent research is available at: {https://github.com/ai-agents-2030/awesome-deep-research-agent}.

Recent advances have demonstrated the promising capabilities of large language models (LLMs) in generating register-transfer level (RTL) code, such as Verilog. However, existing LLM-based frameworks still face significant challenges in accurately handling the complexity of real-world RTL designs, particularly those that are large-scale and involve multi-level module instantiations. To address this issue, we present ComplexVCoder, an open-source LLM-driven framework that enhances both the generation quality and efficiency of complex Verilog code. Specifically, we introduce a two-stage generation mechanism, which leverages an intermediate representation to enable a more accurate and structured transition from natural language descriptions to intricate Verilog designs. In addition, we introduce a rule-based alignment method and a domain-specific retrieval-augmented generation (RAG) to further improve the correctness of the synthesized code by incorporating relevant design knowledge during generation. To evaluate our approach, we construct a comprehensive dataset comprising 55 complex Verilog designs derived from real-world implementations. We also release an open-source benchmark suite for systematically assessing the quality of auto-generated RTL code together with the ComplexVCoder framework. Experimental results show that ComplexVCoder outperforms SOTA frameworks such as CodeV and RTLCoder by 14.6% and 22.2%, respectively, in terms of function correctness on complex Verilog benchmarks. Furthermore, ComplexVcoder achieves comparable generation performances in terms of functionality correctness using a lightweight 32B model (Qwen2.5), rivaling larger-scale models such as GPT-3.5 and DeepSeek-V3.

Systematic literature reviews and meta-analyses are essential for synthesizing research insights, but they remain time-intensive and labor-intensive due to the iterative processes of screening, evaluation, and data extraction. This paper introduces and evaluates LatteReview, a Python-based framework that leverages large language models (LLMs) and multi-agent systems to automate key elements of the systematic review process. Designed to streamline workflows while maintaining rigor, LatteReview utilizes modular agents for tasks such as title and abstract screening, relevance scoring, and structured data extraction. These agents operate within orchestrated workflows, supporting sequential and parallel review rounds, dynamic decision-making, and iterative refinement based on user feedback. LatteReview's architecture integrates LLM providers, enabling compatibility with both cloud-based and locally hosted models. The framework supports features such as Retrieval-Augmented Generation (RAG) for incorporating external context, multimodal reviews, Pydantic-based validation for structured inputs and outputs, and asynchronous programming for handling large-scale datasets. The framework is available on the GitHub repository, with detailed documentation and an installable package.

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: [email protected] or [email protected] Key words: Protein Q&A, Early-Fusion, LLM

Empathy indicates an individual's ability to understand others. Over the past few years, empathy has drawn attention from various disciplines, including but not limited to Affective Computing, Cognitive Science, and Psychology. Detecting empathy has potential applications in society, healthcare and education. Despite being a broad and overlapping topic, the avenue of empathy detection leveraging Machine Learning remains underexplored from a systematic literature review perspective. We collected 849 papers from 10 well-known academic databases, systematically screened them and analysed the final 82 papers. Our analyses reveal several prominent task formulations - including empathy on localised utterances or overall expressions, unidirectional or parallel empathy, and emotional contagion - in monadic, dyadic and group interactions. Empathy detection methods are summarised based on four input modalities - text, audiovisual, audio and physiological signals - thereby presenting modality-specific network architecture design protocols. We discuss challenges, research gaps and potential applications in the Affective Computing-based empathy domain, which can facilitate new avenues of exploration. We further enlist the public availability of datasets and codes. This paper, therefore, provides a structured overview of recent advancements and remaining challenges towards developing a robust empathy detection system that could meaningfully contribute to enhancing human well-being.

This paper surveys and organizes research works in a new paradigm in natural language processing, which we dub "prompt-based learning". Unlike traditional supervised learning, which trains a model to take in an input x and predict an output y as P(y|x), prompt-based learning is based on language models that model the probability of text directly. To use these models to perform prediction tasks, the original input x is modified using a template into a textual string prompt x' that has some unfilled slots, and then the language model is used to probabilistically fill the unfilled information to obtain a final string x, from which the final output y can be derived. This framework is powerful and attractive for a number of reasons: it allows the language model to be pre-trained on massive amounts of raw text, and by defining a new prompting function the model is able to perform few-shot or even zero-shot learning, adapting to new scenarios with few or no labeled data. In this paper we introduce the basics of this promising paradigm, describe a unified set of mathematical notations that can cover a wide variety of existing work, and organize existing work along several dimensions, e.g.the choice of pre-trained models, prompts, and tuning strategies. To make the field more accessible to interested beginners, we not only make a systematic review of existing works and a highly structured typology of prompt-based concepts, but also release other resources, e.g., a website http://pretrain.nlpedia.ai/ including constantly-updated survey, and paperlist.

Deep neural networks drive the success of natural language processing. A fundamental property of language is its compositional structure, allowing humans to systematically produce forms for new meanings. For humans, languages with more compositional and transparent structures are typically easier to learn than those with opaque and irregular structures. However, this learnability advantage has not yet been shown for deep neural networks, limiting their use as models for human language learning. Here, we directly test how neural networks compare to humans in learning and generalizing different languages that vary in their degree of compositional structure. We evaluate the memorization and generalization capabilities of a large language model and recurrent neural networks, and show that both deep neural networks exhibit a learnability advantage for more structured linguistic input: neural networks exposed to more compositional languages show more systematic generalization, greater agreement between different agents, and greater similarity to human learners.

Humans can flexibly switch between different modes of thinking based on task complexity: from rapid intuitive judgments to in-depth analytical understanding. However, current Graphical User Interface (GUI) grounding systems which locate interface elements based on natural language instructions rely solely on immediate prediction without reasoning, struggling to understand complex interface layouts with nested structures and hierarchical relationships, limiting their effectiveness on complex interfaces. Inspired by human dual-system cognition, we present Focus, a novel GUI grounding framework that combines fast prediction with systematic analysis. The framework dynamically switches between rapid and deliberate processing through an adaptive system switching based on task complexity, optimizing both efficiency and accuracy. Focus decomposes grounding into progressive stages: interface summarization, visual focused analysis, and precise coordinate prediction. This structured decomposition enables systematic understanding of both interface layouts and visual relationships. Extensive experiments show that Focus achieves state-of-the-art performance using only 300K of the training data with a 2B parameter model compared to existing approaches. Focus demonstrates superior performance particularly in complex GUI scenarios, achieving 77.4% average accuracy on ScreenSpot and 13.3% on the more challenging ScreenSpot-Pro. Our analysis reveals the effectiveness of this dual-system approach while demonstrating its potential for improving complex GUI interaction scenarios.

The scientific literature's exponential growth makes it increasingly challenging to navigate and synthesize knowledge across disciplines. Large language models (LLMs) are powerful tools for understanding scientific text, but they fail to capture detailed relationships across large bodies of work. Unstructured approaches, like retrieval augmented generation, can sift through such corpora to recall relevant facts; however, when millions of facts influence the answer, unstructured approaches become cost prohibitive. Structured representations offer a natural complement -- enabling systematic analysis across the whole corpus. Recent work enhances LLMs with unstructured or semistructured representations of scientific concepts; to complement this, we try extracting structured representations using LLMs. By combining LLMs' semantic understanding with a schema of scientific concepts, we prototype a system that answers precise questions about the literature as a whole. Our schema applies across scientific fields and we extract concepts from it using only 20 manually annotated abstracts. To demonstrate the system, we extract concepts from 30,000 papers on arXiv spanning astrophysics, fluid dynamics, and evolutionary biology. The resulting database highlights emerging trends and, by visualizing the knowledge graph, offers new ways to explore the ever-growing landscape of scientific knowledge. Demo: abby101/surveyor-0 on HF Spaces. Code: https://github.com/chiral-carbon/kg-for-science.

This paper introduce LongViTU, a large-scale (~121k QA pairs, ~900h videos), automatically generated dataset for long-form video understanding. We developed a systematic approach that organizes videos into a hierarchical tree structure and incorporates self-revision mechanisms to ensure high-quality QA pairs. Each QA pair in LongViTU features: 1) long-term context (average certificate length of 4.6 minutes); 2) rich knowledge and condensed reasoning (commonsense, causality, planning, etc.); and 3) explicit timestamp labels for relevant events. LongViTU also serves as a benchmark for instruction following in long-form and streaming video understanding. We evaluate the open-source state-of-the-art long video understanding model, LongVU, and the commercial model, Gemini-1.5-Pro, on our benchmark. They achieve GPT-4 scores of 49.9 and 52.3, respectively, underscoring the substantial challenge posed by our benchmark. Further supervised fine-tuning (SFT) on LongVU led to performance improvements of 12.0% on our benchmark, 2.2% on the in-distribution (ID) benchmark EgoSchema, 1.0%, 2.2% and 1.2% on the out-of-distribution (OOD) benchmarks VideoMME (Long), WorldQA and OpenEQA, respectively. These outcomes demonstrate LongViTU's high data quality and robust OOD generalizability.

Peer review is the cornerstone of scientific publishing, yet it suffers from inconsistencies, reviewer subjectivity, and scalability challenges. We introduce ReviewerToo, a modular framework for studying and deploying AI-assisted peer review to complement human judgment with systematic and consistent assessments. ReviewerToo supports systematic experiments with specialized reviewer personas and structured evaluation criteria, and can be partially or fully integrated into real conference workflows. We validate ReviewerToo on a carefully curated dataset of 1,963 paper submissions from ICLR 2025, where our experiments with the gpt-oss-120b model achieves 81.8% accuracy for the task of categorizing a paper as accept/reject compared to 83.9% for the average human reviewer. Additionally, ReviewerToo-generated reviews are rated as higher quality than the human average by an LLM judge, though still trailing the strongest expert contributions. Our analysis highlights domains where AI reviewers excel (e.g., fact-checking, literature coverage) and where they struggle (e.g., assessing methodological novelty and theoretical contributions), underscoring the continued need for human expertise. Based on these findings, we propose guidelines for integrating AI into peer-review pipelines, showing how AI can enhance consistency, coverage, and fairness while leaving complex evaluative judgments to domain experts. Our work provides a foundation for systematic, hybrid peer-review systems that scale with the growth of scientific publishing.

Reasoning has long been viewed as an emergent property of large language models (LLMs), appearing at or above a certain scale (sim100B parameters). However, recent studies challenge this assumption, showing that small language models (SLMs) can also achieve competitive reasoning performance. SLMs are increasingly favored for their efficiency and deployability. However, there is a lack of systematic study on the reasoning abilities of diverse SLMs, including those trained from scratch or derived from LLMs through quantization, pruning, and distillation. This raises a critical question: Can SLMs achieve reasoning abilities comparable to LLMs? In this work, we systematically survey, benchmark, and analyze 72 SLMs from six model families across 14 reasoning benchmarks. For reliable evaluation, we examine four evaluation methods and compare four LLM judges against human evaluations on 800 data points. We repeat all experiments three times to ensure a robust performance assessment. Additionally, we analyze the impact of different prompting strategies in small models. Beyond accuracy, we also evaluate model robustness under adversarial conditions and intermediate reasoning steps. Our findings challenge the assumption that scaling is the only way to achieve strong reasoning. Instead, we foresee a future where SLMs with strong reasoning capabilities can be developed through structured training or post-training compression. They can serve as efficient alternatives to LLMs for reasoning-intensive tasks.

Coupling together distinct correlated and topologically non-trivial electronic phases of matter can potentially induce novel electronic orders and phase transitions among them. Transition metal dichalcogenide compounds serve as a bedrock for exploration of such hybrid systems. They host a variety of exotic electronic phases and their Van der Waals nature enables to admix them, either by exfoliation and stacking or by stoichiometric growth, and thereby induce novel correlated complexes. Here we investigate the compound 4Hb-TaS_2 that interleaves the Mott-insulating state of 1T-TaS_2 and the putative spin liquid it hosts together with the metallic state of 2H-TaS_2 and the low temperature superconducting phase it harbors. We reveal a thermodynamic phase diagram that hosts a first order quantum phase transition between a correlated Kondo cluster state and a flat band state in which the Kondo cluster becomes depleted. We demonstrate that this intrinsic transition can be induced by an electric field and temperature as well as by manipulation of the interlayer coupling with the probe tip, hence allowing to reversibly toggle between the Kondo cluster and the flat band states. The phase transition is manifested by a discontinuous change of the complete electronic spectrum accompanied by hysteresis and low frequency noise. We find that the shape of the transition line in the phase diagram is determined by the local compressibility and the entropy of the two electronic states. Our findings set such heterogeneous structures as an exciting platform for systematic investigation and manipulation of Mott-metal transitions and strongly correlated phases and quantum phase transitions therein.

Tokenization is the first - and often underappreciated - layer of computation in language models. While Chain-of-Thought (CoT) prompting enables transformer models to approximate recurrent computation by externalizing intermediate steps, we show that the success of such reasoning is fundamentally bounded by the structure of tokenized inputs. This work presents a theoretical and empirical investigation into how tokenization schemes, particularly subword-based methods like byte-pair encoding (BPE), impede symbolic computation by merging or obscuring atomic reasoning units. We introduce the notion of Token Awareness to formalize how poor token granularity disrupts logical alignment and prevents models from generalizing symbolic procedures. Through systematic evaluation on arithmetic and symbolic tasks, we demonstrate that token structure dramatically affect reasoning performance, causing failure even with CoT, while atomically-aligned formats unlock strong generalization, allowing small models (e.g., GPT-4o-mini) to outperform larger systems (e.g., o1) in structured reasoning. Our findings reveal that symbolic reasoning ability in LLMs is not purely architectural, but deeply conditioned on token-level representations.

Recently an influx of studies claim emergent cognitive abilities in large language models (LLMs). Yet, most rely on anecdotes, overlook contamination of training sets, or lack systematic Evaluation involving multiple tasks, control conditions, multiple iterations, and statistical robustness tests. Here we make two major contributions. First, we propose CogEval, a cognitive science-inspired protocol for the systematic evaluation of cognitive capacities in Large Language Models. The CogEval protocol can be followed for the evaluation of various abilities. Second, here we follow CogEval to systematically evaluate cognitive maps and planning ability across eight LLMs (OpenAI GPT-4, GPT-3.5-turbo-175B, davinci-003-175B, Google Bard, Cohere-xlarge-52.4B, Anthropic Claude-1-52B, LLaMA-13B, and Alpaca-7B). We base our task prompts on human experiments, which offer both established construct validity for evaluating planning, and are absent from LLM training sets. We find that, while LLMs show apparent competence in a few planning tasks with simpler structures, systematic evaluation reveals striking failure modes in planning tasks, including hallucinations of invalid trajectories and getting trapped in loops. These findings do not support the idea of emergent out-of-the-box planning ability in LLMs. This could be because LLMs do not understand the latent relational structures underlying planning problems, known as cognitive maps, and fail at unrolling goal-directed trajectories based on the underlying structure. Implications for application and future directions are discussed.

Document understanding is critical for applications from financial analysis to scientific discovery. Current approaches, whether OCR-based pipelines feeding Large Language Models (LLMs) or native Multimodal LLMs (MLLMs), face key limitations: the former loses structural detail, while the latter struggles with context modeling. Retrieval-Augmented Generation (RAG) helps ground models in external data, but documents' multimodal nature, i.e., combining text, tables, charts, and layout, demands a more advanced paradigm: Multimodal RAG. This approach enables holistic retrieval and reasoning across all modalities, unlocking comprehensive document intelligence. Recognizing its importance, this paper presents a systematic survey of Multimodal RAG for document understanding. We propose a taxonomy based on domain, retrieval modality, and granularity, and review advances involving graph structures and agentic frameworks. We also summarize key datasets, benchmarks, and applications, and highlight open challenges in efficiency, fine-grained representation, and robustness, providing a roadmap for future progress in document AI.

Materials discovery and development are critical for addressing global challenges. Yet, the exponential growth in materials science literature comprising vast amounts of textual data has created significant bottlenecks in knowledge extraction, synthesis, and scientific reasoning. Large Language Models (LLMs) offer unprecedented opportunities to accelerate materials research through automated analysis and prediction. Still, their effective deployment requires domain-specific adaptation for understanding and solving domain-relevant tasks. Here, we present LLaMat, a family of foundational models for materials science developed through continued pretraining of LLaMA models on an extensive corpus of materials literature and crystallographic data. Through systematic evaluation, we demonstrate that LLaMat excels in materials-specific NLP and structured information extraction while maintaining general linguistic capabilities. The specialized LLaMat-CIF variant demonstrates unprecedented capabilities in crystal structure generation, predicting stable crystals with high coverage across the periodic table. Intriguingly, despite LLaMA-3's superior performance in comparison to LLaMA-2, we observe that LLaMat-2 demonstrates unexpectedly enhanced domain-specific performance across diverse materials science tasks, including structured information extraction from text and tables, more particularly in crystal structure generation, a potential adaptation rigidity in overtrained LLMs. Altogether, the present work demonstrates the effectiveness of domain adaptation towards developing practically deployable LLM copilots for materials research. Beyond materials science, our findings reveal important considerations for domain adaptation of LLMs, such as model selection, training methodology, and domain-specific performance, which may influence the development of specialized scientific AI systems.

A suitable feature representation that can both preserve the data intrinsic information and reduce data complexity and dimensionality is key to the performance of machine learning models. Deeply rooted in algebraic topology, persistent homology (PH) provides a delicate balance between data simplification and intrinsic structure characterization, and has been applied to various areas successfully. However, the combination of PH and machine learning has been hindered greatly by three challenges, namely topological representation of data, PH-based distance measurements or metrics, and PH-based feature representation. With the development of topological data analysis, progresses have been made on all these three problems, but widely scattered in different literatures. In this paper, we provide a systematical review of PH and PH-based supervised and unsupervised models from a computational perspective. Our emphasizes are the recent development of mathematical models and tools, including PH softwares and PH-based functions, feature representations, kernels, and similarity models. Essentially, this paper can work as a roadmap for the practical application of PH-based machine learning tools. Further, we consider different topological feature representations in different machine learning models, and investigate their impacts on the protein secondary structure classification.

Human interaction with the external world fundamentally involves the exchange of personal memory, whether with other individuals, websites, applications, or, in the future, AI agents. A significant portion of this interaction is redundant, requiring users to repeatedly provide the same information across different contexts. Existing solutions, such as browser-stored credentials, autofill mechanisms, and unified authentication systems, have aimed to mitigate this redundancy by serving as intermediaries that store and retrieve commonly used user data. The advent of large language models (LLMs) presents an opportunity to redefine memory management through an AI-native paradigm: SECOND ME. SECOND ME acts as an intelligent, persistent memory offload system that retains, organizes, and dynamically utilizes user-specific knowledge. By serving as an intermediary in user interactions, it can autonomously generate context-aware responses, prefill required information, and facilitate seamless communication with external systems, significantly reducing cognitive load and interaction friction. Unlike traditional memory storage solutions, SECOND ME extends beyond static data retention by leveraging LLM-based memory parameterization. This enables structured organization, contextual reasoning, and adaptive knowledge retrieval, facilitating a more systematic and intelligent approach to memory management. As AI-driven personal agents like SECOND ME become increasingly integrated into digital ecosystems, SECOND ME further represents a critical step toward augmenting human-world interaction with persistent, contextually aware, and self-optimizing memory systems. We have open-sourced the fully localizable deployment system at GitHub: https://github.com/Mindverse/Second-Me.

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

We demonstrate that unstructured sparsity significantly improves KV cache compression for LLMs, enabling sparsity levels up to 70% without compromising accuracy or requiring fine-tuning. We conduct a systematic exploration of pruning strategies and find per-token magnitude-based pruning as highly effective for both Key and Value caches under unstructured sparsity, surpassing prior structured pruning schemes. The Key cache benefits from prominent outlier elements, while the Value cache surprisingly benefits from a simple magnitude-based pruning despite its uniform distribution. KV cache size is the major bottleneck in decode performance due to high memory overhead for large context lengths. To address this, we use a bitmap-based sparse format and a custom attention kernel capable of compressing and directly computing over compressed caches pruned to arbitrary sparsity patterns, significantly accelerating memory-bound operations in decode computations and thereby compensating for the overhead of runtime pruning and compression. Our custom attention kernel coupled with the bitmap-based format delivers substantial compression of KV cache upto 45% of dense inference and thereby enables longer context length and increased tokens/sec throughput of upto 2.23x compared to dense inference. Our pruning mechanism and sparse attention kernel is available at https://github.com/dhjoo98/mustafar.

Large language models (LLMs) have showcased remarkable reasoning capabilities, yet they remain susceptible to errors, particularly in temporal reasoning tasks involving complex temporal logic. Existing research has explored LLM performance on temporal reasoning using diverse datasets and benchmarks. However, these studies often rely on real-world data that LLMs may have encountered during pre-training or employ anonymization techniques that can inadvertently introduce factual inconsistencies. In this work, we address these limitations by introducing novel synthetic datasets specifically designed to assess LLM temporal reasoning abilities in various scenarios. The diversity of question types across these datasets enables systematic investigation into the impact of the problem structure, size, question type, fact order, and other factors on LLM performance. Our findings provide valuable insights into the strengths and weaknesses of current LLMs in temporal reasoning tasks. To foster further research in this area, we are open-sourcing the datasets and evaluation framework used in our experiments: https://huggingface.co/datasets/baharef/ToT.

Much of the success of deep learning is drawn from building architectures that properly respect underlying symmetry and structure in the data on which they operate - a set of considerations that have been united under the banner of geometric deep learning. Often problems in the physical sciences deal with relatively small sets of points in two- or three-dimensional space wherein translation, rotation, and permutation equivariance are important or even vital for models to be useful in practice. In this work, we present rotation- and permutation-equivariant architectures for deep learning on these small point clouds, composed of a set of products of terms from the geometric algebra and reductions over those products using an attention mechanism. The geometric algebra provides valuable mathematical structure by which to combine vector, scalar, and other types of geometric inputs in a systematic way to account for rotation invariance or covariance, while attention yields a powerful way to impose permutation equivariance. We demonstrate the usefulness of these architectures by training models to solve sample problems relevant to physics, chemistry, and biology.

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

In this technical report, we present the Ring-linear model series, specifically including Ring-mini-linear-2.0 and Ring-flash-linear-2.0. Ring-mini-linear-2.0 comprises 16B parameters and 957M activations, while Ring-flash-linear-2.0 contains 104B parameters and 6.1B activations. Both models adopt a hybrid architecture that effectively integrates linear attention and softmax attention, significantly reducing I/O and computational overhead in long-context inference scenarios. Compared to a 32 billion parameter dense model, this series reduces inference cost to 1/10, and compared to the original Ring series, the cost is also reduced by over 50%. Furthermore, through systematic exploration of the ratio between different attention mechanisms in the hybrid architecture, we have identified the currently optimal model structure. Additionally, by leveraging our self-developed high-performance FP8 operator library-linghe, overall training efficiency has been improved by 50%. Benefiting from the high alignment between the training and inference engine operators, the models can undergo long-term, stable, and highly efficient optimization during the reinforcement learning phase, consistently maintaining SOTA performance across multiple challenging complex reasoning benchmarks.

High-quality mathematical and logical datasets with verifiable answers are essential for strengthening the reasoning capabilities of large language models (LLMs). While recent data augmentation techniques have facilitated the creation of large-scale benchmarks, existing LLM-generated datasets often suffer from limited reliability, diversity, and scalability. To address these challenges, we introduce PuzzleClone, a formal framework for synthesizing verifiable data at scale using Satisfiability Modulo Theories (SMT). Our approach features three key innovations: (1) encoding seed puzzles into structured logical specifications, (2) generating scalable variants through systematic variable and constraint randomization, and (3) ensuring validity via a reproduction mechanism. Applying PuzzleClone, we construct a curated benchmark comprising over 83K diverse and programmatically validated puzzles. The generated puzzles span a wide spectrum of difficulty and formats, posing significant challenges to current state-of-the-art models. We conduct post training (SFT and RL) on PuzzleClone datasets. Experimental results show that training on PuzzleClone yields substantial improvements not only on PuzzleClone testset but also on logic and mathematical benchmarks. Post training raises PuzzleClone average from 14.4 to 56.2 and delivers consistent improvements across 7 logic and mathematical benchmarks up to 12.5 absolute percentage points (AMC2023 from 52.5 to 65.0). Our code and data are available at https://github.com/puzzleclone.

Access to real-world medical data is often restricted due to privacy regulations, posing a significant barrier to the advancement of healthcare research. Synthetic data offers a promising alternative; however, generating realistic, clinically valid, and privacy-conscious records remains a major challenge. Recent advancements in Large Language Models (LLMs) offer new opportunities for structured data generation; however, existing approaches frequently lack systematic prompting strategies and comprehensive, multi-dimensional evaluation frameworks. In this paper, we present SynLLM, a modular framework for generating high-quality synthetic medical tabular data using 20 state-of-the-art open-source LLMs, including LLaMA, Mistral, and GPT variants, guided by structured prompts. We propose four distinct prompt types, ranging from example-driven to rule-based constraints, that encode schema, metadata, and domain knowledge to control generation without model fine-tuning. Our framework features a comprehensive evaluation pipeline that rigorously assesses generated data across statistical fidelity, clinical consistency, and privacy preservation. We evaluate SynLLM across three public medical datasets, including Diabetes, Cirrhosis, and Stroke, using 20 open-source LLMs. Our results show that prompt engineering significantly impacts data quality and privacy risk, with rule-based prompts achieving the best privacy-quality balance. SynLLM establishes that, when guided by well-designed prompts and evaluated with robust, multi-metric criteria, LLMs can generate synthetic medical data that is both clinically plausible and privacy-aware, paving the way for safer and more effective data sharing in healthcare research.

Tabular data, a prevalent data type across various domains, presents unique challenges due to its heterogeneous nature and complex structural relationships. Achieving high predictive performance and robustness in tabular data analysis holds significant promise for numerous applications. Influenced by recent advancements in natural language processing, particularly transformer architectures, new methods for tabular data modeling have emerged. Early techniques concentrated on pre-training transformers from scratch, often encountering scalability issues. Subsequently, methods leveraging pre-trained language models like BERT have been developed, which require less data and yield enhanced performance. The recent advent of large language models, such as GPT and LLaMA, has further revolutionized the field, facilitating more advanced and diverse applications with minimal fine-tuning. Despite the growing interest, a comprehensive survey of language modeling techniques for tabular data remains absent. This paper fills this gap by providing a systematic review of the development of language modeling for tabular data, encompassing: (1) a categorization of different tabular data structures and data types; (2) a review of key datasets used in model training and tasks used for evaluation; (3) a summary of modeling techniques including widely-adopted data processing methods, popular architectures, and training objectives; (4) the evolution from adapting traditional Pre-training/Pre-trained language models to the utilization of large language models; (5) an identification of persistent challenges and potential future research directions in language modeling for tabular data analysis. GitHub page associated with this survey is available at: https://github.com/lanxiang1017/Language-Modeling-on-Tabular-Data-Survey.git.

Medical vision-and-language pre-training (Med-VLP) has received considerable attention owing to its applicability to extracting generic vision-and-language representations from medical images and texts. Most existing methods mainly contain three elements: uni-modal encoders (i.e., a vision encoder and a language encoder), a multi-modal fusion module, and pretext tasks, with few studies considering the importance of medical domain expert knowledge and explicitly exploiting such knowledge to facilitate Med-VLP. Although there exist knowledge-enhanced vision-and-language pre-training (VLP) methods in the general domain, most require off-the-shelf toolkits (e.g., object detectors and scene graph parsers), which are unavailable in the medical domain. In this paper, we propose a systematic and effective approach to enhance Med-VLP by structured medical knowledge from three perspectives. First, considering knowledge can be regarded as the intermediate medium between vision and language, we align the representations of the vision encoder and the language encoder through knowledge. Second, we inject knowledge into the multi-modal fusion model to enable the model to perform reasoning using knowledge as the supplementation of the input image and text. Third, we guide the model to put emphasis on the most critical information in images and texts by designing knowledge-induced pretext tasks. To perform a comprehensive evaluation and facilitate further research, we construct a medical vision-and-language benchmark including three tasks. Experimental results illustrate the effectiveness of our approach, where state-of-the-art performance is achieved on all downstream tasks. Further analyses explore the effects of different components of our approach and various settings of pre-training.

Although large language models (LLMs) have significant potential to advance chemical discovery, current LLMs lack core chemical knowledge, produce unreliable reasoning trajectories, and exhibit suboptimal performance across diverse chemical tasks. To address these challenges, we propose Chem-R, a generalizable Chemical Reasoning model designed to emulate the deliberative processes of chemists. Chem-R is trained through a three-phase framework that progressively builds advanced reasoning capabilities, including: 1) Chemical Foundation Training, which establishes core chemical knowledge. 2) Chemical Reasoning Protocol Distillation, incorporating structured, expert-like reasoning traces to guide systematic and reliable problem solving. 3) Multi-task Group Relative Policy Optimization that optimizes the model for balanced performance across diverse molecular- and reaction-level tasks. This structured pipeline enables Chem-R to achieve state-of-the-art performance on comprehensive benchmarks, surpassing leading large language models, including Gemini-2.5-Pro and DeepSeek-R1, by up to 46% on molecular tasks and 66% on reaction tasks. Meanwhile, Chem-R also consistently outperforms the existing chemical foundation models across both molecular and reaction level tasks. These results highlight Chem-R's robust generalization, interpretability, and potential as a foundation for next-generation AI-driven chemical discovery.

Critical peer review of scientific manuscripts presents a significant challenge for Large Language Models (LLMs), partly due to data limitations and the complexity of expert reasoning. This report introduces Persistent Workflow Prompting (PWP), a potentially broadly applicable prompt engineering methodology designed to bridge this gap using standard LLM chat interfaces (zero-code, no APIs). We present a proof-of-concept PWP prompt for the critical analysis of experimental chemistry manuscripts, featuring a hierarchical, modular architecture (structured via Markdown) that defines detailed analysis workflows. We develop this PWP prompt through iterative application of meta-prompting techniques and meta-reasoning aimed at systematically codifying expert review workflows, including tacit knowledge. Submitted once at the start of a session, this PWP prompt equips the LLM with persistent workflows triggered by subsequent queries, guiding modern reasoning LLMs through systematic, multimodal evaluations. Demonstrations show the PWP-guided LLM identifying major methodological flaws in a test case while mitigating LLM input bias and performing complex tasks, including distinguishing claims from evidence, integrating text/photo/figure analysis to infer parameters, executing quantitative feasibility checks, comparing estimates against claims, and assessing a priori plausibility. To ensure transparency and facilitate replication, we provide full prompts, detailed demonstration analyses, and logs of interactive chats as supplementary resources. Beyond the specific application, this work offers insights into the meta-development process itself, highlighting the potential of PWP, informed by detailed workflow formalization, to enable sophisticated analysis using readily available LLMs for complex scientific tasks.

Although LLM-based agents have attracted significant attention in domains such as software engineering and machine learning research, their role in advancing combinatorial optimization (CO) remains relatively underexplored. This gap underscores the need for a deeper understanding of their potential in tackling structured, constraint-intensive problems-a pursuit currently limited by the absence of comprehensive benchmarks for systematic investigation. To address this, we introduce CO-Bench, a benchmark suite featuring 36 real-world CO problems drawn from a broad range of domains and complexity levels. CO-Bench includes structured problem formulations and curated data to support rigorous investigation of LLM agents. We evaluate multiple agent frameworks against established human-designed algorithms, revealing key strengths and limitations of current approaches and identifying promising directions for future research. CO-Bench is publicly available at https://github.com/sunnweiwei/CO-Bench.

Human-Object Interaction (HOI) detection is a challenging computer vision task that requires visual models to address the complex interactive relationship between humans and objects and predict HOI triplets. Despite the challenges posed by the numerous interaction combinations, they also offer opportunities for multimodal learning of visual texts. In this paper, we present a systematic and unified framework (RmLR) that enhances HOI detection by incorporating structured text knowledge. Firstly, we qualitatively and quantitatively analyze the loss of interaction information in the two-stage HOI detector and propose a re-mining strategy to generate more comprehensive visual representation.Secondly, we design more fine-grained sentence- and word-level alignment and knowledge transfer strategies to effectively address the many-to-many matching problem between multiple interactions and multiple texts.These strategies alleviate the matching confusion problem that arises when multiple interactions occur simultaneously, thereby improving the effectiveness of the alignment process. Finally, HOI reasoning by visual features augmented with textual knowledge substantially improves the understanding of interactions. Experimental results illustrate the effectiveness of our approach, where state-of-the-art performance is achieved on public benchmarks. We further analyze the effects of different components of our approach to provide insights into its efficacy.

Prompts are the interface for eliciting the capabilities of large language models (LLMs). Understanding their structure and components is critical for analyzing LLM behavior and optimizing performance. However, the field lacks a comprehensive framework for systematic prompt analysis and understanding. We introduce PromptPrism, a linguistically-inspired taxonomy that enables prompt analysis across three hierarchical levels: functional structure, semantic component, and syntactic pattern. We show the practical utility of PromptPrism by applying it to three applications: (1) a taxonomy-guided prompt refinement approach that automatically improves prompt quality and enhances model performance across a range of tasks; (2) a multi-dimensional dataset profiling method that extracts and aggregates structural, semantic, and syntactic characteristics from prompt datasets, enabling comprehensive analysis of prompt distributions and patterns; (3) a controlled experimental framework for prompt sensitivity analysis by quantifying the impact of semantic reordering and delimiter modifications on LLM performance. Our experimental results validate the effectiveness of our taxonomy across these applications, demonstrating that PromptPrism provides a foundation for refining, profiling, and analyzing prompts.

Baryonic effects created by feedback processes associated with galaxy formation are an important, poorly constrained systematic effect for models of large-scale structure as probed by weak gravitational lensing. Upcoming surveys require fast methods to predict and marginalize over the potential impact of baryons on the total matter power spectrum. Here we use the FLAMINGO cosmological hydrodynamical simulations to test a recent proposal to approximate the matter power spectrum as the sum of the linear matter power spectrum and a constant multiple, A_{rm mod}, of the difference between the linear and non-linear gravity-only power spectra. We show that replacing this constant multiple with a one-parameter family of sigmoid functions of the wavenumber k allows to us match the predictions of simulations with different feedback strengths for z leq 1, k < 3~hrm Mpc^{-1}, and the different cosmological models in the FLAMINGO suite. The baryonic response predicted by FLAMINGO models that use jet-like AGN feedback instead of the fiducial thermally-driven AGN feedback can also be reproduced, but at the cost of increasing the number of parameters in the sigmoid function from one to three. The assumption that A_{rm mod} depends only on k breaks down for decaying dark matter models, highlighting the need for more advanced baryon response models when studying cosmological models that deviate strongly from LambdaCDM.

Many recent works have discussed the propensity, or lack thereof, for emergent languages to exhibit properties of natural languages. A favorite in the literature is learning compositionality. We note that most of those works have focused on communicative bandwidth as being of primary importance. While important, it is not the only contributing factor. In this paper, we investigate the learning biases that affect the efficacy and compositionality of emergent languages. Our foremost contribution is to explore how capacity of a neural network impacts its ability to learn a compositional language. We additionally introduce a set of evaluation metrics with which we analyze the learned languages. Our hypothesis is that there should be a specific range of model capacity and channel bandwidth that induces compositional structure in the resulting language and consequently encourages systematic generalization. While we empirically see evidence for the bottom of this range, we curiously do not find evidence for the top part of the range and believe that this is an open question for the community.

In this paper, we propose a new approach to construct a system of transformation rules for the Part-of-Speech (POS) tagging task. Our approach is based on an incremental knowledge acquisition method where rules are stored in an exception structure and new rules are only added to correct the errors of existing rules; thus allowing systematic control of the interaction between the rules. Experimental results on 13 languages show that our approach is fast in terms of training time and tagging speed. Furthermore, our approach obtains very competitive accuracy in comparison to state-of-the-art POS and morphological taggers.

Although RLVR has become an essential component for developing advanced reasoning skills in LLMs, contemporary studies have documented training plateaus that emerge following thousands of optimization steps, demonstrating notable decreases in performance gains despite increased computational investment. This limitation stems from the sparse exploration patterns inherent in current RLVR practices, where models rely on limited rollouts that often miss critical reasoning paths and fail to provide systematic coverage of the solution space. We present DeepSearch, a framework that integrates Monte Carlo Tree Search directly into RLVR training. In contrast to existing methods that rely on tree search only at inference, DeepSearch embeds structured search into the training loop, enabling systematic exploration and fine-grained credit assignment across reasoning steps. Through training-time exploration, DeepSearch addresses the fundamental bottleneck of insufficient exploration, which leads to diminishing performance improvements over prolonged training steps. Our contributions include: (1) a global frontier selection strategy that prioritizes promising nodes across the search tree, (2) selection with entropy-based guidance that identifies confident paths for supervision, and (3) adaptive replay buffer training with solution caching for efficiency. Experiments on mathematical reasoning benchmarks show that DeepSearch achieves 62.95% average accuracy and establishes a new state-of-the-art for 1.5B reasoning models - using 5.7x fewer GPU hours than extended training approaches. These results highlight the importance of strategic exploration over brute-force scaling and demonstrate the promise of algorithmic innovation for advancing RLVR methodologies. DeepSearch establishes a new direction for scaling reasoning capabilities through systematic search rather than prolonged computation.

The rapid progress of large language models (LLMs) has opened new opportunities for education. While learners can interact with academic papers through LLM-powered dialogue, limitations still exist: absence of structured organization and high text reliance can impede systematic understanding and engagement with complex concepts. To address these challenges, we propose Auto-Slides, an LLM-driven system that converts research papers into pedagogically structured, multimodal slides (e.g., diagrams and tables). Drawing on cognitive science, it creates a presentation-oriented narrative and allows iterative refinement via an interactive editor, in order to match learners' knowledge level and goals. Auto-Slides further incorporates verification and knowledge retrieval mechanisms to ensure accuracy and contextual completeness. Through extensive user studies, Auto-Slides enhances learners' comprehension and engagement compared to conventional LLM-based reading. Our contributions lie in designing a multi-agent framework for transforming academic papers into pedagogically optimized slides and introducing interactive customization for personalized learning.

Large Language Models (LLMs) are swiftly advancing in architecture and capability, and as they integrate more deeply into complex systems, the urgency to scrutinize their security properties grows. This paper surveys research in the emerging interdisciplinary field of adversarial attacks on LLMs, a subfield of trustworthy ML, combining the perspectives of Natural Language Processing and Security. Prior work has shown that even safety-aligned LLMs (via instruction tuning and reinforcement learning through human feedback) can be susceptible to adversarial attacks, which exploit weaknesses and mislead AI systems, as evidenced by the prevalence of `jailbreak' attacks on models like ChatGPT and Bard. In this survey, we first provide an overview of large language models, describe their safety alignment, and categorize existing research based on various learning structures: textual-only attacks, multi-modal attacks, and additional attack methods specifically targeting complex systems, such as federated learning or multi-agent systems. We also offer comprehensive remarks on works that focus on the fundamental sources of vulnerabilities and potential defenses. To make this field more accessible to newcomers, we present a systematic review of existing works, a structured typology of adversarial attack concepts, and additional resources, including slides for presentations on related topics at the 62nd Annual Meeting of the Association for Computational Linguistics (ACL'24).

This paper examines the encoding of analogy in large-scale pretrained language models, such as BERT and GPT-2. Existing analogy datasets typically focus on a limited set of analogical relations, with a high similarity of the two domains between which the analogy holds. As a more realistic setup, we introduce the Scientific and Creative Analogy dataset (SCAN), a novel analogy dataset containing systematic mappings of multiple attributes and relational structures across dissimilar domains. Using this dataset, we test the analogical reasoning capabilities of several widely-used pretrained language models (LMs). We find that state-of-the-art LMs achieve low performance on these complex analogy tasks, highlighting the challenges still posed by analogy understanding.

Periodicity, as one of the most important basic characteristics, lays the foundation for facilitating structured knowledge acquisition and systematic cognitive processes within human learning paradigms. However, the potential flaws of periodicity modeling in Transformer affect the learning efficiency and establishment of underlying principles from data for large language models (LLMs) built upon it. In this paper, we demonstrate that integrating effective periodicity modeling can improve the learning efficiency and performance of LLMs. We introduce FANformer, which integrates Fourier Analysis Network (FAN) into attention mechanism to achieve efficient periodicity modeling, by modifying the feature projection process of attention mechanism. Extensive experimental results on language modeling show that FANformer consistently outperforms Transformer when scaling up model size and training tokens, underscoring its superior learning efficiency. To further validate the effectiveness of FANformer, we pretrain a FANformer-1B on 1 trillion tokens. FANformer-1B exhibits marked improvements on downstream tasks compared to open-source LLMs with similar model parameters or training tokens. The results position FANformer as an effective and promising architecture for advancing LLMs.

Multimodal learning combines multiple data modalities, broadening the types and complexity of data our models can utilize: for example, from plain text to image-caption pairs. Most multimodal learning algorithms focus on modeling simple one-to-one pairs of data from two modalities, such as image-caption pairs, or audio-text pairs. However, in most real-world settings, entities of different modalities interact with each other in more complex and multifaceted ways, going beyond one-to-one mappings. We propose to represent these complex relationships as graphs, allowing us to capture data with any number of modalities, and with complex relationships between modalities that can flexibly vary from one sample to another. Toward this goal, we propose Multimodal Graph Learning (MMGL), a general and systematic framework for capturing information from multiple multimodal neighbors with relational structures among them. In particular, we focus on MMGL for generative tasks, building upon pretrained Language Models (LMs), aiming to augment their text generation with multimodal neighbor contexts. We study three research questions raised by MMGL: (1) how can we infuse multiple neighbor information into the pretrained LMs, while avoiding scalability issues? (2) how can we infuse the graph structure information among multimodal neighbors into the LMs? and (3) how can we finetune the pretrained LMs to learn from the neighbor context in a parameter-efficient manner? We conduct extensive experiments to answer these three questions on MMGL and analyze the empirical results to pave the way for future MMGL research.

Scientific progress increasingly depends on synthesizing knowledge across vast literature, yet most experimental data remains trapped in semi-structured formats that resist systematic extraction and analysis. Here, we present MatSKRAFT, a computational framework that automatically extracts and integrates materials science knowledge from tabular data at unprecedented scale. Our approach transforms tables into graph-based representations processed by constraint-driven GNNs that encode scientific principles directly into model architecture. MatSKRAFT significantly outperforms state-of-the-art large language models, achieving F1 scores of 88.68 for property extraction and 71.35 for composition extraction, while processing data 19-496times faster than them (compared to the slowest and the fastest models, respectively) with modest hardware requirements. Applied to nearly 69,000 tables from more than 47,000 research publications, we construct a comprehensive database containing over 535,000 entries, including 104,000 compositions that expand coverage beyond major existing databases, pending manual validation. This systematic approach reveals previously overlooked materials with distinct property combinations and enables data-driven discovery of composition-property relationships forming the cornerstone of materials and scientific discovery.

Automatic dependency parsing of Thai sentences has been underexplored, as evidenced by the lack of large Thai dependency treebanks with complete dependency structures and the lack of a published systematic evaluation of state-of-the-art models, especially transformer-based parsers. In this work, we address these problems by introducing Thai Universal Dependency Treebank (TUD), a new largest Thai treebank consisting of 3,627 trees annotated in accordance with the Universal Dependencies (UD) framework. We then benchmark dependency parsing models that incorporate pretrained transformers as encoders and train them on Thai-PUD and our TUD. The evaluation results show that most of our models can outperform other models reported in previous papers and provide insight into the optimal choices of components to include in Thai dependency parsers. The new treebank and every model's full prediction generated in our experiment are made available on a GitHub repository for further study.

The advent of the Transformer has led to the development of large language models (LLM), which appear to demonstrate human-like capabilities. To assess the generality of this class of models and a variety of other base neural network architectures to multimodal domains, we evaluated and compared their capacity for multimodal generalization. We introduce a multimodal question-answer benchmark to evaluate three specific types of out-of-distribution (OOD) generalization performance: distractor generalization (generalization in the presence of distractors), systematic compositional generalization (generalization to new task permutations), and productive compositional generalization (generalization to more complex tasks structures). We found that across model architectures (e.g., RNNs, Transformers, Perceivers, etc.), models with multiple attention layers, or models that leveraged cross-attention mechanisms between input domains, fared better. Our positive results demonstrate that for multimodal distractor and systematic generalization, either cross-modal attention or models with deeper attention layers are key architectural features required to integrate multimodal inputs. On the other hand, neither of these architectural features led to productive generalization, suggesting fundamental limitations of existing architectures for specific types of multimodal generalization. These results demonstrate the strengths and limitations of specific architectural components underlying modern neural models for multimodal reasoning. Finally, we provide Generic COG (gCOG), a configurable benchmark with several multimodal generalization splits, for future studies to explore.

Transformers yield state-of-the-art results across many tasks. However, their heuristically designed architecture impose huge computational costs during inference. This work aims on challenging the common design philosophy of the Vision Transformer (ViT) model with uniform dimension across all the stacked blocks in a model stage, where we redistribute the parameters both across transformer blocks and between different structures within the block via the first systematic attempt on global structural pruning. Dealing with diverse ViT structural components, we derive a novel Hessian-based structural pruning criteria comparable across all layers and structures, with latency-aware regularization for direct latency reduction. Performing iterative pruning on the DeiT-Base model leads to a new architecture family called NViT (Novel ViT), with a novel parameter redistribution that utilizes parameters more efficiently. On ImageNet-1K, NViT-Base achieves a 2.6x FLOPs reduction, 5.1x parameter reduction, and 1.9x run-time speedup over the DeiT-Base model in a near lossless manner. Smaller NViT variants achieve more than 1% accuracy gain at the same throughput of the DeiT Small/Tiny variants, as well as a lossless 3.3x parameter reduction over the SWIN-Small model. These results outperform prior art by a large margin. Further analysis is provided on the parameter redistribution insight of NViT, where we show the high prunability of ViT models, distinct sensitivity within ViT block, and unique parameter distribution trend across stacked ViT blocks. Our insights provide viability for a simple yet effective parameter redistribution rule towards more efficient ViTs for off-the-shelf performance boost.

Recent advances in natural language processing highlight two key factors for improving reasoning in large language models (LLMs): (i) allocating more test-time compute tends to help on harder problems but often introduces redundancy in the reasoning trace, and (ii) compute is most effective when reasoning is systematic and incremental, forming structured chains of thought (CoTs) akin to human problem-solving. To study these factors in isolation, we introduce a controlled setting based on shortest-path tasks in layered graphs. We train decoder-only transformers on question-trace-answer triples using a custom tokenizer, comparing models trained on optimal bottom-up dynamic programming traces with those trained on longer, valid traces involving backtracking. Surprisingly, with the same training-token budget, models trained on inefficient traces generalize better to unseen graphs. This benefit is not due to length alone-injecting arbitrary redundancy into reasoning traces fails to help and can even hurt performance. Instead, we find that generalization correlates with the model's confidence in next-token prediction, suggesting that long, coherent, and locally incremental traces make the training signal easier to optimize.

Can LLMs accurately adjust their confidence when facing opposition? Building on previous studies measuring calibration on static fact-based question-answering tasks, we evaluate Large Language Models (LLMs) in a dynamic, adversarial debate setting, uniquely combining two realistic factors: (a) a multi-turn format requiring models to update beliefs as new information emerges, and (b) a zero-sum structure to control for task-related uncertainty, since mutual high-confidence claims imply systematic overconfidence. We organized 60 three-round policy debates among ten state-of-the-art LLMs, with models privately rating their confidence (0-100) in winning after each round. We observed five concerning patterns: (1) Systematic overconfidence: models began debates with average initial confidence of 72.9% vs. a rational 50% baseline. (2) Confidence escalation: rather than reducing confidence as debates progressed, debaters increased their win probabilities, averaging 83% by the final round. (3) Mutual overestimation: in 61.7% of debates, both sides simultaneously claimed >=75% probability of victory, a logical impossibility. (4) Persistent self-debate bias: models debating identical copies increased confidence from 64.1% to 75.2%; even when explicitly informed their chance of winning was exactly 50%, confidence still rose (from 50.0% to 57.1%). (5) Misaligned private reasoning: models' private scratchpad thoughts sometimes differed from their public confidence ratings, raising concerns about faithfulness of chain-of-thought reasoning. These results suggest LLMs lack the ability to accurately self-assess or update their beliefs in dynamic, multi-turn tasks; a major concern as LLMs are now increasingly deployed without careful review in assistant and agentic roles. Code for our experiments is available at https://github.com/pradyuprasad/llms_overconfidence

This document serves as an overview of the different mechanisms and areas of governance in the BigCode project. It aims to support transparency by providing relevant information about choices that were made during the project to the broader public, and to serve as an example of intentional governance of an open research project that future endeavors can leverage to shape their own approach. The first section, Project Structure, covers the project organization, its stated goals and values, its internal decision processes, and its funding and resources. The second section, Data and Model Governance, covers decisions relating to the questions of data subject consent, privacy, and model release.

Large language models (LLMs) have demonstrated exceptional performance in text generation within current NLP research. However, the lack of factual accuracy is still a dark cloud hanging over the LLM skyscraper. Structural knowledge prompting (SKP) is a prominent paradigm to integrate external knowledge into LLMs by incorporating structural representations, achieving state-of-the-art results in many knowledge-intensive tasks. However, existing methods often focus on specific problems, lacking a comprehensive exploration of the generalization and capability boundaries of SKP. This paper aims to evaluate and rethink the generalization capability of the SKP paradigm from four perspectives including Granularity, Transferability, Scalability, and Universality. To provide a thorough evaluation, we introduce a novel multi-granular, multi-level benchmark called SUBARU, consisting of 9 different tasks with varying levels of granularity and difficulty.

Scientific knowledge is growing rapidly, making it challenging to track progress and high-level conceptual links across broad disciplines. While existing tools like citation networks and search engines make it easy to access a few related papers, they fundamentally lack the flexible abstraction needed to represent the density of activity in various scientific subfields. We motivate SCIENCE HIERARCHOGRAPHY, the goal of organizing scientific literature into a high-quality hierarchical structure that allows for the categorization of scientific work across varying levels of abstraction, from very broad fields to very specific studies. Such a representation can provide insights into which fields are well-explored and which are under-explored. To achieve the goals of SCIENCE HIERARCHOGRAPHY, we develop a range of algorithms. Our primary approach combines fast embedding-based clustering with LLM-based prompting to balance the computational efficiency of embedding methods with the semantic precision offered by LLM prompting. We demonstrate that this approach offers the best trade-off between quality and speed compared to methods that heavily rely on LLM prompting, such as iterative tree construction with LLMs. To better reflect the interdisciplinary and multifaceted nature of research papers, our hierarchy captures multiple dimensions of categorization beyond simple topic labels. We evaluate the utility of our framework by assessing how effectively an LLM-based agent can locate target papers using the hierarchy. Results show that this structured approach enhances interpretability, supports trend discovery, and offers an alternative pathway for exploring scientific literature beyond traditional search methods. Code, data and demo: https://github.com/JHU-CLSP/science-hierarchography{https://github.com/JHU-CLSP/science-hierarchography}

Structure reasoning is a fundamental capability of large language models (LLMs), enabling them to reason about structured commonsense and answer multi-hop questions. However, existing benchmarks for structure reasoning mainly focus on horizontal and coordinate structures (e.g. graphs), overlooking the hierarchical relationships within them. Hierarchical structure reasoning is crucial for human cognition, particularly in memory organization and problem-solving. It also plays a key role in various real-world tasks, such as information extraction and decision-making. To address this gap, we propose HiBench, the first framework spanning from initial structure generation to final proficiency assessment, designed to benchmark the hierarchical reasoning capabilities of LLMs systematically. HiBench encompasses six representative scenarios, covering both fundamental and practical aspects, and consists of 30 tasks with varying hierarchical complexity, totaling 39,519 queries. To evaluate LLMs comprehensively, we develop five capability dimensions that depict different facets of hierarchical structure understanding. Through extensive evaluation of 20 LLMs from 10 model families, we reveal key insights into their capabilities and limitations: 1) existing LLMs show proficiency in basic hierarchical reasoning tasks; 2) they still struggle with more complex structures and implicit hierarchical representations, especially in structural modification and textual reasoning. Based on these findings, we create a small yet well-designed instruction dataset, which enhances LLMs' performance on HiBench by an average of 88.84\% (Llama-3.1-8B) and 31.38\% (Qwen2.5-7B) across all tasks. The HiBench dataset and toolkit are available here, https://github.com/jzzzzh/HiBench, to encourage evaluation.

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

Modern diffusion models encounter a fundamental trade-off between training efficiency and generation quality. While existing representation alignment methods, such as REPA, accelerate convergence through patch-wise alignment, they often fail to capture structural relationships within visual representations and ensure global distribution consistency between pretrained encoders and denoising networks. To address these limitations, we introduce SARA, a hierarchical alignment framework that enforces multi-level representation constraints: (1) patch-wise alignment to preserve local semantic details, (2) autocorrelation matrix alignment to maintain structural consistency within representations, and (3) adversarial distribution alignment to mitigate global representation discrepancies. Unlike previous approaches, SARA explicitly models both intra-representation correlations via self-similarity matrices and inter-distribution coherence via adversarial alignment, enabling comprehensive alignment across local and global scales. Experiments on ImageNet-256 show that SARA achieves an FID of 1.36 while converging twice as fast as REPA, surpassing recent state-of-the-art image generation methods. This work establishes a systematic paradigm for optimizing diffusion training through hierarchical representation alignment.

This work presents a probabilistic digital twin framework for response prediction in dynamical systems governed by misspecified physics. The approach integrates Gaussian Process Latent Force Models (GPLFM) and Bayesian Neural Networks (BNNs) to enable end-to-end uncertainty-aware inference and prediction. In the diagnosis phase, model-form errors (MFEs) are treated as latent input forces to a nominal linear dynamical system and jointly estimated with system states using GPLFM from sensor measurements. A BNN is then trained on posterior samples to learn a probabilistic nonlinear mapping from system states to MFEs, while capturing diagnostic uncertainty. For prognosis, this mapping is used to generate pseudo-measurements, enabling state prediction via Kalman filtering. The framework allows for systematic propagation of uncertainty from diagnosis to prediction, a key capability for trustworthy digital twins. The framework is demonstrated using four nonlinear examples: a single degree of freedom (DOF) oscillator, a multi-DOF system, and two established benchmarks -- the Bouc-Wen hysteretic system and the Silverbox experimental dataset -- highlighting its predictive accuracy and robustness to model misspecification.

Outliers have been widely observed in Large Language Models (LLMs), significantly impacting model performance and posing challenges for model compression. Understanding the functionality and formation mechanisms of these outliers is critically important. Existing works, however, largely focus on reducing the impact of outliers from an algorithmic perspective, lacking an in-depth investigation into their causes and roles. In this work, we provide a detailed analysis of the formation process, underlying causes, and functions of outliers in LLMs. We define and categorize three types of outliers-activation outliers, weight outliers, and attention outliers-and analyze their distributions across different dimensions, uncovering inherent connections between their occurrences and their ultimate influence on the attention mechanism. Based on these observations, we hypothesize and explore the mechanisms by which these outliers arise and function, demonstrating through theoretical derivations and experiments that they emerge due to the self-attention mechanism's softmax operation. These outliers act as implicit context-aware scaling factors within the attention mechanism. As these outliers stem from systematic influences, we term them systematic outliers. Our study not only enhances the understanding of Transformer-based LLMs but also shows that structurally eliminating outliers can accelerate convergence and improve model compression. The code is avilable at https://github.com/an-yongqi/systematic-outliers.

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

Implicit Personalization (IP) is a phenomenon of language models inferring a user's background from the implicit cues in the input prompts and tailoring the response based on this inference. While previous work has touched upon various instances of this problem, there lacks a unified framework to study this behavior. This work systematically studies IP through a rigorous mathematical formulation, a multi-perspective moral reasoning framework, and a set of case studies. Our theoretical foundation for IP relies on a structural causal model and introduces a novel method, indirect intervention, to estimate the causal effect of a mediator variable that cannot be directly intervened upon. Beyond the technical approach, we also introduce a set of moral reasoning principles based on three schools of moral philosophy to study when IP may or may not be ethically appropriate. Equipped with both mathematical and ethical insights, we present three diverse case studies illustrating the varied nature of the IP problem and offer recommendations for future research. Our code and data are at https://github.com/jiarui-liu/IP.

Hepatocellular carcinoma (HCC), ranking as the third leading cause of cancer-related mortality worldwide, demands urgent improvements in early detection to enhance patient survival. While ultrasound remains the preferred screening modality due to its cost-effectiveness and real-time capabilities, its sensitivity (59%-78%) heavily relies on radiologists' expertise, leading to inconsistent diagnostic outcomes and operational inefficiencies. Recent advancements in AI technology offer promising solutions to bridge this gap. This study introduces the Hierarchical Sparse Query Transformer (HSQformer), a novel hybrid architecture that synergizes CNNs' local feature extraction with Vision Transformers' global contextual awareness through latent space representation and sparse learning. By dynamically activating task-specific experts via a Mixture-of-Experts (MoE) framework, HSQformer achieves hierarchical feature integration without structural redundancy. Evaluated across three clinical scenarios: single-center, multi-center, and high-risk patient cohorts, HSQformer outperforms state-of-the-art models (e.g., 95.38% AUC in multi-center testing) and matches senior radiologists' diagnostic accuracy while significantly surpassing junior counterparts. These results highlight the potential of AI-assisted tools to standardize HCC screening, reduce dependency on human expertise, and improve early diagnosis rates. The full code is available at https://github.com/Asunatan/HSQformer.

Linear structural equation models are multivariate statistical models encoded by mixed graphs. In particular, the set of covariance matrices for distributions belonging to a linear structural equation model for a fixed mixed graph G=(V, D,B) is parameterized by a rational function with parameters for each vertex and edge in G. This rational parametrization naturally allows for the study of these models from an algebraic and combinatorial point of view. Indeed, this point of view has led to a collection of results in the literature, mainly focusing on questions related to identifiability and determining relationships between covariances (i.e., finding polynomials in the Gaussian vanishing ideal). So far, a large proportion of these results has focused on the case when D, the directed part of the mixed graph G, is acyclic. This is due to the fact that in the acyclic case, the parametrization becomes polynomial and there is a description of the entries of the covariance matrices in terms of a finite sum. We move beyond the acyclic case and give a closed form expression for the entries of the covariance matrices in terms of the one-connections in a graph obtained from D through some small operations. This closed form expression then allows us to show that if G is simple, then the parametrization map is generically finite-to-one. Finally, having a closed form expression for the covariance matrices allows for the development of an algorithm for systematically exploring possible polynomials in the Gaussian vanishing ideal.

Task-oriented dialogue systems often face difficulties when user utterances seem semantically complete but lack necessary structural information for appropriate system action. This arises because users frequently do not fully understand their own needs, while systems require precise intent definitions. Current LLM-based agents cannot effectively distinguish between linguistically complete and contextually triggerable expressions, lacking frameworks for collaborative intent formation. We present STORM, a framework modeling asymmetric information dynamics through conversations between UserLLM (full internal access) and AgentLLM (observable behavior only). STORM produces annotated corpora capturing expression trajectories and latent cognitive transitions, enabling systematic analysis of collaborative understanding development. Our contributions include: (1) formalizing asymmetric information processing in dialogue systems; (2) modeling intent formation tracking collaborative understanding evolution; and (3) evaluation metrics measuring internal cognitive improvements alongside task performance. Experiments across four language models reveal that moderate uncertainty (40-60%) can outperform complete transparency in certain scenarios, with model-specific patterns suggesting reconsideration of optimal information completeness in human-AI collaboration. These findings contribute to understanding asymmetric reasoning dynamics and inform uncertainty-calibrated dialogue system design.

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.

The exponential growth of scientific literature necessitates advanced tools for effective knowledge exploration. We present Knowledge Navigator, a system designed to enhance exploratory search abilities by organizing and structuring the retrieved documents from broad topical queries into a navigable, two-level hierarchy of named and descriptive scientific topics and subtopics. This structured organization provides an overall view of the research themes in a domain, while also enabling iterative search and deeper knowledge discovery within specific subtopics by allowing users to refine their focus and retrieve additional relevant documents. Knowledge Navigator combines LLM capabilities with cluster-based methods to enable an effective browsing method. We demonstrate our approach's effectiveness through automatic and manual evaluations on two novel benchmarks, CLUSTREC-COVID and SCITOC. Our code, prompts, and benchmarks are made publicly available.

Literature review requires researchers to synthesize a large amount of information and is increasingly challenging as the scientific literature expands. In this work, we investigate the potential of LLMs for producing hierarchical organizations of scientific studies to assist researchers with literature review. We define hierarchical organizations as tree structures where nodes refer to topical categories and every node is linked to the studies assigned to that category. Our naive LLM-based pipeline for hierarchy generation from a set of studies produces promising yet imperfect hierarchies, motivating us to collect CHIME, an expert-curated dataset for this task focused on biomedicine. Given the challenging and time-consuming nature of building hierarchies from scratch, we use a human-in-the-loop process in which experts correct errors (both links between categories and study assignment) in LLM-generated hierarchies. CHIME contains 2,174 LLM-generated hierarchies covering 472 topics, and expert-corrected hierarchies for a subset of 100 topics. Expert corrections allow us to quantify LLM performance, and we find that while they are quite good at generating and organizing categories, their assignment of studies to categories could be improved. We attempt to train a corrector model with human feedback which improves study assignment by 12.6 F1 points. We release our dataset and models to encourage research on developing better assistive tools for literature review.

A central problem in machine learning involves modeling complex data-sets using highly flexible families of probability distributions in which learning, sampling, inference, and evaluation are still analytically or computationally tractable. Here, we develop an approach that simultaneously achieves both flexibility and tractability. The essential idea, inspired by non-equilibrium statistical physics, is to systematically and slowly destroy structure in a data distribution through an iterative forward diffusion process. We then learn a reverse diffusion process that restores structure in data, yielding a highly flexible and tractable generative model of the data. This approach allows us to rapidly learn, sample from, and evaluate probabilities in deep generative models with thousands of layers or time steps, as well as to compute conditional and posterior probabilities under the learned model. We additionally release an open source reference implementation of the algorithm.

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

We study the relationship between vocabulary size and text length in a corpus of 75 literary works in English, authored by six writers, distinguishing between the contributions of three grammatical classes (or ``tags,'' namely, {\it nouns}, {\it verbs}, and {\it others}), and analyze the progressive appearance of new words of each tag along each individual text. While the power-law relation prescribed by Heaps' law is satisfactorily fulfilled by total vocabulary sizes and text lengths, the appearance of new words in each text is on the whole well described by the average of random shufflings of the text, which does not obey a power law. Deviations from this average, however, are statistically significant and show a systematic trend across the corpus. Specifically, they reveal that the appearance of new words along each text is predominantly retarded with respect to the average of random shufflings. Moreover, different tags are shown to add systematically distinct contributions to this tendency, with {\it verbs} and {\it others} being respectively more and less retarded than the mean trend, and {\it nouns} following instead this overall mean. These statistical systematicities are likely to point to the existence of linguistically relevant information stored in the different variants of Heaps' law, a feature that is still in need of extensive assessment.

Code data has been shown to enhance the reasoning capabilities of large language models (LLMs), but it remains unclear which aspects of code are most responsible. We investigate this question with a systematic, data-centric framework. We construct parallel instruction datasets in ten programming languages and apply controlled perturbations that selectively disrupt structural or semantic properties of code. We then finetune LLMs from five model families and eight scales on each variant and evaluate their performance on natural language, math, and code tasks. Across 3,331 experiments, our results show that LLMs are more vulnerable to structural perturbations than semantic ones, particularly on math and code tasks. Appropriate abstractions like pseudocode and flowcharts can be as effective as code, while encoding the same information with fewer tokens without adhering to original syntax can often retain or even improve performance. Remarkably, even corrupted code with misleading signals remains competitive when surface-level regularities persist. Finally, syntactic styles also shape task-specific gains with Python favoring natural language reasoning and lower-level languages such as Java and Rust favoring math. Through our systematic framework, we aim to provide insight into how different properties of code influence reasoning and inform the design of training data for enhancing LLM reasoning capabilities.

The groundbreaking advance in materials and chemical research has been driven by the development of atomistic simulations. However, the broader applicability of the atomistic simulations remains restricted, as they inherently depend on energy models that are either inaccurate or computationally prohibitive. Machine learning interatomic potentials (MLIPs) have recently emerged as a promising class of energy models, but their deployment remains challenging due to the lack of systematic protocols for generating diverse training data. Here we automate the construction of training datasets to enable the development of general-purpose MLIPs, by introducing GAIA, an end-to-end framework to build a wide range of atomic arrangements. By employing systematic evaluation of metadynamics for effective structural exploration, GAIA overcomes the heuristic nature of conventional dataset generation. Using GAIA, we constructed Titan25, a benchmark-scale dataset, and trained MLIPs that closely match both static and dynamic density functional theory results. The models further reproduce experimental observations across reactive regimes, including detonation, coalescence, and catalytic activity. GAIA narrows the gap between experiment and simulation, and paves the way for the development of universal MLIPs that can reliably describe a wide spectrum of materials and chemical processes.

The problem of Question Answering (QA) has attracted significant research interest for long. Its relevance to language understanding and knowledge retrieval tasks, along with the simple setting makes the task of QA crucial for strong AI systems. Recent success on simple QA tasks has shifted the focus to more complex settings. Among these, Multi-Hop QA (MHQA) is one of the most researched tasks over the recent years. The ability to answer multi-hop questions and perform multi step reasoning can significantly improve the utility of NLP systems. Consequently, the field has seen a sudden surge with high quality datasets, models and evaluation strategies. The notion of `multiple hops' is somewhat abstract which results in a large variety of tasks that require multi-hop reasoning. This implies that different datasets and models differ significantly which makes the field challenging to generalize and survey. This work aims to provide a general and formal definition of MHQA task, and organize and summarize existing MHQA frameworks. We also outline the best methods to create MHQA datasets. The paper provides a systematic and thorough introduction as well as the structuring of the existing attempts to this highly interesting, yet quite challenging task.