Daily Papers

Large Language Model (LLM) coding agents have achieved strong results on software engineering tasks, yet repository exploration remains a major bottleneck: locating relevant code consumes substantial token budget and pollutes the agent's context with irrelevant snippets. In most agents, the same model explores the repository and solves the task, leaving exploratory reads and searches in the solver's history. We present FastContext, a dedicated exploration subagent that separates repository exploration from solving. Invoked on demand, FastContext issues parallel tool calls and returns concise file paths and line ranges as focused context. FastContext is powered by specialized exploration models spanning 4B--30B parameters. We bootstrap them from strong reference-model trajectories and refine them with task-grounded rewards for broad first-turn search, multi-turn evidence gathering, and precise citation generation. Across SWE-bench Multilingual, SWE-bench Pro, and SWE-QA, integrating FastContext into Mini-SWE-Agent improves end-to-end resolution rates up to 5.5\% while reducing coding-agent token consumption up to 60\%, with marginal overhead. These results show that repository exploration can be separated from solving and handled effectively by specialized models. Code and data: https://github.com/microsoft/fastcontext

Recently, Large Language Model (LLM) based agents have advanced the significant development of Automatic Software Engineering (ASE). Although verified effectiveness, the designs of the existing methods mainly focus on the local information of codes, e.g., issues, classes, and functions, leading to limitations in capturing the global context and interdependencies within the software system. From the practical experiences of the human SE developers, we argue that an excellent understanding of the whole repository will be the critical path to ASE. However, understanding the whole repository raises various challenges, e.g., the extremely long code input, the noisy code information, the complex dependency relationships, etc. To this end, we develop a novel ASE method named RepoUnderstander by guiding agents to comprehensively understand the whole repositories. Specifically, we first condense the critical information of the whole repository into the repository knowledge graph in a top-to-down mode to decrease the complexity of repository. Subsequently, we empower the agents the ability of understanding whole repository by proposing a Monte Carlo tree search based repository exploration strategy. In addition, to better utilize the repository-level knowledge, we guide the agents to summarize, analyze, and plan. Then, they can manipulate the tools to dynamically acquire information and generate the patches to solve the real-world GitHub issues. Extensive experiments demonstrate the superiority and effectiveness of the proposed RepoUnderstander. It achieved 18.5\% relative improvement on the SWE-bench Lite benchmark compared to SWE-agent.

Repository-level coding benchmarks such as SWE-bench have driven a rapid surge in the capabilities of coding agents. Yet they usually treat coding tasks as a holistic, binary prediction problem (e.g., resolved or unresolved), neglecting fine-grained agent capabilities such as repository understanding, context retrieval, code localization, and bug diagnosis. In this paper, we introduce SWE-Explore, a benchmark that isolates the evaluation of repository exploration, a critical capability of coding agents. Given a repository and an issue, SWE-Explore asks an explorer to return a ranked list of relevant code regions under a fixed line budget. SWE-Explore covers 848 issues across 10 programming languages and 203 open-source repositories. For each instance, we derive line-level ground truth from independent agent trajectories that successfully solved the same issue, distilling the specific code regions their solution paths actually consulted. We evaluate exploration along coverage, ranking, and context-efficiency dimensions, showing that these metrics strongly track downstream repair behavior. Across a broad set of retrieval methods, general coding agents, and specialized localizers, we find that agentic explorers form a clear tier above classical retrieval. While file-level localization is already strong for modern methods, line-level coverage and efficient ranking remain the key axes differentiating state-of-the-art explorers.

Test-time scaling has been widely adopted to enhance the capabilities of Large Language Model (LLM) agents in software engineering (SWE) tasks. However, the standard approach of repeatedly sampling trajectories from scratch is computationally expensive. While recent methods have attempted to mitigate costs using specialized value agents, they can suffer from model miscalibration and fail to generalize to modern agents that synthesize custom bash scripts as tools. In this paper, we introduce SWE-Replay, the first efficient and generalizable test-time scaling technique for modern agents without reliance on potentially noisy value estimates. SWE-Replay optimizes the scaling process by recycling trajectories from prior trials, dynamically choosing to either explore from scratch or exploit archived experience by branching at critical intermediate steps. This selection of intermediate steps is driven by the potential and reasoning significance of repository exploration, rather than external LLM-based quality estimates. Our evaluation shows that, on SWE-Bench Verified, SWE-Replay consistently outperforms naive scaling, reducing costs by up to 17.4% while maintaining or even improving performance by up to 3.8%. Further evaluation on SWE-Bench Pro and Multilingual validates the generalizability of SWE-Replay, establishing it as a robust foundation for efficient test-time scaling of software engineering agents.

The evolution of Large Language Models (LLMs) into autonomous agents has expanded the scope of AI coding from localized code generation to complex, repository-level, and execution-driven problem solving. However, current benchmarks predominantly evaluate code logic in static contexts, neglecting the dynamic, full-process requirements of real-world engineering, particularly in backend development which demands rigorous environment configuration and service deployment. To address this gap, we introduce ABC-Bench, a benchmark explicitly designed to evaluate agentic backend coding within a realistic, executable workflow. Using a scalable automated pipeline, we curated 224 practical tasks spanning 8 languages and 19 frameworks from open-source repositories. Distinct from previous evaluations, ABC-Bench require the agents to manage the entire development lifecycle from repository exploration to instantiating containerized services and pass the external end-to-end API tests. Our extensive evaluation reveals that even state-of-the-art models struggle to deliver reliable performance on these holistic tasks, highlighting a substantial disparity between current model capabilities and the demands of practical backend engineering. Our code is available at https://github.com/OpenMOSS/ABC-Bench.

Training capable software engineering (SWE) agents demands large-scale, executable, and verifiable environments that provide dynamic feedback loops for iterative code editing, test execution, and solution refinement. However, existing open-source datasets remain limited in scale and repository diversity, while industrial solutions are opaque with unreleased infrastructure, creating a prohibitive barrier for most academic research groups. We present OpenSWE, the largest fully transparent framework for SWE agent training in Python, comprising 45,320 executable Docker environments spanning over 12.8k repositories, with all Dockerfiles, evaluation scripts, and infrastructure fully open-sourced for reproducibility. OpenSWE is built through a multi-agent synthesis pipeline deployed across a 64-node distributed cluster, automating repository exploration, Dockerfile construction, evaluation script generation, and iterative test analysis. Beyond scale, we propose a quality-centric filtering pipeline that characterizes the inherent difficulty of each environment, filtering out instances that are either unsolvable or insufficiently challenging and retaining only those that maximize learning efficiency. With 891K spent on environment construction and an additional 576K on trajectory sampling and difficulty-aware curation, the entire project represents a total investment of approximately $1.47 million, yielding about 13,000 curated trajectories from roughly 9,000 quality guaranteed environments. Extensive experiments validate OpenSWE's effectiveness: OpenSWE-32B and OpenSWE-72B achieve 62.4% and 66.0% on SWE-bench Verified, establishing SOTA among Qwen2.5 series. Moreover, SWE-focused training yields substantial out-of-domain improvements, including up to 12 points on mathematical reasoning and 5 points on science benchmarks, without degrading factual recall.

Program verifiers play a central role in training coding agents, including selecting trajectories for supervised fine-tuning (SFT) and providing rewards for reinforcement learning (RL). Standard execution-based verification requires running unit tests inside per-repository environments such as Docker images, incurring substantial environment setup costs. We propose Dockerless, an environment-free agentic patch verifier that evaluates generated code patches without executing them. Rather than simply matching candidate patches to references, Dockerless judges patch correctness using evidence gathered through agentic repository exploration. On a verifier evaluation benchmark, Dockerless outperforms the strongest open-source verifier by 14.3 AUC points. Using Dockerless as both the SFT trajectory filter and the RL reward enables a fully environment-free post-training pipeline. The resulting model reaches 62.0%, 50.0%, and 35.2% resolve rate on SWE-bench Verified, Multilingual, and Pro, respectively. It surpasses the Qwen3.5-9B baseline by 2.4, 8.7, and 2.9 points, matching environment-based post-training.

The rapid advancement of conversational and chat-based language models has led to remarkable progress in complex task-solving. However, their success heavily relies on human input to guide the conversation, which can be challenging and time-consuming. This paper explores the potential of building scalable techniques to facilitate autonomous cooperation among communicative agents and provide insight into their "cognitive" processes. To address the challenges of achieving autonomous cooperation, we propose a novel communicative agent framework named role-playing. Our approach involves using inception prompting to guide chat agents toward task completion while maintaining consistency with human intentions. We showcase how role-playing can be used to generate conversational data for studying the behaviors and capabilities of chat agents, providing a valuable resource for investigating conversational language models. Our contributions include introducing a novel communicative agent framework, offering a scalable approach for studying the cooperative behaviors and capabilities of multi-agent systems, and open-sourcing our library to support research on communicative agents and beyond. The GitHub repository of this project is made publicly available on: https://github.com/lightaime/camel.

Code agents increasingly help developers work with unfamiliar repositories, but every such task depends on a costly prerequisite: bootstrapping the repository into a usable development state. This process requires substantial trial-and-error exploration, yet the resulting knowledge--resolved dependencies, repair strategies--stays trapped in a single conversation, unavailable to future agents. We therefore formulate repository bootstrapping as a reusable startup knowledge problem and introduce BootstrapAgent, a multi-agent framework that distills the heuristics discovered during bootstrap exploration into a persistent, verifiable, agent-consumable .bootstrap contract. Through evidence extraction, structured planning, deterministic Docker-based verification, and trace-driven repair, BootstrapAgent generates a contract covering environment setup, diagnostic checks, minimal verification, and accumulated repair knowledge. We further propose warm repair with clean replay to accelerate iterative debugging without sacrificing cold-start reproducibility, and a delta repair with sanity check to prevent reward hacking. Experiments on three benchmarks show that BootstrapAgent achieves a 92.9% success rate, outperforming the baseline by over 10% while reducing downstream agent token usage by 25.9% and build time by 22.3%. Our code is available at https://github.com/Vossera/BootstrapAgent.

Wikidata is the largest collaborative general knowledge graph supported by a worldwide community. It includes many helpful topics for knowledge exploration and data science applications. However, due to the enormous size of Wikidata, it is challenging to retrieve a large amount of data with millions of results, make complex queries requiring large aggregation operations, or access too many statement references. This paper introduces our preliminary works on Wikidata-lite, a toolkit to build a database offline for knowledge extraction and exploration, e.g., retrieving item information, statements, provenances, or searching entities by their keywords and attributes. Wikidata-lite has high performance and memory efficiency, much faster than the official Wikidata SPARQL endpoint for big queries. The Wikidata-lite repository is available at https://github.com/phucty/wikidb.

Software engineering tools increasingly rely on LLM based agents to localize files to change to resolve a software issue. Most AI agents explore repositories linearly, that is, visiting one directory or file per step. We postulate that this is a structural mismatch for changes that span several subsystems. We compare linear sequential exploration against non-linear, domain-scoped parallel agentic exploration. Using SWE Bench Pro as initial benchmark, we focus on ansible as an exemplar. We construct an approach for persistent-session evaluation of GitHub issues anchored at a single base commit. We compare our non-linear domain-agent file traversal system against a base LLM without direct repository access, a single agent Recursive Language Model (RLM) baseline with a persistent Python REPL and an external CLI baseline using Codex 5.5 High. Domain scoped parallel agent spawning with a small Haiku-class model achieves the highest micro F1 among Haiku class models by a large margin. Domain-agents is the second highest behind only the much larger Codex 5.5 High on our own expanded benchmark including over more recent PRs from 2025 and 2026. On the original, curated, 2020 SWE-bench Pro benchmark, a larger Sonnet plain LLM baseline attains higher micro F1 by predicting few files, leading to higher precision, but at significantly lower all gold recall. We also present three additional findings. First, documentation evolution is a latent dependency unresolved by any approach. Second, naive file system access can degrade localization driven by test-file over prediction. Lastly, forced multi-agent consultation does not measurably help and raises token cost substantially.

A widespread practice in software development is to tailor coding agents to repositories using context files, such as AGENTS.md, by either manually or automatically generating them. Although this practice is strongly encouraged by agent developers, there is currently no rigorous investigation into whether such context files are actually effective for real-world tasks. In this work, we study this question and evaluate coding agents' task completion performance in two complementary settings: established SWE-bench tasks from popular repositories, with LLM-generated context files following agent-developer recommendations, and a novel collection of issues from repositories containing developer-committed context files. Across multiple coding agents and LLMs, we find that context files tend to reduce task success rates compared to providing no repository context, while also increasing inference cost by over 20%. Behaviorally, both LLM-generated and developer-provided context files encourage broader exploration (e.g., more thorough testing and file traversal), and coding agents tend to respect their instructions. Ultimately, we conclude that unnecessary requirements from context files make tasks harder, and human-written context files should describe only minimal requirements.

While Large Language Models (LLMs) have made significant strides in replicating human-like abilities, there are concerns about a reduction in the linguistic diversity of their outputs. This results in the homogenization of viewpoints and perspectives, as well as the underrepresentation of specific demographic groups. Although several fine-tuning and prompting techniques have been suggested to tackle the issue, they are often tailored to specific tasks or come with a substantial increase in computational cost and latency. This makes them challenging to apply to applications that demand very low latency, such as chatbots and virtual assistants. We propose Possibility Exploration Fine-Tuning (PEFT), a task-agnostic framework that enhances the text diversity of LLMs without increasing latency or computational cost. Given the same prompt, models fine-tuned with PEFT can simultaneously generate multiple diverse responses, each corresponding with a controllable possibility number. Experiments on dialogue and story generation tasks demonstrate that PEFT significantly enhances the diversity of LLM outputs, as evidenced by lower similarity between candidate responses. Since PEFT emphasizes semantic diversity over lexical diversity, it can also notably reduce demographic bias in dialogue systems. The implementations and datasets are available in our repository: https://github.com/mailong25/peft_diversity

Agentic repository-level code understanding is essential for automating complex software engineering tasks, yet the field lacks reliable benchmarks. Existing evaluations often overlook the long tail topics and rely on popular repositories where Large Language Models (LLMs) can cheat via memorized knowledge. To address this, we introduce SWE-QA-Pro, a benchmark constructed from diverse, long-tail repositories with executable environments. We enforce topical balance via issue-driven clustering to cover under-represented task types and apply a rigorous difficulty calibration process: questions solvable by direct-answer baselines are filtered out. This results in a dataset where agentic workflows significantly outperform direct answering (e.g., a ~13-point gap for Claude Sonnet 4.5), confirming the necessity of agentic codebase exploration. Furthermore, to tackle the scarcity of training data for such complex behaviors, we propose a scalable synthetic data pipeline that powers a two-stage training recipe: Supervised Fine-Tuning (SFT) followed by Reinforcement Learning from AI Feedback (RLAIF). This approach allows small open models to learn efficient tool usage and reasoning. Empirically, a Qwen3-8B model trained with our recipe surpasses GPT-4o by 2.3 points on SWE-QA-Pro and substantially narrows the gap to state-of-the-art proprietary models, demonstrating both the validity of our evaluation and the effectiveness of our agentic training workflow.

Traditional Celluloid (Cel) Animation production pipeline encompasses multiple essential steps, including storyboarding, layout design, keyframe animation, inbetweening, and colorization, which demand substantial manual effort, technical expertise, and significant time investment. These challenges have historically impeded the efficiency and scalability of Cel-Animation production. The rise of generative artificial intelligence (GenAI), encompassing large language models, multimodal models, and diffusion models, offers innovative solutions by automating tasks such as inbetween frame generation, colorization, and storyboard creation. This survey explores how GenAI integration is revolutionizing traditional animation workflows by lowering technical barriers, broadening accessibility for a wider range of creators through tools like AniDoc, ToonCrafter, and AniSora, and enabling artists to focus more on creative expression and artistic innovation. Despite its potential, issues such as maintaining visual consistency, ensuring stylistic coherence, and addressing ethical considerations continue to pose challenges. Furthermore, this paper discusses future directions and explores potential advancements in AI-assisted animation. For further exploration and resources, please visit our GitHub repository: https://github.com/yunlong10/Awesome-AI4Animation

The rapid evolution of software libraries presents a significant challenge for code generation models, which must adapt to frequent version updates while maintaining compatibility with previous versions. Existing code completion benchmarks often overlook this dynamic aspect, and the one that does consider it relies on static code prediction tasks without execution-based evaluation, offering a limited perspective on a model's practical usability. To address this gap, we introduce \GitChameleon{}, a novel, manually curated dataset comprising 116 Python code completion problems, each conditioned on specific library versions and accompanied by executable unit tests. is designed to rigorously assess the ability of modern large language models (LLMs) to generate version-specific code that is not only syntactically correct but also functionally accurate upon execution. Our comprehensive evaluations reveal that state-of-the-art LLMs struggle with this task; for instance, GPT-4o achieves a pass@10 of only 39.9\% (43.7\% when provided with error feedback), highlighting the complexity of the problem and the limitations of current models. By providing an execution-based benchmark that emphasizes the dynamic nature of code libraries, serves as a critical tool to advance the development of more adaptable and reliable code generation models. For facilitation for further exploration of version-conditioned code generation, we make our code repository publicly accessible at https://github.com/NizarIslah/GitChameleon.

Many recent advances in robotic manipulation have come through imitation learning, yet these rely largely on mimicking a particularly hard-to-acquire form of demonstrations: those collected on the same robot in the same room with the same objects as the trained policy must handle at test time. In contrast, large pre-recorded human video datasets demonstrating manipulation skills in-the-wild already exist, which contain valuable information for robots. Is it possible to distill a repository of useful robotic skill policies out of such data without any additional requirements on robot-specific demonstrations or exploration? We present the first such system ZeroMimic, that generates immediately deployable image goal-conditioned skill policies for several common categories of manipulation tasks (opening, closing, pouring, pick&place, cutting, and stirring) each capable of acting upon diverse objects and across diverse unseen task setups. ZeroMimic is carefully designed to exploit recent advances in semantic and geometric visual understanding of human videos, together with modern grasp affordance detectors and imitation policy classes. After training ZeroMimic on the popular EpicKitchens dataset of ego-centric human videos, we evaluate its out-of-the-box performance in varied real-world and simulated kitchen settings with two different robot embodiments, demonstrating its impressive abilities to handle these varied tasks. To enable plug-and-play reuse of ZeroMimic policies on other task setups and robots, we release software and policy checkpoints of our skill policies.

Bug localization in multi-repository microservice architectures is challenging due to the semantic gap between natural language bug reports and code, LLM context limitations, and the need to first identify the correct repository. We propose reframing this as a natural language reasoning task by transforming codebases into hierarchical NL summaries and performing NL-to-NL search instead of cross-modal retrieval. Our approach builds context-aware summaries at file, directory, and repository levels, then uses a two-phase search: first routing bug reports to relevant repositories, then performing top-down localization within those repositories. Evaluated on DNext, an industrial system with 46 repositories and 1.1M lines of code, our method achieves Pass@10 of 0.82 and MRR of 0.50, significantly outperforming retrieval baselines and agentic RAG systems like GitHub Copilot and Cursor. This work demonstrates that engineered natural language representations can be more effective than raw source code for scalable bug localization, providing an interpretable repository -> directory -> file search path, which is vital for building trust in enterprise AI tools by providing essential transparency.

The rapid acceleration of scientific publishing has created substantial challenges for researchers attempting to discover, contextualize, and interpret relevant literature. Traditional keyword-based search systems provide limited semantic understanding, while existing AI-driven tools typically focus on isolated tasks such as retrieval, clustering, or bibliometric visualization. This paper presents an integrated system for scientific literature exploration that combines large-scale data acquisition, hybrid retrieval, semantic topic modeling, and heterogeneous knowledge graph construction. The system builds a comprehensive corpus by merging full-text data from arXiv with structured metadata from OpenAlex. A hybrid retrieval architecture fuses BM25 lexical search with embedding-based semantic search using Reciprocal Rank Fusion. Topic modeling is performed on retrieved results using BERTopic or non-negative matrix factorization depending on computational resources. A knowledge graph unifies papers, authors, institutions, countries, and extracted topics into an interpretable structure. The system provides a multi-layered exploration environment that reveals not only relevant publications but also the conceptual and relational landscape surrounding a query. Evaluation across multiple queries demonstrates improvements in retrieval relevance, topic coherence, and interpretability. The proposed framework contributes an extensible foundation for AI-assisted scientific discovery.

We present SymbioticRAG, a novel framework that fundamentally reimagines Retrieval-Augmented Generation~(RAG) systems by establishing a bidirectional learning relationship between humans and machines. Our approach addresses two critical challenges in current RAG systems: the inherently human-centered nature of relevance determination and users' progression from "unconscious incompetence" in query formulation. SymbioticRAG introduces a two-tier solution where Level 1 enables direct human curation of retrieved content through interactive source document exploration, while Level 2 aims to build personalized retrieval models based on captured user interactions. We implement Level 1 through three key components: (1)~a comprehensive document processing pipeline with specialized models for layout detection, OCR, and extraction of tables, formulas, and figures; (2)~an extensible retriever module supporting multiple retrieval strategies; and (3)~an interactive interface that facilitates both user engagement and interaction data logging. We experiment Level 2 implementation via a retriever strategy incorporated LLM summarized user intention from user interaction logs. To maintain high-quality data preparation, we develop a human-on-the-loop validation interface that improves pipeline output while advancing research in specialized extraction tasks. Evaluation across three scenarios (literature review, geological exploration, and education) demonstrates significant improvements in retrieval relevance and user satisfaction compared to traditional RAG approaches. To facilitate broader research and further advancement of SymbioticRAG Level 2 implementation, we will make our system openly accessible to the research community.

Software repositories is one of the sources of data in Empirical Software Engineering, primarily in the Mining Software Repositories field, aimed at extracting knowledge from the dynamics and practice of software projects. With the emergence of social coding platforms such as GitHub, researchers have now access to millions of software repositories to use as source data for their studies. With this massive amount of data, sampling techniques are needed to create more manageable datasets. The creation of these datasets is a crucial step, and researchers have to carefully select the repositories to create representative samples according to a set of variables of interest. However, current sampling methods are often based on random selection or rely on variables which may not be related to the research study (e.g., popularity or activity). In this paper, we present a methodology for creating representative samples of software repositories, where such representativeness is properly aligned with both the characteristics of the population of repositories and the requirements of the empirical study. We illustrate our approach with use cases based on Hugging Face repositories.

Pharo offers a sophisticated completion engine based on semantic heuristics, which coordinates specific fetchers within a lazy architecture. These heuristics can be recomposed to support various activities (e.g., live programming or history usage navigation). While this system is powerful, it does not account for the repository structure when suggesting global names such as class names, class variables, or global variables. As a result, it does not prioritize classes within the same package or project, treating all global names equally. In this paper, we present a new heuristic that addresses this limitation. Our approach searches variable names in a structured manner: it begins with the package of the requesting class, then expands to other packages within the same repository, and finally considers the global namespace. We describe the logic behind this heuristic and evaluate it against the default semantic heuristic and one that directly queries the global namespace. Preliminary results indicate that the Mean Reciprocal Rank (MRR) improves, confirming that package-awareness completions deliver more accurate and relevant suggestions than the previous flat global approach.

Repository-level code completion aims to generate code for unfinished code snippets within the context of a specified repository. Existing approaches mainly rely on retrieval-augmented generation strategies due to limitations in input sequence length. However, traditional lexical-based retrieval methods like BM25 struggle to capture code semantics, while model-based retrieval methods face challenges due to the lack of labeled data for training. Therefore, we propose RLCoder, a novel reinforcement learning framework, which can enable the retriever to learn to retrieve useful content for code completion without the need for labeled data. Specifically, we iteratively evaluate the usefulness of retrieved content based on the perplexity of the target code when provided with the retrieved content as additional context, and provide feedback to update the retriever parameters. This iterative process enables the retriever to learn from its successes and failures, gradually improving its ability to retrieve relevant and high-quality content. Considering that not all situations require information beyond code files and not all retrieved context is helpful for generation, we also introduce a stop signal mechanism, allowing the retriever to decide when to retrieve and which candidates to retain autonomously. Extensive experimental results demonstrate that RLCoder consistently outperforms state-of-the-art methods on CrossCodeEval and RepoEval, achieving 12.2% EM improvement over previous methods. Moreover, experiments show that our framework can generalize across different programming languages and further improve previous methods like RepoCoder. We provide the code and data at https://github.com/DeepSoftwareAnalytics/RLCoder.

Formulating effective search queries remains a challenging task, particularly when users lack expertise in a specific domain or are not proficient in the language of the content. Providing example documents of interest might be easier for a user. However, such query-by-example scenarios are prone to concept drift, and the retrieval effectiveness is highly sensitive to the query generation method, without a clear way to incorporate user feedback. To enable exploration and to support Human-In-The-Loop experiments we propose QueryExplorer -- an interactive query generation, reformulation, and retrieval interface with support for HuggingFace generation models and PyTerrier's retrieval pipelines and datasets, and extensive logging of human feedback. To allow users to create and modify effective queries, our demo supports complementary approaches of using LLMs interactively, assisting the user with edits and feedback at multiple stages of the query formulation process. With support for recording fine-grained interactions and user annotations, QueryExplorer can serve as a valuable experimental and research platform for annotation, qualitative evaluation, and conducting Human-in-the-Loop (HITL) experiments for complex search tasks where users struggle to formulate queries.

The advent of large language models (LLMs) has transformed information access and reasoning through open-ended natural language interaction. However, LLMs remain limited by static knowledge, factual hallucinations, and the inability to retrieve real-time or domain-specific information. Retrieval-Augmented Generation (RAG) mitigates these issues by grounding model outputs in external evidence, but traditional RAG pipelines are often single turn and heuristic, lacking adaptive control over retrieval and reasoning. Recent advances in agentic search address these limitations by enabling LLMs to plan, retrieve, and reflect through multi-step interaction with search environments. Within this paradigm, reinforcement learning (RL) offers a powerful mechanism for adaptive and self-improving search behavior. This survey provides the first comprehensive overview of RL-based agentic search, organizing the emerging field along three complementary dimensions: (i) What RL is for (functional roles), (ii) How RL is used (optimization strategies), and (iii) Where RL is applied (scope of optimization). We summarize representative methods, evaluation protocols, and applications, and discuss open challenges and future directions toward building reliable and scalable RL driven agentic search systems. We hope this survey will inspire future research on the integration of RL and agentic search. Our repository is available at https://github.com/ventr1c/Awesome-RL-based-Agentic-Search-Papers.

Go-Explore is a powerful family of algorithms designed to solve hard-exploration problems, built on the principle of archiving discovered states, and iteratively returning to and exploring from the most promising states. This approach has led to superhuman performance across a wide variety of challenging problems including Atari games and robotic control, but requires manually designing heuristics to guide exploration, which is time-consuming and infeasible in general. To resolve this, we propose Intelligent Go-Explore (IGE) which greatly extends the scope of the original Go-Explore by replacing these heuristics with the intelligence and internalized human notions of interestingness captured by giant foundation models (FMs). This provides IGE with a human-like ability to instinctively identify how interesting or promising any new state is (e.g. discovering new objects, locations, or behaviors), even in complex environments where heuristics are hard to define. Moreover, IGE offers the exciting and previously impossible opportunity to recognize and capitalize on serendipitous discoveries that cannot be predicted ahead of time. We evaluate IGE on a range of language-based tasks that require search and exploration. In Game of 24, a multistep mathematical reasoning problem, IGE reaches 100% success rate 70.8% faster than the best classic graph search baseline. Next, in BabyAI-Text, a challenging partially observable gridworld, IGE exceeds the previous SOTA with orders of magnitude fewer online samples. Finally, in TextWorld, we show the unique ability of IGE to succeed in settings requiring long-horizon exploration where prior SOTA FM agents like Reflexion completely fail. Overall, IGE combines the tremendous strengths of FMs and the powerful Go-Explore algorithm, opening up a new frontier of research into creating more generally capable agents with impressive exploration capabilities.

When a human requests an LLM to complete a coding task using functionality from a large code repository, how do we provide context from the repo to the LLM? One approach is to add the entire repo to the LLM's context window. However, most tasks involve only fraction of symbols from a repo, longer contexts are detrimental to the LLM's reasoning abilities, and context windows are not unlimited. Alternatively, we could emulate the human ability to navigate a large repo, pick out the right functionality, and form a plan to solve the task. We propose MutaGReP (Mutation-guided Grounded Repository Plan Search), an approach to search for plans that decompose a user request into natural language steps grounded in the codebase. MutaGReP performs neural tree search in plan space, exploring by mutating plans and using a symbol retriever for grounding. On the challenging LongCodeArena benchmark, our plans use less than 5% of the 128K context window for GPT-4o but rival the coding performance of GPT-4o with a context window filled with the repo. Plans produced by MutaGReP allow Qwen 2.5 Coder 32B and 72B to match the performance of GPT-4o with full repo context and enable progress on the hardest LongCodeArena tasks. Project page: zaidkhan.me/MutaGReP

While the Earth observation community has witnessed a surge in high-impact foundation models and global Earth embedding datasets, a significant barrier remains in translating these academic assets into freely accessible tools. This tutorial introduces EarthEmbeddingExplorer, an interactive web application designed to bridge this gap, transforming static research artifacts into dynamic, practical workflows for discovery. We will provide a comprehensive hands-on guide to the system, detailing its cloud-native software architecture, demonstrating cross-modal queries (natural language, visual, and geolocation), and showcasing how to derive scientific insights from retrieval results. By democratizing access to precomputed Earth embeddings, this tutorial empowers researchers to seamlessly transition from state-of-the-art models and data archives to real-world application and analysis. The web application is available at https://modelscope.ai/studios/Major-TOM/EarthEmbeddingExplorer.

Current repository agents encounter a reasoning disconnect due to fragmented representations, as existing methods rely on isolated API documentation or dependency graphs that lack semantic depth. We consider repository comprehension and generation to be inverse processes within a unified cycle: generation expands intent into implementation, while comprehension compresses implementation back into intent. To address this, we propose RPG-Encoder, a framework that generalizes the Repository Planning Graph (RPG) from a static generative blueprint into a unified, high-fidelity representation. RPG-Encoder closes the reasoning loop through three mechanisms: (1) Encoding raw code into the RPG that combines lifted semantic features with code dependencies; (2) Evolving the topology incrementally to decouple maintenance costs from repository scale, reducing overhead by 95.7%; and (3) Operating as a unified interface for structure-aware navigation. In evaluations, RPG-Encoder establishes state-of-the-art repository understanding on SWE-bench Verified with 93.7% Acc@5 and exceeds the best baseline by over 10% on SWE-bench Live Lite. These results highlight our superior fine-grained localization accuracy in complex codebases. Furthermore, it achieves 98.5% reconstruction coverage on RepoCraft, confirming RPG's high-fidelity capacity to mirror the original codebase and closing the loop between intent and implementation.

The task of repository-level code completion is to continue writing the unfinished code based on a broader context of the repository. While for automated code completion tools, it is difficult to utilize the useful information scattered in different files. We propose RepoCoder, a simple, generic, and effective framework to address the challenge. It streamlines the repository-level code completion process by incorporating a similarity-based retriever and a pre-trained code language model in an iterative retrieval-generation pipeline. RepoCoder makes effective utilization of repository-level information for code completion and has the ability to generate code at various levels of granularity. Moreover, we propose a new benchmark RepoEval, which consists of the latest and high-quality real-world repositories covering line, API invocation, and function body completion scenarios. Experimental results indicate that RepoCoder significantly improves the In-File completion baseline by over 10% in all settings and consistently outperforms the vanilla retrieval-augmented code completion approach. Furthermore, we validate the effectiveness of RepoCoder through comprehensive analysis, providing valuable insights for future research. Our source code and benchmark are publicly available: https://github.com/microsoft/CodeT/tree/main/RepoCoder

Large language models (LLMs) are increasingly applied to scientific research, yet prevailing science benchmarks probe decontextualized knowledge and overlook the iterative reasoning, hypothesis generation, and observation interpretation that drive scientific discovery. We introduce a scenario-grounded benchmark that evaluates LLMs across biology, chemistry, materials, and physics, where domain experts define research projects of genuine interest and decompose them into modular research scenarios from which vetted questions are sampled. The framework assesses models at two levels: (i) question-level accuracy on scenario-tied items and (ii) project-level performance, where models must propose testable hypotheses, design simulations or experiments, and interpret results. Applying this two-phase scientific discovery evaluation (SDE) framework to state-of-the-art LLMs reveals a consistent performance gap relative to general science benchmarks, diminishing return of scaling up model sizes and reasoning, and systematic weaknesses shared across top-tier models from different providers. Large performance variation in research scenarios leads to changing choices of the best performing model on scientific discovery projects evaluated, suggesting all current LLMs are distant to general scientific "superintelligence". Nevertheless, LLMs already demonstrate promise in a great variety of scientific discovery projects, including cases where constituent scenario scores are low, highlighting the role of guided exploration and serendipity in discovery. This SDE framework offers a reproducible benchmark for discovery-relevant evaluation of LLMs and charts practical paths to advance their development toward scientific discovery.

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.

The advent of Large Language Models (LLMs) has significantly revolutionized web search. The emergence of LLM-based Search Agents marks a pivotal shift towards deeper, dynamic, autonomous information seeking. These agents can comprehend user intentions and environmental context and execute multi-turn retrieval with dynamic planning, extending search capabilities far beyond the web. Leading examples like OpenAI's Deep Research highlight their potential for deep information mining and real-world applications. This survey provides the first systematic analysis of search agents. We comprehensively analyze and categorize existing works from the perspectives of architecture, optimization, application, and evaluation, ultimately identifying critical open challenges and outlining promising future research directions in this rapidly evolving field. Our repository is available on https://github.com/YunjiaXi/Awesome-Search-Agent-Papers.

Public repositories host millions of fine-tuned models, yet community usage remains disproportionately concentrated on a small number of foundation checkpoints. We investigate whether this concentration reflects efficient market selection or if superior models are systematically overlooked. Through an extensive evaluation of over 2,000 models, we show the prevalence of "hidden gems", unpopular fine-tunes that significantly outperform their popular counterparts. Notably, within the Llama-3.1-8B family, we find rarely downloaded checkpoints that improve math performance from 83.2% to 96.0% without increasing inference costs. However, discovering these models through exhaustive evaluation of every uploaded model is computationally infeasible. We therefore formulate model discovery as a Multi-Armed Bandit problem and accelerate the Sequential Halving search algorithm by using shared query sets and aggressive elimination schedules. Our method retrieves top models with as few as 50 queries per candidate, accelerating discovery by over 50x.

The deployment of coding agents in privacy-sensitive and resource-constrained environments drives the demand for capable open-weight Small Language Models (SLMs). However, they suffer from a fundamental capability gap: unlike frontier large models, they lack the inference-time strong generalization to work with complicated, unfamiliar codebases. We identify that the prevailing Task-Centric Learning (TCL) paradigm, which scales exposure across disparate repositories, fails to address this limitation. In response, we propose Repository-Centric Learning (RCL), a paradigm shift that prioritizes vertical repository depth over horizontal task breadth, suggesting SLMs must internalize the "physics" of a target software environment through parametric knowledge acquisition, rather than attempting to recover it via costly inference-time search. Following this new paradigm, we design a four-unit Repository-Centric Experience, transforming static codebases into interactive learning signals, to train SWE-Spot-4B, a family of highly compact models built as repo-specialized experts that breaks established scaling trends, outperforming open-weight models up to larger (e.g., CWM by Meta, Qwen3-Coder-30B) and surpassing/matching efficiency-focused commercial models (e.g., GPT-4.1-mini, GPT-5-nano) across multiple SWE tasks. Further analysis reveals that RCL yields higher training sample efficiency and lower inference costs, emphasizing that for building efficient intelligence, repository mastery is a distinct and necessary dimension that complements general coding capability.

Large Language Models (LLMs) are catalyzing a paradigm shift in scientific discovery, evolving from task-specific automation tools into increasingly autonomous agents and fundamentally redefining research processes and human-AI collaboration. This survey systematically charts this burgeoning field, placing a central focus on the changing roles and escalating capabilities of LLMs in science. Through the lens of the scientific method, we introduce a foundational three-level taxonomy-Tool, Analyst, and Scientist-to delineate their escalating autonomy and evolving responsibilities within the research lifecycle. We further identify pivotal challenges and future research trajectories such as robotic automation, self-improvement, and ethical governance. Overall, this survey provides a conceptual architecture and strategic foresight to navigate and shape the future of AI-driven scientific discovery, fostering both rapid innovation and responsible advancement. Github Repository: https://github.com/HKUST-KnowComp/Awesome-LLM-Scientific-Discovery.

Repository-level code generation remains challenging due to complex code dependencies and the limitations of large language models (LLMs) in processing long contexts. While retrieval-augmented generation (RAG) frameworks are widely adopted, the effectiveness of different retrieved information sources-contextual code, APIs, and similar snippets-has not been rigorously analyzed. Through an empirical study on two benchmarks, we demonstrate that in-context code and potential API information significantly enhance LLM performance, whereas retrieved similar code often introduces noise, degrading results by up to 15%. Based on the preliminary results, we propose AllianceCoder, a novel context-integrated method that employs chain-of-thought prompting to decompose user queries into implementation steps and retrieves APIs via semantic description matching. Through extensive experiments on CoderEval and RepoExec, AllianceCoder achieves state-of-the-art performance, improving Pass@1 by up to 20% over existing approaches.

In recent years, the rapid advancement of Large Language Models (LLMs) has transformed the landscape of scientific research, offering unprecedented support across various stages of the research cycle. This paper presents the first systematic survey dedicated to exploring how LLMs are revolutionizing the scientific research process. We analyze the unique roles LLMs play across four critical stages of research: hypothesis discovery, experiment planning and implementation, scientific writing, and peer reviewing. Our review comprehensively showcases the task-specific methodologies and evaluation benchmarks. By identifying current challenges and proposing future research directions, this survey not only highlights the transformative potential of LLMs, but also aims to inspire and guide researchers and practitioners in leveraging LLMs to advance scientific inquiry. Resources are available at the following repository: https://github.com/du-nlp-lab/LLM4SR

We introduce ResearchGym, a benchmark and execution environment for evaluating AI agents on end-to-end research. To instantiate this, we repurpose five oral and spotlight papers from ICML, ICLR, and ACL. From each paper's repository, we preserve the datasets, evaluation harness, and baseline implementations but withhold the paper's proposed method. This results in five containerized task environments comprising 39 sub-tasks in total. Within each environment, agents must propose novel hypotheses, run experiments, and attempt to surpass strong human baselines on the paper's metrics. In a controlled evaluation of an agent powered by GPT-5, we observe a sharp capability--reliability gap. The agent improves over the provided baselines from the repository in just 1 of 15 evaluations (6.7%) by 11.5%, and completes only 26.5% of sub-tasks on average. We identify recurring long-horizon failure modes, including impatience, poor time and resource management, overconfidence in weak hypotheses, difficulty coordinating parallel experiments, and hard limits from context length. Yet in a single run, the agent surpasses the solution of an ICML 2025 Spotlight task, indicating that frontier agents can occasionally reach state-of-the-art performance, but do so unreliably. We additionally evaluate proprietary agent scaffolds including Claude Code (Opus-4.5) and Codex (GPT-5.2) which display a similar gap. ResearchGym provides infrastructure for systematic evaluation and analysis of autonomous agents on closed-loop research.

Many works have recently proposed the use of Large Language Model (LLM) based agents for performing `repository level' tasks, loosely defined as a set of tasks whose scopes are greater than a single file. This has led to speculation that the orchestration of these repository-level tasks could lead to software engineering agents capable of performing almost independently of human intervention. However, of the suite of tasks that would need to be performed by this autonomous software engineering agent, we argue that one important task is missing, which is to fulfil project level dependency by installing other repositories. To investigate the feasibility of this repository level installation task, we introduce a benchmark of of repository installation tasks curated from 40 open source Python projects, which includes a ground truth installation process for each target repository. Further, we propose Installamatic, an agent which aims to perform and verify the installation of a given repository by searching for relevant instructions from documentation in the repository. Empirical experiments reveal that that 55% of the studied repositories can be automatically installed by our agent at least one out of ten times. Through further analysis, we identify the common causes for our agent's inability to install a repository, discuss the challenges faced in the design and implementation of such an agent and consider the implications that such an agent could have for developers.

This paper introduces a pioneering approach to artificial intelligence research, embodied in our O1 Replication Journey. In response to the announcement of OpenAI's groundbreaking O1 model, we embark on a transparent, real-time exploration to replicate its capabilities while reimagining the process of conducting and communicating AI research. Our methodology addresses critical challenges in modern AI research, including the insularity of prolonged team-based projects, delayed information sharing, and the lack of recognition for diverse contributions. By providing comprehensive, real-time documentation of our replication efforts, including both successes and failures, we aim to foster open science, accelerate collective advancement, and lay the groundwork for AI-driven scientific discovery. Our research progress report diverges significantly from traditional research papers, offering continuous updates, full process transparency, and active community engagement throughout the research journey. Technologically, we proposed the journey learning paradigm, which encourages models to learn not just shortcuts, but the complete exploration process, including trial and error, reflection, and backtracking. With only 327 training samples and without any additional tricks, journey learning outperformed conventional supervised learning by over 8\% on the MATH dataset, demonstrating its extremely powerful potential. We believe this to be the most crucial component of O1 technology that we have successfully decoded. We share valuable resources including technical hypotheses and insights, cognitive exploration maps, custom-developed tools, etc at https://github.com/GAIR-NLP/O1-Journey.

Retrieval-Augmented Generation (RAG) enhances language models by retrieving and incorporating relevant external knowledge. However, traditional retrieve-and-generate processes may not be optimized for real-world scenarios, where queries might require multiple retrieval steps or none at all. In this paper, we propose a Probing-RAG, which utilizes the hidden state representations from the intermediate layers of language models to adaptively determine the necessity of additional retrievals for a given query. By employing a pre-trained prober, Probing-RAG effectively captures the model's internal cognition, enabling reliable decision-making about retrieving external documents. Experimental results across five open-domain QA datasets demonstrate that Probing-RAG outperforms previous methods while reducing the number of redundant retrieval steps.

Conventional Retrieval-Augmented Generation (RAG) systems enhance Large Language Models (LLMs) but often fall short on complex queries, delivering limited, extractive answers and struggling with multiple targeted retrievals or navigating intricate entity relationships. This is a critical gap in knowledge-intensive domains. We introduce INRAExplorer, an agentic RAG system for exploring the scientific data of INRAE (France's National Research Institute for Agriculture, Food and Environment). INRAExplorer employs an LLM-based agent with a multi-tool architecture to dynamically engage a rich knowledge base, through a comprehensive knowledge graph derived from open access INRAE publications. This design empowers INRAExplorer to conduct iterative, targeted queries, retrieve exhaustive datasets (e.g., all publications by an author), perform multi-hop reasoning, and deliver structured, comprehensive answers. INRAExplorer serves as a concrete illustration of enhancing knowledge interaction in specialized fields.

There has been a surge of interest in harnessing the reasoning capabilities of Large Language Models (LLMs) to accelerate scientific discovery. While existing approaches rely on grounding the discovery process within the relevant literature, effectiveness varies significantly with the quality and nature of the retrieved literature. We address the challenge of retrieving prior work whose concepts can inspire solutions for a given research problem, a task we define as Methodology Inspiration Retrieval (MIR). We construct a novel dataset tailored for training and evaluating retrievers on MIR, and establish baselines. To address MIR, we build the Methodology Adjacency Graph (MAG); capturing methodological lineage through citation relationships. We leverage MAG to embed an "intuitive prior" into dense retrievers for identifying patterns of methodological inspiration beyond superficial semantic similarity. This achieves significant gains of +5.4 in Recall@3 and +7.8 in Mean Average Precision (mAP) over strong baselines. Further, we adapt LLM-based re-ranking strategies to MIR, yielding additional improvements of +4.5 in Recall@3 and +4.8 in mAP. Through extensive ablation studies and qualitative analyses, we exhibit the promise of MIR in enhancing automated scientific discovery and outline avenues for advancing inspiration-driven retrieval.

Reinforcement learning with verifiable rewards (RLVR) is a powerful paradigm for enhancing the reasoning capabilities of large language models (LLMs), yet its success hinges on effective exploration. An ideal exploration strategy must navigate two fundamental challenges: it must preserve sample quality while also ensuring training stability. While standard fixed-temperature sampling is simple, it struggles to balance these competing demands, as high temperatures degrade sample quality and low temperatures limit discovery. In this work, we propose a simpler and more effective strategy, Exploratory Annealed Decoding (EAD), grounded in the insight that exploration is most impactful on early tokens which define a sequence's semantic direction. EAD implements an intuitive **explore-at-the-beginning, exploit-at-the-end** strategy by annealing the sampling temperature from high to low during generation. This dynamic schedule encourages meaningful, high-level diversity at the start, then gradually lowers the temperature to preserve sample quality and keep the sampling distribution close to the target policy, which is essential for stable training. We demonstrate that EAD is a lightweight, plug-and-play method that significantly improves sample efficiency, consistently outperforming fixed-temperature sampling across various RLVR algorithms and model sizes. Our work suggests that aligning exploration with the natural dynamics of sequential generation offers a robust path to improving LLM reasoning.

With the increasing numbers of publicly available models, there are probably pretrained, online models for most tasks users require. However, current model search methods are rudimentary, essentially a text-based search in the documentation, thus users cannot find the relevant models. This paper presents ProbeLog, a method for retrieving classification models that can recognize a target concept, such as "Dog", without access to model metadata or training data. Differently from previous probing methods, ProbeLog computes a descriptor for each output dimension (logit) of each model, by observing its responses on a fixed set of inputs (probes). Our method supports both logit-based retrieval ("find more logits like this") and zero-shot, text-based retrieval ("find all logits corresponding to dogs"). As probing-based representations require multiple costly feedforward passes through the model, we develop a method, based on collaborative filtering, that reduces the cost of encoding repositories by 3x. We demonstrate that ProbeLog achieves high retrieval accuracy, both in real-world and fine-grained search tasks and is scalable to full-size repositories.

Deep Research agents driven by LLMs have automated the scholarly discovery pipeline, from planning and query formulation to iterative web exploration. Yet they remain constrained by a static, ``one-size-fits-all'' retrieval paradigm. Current systems fail to adaptively adjust the depth and breadth of exploration based on the user's existing expertise or latent interests, frequently resulting in reports that are either redundant for experts or overly dense for novices. To address this, we introduce Personalized Deep Research (PDR), a framework that integrates dynamic user context into the core retrieval-reasoning loop. Rather than treating personalization as a post-hoc formatting step, PDR unifies user profile modeling with iterative query development, dual-stage (private/public) retrieval, and context-aware synthesis. This allows the system to autonomously align research sub-goals with user intent and optimize the stopping criteria for evidence collection. To facilitate benchmarking, we release the PDR Dataset, covering four realistic user tasks, and propose a hybrid evaluation framework combining lexical metrics with LLM-based judgments to assess factual accuracy and personalization alignment. Experimental results against commercial baselines demonstrate that PDR significantly improves retrieval utility and report relevance, effectively bridging the gap between generic information retrieval and personalized knowledge acquisition. The resource is available to the public at https://github.com/Applied-Machine-Learning-Lab/SIGIR2026_PDR.

Despite the huge success of Large Language Models (LLMs) in coding assistants like GitHub Copilot, these models struggle to understand the context present in the repository (e.g., imports, parent classes, files with similar names, etc.), thereby producing inaccurate code completions. This effect is more pronounced when using these assistants for repositories that the model has not seen during training, such as proprietary software or work-in-progress code projects. Recent work has shown the promise of using context from the repository during inference. In this work, we extend this idea and propose RepoFusion, a framework to train models to incorporate relevant repository context. Experiments on single-line code completion show that our models trained with repository context significantly outperform much larger code models as CodeGen-16B-multi (sim73times larger) and closely match the performance of the sim 70times larger StarCoderBase model that was trained with the Fill-in-the-Middle objective. We find these results to be a novel and compelling demonstration of the gains that training with repository context can bring. We carry out extensive ablation studies to investigate the impact of design choices such as context type, number of contexts, context length, and initialization within our framework. Lastly, we release Stack-Repo, a dataset of 200 Java repositories with permissive licenses and near-deduplicated files that are augmented with three types of repository contexts. Additionally, we are making available the code and trained checkpoints for our work. Our released resources can be found at https://huggingface.co/RepoFusion.

Locating the files and functions requiring modification in large open-source software (OSS) repositories is challenging due to their scale and structural complexity. Existing large language model (LLM)-based methods typically treat this as a repository-level retrieval task and rely on multiple auxiliary tools, which overlook code execution logic and complicate model control. We propose RepoNavigator, an LLM agent equipped with a single execution-aware tool-jumping to the definition of an invoked symbol. This unified design reflects the actual flow of code execution while simplifying tool manipulation. RepoNavigator is trained end-to-end via Reinforcement Learning (RL) directly from a pretrained model, without any closed-source distillation. Experiments demonstrate that RL-trained RepoNavigator achieves state-of-the-art performance, with the 7B model outperforming 14B baselines, the 14B model surpassing 32B competitors, and even the 32B model exceeding closed-source models such as Claude-3.7. These results confirm that integrating a single, structurally grounded tool with RL training provides an efficient and scalable solution for repository-level issue localization.

Reinforcement Learning from Verifiable Rewards (RLVR) improves the reasoning abilities of Large Language Models (LLMs) but it struggles with unstable exploration. We propose FR3E (First Return, Entropy-Eliciting Explore), a structured exploration framework that identifies high-uncertainty decision points in reasoning trajectories and performs targeted rollouts to construct semantically grounded intermediate feedback. Our method provides targeted guidance without relying on dense supervision. Empirical results on mathematical reasoning benchmarks(AIME24) show that FR3E promotes more stable training, produces longer and more coherent responses, and increases the proportion of fully correct trajectories. These results highlight the framework's effectiveness in improving LLM reasoning through more robust and structured exploration.

We introduce Trove, an easy-to-use open-source retrieval toolkit that simplifies research experiments without sacrificing flexibility or speed. For the first time, we introduce efficient data management features that load and process (filter, select, transform, and combine) retrieval datasets on the fly, with just a few lines of code. This gives users the flexibility to easily experiment with different dataset configurations without the need to compute and store multiple copies of large datasets. Trove is highly customizable: in addition to many built-in options, it allows users to freely modify existing components or replace them entirely with user-defined objects. It also provides a low-code and unified pipeline for evaluation and hard negative mining, which supports multi-node execution without any code changes. Trove's data management features reduce memory consumption by a factor of 2.6. Moreover, Trove's easy-to-use inference pipeline incurs no overhead, and inference times decrease linearly with the number of available nodes. Most importantly, we demonstrate how Trove simplifies retrieval experiments and allows for arbitrary customizations, thus facilitating exploratory research.

Language Model (LM) agents are increasingly used in complex open-ended decision-making tasks, from AI coding to physical AI. A core requirement in these settings is the ability to both explore the problem space and exploit acquired knowledge effectively. However, systematically distinguishing and quantifying exploration and exploitation from observed actions without access to the agent's internal policy remains challenging. To address this, we design controllable environments inspired by practical embodied AI scenarios. Each environment consists of a partially observable 2D grid map and an unknown task Directed Acyclic Graph (DAG). The map generation can be programmatically adjusted to emphasize exploration or exploitation difficulty. To enable policy-agnostic evaluation, we design a metric to quantify exploration and exploitation errors from agent's actions. We evaluate a variety of frontier LM agents and find that even state-of-the-art models struggle on our task, with different models exhibiting distinct failure modes. We further observe that reasoning models solve the task more effectively and show both exploration and exploitation can be significantly improved through minimal harness engineering. We release our code https://github.com/jjj-madison/measurable-explore-exploit{here}.

Large language models excel at function- and file-level code generation, yet generating complete repositories from scratch remains a fundamental challenge. This process demands coherent and reliable planning across proposal- and implementation-level stages, while natural language, due to its ambiguity and verbosity, is ill-suited for faithfully representing complex software structures. To address this, we introduce the Repository Planning Graph (RPG), a persistent representation that unifies proposal- and implementation-level planning by encoding capabilities, file structures, data flows, and functions in one graph. RPG replaces ambiguous natural language with an explicit blueprint, enabling long-horizon planning and scalable repository generation. Building on RPG, we develop ZeroRepo, a graph-driven framework for repository generation from scratch. It operates in three stages: proposal-level planning and implementation-level refinement to construct the graph, followed by graph-guided code generation with test validation. To evaluate this setting, we construct RepoCraft, a benchmark of six real-world projects with 1,052 tasks. On RepoCraft, ZeroRepo produces repositories averaging nearly 36K LOC, roughly 3.9times the strongest baseline (Claude Code) and about 64times other baselines. It attains 81.5% functional coverage and a 69.7% pass rate, exceeding Claude Code by 27.3 and 35.8 percentage points, respectively. Further analysis shows that RPG models complex dependencies, enables progressively more sophisticated planning through near-linear scaling, and enhances LLM understanding of repositories, thereby accelerating agent localization.

Repository summarization is a crucial research question in development and maintenance for software engineering. Existing repository summarization techniques primarily focus on summarizing code according to the directory tree, which is insufficient for tracing high-level features to the methods that collaboratively implement them. To address these limitations, we propose RepoSummary, a feature-oriented code repository summarization approach that simultaneously generates repository documentation automatically. Furthermore, it establishes more accurate traceability links from functional features to the corresponding code elements, enabling developers to rapidly locate relevant methods and files during code comprehension and maintenance. Comprehensive experiments against the state-of-the-art baseline (HGEN) demonstrate that RepoSummary achieves higher feature coverage and more accurate traceability. On average, it increases the rate of completely covered features in manual documentation from 61.2% to 71.1%, improves file-level traceability recall from 29.9% to 53.0%, and generates documentation that is more conceptually consistent, easier to understand, and better formatted than that produced by existing approaches.

The Archives Unleashed project aims to improve scholarly access to web archives through a multi-pronged strategy involving tool creation, process modeling, and community building - all proceeding concurrently in mutually-reinforcing efforts. As we near the end of our initially-conceived three-year project, we report on our progress and share lessons learned along the way. The main contribution articulated in this paper is a process model that decomposes scholarly inquiries into four main activities: filter, extract, aggregate, and visualize. Based on the insight that these activities can be disaggregated across time, space, and tools, it is possible to generate "derivative products", using our Archives Unleashed Toolkit, that serve as useful starting points for scholarly inquiry. Scholars can download these products from the Archives Unleashed Cloud and manipulate them just like any other dataset, thus providing access to web archives without requiring any specialized knowledge. Over the past few years, our platform has processed over a thousand different collections from about two hundred users, totaling over 280 terabytes of web archives.

A prerequisite for coding agents to perform tasks on large repositories is code localization - the identification of relevant files, classes, and functions to work on. While repository-level code localization has been performed using embedding-based retrieval approaches such as vector search, recent work has focused on developing agents to localize relevant code either as a standalone precursor to or interleaved with performing actual work. Most prior methods on agentic code search equip the agent with complex, specialized tools, such as repository graphs derived from static analysis. In this paper, we demonstrate that, with an effective reinforcement learning recipe, a coding agent equipped with nothing more than a standard Unix terminal can be trained to achieve strong results. Our experiments on three benchmarks (SWE-Bench Verified, Pro, and Lite) reveal that our models consistently achieve superior or competitive performance over 2-18x larger base and post-trained LLMs and sometimes approach performance provided by closed models like Claude Sonnet, even when using specialized scaffolds. Our work particularly focuses on techniques for re-purposing existing coding agent environments for code search, reward design, and RL optimization. We release the resulting model family, CodeScout, along with all our code and data for the community to build upon.

We are at the cusp of a transition from "learning from data" to "learning what data to learn from" as a central focus of artificial intelligence (AI) research. While the first-order learning problem is not completely solved, large models under unified architectures, such as transformers, have shifted the learning bottleneck from how to effectively train our models to how to effectively acquire and use task-relevant data. This problem, which we frame as exploration, is a universal aspect of learning in open-ended domains, such as the real world. Although the study of exploration in AI is largely limited to the field of reinforcement learning, we argue that exploration is essential to all learning systems, including supervised learning. We propose the problem of generalized exploration to conceptually unify exploration-driven learning between supervised learning and reinforcement learning, allowing us to highlight key similarities across learning settings and open research challenges. Importantly, generalized exploration serves as a necessary objective for maintaining open-ended learning processes, which in continually learning to discover and solve new problems, provides a promising path to more general intelligence.

Repository-level bug localization-the task of identifying where code must be modified to fix a bug-is a critical software engineering challenge. Standard Large Language Modles (LLMs) are often unsuitable for this task due to context window limitations that prevent them from processing entire code repositories. As a result, various retrieval methods are commonly used, including keyword matching, text similarity, and simple graph-based heuristics such as Breadth-First Search. Graph Neural Networks (GNNs) offer a promising alternative due to their ability to model complex, repository-wide dependencies; however, their application has been hindered by the lack of a dedicated benchmark. To address this gap, we introduce GREPO, the first GNN benchmark for repository-scale bug localization tasks. GREPO comprises 86 Python repositories and 47294 bug-fixing tasks, providing graph-based data structures ready for direct GNN processing. Our evaluation of various GNN architectures shows outstanding performance compared to established information retrieval baselines. This work highlights the potential of GNNs for bug localization and established GREPO as a foundation resource for future research, The code is available at https://github.com/qingpingmo/GREPO.

Repository-level code generation has attracted growing attention in recent years. Unlike function-level code generation, it requires the model to understand the entire repository, reasoning over complex dependencies across functions, classes, and modules. However, existing approaches such as retrieval-augmented generation (RAG) or context-based function selection often fall short: they primarily rely on surface-level similarity and struggle to capture the rich dependencies that govern repository-level semantics. In this paper, we introduce InlineCoder, a novel framework for repository-level code generation. InlineCoder enhances the understanding of repository context by inlining the unfinished function into its call graph, thereby reframing the challenging repository understanding as an easier function-level coding task. Given a function signature, InlineCoder first generates a draft completion, termed an anchor, which approximates downstream dependencies and enables perplexity-based confidence estimation. This anchor drives a bidirectional inlining process: (i) Upstream Inlining, which embeds the anchor into its callers to capture diverse usage scenarios; and (ii) Downstream Retrieval, which integrates the anchor's callees into the prompt to provide precise dependency context. The enriched context, combining draft completion with upstream and downstream perspectives, equips the LLM with a comprehensive repository view.

Scientific discovery is a cumulative process and requires new ideas to be situated within an ever-expanding landscape of existing knowledge. An emerging and critical challenge is how to identify conceptually relevant prior work from rapidly growing literature, and assess how a new idea differentiates from existing research. Current embedding approaches typically conflate distinct conceptual aspects into single representations and cannot support fine-grained literature retrieval; meanwhile, LLM-based evaluators are subject to sycophancy biases, failing to provide discriminative novelty assessment. To tackle these challenges, we introduce the Ideation Space, a structured representation that decomposes scientific knowledge into three distinct dimensions, i.e., research problem, methodology, and core findings, each learned through contrastive training. This framework enables principled measurement of conceptual distance between ideas, and modeling of ideation transitions that capture the logical connections within a proposed idea. Building upon this representation, we propose a Hierarchical Sub-Space Retrieval framework for efficient, targeted literature retrieval, and a Decomposed Novelty Assessment algorithm that identifies which aspects of an idea are novel. Extensive experiments demonstrate substantial improvements, where our approach achieves Recall@30 of 0.329 (16.7% over baselines), our ideation transition retrieval reaches Hit Rate@30 of 0.643, and novelty assessment attains 0.37 correlation with expert judgments. In summary, our work provides a promising paradigm for future research on accelerating and evaluating scientific discovery.

In open-ended environments, exploration is fundamental for autonomous agents, yet current language model agents struggle with this. Effective exploration requires memory, but retaining raw interaction histories is computationally expensive over long trajectories. While latent memory offers a solution to compress interaction histories, its training lacks reliable supervisory signals. We introduce Joint Agent Memory and Exploration Learning (JAMEL), a framework that trains agentic memory and exploration policy together through novelty-driven interaction. We observe that memory and exploration form a mutually dependent loop: sustained exploration requires memory to distinguish exhausted behaviors from unseen ones, while novelty-seeking interaction provides the supervision needed to make memory useful for future exploration. By utilizing deterministic and persistent novelty signals such as code coverage in the GUI domain, we provide natural, annotation-free supervision for the memory module. Empirical evaluations demonstrate that \ours successfully generalizes to unseen environments. Its exploration capability outperforms open-weight baselines and rivals the exploration depth of a closed-source model while reducing token consumption. Our code and model are open-sourced at https://github.com/MobileLLM/JAMEL.

Currently, there is limited research investigating the phenomenon of research data repositories being shut down, and the impact this has on the long-term availability of data. This paper takes an infrastructure perspective on the preservation of research data by using a registry to identify 191 research data repositories that have been closed and presenting information on the shutdown process. The results show that 6.2 % of research data repositories indexed in the registry were shut down. The risks resulting in repository shutdown are varied. The median age of a repository when shutting down is 12 years. Strategies to prevent data loss at the infrastructure level are pursued to varying extent. 44 % of the repositories in the sample migrated data to another repository, and 12 % maintain limited access to their data collection. However, both strategies are not permanent solutions. Finally, the general lack of information on repository shutdown events as well as the effect on the findability of data and the permanence of the scholarly record are discussed.

Repository-level code review requires reasoning over project structure, repository context, and file-level implementation details. Existing automated review workflows often collapse these tasks into a single pass, which can reduce relevance, increase duplication, and weaken prioritization. We present RepoReviewer, a local-first multi-agent system for automated GitHub repository review with a Python CLI, FastAPI API, LangGraph orchestration layer, and Next.js user interface. RepoReviewer decomposes review into repository acquisition, context synthesis, file-level analysis, finding prioritization, and summary generation. We describe the system design, implementation tradeoffs, developer-facing interfaces, and practical failure modes. Rather than claiming benchmark superiority, we frame RepoReviewer as a technical systems contribution: a pragmatic architecture for repository-level automated review, accompanied by reusable evaluation and reporting infrastructure for future empirical study.

LLM-powered search agents are increasingly being used for multi-step information seeking tasks, yet the IR community lacks empirical understanding of how agentic search sessions unfold and how retrieved evidence is used. This paper presents a large-scale log analysis of agentic search based on 14.44M search requests (3.97M sessions) collected from DeepResearchGym, i.e. an open-source search API accessed by external agentic clients. We sessionize the logs, assign session-level intents and step-wise query-reformulation labels using LLM-based annotation, and propose Context-driven Term Adoption Rate (CTAR) to quantify whether newly introduced query terms are traceable to previously retrieved evidence. Our analyses reveal distinctive behavioral patterns. First, over 90% of multi-turn sessions contain at most ten steps, and 89% of inter-step intervals fall under one minute. Second, behavior varies by intent. Fact-seeking sessions exhibit high repetition that increases over time, while sessions requiring reasoning sustain broader exploration. Third, agents reuse evidence across steps. On average, 54% of newly introduced query terms appear in the accumulated evidence context, with contributions from earlier steps beyond the most recent retrieval. The findings suggest that agentic search may benefit from repetition-aware early stopping, intent-adaptive retrieval budgets, and explicit cross-step context tracking. We plan to release the anonymized logs to support future research.

Scientific discovery is not only answer generation but revision of the representational regime in which evidence, artifacts, operations, and verifiers are typed. We develop a category-theoretic account of agentic discovery for materials science. In a fixed regime b with schema category S_b, the system state is a copresheaf I_t: S_b -> Set, and provenance is the category of elements \int_{S_b} I_t. Fixed-regime operation is an update on such states, endofunctorial only when provenance-preserving refinements are specified and preserved. Discovery is instead a verified regime transition u: S_b -> S_b': old artifacts are preserved, transported by the left Kan extension Lan_u I_t, and compared with the post-transition state to identify residual content beyond functorial transport. This separates retrieval, search, and discovery without subjective novelty. We instantiate the framework in two systems. In Builder/Breaker, a protein-mechanics world model is revised under a Minimum Description Length gate; the accepted law expresses within-chain flexibility as all-mode elastic compliance conditioned by slow collective-mode participation, or mode-conditioned compliance. In CategoryScienceClaw, typed skills, artifacts, open needs, workflow mutation, gates, stress tests, and public discourse become a proof-carrying knowledge-computation graph. A fiber-network example records candidate models, rejected alternatives, an AIC gate, perturbation tests, and an accepted orientation-tensor anisotropic stiffness surrogate over an isotropic fiber-count descriptor. Together, the cases show how category theory can be both a mathematical language for discovery and an engineering specification for self-revising AI discovery systems.

Public funding plays a central role in driving scientific discovery. To better understand the link between research inputs and outputs, we introduce FIND (Funding-Impact NSF Database), an open-access dataset that systematically links NSF grant proposals to their downstream research outputs, including publication metadata and abstracts. The primary contribution of this project is the creation of a large-scale, structured dataset that enables transparency, impact evaluation, and metascience research on the returns to public funding. To illustrate the potential of FIND, we present two proof-of-concept NLP applications. First, we analyze whether the language of grant proposals can predict the subsequent citation impact of funded research. Second, we leverage large language models to extract scientific claims from both proposals and resulting publications, allowing us to measure the extent to which funded projects deliver on their stated goals. Together, these applications highlight the utility of FIND for advancing metascience, informing funding policy, and enabling novel AI-driven analyses of the scientific process.

Exploration is a prerequisite for learning useful behaviors in sparse-reward, long-horizon tasks, particularly within 3D environments. Curiosity-driven reinforcement learning addresses this via intrinsic rewards derived from the mismatch between the agent's predictive model of the world and reality. However, translating this intrinsic motivation to complex, photorealistic environments remains difficult, as agents can become trapped in local loops and receive fresh rewards for revisiting forgotten states. In this work, we demonstrate that this failure stems from a lack of spatial persistence and episodic context. We show that effective curiosity requires a model of the world that is persistent and continuously updated, paired with an agent that maintains an episodic trajectory history to navigate toward novel regions. We achieve this using an online 3D reconstruction as a persistent model of the world, while the agent policy is parameterized as a sequence model over RGB observations to maintain episodic context. This design enables effective exploration during training while allowing the agent to navigate using solely RGB frames at deployment. Trained purely via curiosity on HM3D, our agent outperforms RL-based active mapping baselines and generalizes zero-shot to Gibson and AI-generated worlds. Our end-to-end policy enables efficient adaptation to downstream tasks, such as apple picking and image-goal navigation, outperforming from-scratch baselines. Please see video results at https://recuriosity.github.io/.

Achieving effective test-time scaling requires models to engage in In-Context Exploration -- the intrinsic ability to generate, verify, and refine multiple reasoning hypotheses within a single continuous context. Grounded in State Coverage theory, our analysis identifies a critical bottleneck to enabling this capability: while broader state coverage requires longer reasoning trajectories, the probability of sampling such sequences decays exponentially during autoregressive generation, a phenomenon we term the ``Shallow Exploration Trap''. To bridge this gap, we propose Length-Incentivized Exploration(\method). This simple yet effective recipe explicitly encourages models to explore more via a length-based reward coupled with a redundancy penalty, thereby maximizing state coverage in two-step manner. Comprehensive experiments across different models (Qwen3, Llama) demonstrate that \method effectively incentivize in-context exploration. As a result, our method achieves an average improvement of 4.4\% on in-domain tasks and a 2.7\% gain on out-of-domain benchmarks.

Issue localization, the process of identifying code locations that need modification to resolve software issues, is a critical yet challenging task in software development. The semantic gap between natural language issue descriptions and faulty code requires complex multi-hop reasoning through code dependencies. Existing LLM-based agents attempt to address this by integrating repository retrieval tools. However, this transforms issue localization into a demanding task we call Repo Deep Search, which requires the LLM to effectively utilize various repository retrieval tools throughout a multi-step reasoning and navigation process. To tackle this challenge, we present ToolTrain, a two-stage tool-integrated training framework combining rejection-sampled supervised fine-tuning and tool-integrated reinforcement learning to enhance LLMs' ability to use retrieval tools for issue localization. Experimental results show that ToolTrain-trained models achieve state-of-the-art performance, with our 32B model even surpassing Claude-3.7 on function-level localization. The results also show that improved localization performance translates to better end-to-end issue resolution performance. This further demonstrates that training for issue localization is a viable and effective strategy for improving automated software development.

Evaluating novelty is critical yet challenging in peer review, as reviewers must assess submissions against a vast, rapidly evolving literature. This report presents OpenNovelty, an LLM-powered agentic system for transparent, evidence-based novelty analysis. The system operates through four phases: (1) extracting the core task and contribution claims to generate retrieval queries; (2) retrieving relevant prior work based on extracted queries via semantic search engine; (3) constructing a hierarchical taxonomy of core-task-related work and performing contribution-level full-text comparisons against each contribution; and (4) synthesizing all analyses into a structured novelty report with explicit citations and evidence snippets. Unlike naive LLM-based approaches, OpenNovelty grounds all assessments in retrieved real papers, ensuring verifiable judgments. We deploy our system on 500+ ICLR 2026 submissions with all reports publicly available on our website, and preliminary analysis suggests it can identify relevant prior work, including closely related papers that authors may overlook. OpenNovelty aims to empower the research community with a scalable tool that promotes fair, consistent, and evidence-backed peer review.

Reinforcement learning (RL) promises to expand the capabilities of language models, but it is unclear if current RL techniques promote the discovery of novel behaviors, or simply sharpen those already present in the base model. In this paper, we investigate the value of deliberate exploration -- explicitly incentivizing the model to discover novel and diverse behaviors -- and aim to understand how the knowledge in pre-trained models can guide this search. Our main finding is that exploration with a simple, principled, representation-based bonus derived from the pre-trained language model's hidden states significantly improves diversity and pass@k rates -- both for post-training, and in a novel inference-time scaling setting we introduce. For inference-time, exploration with representation-based diversity improves efficiency, consistently improving pass@k rates across a variety of models and reasoning tasks. For example, for Qwen-2.5-14b-Instruct we obtain over 50% improvement in verifier efficiency on almost all tasks. For post-training, we show that integrating this exploration strategy into an RL pipeline improves reasoning performance over that of the initial model and over standard RL post-training. For example, on AIME 2024, our post-trained Qwen-2.5-7b-Instruct's pass@80 matches the pass@256 of GRPO on the same model, demonstrating a 3x improvement in test-time sample efficiency. Overall, our findings suggest that deliberate exploration -- with the right notion of diversity -- is a practical path toward discovery of new behaviors beyond sharpening.

Scientific discovery is an inherently creative and uncertain process, requiring reasoning beyond the recall of known knowledge. While many benchmarks have been proposed to evaluate large language model (LLM) performance on deep research tasks via multi-hop retrieval, their innovative reasoning abilities essential for true scientific discovery remain largely untested. We introduce a benchmark framework for evaluating model performance in scientific discovery and reasoning, building up from a raw problem to the classical null hypothesis test. In our framework, models initially receive only the topic and research question from a recent paper, with technical details progressively revealed. At each stage of information disclosure, the model is tasked with generating hypotheses that address the research question, which is compared with the conclusions from the original paper and evaluated via automated semantic similarity of constituent atomic claims. This progressive evaluation of semantic divergence from ground-truth conclusions enables assessment of a model's innovativeness (under minimal information) to grounded reasoning capabilities (under full experimental details), both critical for using LLMs for scientific discovery purposes. Our framework provides a foundation for systematically evaluating scientific reasoning and discovery capabilities in LLMs, crucial for advancing the development of next-generation AI scientist/co-scientist systems. Specifically, here we evaluate GPT-5, GPT-5.4, Gemini 2.5 pro, and Gemini 3.1 pro preview across 45 papers spanning bioactive materials, mechanical materials, and nanomaterials. We find that GPT-5.4 and Gemini 3.1 pro outperform their previous generation counterparts as expected, and GPT-5.4 in particular maintains 0.7 F1 score alignment with ground truth conclusions even under minimal context.

In this paper, we present a novel approach to knowledge extraction and retrieval using Natural Language Processing (NLP) techniques for material science. Our goal is to automatically mine structured knowledge from millions of research articles in the field of polycrystalline materials and make it easily accessible to the broader community. The proposed method leverages NLP techniques such as entity recognition and document classification to extract relevant information and build an extensive knowledge base, from a collection of 9.5 Million publications. The resulting knowledge base is integrated into a search engine, which enables users to search for information about specific materials, properties, and experiments with greater precision than traditional search engines like Google. We hope our results can enable material scientists quickly locate desired experimental procedures, compare their differences, and even inspire them to design new experiments. Our website will be available at Github https://github.com/Xianjun-Yang/PcMSP.git soon.

Coding agents powered by large language models have demonstrated strong performance on software engineering tasks. Yet most agents consume repositories almost entirely as text, which differs from how human developers use visual structure such as folder hierarchies and dependency relationships to orient themselves in large codebases. With multimodal large language models (MLLMs), it is an open question whether agents can effectively benefit from visual representations of repositories. This paper presents the first systematic empirical study of visual repository representations for LLM-based agents on repository-level issue resolution. We evaluate four recent multimodal models. Our results show that a strictly vision-only setup degrades accuracy and increases token cost, because agents lack sufficient symbolic detail and compensate with repeated visual queries. In contrast, integrating visual graphs of repository structure as a supplementary modality alongside standard text interfaces helps agents understand structure more efficiently: input token consumption decreases by up to 26% while issue-resolution accuracy is maintained or improved. Visualization is most useful during fault localization and when the agent autonomously controls exploration depth. These findings point to a practical hybrid text-and-vision design for next-generation coding agents.

As the capabilities of LLM-based code agents continue to advance, their expected role is expanding beyond localized bug fixing in existing codebases toward architecting and implementing complete software repositories from high-level specifications. However, training agents for such long-horizon software engineering tasks remains difficult due to the scarcity of large-scale, verifiable whole-repository generation data. In this paper, we introduce DeNovoSWE, a large-scale dataset for whole-repository generation. DeNovoSWE comprises 4,818 high-quality instances, where each instance requires generating a complete repository from documentation. Our dataset is automatically constructed through a carefully designed sandboxed agentic workflow, enabling scalable curation without human annotation. DeNovoSWE is constructed with "divide and conquer" and critic-repair philosophy. To balance data quality and diversity, we further introduce a difficulty-aware trajectory filtering strategy. Fine-tuning Qwen3-30B-A3B on DeNovoSWE substantially improves long-horizon SWE performance, raising its score on the challenging BeyondSWE-Doc2Repo benchmark from 5.8% to 47.2%.

Large language models (LLMs) exhibit remarkable problem-solving abilities, but struggle with complex tasks due to static internal knowledge. Retrieval-Augmented Generation (RAG) enhances access to external information, yet remains limited in multi-hop reasoning and strategic search due to rigid workflows. Recent advancements in agentic deep research empower LLMs to autonomously reason, search, and synthesize information. However, current approaches relying on outcome-based reinforcement learning (RL) face critical issues such as conflicting gradients and reward sparsity, limiting performance gains and training efficiency. To address these, we first propose Atomic Thought, a novel LLM thinking paradigm that decomposes reasoning into fine-grained functional units. These units are supervised by Reasoning Reward Models (RRMs), which provide Atomic Thought Rewards (ATR) for fine-grained guidance. Building on this, we propose Atom-Searcher, a novel RL framework for agentic deep research that integrates Atomic Thought and ATR. Atom-Searcher uses a curriculum-inspired reward schedule, prioritizing process-level ATR early and transitioning to outcome rewards, accelerating convergence on effective reasoning paths. Experiments on seven benchmarks show consistent improvements over the state-of-the-art. Key advantages include: (1) Atom-Searcher scales computation at test-time. (2) Atomic Thought provides supervision anchors for RRMs, bridging deep research tasks and RRMs. (3) Atom-Searcher exhibits more interpretable, human-like reasoning patterns.

Retrieval-augmented generation (RAG) has recently demonstrated considerable potential for repository-level code completion, as it integrates cross-file knowledge with in-file preceding code to provide comprehensive contexts for generation. To better understand the contribution of the retrieved cross-file contexts, we introduce a likelihood-based metric to evaluate the impact of each retrieved code chunk on the completion. Our analysis reveals that, despite retrieving numerous chunks, only a small subset positively contributes to the completion, while some chunks even degrade performance. To address this issue, we leverage this metric to construct a repository-level dataset where each retrieved chunk is labeled as positive, neutral, or negative based on its relevance to the target completion. We then propose an adaptive retrieval context filtering framework, CODEFILTER, trained on this dataset to mitigate the harmful effects of negative retrieved contexts in code completion. Extensive evaluation on the RepoEval and CrossCodeLongEval benchmarks demonstrates that CODEFILTER consistently improves completion accuracy compared to approaches without filtering operations across various tasks. Additionally, CODEFILTER significantly reduces the length of the input prompt, enhancing computational efficiency while exhibiting strong generalizability across different models. These results underscore the potential of CODEFILTER to enhance the accuracy, efficiency, and attributability of repository-level code completion.

This paper introduces a centralized, open-source dataset repository designed to advance NLP and NMT for Assamese, a low-resource language. The repository, available at GitHub, supports various tasks like sentiment analysis, named entity recognition, and machine translation by providing both pre-training and fine-tuning corpora. We review existing datasets, highlighting the need for standardized resources in Assamese NLP, and discuss potential applications in AI-driven research, such as LLMs, OCR, and chatbots. While promising, challenges like data scarcity and linguistic diversity remain. The repository aims to foster collaboration and innovation, promoting Assamese language research in the digital age.

Large language models have made significant progress in complex but easy-to-verify problems, yet they still struggle with discovering the unknown. In this paper, we present AlphaResearch, an autonomous research agent designed to discover new algorithms on open-ended problems. To synergize the feasibility and innovation of the discovery process, we construct a novel dual research environment by combining the execution-based verify and simulated real-world peer review environment. AlphaResearch discovers new algorithm by iteratively running the following steps: (1) propose new ideas (2) verify the ideas in the dual research environment (3) optimize the research proposals for better performance. To promote a transparent evaluation process, we construct AlphaResearchComp, a new evaluation benchmark that includes an eight open-ended algorithmic problems competition, with each problem carefully curated and verified through executable pipelines, objective metrics, and reproducibility checks. AlphaResearch gets a 2/8 win rate in head-to-head comparison with human researchers, demonstrate the possibility of accelerating algorithm discovery with LLMs. Notably, the algorithm discovered by AlphaResearch on the ``packing circles'' problem achieves the best-of-known performance, surpassing the results of human researchers and strong baselines from recent work (e.g., AlphaEvolve). Additionally, we conduct a comprehensive analysis of the remaining challenges of the 6/8 failure cases, providing valuable insights for future research.

Code completion models have made significant progress in recent years. Recently, repository-level code completion has drawn more attention in modern software development, and several baseline methods and benchmarks have been proposed. However, existing repository-level code completion methods often fall short of fully using the extensive context of a project repository, such as the intricacies of relevant files and class hierarchies. Besides, the existing benchmarks usually focus on limited code completion scenarios, which cannot reflect the repository-level code completion abilities well of existing methods. To address these limitations, we propose the R2C2-Coder to enhance and benchmark the real-world repository-level code completion abilities of code Large Language Models, where the R2C2-Coder includes a code prompt construction method R2C2-Enhance and a well-designed benchmark R2C2-Bench. Specifically, first, in R2C2-Enhance, we first construct the candidate retrieval pool and then assemble the completion prompt by retrieving from the retrieval pool for each completion cursor position. Second, based on R2C2 -Enhance, we can construct a more challenging and diverse R2C2-Bench with training, validation and test splits, where a context perturbation strategy is proposed to simulate the real-world repository-level code completion well. Extensive results on multiple benchmarks demonstrate the effectiveness of our R2C2-Coder.

Neural Information Retrieval (NIR) has significantly improved upon heuristic-based IR systems. Yet, failures remain frequent, the models used often being unable to retrieve documents relevant to the user's query. We address this challenge by proposing a lightweight abstention mechanism tailored for real-world constraints, with particular emphasis placed on the reranking phase. We introduce a protocol for evaluating abstention strategies in a black-box scenario, demonstrating their efficacy, and propose a simple yet effective data-driven mechanism. We provide open-source code for experiment replication and abstention implementation, fostering wider adoption and application in diverse contexts.

Advancements in Large Language Models (LLMs) drive interest in scientific applications, necessitating specialized benchmarks such as Earth science. Existing benchmarks either present a general science focus devoid of Earth science specificity or cover isolated subdomains, lacking holistic evaluation. Furthermore, current benchmarks typically neglect the assessment of LLMs' capabilities in open-ended scientific exploration. In this paper, we present a comprehensive and professional benchmark for the Earth sciences, designed to evaluate the capabilities of LLMs in scientific exploration within this domain, spanning from fundamental to advanced levels. Leveraging a corpus of 100,000 research papers, we first construct two Question Answering (QA) datasets: Earth-Iron, which offers extensive question coverage for broad assessment, and Earth-Silver, which features a higher level of difficulty to evaluate professional depth. These datasets encompass five Earth spheres, 114 disciplines, and 11 task categories, assessing foundational knowledge crucial for scientific exploration. Most notably, we introduce Earth-Gold with new metrics, a dataset comprising open-ended multi-turn dialogues specifically designed to evaluate the advanced capabilities of LLMs in scientific exploration, including methodology induction, limitation analysis, and concept proposal. Extensive experiments reveal limitations in 11 leading LLMs across different domains and tasks, highlighting considerable room for improvement in their scientific exploration capabilities. The benchmark is available on https://huggingface.co/ai-earth .

Chain-of-Thought (CoT) and its variants have markedly advanced the reasoning abilities of Large Language Models (LLMs), yet their monolithic and auto-regressive architecture inherently conflates high-level strategic planning with low-level step-by-step execution, leading to computational inefficiency, limited exploration of reasoning paths, and reduced interpretability. To overcome these issues, we propose the Explore-Execute Chain (E^2C), a structured reasoning framework that decouples reasoning into two distinct phases: an exploratory phase that stochastically generates succinct high-level plans, followed by an execution phase that deterministically carries out the chosen plan. Our approach incorporates a two-stage training methodology, which combines Supervised Fine-Tuning (SFT) - augmented by a novel data generation algorithm enforcing strict plan adherence - with a subsequent Reinforcement Learning (RL) stage that capitalizes on the informativeness of exploration and reinforces the determinism of execution. This decomposition enables an efficient test-time scaling strategy: on AIME'2024, E^2C Test Time Scaling reaches 58.1% accuracy using <10% of the decoding tokens required by comparable methods (e.g., Forest-of-Thought), sharply cutting self-consistency overhead. For cross-domain adaptation, our Exploration-Focused SFT (EF-SFT) fine-tunes with only 3.5% of the tokens used by standard SFT yet yields up to 14.5% higher accuracy than standard SFT on medical benchmarks, delivering state-of-the-art performance, strong generalization, and greater interpretability by separating planning from execution. The code and pre-trained models for the project are available at: https://github.com/yks23/Explore-Execute-Chain.git

Research Agents enable models to gather information from the web using tools to answer user queries, requiring them to dynamically interleave internal reasoning with tool use. While such capabilities can in principle be learned via reinforcement learning with verifiable rewards (RLVR), we observe that agents often exhibit poor exploration behaviors, including premature termination and biased tool usage. As a result, RLVR alone yields limited improvements. We propose SynPlanResearch-R1, a framework that synthesizes tool-use trajectories that encourage deeper exploration to shape exploration during cold-start supervised fine-tuning, providing a strong initialization for subsequent RL. Across seven multi-hop and open-web benchmarks, \framework improves performance by up to 6.0% on Qwen3-8B and 5.8% on Qwen3-4B backbones respectively compared to SOTA baselines. Further analyses of tool-use patterns and training dynamics compared to baselines shed light on the factors underlying these gains. Our code is publicly available at https://github.com/HansiZeng/syn-plan-research.

LLMs have demonstrated significant potential in code generation tasks, achieving promising results at the function or statement level across various benchmarks. However, the complexities associated with creating code artifacts like classes, particularly within the context of real-world software repositories, remain underexplored. Prior research treats class-level generation as an isolated task, neglecting the intricate dependencies & interactions that characterize real-world software environments. To address this gap, we introduce RepoClassBench, a comprehensive benchmark designed to rigorously evaluate LLMs in generating complex, class-level code within real-world repositories. RepoClassBench includes "Natural Language to Class generation" tasks across Java, Python & C# from a selection of repositories. We ensure that each class in our dataset not only has cross-file dependencies within the repository but also includes corresponding test cases to verify its functionality. We find that current models struggle with the realistic challenges posed by our benchmark, primarily due to their limited exposure to relevant repository contexts. To address this shortcoming, we introduce Retrieve-Repotools-Reflect (RRR), a novel approach that equips LLMs with static analysis tools to iteratively navigate & reason about repository-level context in an agent-based framework. Our experiments demonstrate that RRR significantly outperforms existing baselines on RepoClassBench, showcasing its effectiveness across programming languages & under various settings. Our findings emphasize the critical need for code-generation benchmarks to incorporate repo-level dependencies to more accurately reflect the complexities of software development. Our work shows the benefits of leveraging specialized tools to enhance LLMs' understanding of repository context. We plan to make our dataset & evaluation harness public.

Retrieval Augmented Generation (RAG) has proven to be highly effective in boosting the generative performance of language model in knowledge-intensive tasks. However, existing RAG framework either indiscriminately perform retrieval or rely on rigid single-class classifiers to select retrieval methods, leading to inefficiencies and suboptimal performance across queries of varying complexity. To address these challenges, we propose a reinforcement learning-based framework that dynamically selects the most suitable retrieval strategy based on query complexity. % our solution Our approach leverages a multi-armed bandit algorithm, which treats each retrieval method as a distinct ``arm'' and adapts the selection process by balancing exploration and exploitation. Additionally, we introduce a dynamic reward function that balances accuracy and efficiency, penalizing methods that require more retrieval steps, even if they lead to a correct result. Our method achieves new state of the art results on multiple single-hop and multi-hop datasets while reducing retrieval costs. Our code are available at https://github.com/FUTUREEEEEE/MBA .

Deep research systems represent an emerging class of agentic information retrieval methods that generate comprehensive and well-supported reports to complex queries. However, most existing frameworks rely on dynamic commercial search APIs, which pose reproducibility and transparency challenges in addition to their cost. To address these limitations, we introduce DeepResearchGym, an open-source sandbox that combines a reproducible search API with a rigorous evaluation protocol for benchmarking deep research systems. The API indexes large-scale public web corpora, namely ClueWeb22 and FineWeb, using a state-of-the-art dense retriever and approximate nearest neighbor search via DiskANN. It achieves lower latency than popular commercial APIs while ensuring stable document rankings across runs, and is freely available for research use. To evaluate deep research systems' outputs, we extend the Researchy Questions benchmark with automatic metrics through LLM-as-a-judge assessments to measure alignment with users' information needs, retrieval faithfulness, and report quality. Experimental results show that systems integrated with DeepResearchGym achieve performance comparable to those using commercial APIs, with performance rankings remaining consistent across evaluation metrics. A human evaluation study further confirms that our automatic protocol aligns with human preferences, validating the framework's ability to help support controlled assessment of deep research systems. Our code and API documentation are available at https://www.deepresearchgym.ai.

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

Did you try out the new Bing Search? Or maybe you fiddled around with Google AI~Overviews? These might sound familiar because the modern-day search stack has recently evolved to include retrieval-augmented generation (RAG) systems. They allow searching and incorporating real-time data into large language models (LLMs) to provide a well-informed, attributed, concise summary in contrast to the traditional search paradigm that relies on displaying a ranked list of documents. Therefore, given these recent advancements, it is crucial to have an arena to build, test, visualize, and systematically evaluate RAG-based search systems. With this in mind, we propose the TREC 2024 RAG Track to foster innovation in evaluating RAG systems. In our work, we lay out the steps we've made towards making this track a reality -- we describe the details of our reusable framework, Ragnar\"ok, explain the curation of the new MS MARCO V2.1 collection choice, release the development topics for the track, and standardize the I/O definitions which assist the end user. Next, using Ragnar\"ok, we identify and provide key industrial baselines such as OpenAI's GPT-4o or Cohere's Command R+. Further, we introduce a web-based user interface for an interactive arena allowing benchmarking pairwise RAG systems by crowdsourcing. We open-source our Ragnar\"ok framework and baselines to achieve a unified standard for future RAG systems.

While Large Language Models (LLMs) have demonstrated proficiency in Deep Research or Wide Search, their capacity to solve highly complex questions-those requiring long-horizon planning, massive evidence gathering, and synthesis across heterogeneous sources-remains largely unexplored. We introduce Super Research, a task for complex autonomous research tasks that integrates (i) structured decomposition into a research plan, (ii) super wide retrieval for diverse perspectives, and (iii) super deep investigation to resolve uncertainties through iterative queries. To evaluate this capability, we curated a benchmark of 300 expert-written questions across diverse domains, each requiring up to 100+ retrieval steps and 1,000+ web pages to reconcile conflicting evidence. Super Research produces verifiable reports with fine-grained citations and intermediate artifacts (e.g., outlines and tables) to ensure traceable reasoning. Furthermore, we present a graph-anchored auditing protocol that evaluates Super Research along five dimensions: Coverage, Logical Consistency, Report Utility, Objectivity and Citation Health. While super-complex questions may be infrequent in standard applications, Super Research serves as a critical ceiling evaluation and stress test for LLM capabilities. A model's proficiency within Super Research acts as a powerful proxy for its general research competence; success here suggests the robustness necessary to navigate nearly any subordinate research task. Leaderboard is available at: https://cnsdqd-dyb.github.io/Super-Research-Benchmark/

One of the challenges in online reinforcement learning (RL) is that the agent needs to trade off the exploration of the environment and the exploitation of the samples to optimize its behavior. Whether we optimize for regret, sample complexity, state-space coverage or model estimation, we need to strike a different exploration-exploitation trade-off. In this paper, we propose to tackle the exploration-exploitation problem following a decoupled approach composed of: 1) An "objective-specific" algorithm that (adaptively) prescribes how many samples to collect at which states, as if it has access to a generative model (i.e., a simulator of the environment); 2) An "objective-agnostic" sample collection exploration strategy responsible for generating the prescribed samples as fast as possible. Building on recent methods for exploration in the stochastic shortest path problem, we first provide an algorithm that, given as input the number of samples b(s,a) needed in each state-action pair, requires O(B D + D^{3/2} S^2 A) time steps to collect the B=sum_{s,a} b(s,a) desired samples, in any unknown communicating MDP with S states, A actions and diameter D. Then we show how this general-purpose exploration algorithm can be paired with "objective-specific" strategies that prescribe the sample requirements to tackle a variety of settings -- e.g., model estimation, sparse reward discovery, goal-free cost-free exploration in communicating MDPs -- for which we obtain improved or novel sample complexity guarantees.

Scientific innovation is undergoing a paradigm shift driven by the rapid advancement of Large Language Models (LLMs). As science faces mounting challenges including information overload, disciplinary silos, and diminishing returns on conventional research methods, LLMs are emerging as powerful agents capable not only of enhancing scientific workflows but also of participating in and potentially leading the innovation process. Existing surveys mainly focus on different perspectives, phrases, and tasks in scientific research and discovery, while they have limitations in understanding the transformative potential and role differentiation of LLM. This survey proposes a comprehensive framework to categorize the evolving roles of LLMs in scientific innovation across three hierarchical levels: Evaluator, Collaborator, and Scientist. We distinguish between LLMs' contributions to structured scientific research processes and open-ended scientific discovery, thereby offering a unified taxonomy that clarifies capability boundaries, evaluation criteria, and human-AI interaction patterns at each level. Through an extensive analysis of current methodologies, benchmarks, systems, and evaluation metrics, this survey delivers an in-depth and systematic synthesis on LLM-driven scientific innovation. We present LLMs not only as tools for automating existing processes, but also as catalysts capable of reshaping the epistemological foundations of science itself. This survey offers conceptual clarity, practical guidance, and theoretical foundations for future research, while also highlighting open challenges and ethical considerations in the pursuit of increasingly autonomous AI-driven science. Resources related to this survey can be accessed on GitHub at: https://github.com/haoxuan-unt2024/llm4innovation.

Recent advances have been improving the context windows of Large Language Models (LLMs). To quantify the real long-context capabilities of LLMs, evaluators such as the popular Needle in a Haystack have been developed to test LLMs over a large chunk of raw texts. While effective, current evaluations overlook the insight of how LLMs work with long-context code, i.e., repositories. To this end, we initiate the RepoQA benchmark to evaluate LLMs on long-context code understanding. Traditional needle testers ask LLMs to directly retrieve the answer from the context without necessary deep understanding. In RepoQA, we built our initial task, namely Searching Needle Function (SNF), which exercises LLMs to search functions given their natural-language description, i.e., LLMs cannot find the desired function if they cannot understand the description and code. RepoQA is multilingual and comprehensive: it includes 500 code search tasks gathered from 50 popular repositories across 5 modern programming languages. By evaluating 26 general and code-specific LLMs on RepoQA, we show (i) there is still a small gap between the best open and proprietary models; (ii) different models are good at different languages; and (iii) models may understand code better without comments.

We present Spacerini, a modular framework for seamless building and deployment of interactive search applications, designed to facilitate the qualitative analysis of large scale research datasets. Spacerini integrates features from both the Pyserini toolkit and the Hugging Face ecosystem to ease the indexing text collections and deploy them as search engines for ad-hoc exploration and to make the retrieval of relevant data points quick and efficient. The user-friendly interface enables searching through massive datasets in a no-code fashion, making Spacerini broadly accessible to anyone looking to qualitatively audit their text collections. This is useful both to IR~researchers aiming to demonstrate the capabilities of their indexes in a simple and interactive way, and to NLP~researchers looking to better understand and audit the failure modes of large language models. The framework is open source and available on GitHub: https://github.com/castorini/hf-spacerini, and includes utilities to load, pre-process, index, and deploy local and web search applications. A portfolio of applications created with Spacerini for a multitude of use cases can be found by visiting https://hf.co/spacerini.

We present BYOL-Explore, a conceptually simple yet general approach for curiosity-driven exploration in visually-complex environments. BYOL-Explore learns a world representation, the world dynamics, and an exploration policy all-together by optimizing a single prediction loss in the latent space with no additional auxiliary objective. We show that BYOL-Explore is effective in DM-HARD-8, a challenging partially-observable continuous-action hard-exploration benchmark with visually-rich 3-D environments. On this benchmark, we solve the majority of the tasks purely through augmenting the extrinsic reward with BYOL-Explore s intrinsic reward, whereas prior work could only get off the ground with human demonstrations. As further evidence of the generality of BYOL-Explore, we show that it achieves superhuman performance on the ten hardest exploration games in Atari while having a much simpler design than other competitive agents.

Code retrieval is becoming central to coding agents, but agentic coding requires more than matching a natural-language query to an isolated snippet. Given a user request, a coding agent needs to navigate a concrete repository state, locate relevant files and functions, gather supporting context, and filter similar in-repository distractors. Existing code retrieval benchmarks mainly evaluate docstring-to-function or snippet-level matching, thereby missing this requirement-driven repository search problem. To address this gap, we introduce CORE-Bench, a comprehensive benchmark for code retrieval in the era of agentic coding. CORE-Bench evaluates code retrieval ability at three levels: code understanding, issue-to-edit localization, and broader context retrieval. Built from curated code-search tasks and SWE-bench-series instances, CORE-Bench contains over 180K queries and 106K broader-context relevance labels. Experiments with representative embedding models show a sharp drop from traditional code search to code retrieval in agentic coding settings. Simple supervised fine-tuning of existing embedding models significantly improves performance in this setting, suggesting substantial room for further progress.

Reinforcement Learning with Verifiable Rewards (RLVR) is a powerful paradigm for enhancing the reasoning ability of Large Language Models (LLMs). Yet current RLVR methods often explore poorly, leading to premature convergence and entropy collapse. To address this challenge, we introduce Curiosity-Driven Exploration (CDE), a framework that leverages the model's own intrinsic sense of curiosity to guide exploration. We formalize curiosity with signals from both the actor and the critic: for the actor, we use perplexity over its generated response, and for the critic, we use the variance of value estimates from a multi-head architecture. Both signals serve as an exploration bonus within the RLVR framework to guide the model. Our theoretical analysis shows that the actor-wise bonus inherently penalizes overconfident errors and promotes diversity among correct responses; moreover, we connect the critic-wise bonus to the well-established count-based exploration bonus in RL. Empirically, our method achieves an approximate +3 point improvement over standard RLVR using GRPO/PPO on AIME benchmarks. Further analysis identifies a calibration collapse mechanism within RLVR, shedding light on common LLM failure modes.

Deep research has emerged as an important task that aims to address hard queries through extensive open-web exploration. To tackle it, most prior work equips large language model (LLM)-based agents with opaque web search APIs, enabling agents to iteratively issue search queries, retrieve external evidence, and reason over it. Despite search's essential role in deep research, black-box web search APIs hinder systematic analysis of search components, leaving the behaviour of established text ranking methods in deep research largely unclear. To fill this gap, we reproduce a selection of key findings and best practices for IR text ranking methods in the deep research setting. In particular, we examine their effectiveness from three perspectives: (i) retrieval units (documents vs. passages), (ii) pipeline configurations (different retrievers, re-rankers, and re-ranking depths), and (iii) query characteristics (the mismatch between agent-issued queries and the training queries of text rankers). We perform experiments on BrowseComp-Plus, a deep research dataset with a fixed corpus, evaluating 2 open-source agents, 5 retrievers, and 3 re-rankers across diverse setups. We find that agent-issued queries typically follow web-search-style syntax (e.g., quoted exact matches), favouring lexical, learned sparse, and multi-vector retrievers; passage-level units are more efficient under limited context windows, and avoid the difficulties of document length normalisation in lexical retrieval; re-ranking is highly effective; translating agent-issued queries into natural-language questions significantly bridges the query mismatch.

A grand challenge in reinforcement learning is intelligent exploration, especially when rewards are sparse or deceptive. Two Atari games serve as benchmarks for such hard-exploration domains: Montezuma's Revenge and Pitfall. On both games, current RL algorithms perform poorly, even those with intrinsic motivation, which is the dominant method to improve performance on hard-exploration domains. To address this shortfall, we introduce a new algorithm called Go-Explore. It exploits the following principles: (1) remember previously visited states, (2) first return to a promising state (without exploration), then explore from it, and (3) solve simulated environments through any available means (including by introducing determinism), then robustify via imitation learning. The combined effect of these principles is a dramatic performance improvement on hard-exploration problems. On Montezuma's Revenge, Go-Explore scores a mean of over 43k points, almost 4 times the previous state of the art. Go-Explore can also harness human-provided domain knowledge and, when augmented with it, scores a mean of over 650k points on Montezuma's Revenge. Its max performance of nearly 18 million surpasses the human world record, meeting even the strictest definition of "superhuman" performance. On Pitfall, Go-Explore with domain knowledge is the first algorithm to score above zero. Its mean score of almost 60k points exceeds expert human performance. Because Go-Explore produces high-performing demonstrations automatically and cheaply, it also outperforms imitation learning work where humans provide solution demonstrations. Go-Explore opens up many new research directions into improving it and weaving its insights into current RL algorithms. It may also enable progress on previously unsolvable hard-exploration problems in many domains, especially those that harness a simulator during training (e.g. robotics).

Large Language Models (LLMs) are powerful but prone to hallucinations due to static knowledge. Retrieval-Augmented Generation (RAG) helps by injecting external information, but current methods often are costly, generalize poorly, or ignore the internal knowledge of the model. In this paper, we introduce R1-Searcher++, a novel framework designed to train LLMs to adaptively leverage both internal and external knowledge sources. R1-Searcher++ employs a two-stage training strategy: an initial SFT Cold-start phase for preliminary format learning, followed by RL for Dynamic Knowledge Acquisition. The RL stage uses outcome-supervision to encourage exploration, incorporates a reward mechanism for internal knowledge utilization, and integrates a memorization mechanism to continuously assimilate retrieved information, thereby enriching the model's internal knowledge. By leveraging internal knowledge and external search engine, the model continuously improves its capabilities, enabling efficient retrieval-augmented reasoning. Our experiments demonstrate that R1-Searcher++ outperforms previous RAG and reasoning methods and achieves efficient retrieval. The code is available at https://github.com/RUCAIBox/R1-Searcher-plus.

Recent advances in Large Language Models (LLMs) have enabled researchers to focus on practical repository-level tasks in software engineering domain. In this work, we consider a cornerstone task for automating work with software repositories-environment setup, i.e., a task of configuring a repository-specific development environment on a system. Existing studies on environment setup introduce innovative agentic strategies, but their evaluation is often based on small datasets that may not capture the full range of configuration challenges encountered in practice. To address this gap, we introduce a comprehensive environment setup benchmark EnvBench. It encompasses 329 Python and 665 JVM-based (Java, Kotlin) repositories, with a focus on repositories that present genuine configuration challenges, excluding projects that can be fully configured by simple deterministic scripts. To enable further benchmark extension and usage for model tuning, we implement two automatic metrics: a static analysis check for missing imports in Python and a compilation check for JVM languages. We demonstrate the applicability of our benchmark by evaluating three environment setup approaches, including a simple zero-shot baseline and two agentic workflows, that we test with two powerful LLM backbones, GPT-4o and GPT-4o-mini. The best approach manages to successfully configure 6.69% repositories for Python and 29.47% repositories for JVM, suggesting that EnvBench remains challenging for current approaches. Our benchmark suite is publicly available at https://github.com/JetBrains-Research/EnvBench. The dataset and experiment trajectories are available at https://jb.gg/envbench.

Current deep-research agents run in a ''fire-and-forget'' mode: once started, they give users no way to fix errors or add expert knowledge during execution. We present ResearStudio, the first open-source framework that places real-time human control at its core. The system follows a Collaborative Workshop design. A hierarchical Planner-Executor writes every step to a live ''plan-as-document,'' a fast communication layer streams each action, file change, and tool call to a web interface. At any moment, the user can pause the run, edit the plan or code, run custom commands, and resume -- switching smoothly between AI-led, human-assisted and human-led, AI-assisted modes. In fully autonomous mode, ResearStudio achieves state-of-the-art results on the GAIA benchmark, surpassing systems like OpenAI's DeepResearch and Manus. These results show that strong automated performance and fine-grained human control can coexist. The full code, protocol, and evaluation scripts are available at https://github.com/ResearAI/ResearStudio. We will continue to update the repository to encourage further work on safe and controllable research agents. Our live demo is publicly accessible at http://ai-researcher.net:3000/. We support the development of DeepScientist, which can be accessed at https://github.com/ResearAI/DeepScientist.

Autonomous scientific discovery systems offer the potential to accelerate research by automating the process of hypothesis generation and validation. However, current systems operate within constrained search spaces or require predefined research questions, limiting their capacity for true open-ended inquiry. Furthermore, while they generate hypotheses iteratively, they largely lack the ability to explicitly synthesize their own accumulated findings to uncover complex, interconnected phenomena. We introduce DiscoPER, an autonomous large language model-powered framework that conducts open-ended research by dynamically generating and executing code to explore datasets without pre-specified research objectives. To ensure rigorous scientific validity, every proposed discovery must pass statistical testing. To overcome the limitations of isolated search, our framework introduces a second-order reasoning mechanism that periodically analyzes its own accumulated discoveries. By treating prior discoveries as empirical data, DiscoPER identifies structural patterns, confounds, and epistemic gaps, actively redirecting hypothesis exploration toward uncharted regions of the search space. The search space is further expanded by incorporating tool use, enabling the system to explore hypotheses beyond structured metadata by seamlessly processing and extracting useful information from multimodal sources like images. Evaluated on iNatDisco, a new multimodal ecological knowledge benchmark with pattern-level ground truth obtained from peer-reviewed literature, DiscoPER recovers 8 of 9 known patterns with a 72.7% hypothesis support rate, outperforming both classical causal discovery and LLM-guided baselines. Ablations show that DiscoPER scales with more data, and confirms the benefits of second-order meta-reflection.

Using LLMs (Large Language Models) in conjunction with external documents has made RAG (Retrieval-Augmented Generation) an essential technology. Numerous techniques and modules for RAG are being researched, but their performance can vary across different datasets. Finding RAG modules that perform well on specific datasets is challenging. In this paper, we propose the AutoRAG framework, which automatically identifies suitable RAG modules for a given dataset. AutoRAG explores and approximates the optimal combination of RAG modules for the dataset. Additionally, we share the results of optimizing a dataset using AutoRAG. All experimental results and data are publicly available and can be accessed through our GitHub repository https://github.com/Marker-Inc-Korea/AutoRAG_ARAGOG_Paper .

Reinforcement learning (RL) agents improve through trial-and-error, but when reward is sparse and the agent cannot discover successful action sequences, learning stagnates. This has been a notable problem in training deep RL agents to perform web-based tasks, such as booking flights or replying to emails, where a single mistake can ruin the entire sequence of actions. A common remedy is to "warm-start" the agent by pre-training it to mimic expert demonstrations, but this is prone to overfitting. Instead, we propose to constrain exploration using demonstrations. From each demonstration, we induce high-level "workflows" which constrain the allowable actions at each time step to be similar to those in the demonstration (e.g., "Step 1: click on a textbox; Step 2: enter some text"). Our exploration policy then learns to identify successful workflows and samples actions that satisfy these workflows. Workflows prune out bad exploration directions and accelerate the agent's ability to discover rewards. We use our approach to train a novel neural policy designed to handle the semi-structured nature of websites, and evaluate on a suite of web tasks, including the recent World of Bits benchmark. We achieve new state-of-the-art results, and show that workflow-guided exploration improves sample efficiency over behavioral cloning by more than 100x.

Recent text-to-SQL systems powered by large language models (LLMs) have demonstrated remarkable performance in translating natural language queries into SQL. However, these systems often struggle with complex database structures and domain-specific queries, as they primarily focus on enhancing logical reasoning and SQL syntax while overlooking the critical need for comprehensive database understanding. To address this limitation, we propose DB-Explore, a novel framework that systematically aligns LLMs with database knowledge through automated exploration and instruction synthesis. DB-Explore constructs database graphs to capture complex relational schemas, leverages GPT-4 to systematically mine structural patterns and semantic knowledge, and synthesizes instructions to distill this knowledge for efficient fine-tuning of LLMs. Our framework enables comprehensive database understanding through diverse sampling strategies and automated instruction generation, bridging the gap between database structures and language models. Experiments conducted on the SPIDER and BIRD benchmarks validate the effectiveness of DB-Explore, achieving an execution accuracy of 52.1% on BIRD and 84.0% on SPIDER. Notably, our open-source implementation, based on the Qwen2.5-coder-7B model, outperforms multiple GPT-4-driven text-to-SQL systems in comparative evaluations, and achieves near state-of-the-art performance with minimal computational cost.

The evolution of Large Language Models (LLMs) towards autonomous agents has catalyzed progress in Deep Research. While retrieval capabilities are well-benchmarked, the post-retrieval synthesis stage--where agents must digest massive amounts of context and consolidate fragmented evidence into coherent, long-form reports--remains under-evaluated due to the subjectivity of open-ended writing. To bridge this gap, we introduce DeepSynth-Eval, a benchmark designed to objectively evaluate information consolidation capabilities. We leverage high-quality survey papers as gold standards, reverse-engineering research requests and constructing "Oracle Contexts" from their bibliographies to isolate synthesis from retrieval noise. We propose a fine-grained evaluation protocol using General Checklists (for factual coverage) and Constraint Checklists (for structural organization), transforming subjective judgment into verifiable metrics. Experiments across 96 tasks reveal that synthesizing information from hundreds of references remains a significant challenge. Our results demonstrate that agentic plan-and-write workflows significantly outperform single-turn generation, effectively reducing hallucinations and improving adherence to complex structural constraints.

Repository-level code comprehension and knowledge sharing remain core challenges in software engineering. Large language models (LLMs) have shown promise by generating explanations of program structure and logic. However, these approaches still face limitations: First, relevant knowledge is distributed across multiple files within a repository, aka semantic fragmentation. Second, retrieval inefficiency and attention saturation degrade performance in RAG pipelines, where long, unaligned contexts overwhelm attention. Third, repository specific training data is scarce and often outdated. Finally, proprietary LLMs hinder industrial adoption due to privacy and deployment constraints. To address these issues, we propose Key-Augmented Neural Triggers (KANT), a novel approach that embeds knowledge anchors into both training and inference. Unlike prior methods, KANT enables internal access to repository specific knowledge, reducing fragmentation and grounding inference in localized context. Moreover, we synthesize specialized data directly from code. At inference, knowledge anchors replace verbose context, reducing token overhead and latency while supporting efficient, on premise deployment. We evaluate KANT via: a qualitative human evaluation of the synthesized dataset's intent coverage and quality across five dimensions; compare against SOTA baselines across five qualitative dimensions and inference speed; and replication across different LLMs to assess generalizability. Results show that the synthetic training data aligned with information-seeking needs. KANT achieved over 60% preference from human annotators and a LocalStack expert (preferring 79% of cases). Also, KANT reduced inference latency by up to 85% across all models. Overall, it is well-suited for scalable, low-latency, on-premise deployments, providing a strong foundation for code comprehension.

The ultimate goal of code agents is to solve complex tasks autonomously. Although large language models (LLMs) have made substantial progress in code generation, real-world tasks typically demand full-fledged code repositories rather than simple scripts. Building such repositories from scratch remains a major challenge. Fortunately, GitHub hosts a vast, evolving collection of open-source repositories, which developers frequently reuse as modular components for complex tasks. Yet, existing frameworks like OpenHands and SWE-Agent still struggle to effectively leverage these valuable resources. Relying solely on README files provides insufficient guidance, and deeper exploration reveals two core obstacles: overwhelming information and tangled dependencies of repositories, both constrained by the limited context windows of current LLMs. To tackle these issues, we propose RepoMaster, an autonomous agent framework designed to explore and reuse GitHub repositories for solving complex tasks. For efficient understanding, RepoMaster constructs function-call graphs, module-dependency graphs, and hierarchical code trees to identify essential components, providing only identified core elements to the LLMs rather than the entire repository. During autonomous execution, it progressively explores related components using our exploration tools and prunes information to optimize context usage. Evaluated on the adjusted MLE-bench, RepoMaster achieves a 110% relative boost in valid submissions over the strongest baseline OpenHands. On our newly released GitTaskBench, RepoMaster lifts the task-pass rate from 40.7% to 62.9% while reducing token usage by 95%. Our code and demonstration materials are publicly available at https://github.com/QuantaAlpha/RepoMaster.

In this paper, we introduce Latent Go-Explore (LGE), a simple and general approach based on the Go-Explore paradigm for exploration in reinforcement learning (RL). Go-Explore was initially introduced with a strong domain knowledge constraint for partitioning the state space into cells. However, in most real-world scenarios, drawing domain knowledge from raw observations is complex and tedious. If the cell partitioning is not informative enough, Go-Explore can completely fail to explore the environment. We argue that the Go-Explore approach can be generalized to any environment without domain knowledge and without cells by exploiting a learned latent representation. Thus, we show that LGE can be flexibly combined with any strategy for learning a latent representation. Our results indicate that LGE, although simpler than Go-Explore, is more robust and outperforms state-of-the-art algorithms in terms of pure exploration on multiple hard-exploration environments including Montezuma's Revenge. The LGE implementation is available as open-source at https://github.com/qgallouedec/lge.

Retrieval-Augmented Generation (RAG) improves the accuracy and relevance of large language model outputs by incorporating knowledge retrieval. However, implementing RAG in enterprises poses challenges around data security, accuracy, scalability, and integration. This paper explores the unique requirements for enterprise RAG, surveys current approaches and limitations, and discusses potential advances in semantic search, hybrid queries, and optimized retrieval. It proposes an evaluation framework to validate enterprise RAG solutions, including quantitative testing, qualitative analysis, ablation studies, and industry case studies. This framework aims to help demonstrate the ability of purpose-built RAG architectures to deliver accuracy and relevance improvements with enterprise-grade security, compliance and integration. The paper concludes with implications for enterprise deployments, limitations, and future research directions. Close collaboration between researchers and industry partners may accelerate progress in developing and deploying retrieval-augmented generation technology.

Scientific literature searches are often exploratory, whereby users are not yet familiar with a particular field or concept but are interested in learning more about it. However, existing systems for scientific literature search are typically tailored to keyword-based lookup searches, limiting the possibilities for exploration. We propose NLP-KG, a feature-rich system designed to support the exploration of research literature in unfamiliar natural language processing (NLP) fields. In addition to a semantic search, NLP-KG allows users to easily find survey papers that provide a quick introduction to a field of interest. Further, a Fields of Study hierarchy graph enables users to familiarize themselves with a field and its related areas. Finally, a chat interface allows users to ask questions about unfamiliar concepts or specific articles in NLP and obtain answers grounded in knowledge retrieved from scientific publications. Our system provides users with comprehensive exploration possibilities, supporting them in investigating the relationships between different fields, understanding unfamiliar concepts in NLP, and finding relevant research literature. Demo, video, and code are available at: https://github.com/NLP-Knowledge-Graph/NLP-KG-WebApp.

The rapid growth of scientific literature imposes significant challenges for researchers endeavoring to stay updated with the latest advancements in their fields and delve into new areas. We introduce OpenResearcher, an innovative platform that leverages Artificial Intelligence (AI) techniques to accelerate the research process by answering diverse questions from researchers. OpenResearcher is built based on Retrieval-Augmented Generation (RAG) to integrate Large Language Models (LLMs) with up-to-date, domain-specific knowledge. Moreover, we develop various tools for OpenResearcher to understand researchers' queries, search from the scientific literature, filter retrieved information, provide accurate and comprehensive answers, and self-refine these answers. OpenResearcher can flexibly use these tools to balance efficiency and effectiveness. As a result, OpenResearcher enables researchers to save time and increase their potential to discover new insights and drive scientific breakthroughs. Demo, video, and code are available at: https://github.com/GAIR-NLP/OpenResearcher.

Does a lexical retriever suffice as large language models (LLMs) become more capable in an agentic loop? This question naturally arises when building deep research systems. We revisit it by pairing BM25 with frontier LLMs that have better reasoning and tool-use abilities. To support researchers asking the same question, we introduce Pi-Serini, a search agent equipped with three tools for retrieving, browsing, and reading documents. Our results show that, on BrowseComp-Plus, a well-configured lexical retriever with sufficient retrieval depth can support effective deep research when paired with more capable LLMs. Specifically, Pi-Serini with gpt-5.5 achieves 83.1% answer accuracy and 94.7% surfaced evidence recall, outperforming released search agents that use dense retrievers. Controlled ablations further show that BM25 tuning improves answer accuracy by 18.0% and surfaced evidence recall by 11.1% over the default BM25 setting, while increasing retrieval depth further improves surfaced evidence recall by 25.3% over the shallow-retrieval setting. Source code is available at https://github.com/justram/pi-serini.

Repository-level pretraining is commonly used to enable large language models for code to leverage codebase-wide context. This enhances their ability to generate accurate and context-aware code completions. In this work, we investigate how different repository-processing strategies affect in-context learning in OpenCoder, a 1.5B-parameter model. We extend its context window from 4,096 to 16,384 tokens by training on additional 1B tokens of curated repository-level data. Despite relying on a smaller dataset than competing models (which often use hundreds of billions of tokens), our model achieves comparable performance on the Long Code Arena benchmark. We find that various repository-processing techniques yield similarly strong results, with the primary gain coming from adapting to a new rotary positional embedding (RoPE) scaling parameter. Finally, we show that a simpler file-level training approach at the original sequence length remains highly effective, opening up repository-level code completion research to settings with more constrained data and compute resources.

The standard post-training recipe for large reasoning models, supervised fine-tuning followed by reinforcement learning (SFT-then-RL), may limit the benefits of the RL stage: while SFT imitates expert demonstrations, it often causes overconfidence and reduces generation diversity, leaving RL with a narrowed solution space to explore. Adding entropy regularization during SFT is not a cure-all; it tends to flatten token distributions toward uniformity, increasing entropy without improving meaningful exploration capability. In this paper, we propose CurioSFT, an entropy-preserving SFT method designed to enhance exploration capabilities through intrinsic curiosity. It consists of (a) Self-Exploratory Distillation, which distills the model toward a self-generated, temperature-scaled teacher to encourage exploration within its capability; and (b) Entropy-Guided Temperature Selection, which adaptively adjusts distillation strength to mitigate knowledge forgetting by amplifying exploration at reasoning tokens while stabilizing factual tokens. Extensive experiments on mathematical reasoning tasks demonstrate that, in SFT stage, CurioSFT outperforms the vanilla SFT by 2.5 points on in-distribution tasks and 2.9 points on out-of-distribution tasks. We also verify that exploration capabilities preserved during SFT successfully translate into concrete gains in RL stage, yielding an average improvement of 5.0 points.

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}

The rapidly evolving fields of Machine Learning (ML) and Artificial Intelligence have witnessed the emergence of platforms like Hugging Face (HF) as central hubs for model development and sharing. This experience report synthesizes insights from two comprehensive studies conducted on HF, focusing on carbon emissions and the evolutionary and maintenance aspects of ML models. Our objective is to provide a practical guide for future researchers embarking on mining software repository studies within the HF ecosystem to enhance the quality of these studies. We delve into the intricacies of the replication package used in our studies, highlighting the pivotal tools and methodologies that facilitated our analysis. Furthermore, we propose a nuanced stratified sampling strategy tailored for the diverse HF Hub dataset, ensuring a representative and comprehensive analytical approach. The report also introduces preliminary guidelines, transitioning from repository mining to cohort studies, to establish causality in repository mining studies, particularly within the ML model of HF context. This transition is inspired by existing frameworks and is adapted to suit the unique characteristics of the HF model ecosystem. Our report serves as a guiding framework for researchers, contributing to the responsible and sustainable advancement of ML, and fostering a deeper understanding of the broader implications of ML models.

Frontier language models have demonstrated strong reasoning and long-horizon tool-use capabilities. However, existing RAG systems fail to leverage these capabilities. They still rely on two paradigms: (1) designing an algorithm that retrieves passages in a single shot and concatenates them into the model's input, or (2) predefining a workflow and prompting the model to execute it step-by-step. Neither paradigm allows the model to participate in retrieval decisions, preventing efficient scaling with model improvements. In this paper, we introduce A-RAG, an Agentic RAG framework that exposes hierarchical retrieval interfaces directly to the model. A-RAG provides three retrieval tools: keyword search, semantic search, and chunk read, enabling the agent to adaptively search and retrieve information across multiple granularities. Experiments on multiple open-domain QA benchmarks show that A-RAG consistently outperforms existing approaches with comparable or lower retrieved tokens, demonstrating that A-RAG effectively leverages model capabilities and dynamically adapts to different RAG tasks. We further systematically study how A-RAG scales with model size and test-time compute. We will release our code and evaluation suite to facilitate future research. Code and evaluation suite are available at https://github.com/Ayanami0730/arag.

The surge in scientific publications challenges traditional review methods, demanding tools that integrate structured metadata with full-text analysis. Hybrid Retrieval Augmented Generation (RAG) systems, combining graph queries with vector search offer promise but are typically static, rely on proprietary tools, and lack uncertainty estimates. We present an agentic approach that encapsulates the hybrid RAG pipeline within an autonomous agent capable of (1) dynamically selecting between GraphRAG and VectorRAG for each query, (2) adapting instruction-tuned generation in real time to researcher needs, and (3) quantifying uncertainty during inference. This dynamic orchestration improves relevance, reduces hallucinations, and promotes reproducibility. Our pipeline ingests bibliometric open-access data from PubMed, arXiv, and Google Scholar APIs, builds a Neo4j citation-based knowledge graph (KG), and embeds full-text PDFs into a FAISS vector store (VS) using the all-MiniLM-L6-v2 model. A Llama-3.3-70B agent selects GraphRAG (translating queries to Cypher for KG) or VectorRAG (combining sparse and dense retrieval with re-ranking). Instruction tuning refines domain-specific generation, and bootstrapped evaluation yields standard deviation for evaluation metrics. On synthetic benchmarks mimicking real-world queries, the Instruction-Tuned Agent with Direct Preference Optimization (DPO) outperforms the baseline, achieving a gain of 0.63 in VS Context Recall and a 0.56 gain in overall Context Precision. Additional gains include 0.24 in VS Faithfulness, 0.12 in both VS Precision and KG Answer Relevance, 0.11 in overall Faithfulness score, 0.05 in KG Context Recall, and 0.04 in both VS Answer Relevance and overall Precision. These results highlight the system's improved reasoning over heterogeneous sources and establish a scalable framework for autonomous, agentic scientific discovery.