Daily Papers

Code completion, a key downstream task in code generation, is one of the most frequent and impactful methods for enhancing developer productivity in software development. As intelligent completion tools evolve, we need a robust evaluation benchmark that enables meaningful comparisons between products and guides future advancements. However, existing benchmarks focus more on coarse-grained tasks without industrial analysis resembling general code generation rather than the real-world scenarios developers encounter. Moreover, these benchmarks often rely on costly and time-consuming human annotation, and the standalone test cases fail to leverage minimal tests for maximum repository-level understanding and code coverage. To address these limitations, we first analyze business data from an industrial code completion tool and redefine the evaluation criteria to better align with the developer's intent and desired completion behavior throughout the coding process. Based on these insights, we introduce Codev-Agent, an agent-based system that automates repository crawling, constructs execution environments, extracts dynamic calling chains from existing unit tests, and generates new test samples to avoid data leakage, ensuring fair and effective comparisons. Using Codev-Agent, we present the Code-Development Benchmark (Codev-Bench), a fine-grained, real-world, repository-level, and developer-centric evaluation framework. Codev-Bench assesses whether a code completion tool can capture a developer's immediate intent and suggest appropriate code across diverse contexts, providing a more realistic benchmark for code completion in modern software development.

Software issue resolution is a critical challenge in software engineering and has garnered increasing attention in recent years. With the rapid advancement of large language models (LLMs), substantial progress has been made in addressing real-world software engineering tasks. Recent studies have introduced ensemble reasoning techniques to enhance the performance of LLM-based issue resolution. However, existing prompting-based methods still face limitations in effectively exploring large ensemble spaces and lack the capacity for repository-level understanding, both of which constrain their overall effectiveness. In this paper, we propose Trae Agent, the first agent-based ensemble reasoning approach for repository-level issue resolution. Trae Agent formulates our goal as an optimal solution search problem and addresses two key challenges, i.e., large ensemble spaces and repository-level understanding, through modular agents for generation, pruning, and selection. We conduct extensive experiments using three leading LLMs on the widely-adopted SWE-bench benchmark, comparing Trae Agent against four state-of-the-art ensemble reasoning techniques. Experimental results demonstrate that Trae Agent consistently achieves superior performance, with an average improvement of 10.22% over all baselines in terms of Pass@1. Trae Agent has achieved first place on the SWE-bench Verified leaderboard, with a notable Pass@1 score of 75.20%. We are pleased to release Trae Agent as an open-source project to support the research community, with all resources available at https://github.com/bytedance/trae-agent.

While large language models (LLMs) have shown considerable promise in code generation, real-world software development demands advanced repository-level reasoning. This includes understanding dependencies, project structures, and managing multi-file changes. However, the ability of LLMs to effectively comprehend and handle complex code repositories has yet to be fully explored. To address challenges, we introduce a hierarchical benchmark designed to evaluate repository dependency understanding (DependEval). Benchmark is based on 15,576 repositories collected from real-world websites. It evaluates models on three core tasks: Dependency Recognition, Repository Construction, and Multi-file Editing, across 8 programming languages from actual code repositories. Our evaluation of over 25 LLMs reveals substantial performance gaps and provides valuable insights into repository-level code understanding.

Large Language Models (LLMs) excel in code generation yet struggle with modern AI software engineering tasks. Unlike traditional function-level or file-level coding tasks, AI software engineering requires not only basic coding proficiency but also advanced skills in managing and interacting with code repositories. However, existing methods often overlook the need for repository-level code understanding, which is crucial for accurately grasping the broader context and developing effective solutions. On this basis, we present RepoGraph, a plug-in module that manages a repository-level structure for modern AI software engineering solutions. RepoGraph offers the desired guidance and serves as a repository-wide navigation for AI software engineers. We evaluate RepoGraph on the SWE-bench by plugging it into four different methods of two lines of approaches, where RepoGraph substantially boosts the performance of all systems, leading to a new state-of-the-art among open-source frameworks. Our analyses also demonstrate the extensibility and flexibility of RepoGraph by testing on another repo-level coding benchmark, CrossCodeEval. Our code is available at https://github.com/ozyyshr/RepoGraph.

Language models have been applied to various software development tasks, but the performance varies according to the scale of the models. Large Language Models (LLMs) outperform Small Language Models (SLMs) in complex tasks like repository-level issue resolving, but raise concerns about privacy and cost. In contrast, SLMs are more accessible but under-perform in complex tasks. In this paper, we introduce ReSAT (Repository Structure-Aware Training), construct training data based on a large number of issues and corresponding pull requests from open-source communities to enhance the model's understanding of repository structure and issue resolving ability. We construct two types of training data: (1) localization training data, a multi-level progressive localization data to improve code understanding and localization capability; (2) code edit training data, which improves context-based code editing capability. The evaluation results on SWE-Bench-verified and RepoQA demonstrate that ReSAT effectively enhances SLMs' issue-resolving and repository-level long-context understanding capabilities.

Understanding and reasoning about entire software repositories is an essential capability for intelligent software engineering tools. While existing benchmarks such as CoSQA and CodeQA have advanced the field, they predominantly focus on small, self-contained code snippets. These setups fail to capture the complexity of real-world repositories, where effective understanding and reasoning often require navigating multiple files, understanding software architecture, and grounding answers in long-range code dependencies. In this paper, we present SWE-QA, a repository-level code question answering (QA) benchmark designed to facilitate research on automated QA systems in realistic code environments. SWE-QA involves 576 high-quality question-answer pairs spanning diverse categories, including intention understanding, cross-file reasoning, and multi-hop dependency analysis. To construct SWE-QA, we first crawled 77,100 GitHub issues from 11 popular repositories. Based on an analysis of naturally occurring developer questions extracted from these issues, we developed a two-level taxonomy of repository-level questions and constructed a set of seed questions for each category. For each category, we manually curated and validated questions and collected their corresponding answers. As a prototype application, we further develop SWE-QA-Agent, an agentic framework in which LLM agents reason and act to find answers automatically. We evaluate six advanced LLMs on SWE-QA under various context augmentation strategies. Experimental results highlight the promise of LLMs, particularly our SWE-QA-Agent framework, in addressing repository-level QA, while also revealing open challenges and pointing to future research directions.

Large Language Models (LLMs) have exhibited significant proficiency in code debugging, especially in automatic program repair, which may substantially reduce the time consumption of developers and enhance their efficiency. Significant advancements in debugging datasets have been made to promote the development of code debugging. However, these datasets primarily focus on assessing the LLM's function-level code repair capabilities, neglecting the more complex and realistic repository-level scenarios, which leads to an incomplete understanding of the LLM's challenges in repository-level debugging. While several repository-level datasets have been proposed, they often suffer from limitations such as limited diversity of tasks, languages, and error types. To mitigate this challenge, this paper introduces RepoDebug, a multi-task and multi-language repository-level code debugging dataset with 22 subtypes of errors that supports 8 commonly used programming languages and 3 debugging tasks. Furthermore, we conduct evaluation experiments on 10 LLMs, where Claude 3.5 Sonnect, the best-performing model, still cannot perform well in repository-level debugging.

Large Language Models (LLMs) have demonstrated impressive capabilities in code generation. However, current evaluation datasets suffer from issues such as the lack of runnable test cases, deviation from the distribution of real-world code, and the ability to evaluate only the Python language. These limitations undermine the credibility of the evaluation results. To address these limitations, we introduce MRG-Bench (Multi-language Repository-level Code Generation Benchmark), a novel dataset that provides a more accurate evaluation of LLMs in practical repository-level code generation tasks. MRG-Bench has three main features: (1) practical data sourced from real-world code repositories that align to the practical distribution, (2) multiple programming languages support, including Python, Java, and Go, and (3) project-level runnable test cases to assess the quality of the generated code. Based on MRG-Bench, we conducted extensive experiments including large language models, long-context models, and RAG-related methods. These evaluation results demonstrate that current repository-level code generation techniques suffer from significant performance deficiencies. To further investigate why models fail, we designed novel experiments to annotate the underlying causes of generation errors. The results explicitly show that the majority of methods suffer from "difficulty in understanding user requirements," failing to comprehend their assigned tasks accurately. Moreover, the impact of different repository-level contexts on this issue exhibits significant disparities across different programming languages, suggesting that, in practice, specialized contextual information needs to be designed for different languages.

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.

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.

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.

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.

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

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.

Large language models that enhance software development tasks, such as code generation, code completion, and code question answering (QA), have been extensively studied in both academia and the industry. The models are integrated into popular intelligent IDEs like JetBrains and Cursor. Current benchmarks for evaluating models' code comprehension capabilities primarily focus on code generation or completion, often neglecting QA, which is a crucial aspect of understanding code. Existing code QA benchmarks are derived from code comments with predefined patterns (e.g., CodeQA) or focus on specific domains, such as education (e.g., CS1QA). These benchmarks fail to capture the real-world complexity of software engineering and user requirements for understanding code repositories. To address this gap, we introduce CoReQA, a benchmark for Code Repository-level question answering, constructed from GitHub issues and comments from 176 popular repositories across four programming languages. Since questions and answers may include both natural language and code snippets, traditional evaluation metrics such as BLEU are inadequate for assessing repository-level QA performance. Thus, we provide an LLM-as-a-judge framework to evaluate QA performance from five aspects. Based on CoReQA, we evaluate the performance of three baselines, including two short-context models using generic retrieval strategies and one long-context model that utilizes the entire repository context. Evaluation results show that state-of-the-art proprietary and long-context models struggle to address repository-level questions effectively. Our analysis highlights the limitations of language models in assisting developers in understanding repositories and suggests future directions for improving repository comprehension systems through effective context retrieval methodologies.

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.

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.

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.

Code summarization is a critical task in natural language processing and software engineering, which aims to generate concise descriptions of source code. Recent advancements have improved the quality of these summaries, enhancing code readability and maintainability. However, the content of a repository or a class has not been considered in function code summarization. This study investigated the effectiveness of code summarization models beyond the function level, exploring the impact of class and repository contexts on the summary quality. The study involved revising benchmarks for evaluating models at class and repository levels, assessing baseline models, and evaluating LLMs with in-context learning to determine the enhancement of summary quality with additional context. The findings revealed that the fine-tuned state-of-the-art CodeT5+ base model excelled in code summarization, while incorporating few-shot learning and retrieved code chunks from RAG significantly enhanced the performance of LLMs in this task. Notably, the Deepseek Coder 1.3B and Starcoder2 15B models demonstrated substantial improvements in metrics such as BLEURT, METEOR, and BLEU-4 at both class and repository levels. Repository-level summarization exhibited promising potential but necessitates significant computational resources and gains from the inclusion of structured context. Lastly, we employed the recent SIDE code summarization metric in our evaluation. This study contributes to refining strategies for prompt engineering, few-shot learning, and RAG, addressing gaps in benchmarks for code summarization at various levels. Finally, we publish all study details, code, datasets, and results of evaluation in the GitHub repository available at https://github.com/kilimanj4r0/code-summarization-beyond-function-level.

Recent advances in Large Language Models (LLMs) have shown promise in function-level code generation, yet repository-level software engineering tasks remain challenging. Current solutions predominantly rely on proprietary LLM agents, which introduce unpredictability and limit accessibility, raising concerns about data privacy and model customization. This paper investigates whether open-source LLMs can effectively address repository-level tasks without requiring agent-based approaches. We demonstrate this is possible by enabling LLMs to comprehend functions and files within codebases through their semantic information and structural dependencies. To this end, we introduce Code Graph Models (CGMs), which integrate repository code graph structures into the LLM's attention mechanism and map node attributes to the LLM's input space using a specialized adapter. When combined with an agentless graph RAG framework, our approach achieves a 43.00% resolution rate on the SWE-bench Lite benchmark using the open-source Qwen2.5-72B model. This performance ranks first among open weight models, second among methods with open-source systems, and eighth overall, surpassing the previous best open-source model-based method by 12.33%.

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.

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.

Recent advancements in code-fluent Large Language Models (LLMs) enabled the research on repository-level code editing. In such tasks, the model navigates and modifies the entire codebase of a project according to request. Hence, such tasks require efficient context retrieval, i.e., navigating vast codebases to gather relevant context. Despite the recognized importance of context retrieval, existing studies tend to approach repository-level coding tasks in an end-to-end manner, rendering the impact of individual components within these complicated systems unclear. In this work, we decouple the task of context retrieval from the other components of the repository-level code editing pipelines. We lay the groundwork to define the strengths and weaknesses of this component and the role that reasoning plays in it by conducting experiments that focus solely on context retrieval. We conclude that while the reasoning helps to improve the precision of the gathered context, it still lacks the ability to identify its sufficiency. We also outline the ultimate role of the specialized tools in the process of context gathering. The code supplementing this paper is available at https://github.com/JetBrains-Research/ai-agents-code-editing.

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.

Recent advances in retrieval-augmented generation (RAG) have initiated a new era in repository-level code completion. However, the invariable use of retrieval in existing methods exposes issues in both efficiency and robustness, with a large proportion of the retrieved contexts proving unhelpful or harmful to code language models (code LMs). In this paper, we propose a selective RAG framework to avoid retrieval when unnecessary. To power this framework, we design a self-supervised learning approach to enable a code LM to accurately self-evaluate whether retrieval can improve its output quality and robustly leverage the potentially noisy retrieved contexts. Using this LM as both the selective RAG policy and the generation model, our framework achieves state-of-the-art repository-level code completion performance on diverse benchmarks including RepoEval, CrossCodeEval, and CrossCodeLongEval, a new long-form code completion benchmark. Meanwhile, our analyses show that selectively retrieving brings as much as 70% inference speedup in the online serving setting without harming the performance. We further demonstrate that our framework is able to accommodate different generation models, retrievers, and programming languages. These advancements position our framework as an important step towards more accurate and efficient repository-level code completion.

The success of language models in code assistance has spurred the proposal of repository-level code completion as a means to enhance prediction accuracy, utilizing the context from the entire codebase. However, this amplified context can inadvertently increase inference latency, potentially undermining the developer experience and deterring tool adoption - a challenge we termed the Context-Latency Conundrum. This paper introduces REPOFUSE, a pioneering solution designed to enhance repository-level code completion without the latency trade-off. REPOFUSE uniquely fuses two types of context: the analogy context, rooted in code analogies, and the rationale context, which encompasses in-depth semantic relationships. We propose a novel rank truncated generation (RTG) technique that efficiently condenses these contexts into prompts with restricted size. This enables REPOFUSE to deliver precise code completions while maintaining inference efficiency. Through testing with the CrossCodeEval suite, REPOFUSE has demonstrated a significant leap over existing models, achieving a 40.90% to 59.75% increase in exact match (EM) accuracy for code completions and a 26.8% enhancement in inference speed. Beyond experimental validation, REPOFUSE has been integrated into the workflow of a large enterprise, where it actively supports various coding tasks.

Repository-level code completion has drawn great attention in software engineering, and several benchmark datasets have been introduced. However, existing repository-level code completion benchmarks usually focus on a limited number of languages (<5), which cannot evaluate the general code intelligence abilities across different languages for existing code Large Language Models (LLMs). Besides, the existing benchmarks usually report overall average scores of different languages, where the fine-grained abilities in different completion scenarios are ignored. Therefore, to facilitate the research of code LLMs in multilingual scenarios, we propose a massively multilingual repository-level code completion benchmark covering 18 programming languages (called M2RC-EVAL), and two types of fine-grained annotations (i.e., bucket-level and semantic-level) on different completion scenarios are provided, where we obtain these annotations based on the parsed abstract syntax tree. Moreover, we also curate a massively multilingual instruction corpora M2RC- INSTRUCT dataset to improve the repository-level code completion abilities of existing code LLMs. Comprehensive experimental results demonstrate the effectiveness of our M2RC-EVAL and M2RC-INSTRUCT.

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.

Recent Large Reasoning Models (LRMs), such as DeepSeek-R1 and OpenAI o1, have demonstrated strong performance gains by scaling up the length of Chain-of-Thought (CoT) reasoning during inference. However, a growing concern lies in their tendency to produce excessively long reasoning traces, which are often filled with redundant content (e.g., repeated definitions), over-analysis of simple problems, and superficial exploration of multiple reasoning paths for harder tasks. This inefficiency introduces significant challenges for training, inference, and real-world deployment (e.g., in agent-based systems), where token economy is critical. In this survey, we provide a comprehensive overview of recent efforts aimed at improving reasoning efficiency in LRMs, with a particular focus on the unique challenges that arise in this new paradigm. We identify common patterns of inefficiency, examine methods proposed across the LRM lifecycle, i.e., from pretraining to inference, and discuss promising future directions for research. To support ongoing development, we also maintain a real-time GitHub repository tracking recent progress in the field. We hope this survey serves as a foundation for further exploration and inspires innovation in this rapidly evolving area.

Semantic textual similartiy (STS) and information retrieval tasks (IR) tasks have been the two major avenues to record the progress of embedding models in the past few years. Under the emerging Retrieval-augmented Generation (RAG) paradigm, we envision the need to evaluate next-level language understanding abilities of embedding models, and take a conscious look at the reasoning abilities stored in them. Addressing this, we pose the question: Can retrievers solve reasoning problems? By transforming reasoning tasks into retrieval tasks, we find that without specifically trained for reasoning-level language understanding, current state-of-the-art retriever models may still be far from being competent for playing the role of assisting LLMs, especially in reasoning-intensive tasks. Moreover, albeit trained to be aware of instructions, instruction-aware IR models are often better off without instructions in inference time for reasoning tasks, posing an overlooked retriever-LLM behavioral gap for the research community to align. However, recent decoder-based embedding models show great promise in narrowing the gap, highlighting the pathway for embedding models to achieve reasoning-level language understanding. We also show that, although current off-the-shelf re-ranker models fail on these tasks, injecting reasoning abilities into them through fine-tuning still appears easier than doing so to bi-encoders, and we are able to achieve state-of-the-art performance across all tasks by fine-tuning a reranking model. We release Reasoning as Retrieval Benchmark (RAR-b), a holistic suite of tasks and settings to evaluate the reasoning abilities stored in retriever models. RAR-b is available at https://github.com/gowitheflow-1998/RAR-b.

Repositories of large software systems have become commonplace. This massive expansion has resulted in the emergence of various problems in these software platforms including identification of (i) bug-prone packages, (ii) critical bugs, and (iii) severity of bugs. One of the important goals would be to mine these bugs and recommend them to the developers to resolve them. The first step to this is that one has to accurately detect the extent of severity of the bugs. In this paper, we take up this task of predicting the severity of bugs in the near future. Contextualized neural models built on the text description of a bug and the user comments about the bug help to achieve reasonably good performance. Further information on how the bugs are related to each other in terms of the ways they affect packages can be summarised in the form of a graph and used along with the text to get additional benefits.

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.

Progress in Machine Learning is often driven by the availability of large datasets, and consistent evaluation metrics for comparing modeling approaches. To this end, we present a repository of conversational datasets consisting of hundreds of millions of examples, and a standardised evaluation procedure for conversational response selection models using '1-of-100 accuracy'. The repository contains scripts that allow researchers to reproduce the standard datasets, or to adapt the pre-processing and data filtering steps to their needs. We introduce and evaluate several competitive baselines for conversational response selection, whose implementations are shared in the repository, as well as a neural encoder model that is trained on the entire training set.

Large Language Models (LLMs) have shown impressive capabilities in downstream software engineering tasks such as Automated Program Repair (APR). In particular, there has been a lot of research on repository-level issue-resolution benchmarks such as SWE-Bench. Although there has been significant progress on this topic, we notice that in the process of solving such issues, existing agentic systems tend to hyper-localize on immediately suspicious lines of code and fix them in isolation, without a deeper understanding of the issue semantics, code semantics, or execution semantics. Consequently, many existing systems generate patches that overfit to the user issue, even when a more general fix is preferable. To address this limitation, we introduce SemAgent, a novel workflow-based procedure that leverages issue, code, and execution semantics to generate patches that are complete - identifying and fixing all lines relevant to the issue. We achieve this through a novel pipeline that (a) leverages execution semantics to retrieve relevant context, (b) comprehends issue-semantics via generalized abstraction, (c) isolates code-semantics within the context of this abstraction, and (d) leverages this understanding in a two-stage architecture: a repair stage that proposes fine-grained fixes, followed by a reviewer stage that filters relevant fixes based on the inferred issue-semantics. Our evaluations show that our methodology achieves a solve rate of 44.66% on the SWEBench-Lite benchmark beating all other workflow-based approaches, and an absolute improvement of 7.66% compared to our baseline, which lacks such deep semantic understanding. We note that our approach performs particularly well on issues requiring multi-line reasoning (and editing) and edge-case handling, suggesting that incorporating issue and code semantics into APR pipelines can lead to robust and semantically consistent repairs.

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.

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.

Recent advancements in large language models (LLMs) suggest great promises in code and proof generations. However, scaling automated formal verification to real-world projects requires resolving cross-module dependencies and global contexts, which are crucial challenges overlooked by existing LLM-based methods with a special focus on targeting isolated, function-level verification tasks. To systematically explore and address the significant challenges of verifying entire software repositories, we introduce RVBench, the first verification benchmark explicitly designed for repository-level evaluation, constructed from four diverse and complex open-source Verus projects. We further introduce RagVerus, an extensible framework that synergizes retrieval-augmented generation with context-aware prompting to automate proof synthesis for multi-module repositories. RagVerus triples proof pass rates on existing benchmarks under constrained model inference budgets, and achieves a 27% relative improvement on the more challenging RVBench benchmark, demonstrating a scalable and sample-efficient verification solution.

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

The issue-resolving task, where a model generates patches to fix real-world bugs, has emerged as a critical benchmark for evaluating the capabilities of large language models (LLMs). While SWE-bench and its variants have become standard in this domain, they suffer from key limitations: they have not been updated since their initial releases, cover a narrow set of repositories, and depend heavily on manual effort for instance construction and environment setup. These factors hinder scalability and introduce risks of overfitting and data contamination. In this work, we present SWE-bench-Live, a live-updatable benchmark designed to overcome these challenges. Our initial release consists of 1,319 tasks derived from real GitHub issues created since 2024, spanning 93 repositories. Each task is accompanied by a dedicated Docker image to ensure reproducible execution. Central to our benchmark is \method, an automated curation pipeline that streamlines the entire process from instance creation to environment setup, removing manual bottlenecks and enabling scalability and continuous updates. We evaluate a range of state-of-the-art agent frameworks and LLMs on SWE-bench-Live, revealing a substantial performance gap compared to static benchmarks like SWE-bench, even under controlled evaluation conditions. To better understand this discrepancy, we perform detailed analyses across repository origin, issue recency, and task difficulty. By providing a fresh, diverse, and executable benchmark grounded in live repository activity, SWE-bench-Live facilitates rigorous, contamination-resistant evaluation of LLMs and agents in dynamic, real-world software development settings.

Capability evaluation of large language models (LLMs) is increasingly shadowed by rising concerns of data contamination that cast doubts on whether static benchmarks measure genuine reasoning or mere memorization. We present an empirical study using an infinitely scalable framework to synthesize research-level QA directly from arXiv papers, harnessing the natural temporal structure of research publications where performance decay after knowledge cutoffs may indicate potential contamination. We evaluated 4 frontier model represented by 2 models of different knowledge cutoff dates per family on 1,643 multi-step reasoning questions synthesized from 20,277 arXiv papers stratified over 26 months, covering at least 6 months before and after all cutoff dates. Our results consistently showed a lack of significant performance decay near knowledge cutoff dates for models of various sizes, developers, and release dates. We further performed a comparative analysis with previous longitudinal studies that reported significant post-cutoff performance decay using directly retrieved questions based on public data. we hypothesize that the multi-step reasoning required by our synthesis pipeline offered additional complexity that goes deeper than shallow memorization, which effectively serves a mitigation strategy against benchmark contamination. We fully open source our code and dataset to aid reproducibility and advocate for a paradigm shift that prioritize reasoning-driven synthesis to construct benchmarks over simply collecting newly released questions periodically.

Retrieval-augmented generation (RAG) techniques leverage the in-context learning capabilities of large language models (LLMs) to produce more accurate and relevant responses. Originating from the simple 'retrieve-then-read' approach, the RAG framework has evolved into a highly flexible and modular paradigm. A critical component, the Query Rewriter module, enhances knowledge retrieval by generating a search-friendly query. This method aligns input questions more closely with the knowledge base. Our research identifies opportunities to enhance the Query Rewriter module to Query Rewriter+ by generating multiple queries to overcome the Information Plateaus associated with a single query and by rewriting questions to eliminate Ambiguity, thereby clarifying the underlying intent. We also find that current RAG systems exhibit issues with Irrelevant Knowledge; to overcome this, we propose the Knowledge Filter. These two modules are both based on the instruction-tuned Gemma-2B model, which together enhance response quality. The final identified issue is Redundant Retrieval; we introduce the Memory Knowledge Reservoir and the Retriever Trigger to solve this. The former supports the dynamic expansion of the RAG system's knowledge base in a parameter-free manner, while the latter optimizes the cost for accessing external knowledge, thereby improving resource utilization and response efficiency. These four RAG modules synergistically improve the response quality and efficiency of the RAG system. The effectiveness of these modules has been validated through experiments and ablation studies across six common QA datasets. The source code can be accessed at https://github.com/Ancientshi/ERM4.

The impressive performance of large language models (LLMs) on code-related tasks has shown the potential of fully automated software development. In light of this, we introduce a new software engineering task, namely Natural Language to code Repository (NL2Repo). This task aims to generate an entire code repository from its natural language requirements. To address this task, we propose a simple yet effective framework CodeS, which decomposes NL2Repo into multiple sub-tasks by a multi-layer sketch. Specifically, CodeS includes three modules: RepoSketcher, FileSketcher, and SketchFiller. RepoSketcher first generates a repository's directory structure for given requirements; FileSketcher then generates a file sketch for each file in the generated structure; SketchFiller finally fills in the details for each function in the generated file sketch. To rigorously assess CodeS on the NL2Repo task, we carry out evaluations through both automated benchmarking and manual feedback analysis. For benchmark-based evaluation, we craft a repository-oriented benchmark, SketchEval, and design an evaluation metric, SketchBLEU. For feedback-based evaluation, we develop a VSCode plugin for CodeS and engage 30 participants in conducting empirical studies. Extensive experiments prove the effectiveness and practicality of CodeS on the NL2Repo task.

With the success of large language models (LLMs) of code and their use as code assistants (e.g. Codex used in GitHub Copilot), techniques for introducing domain-specific knowledge in the prompt design process become important. In this work, we propose a framework called Repo-Level Prompt Generator that learns to generate example-specific prompts using prompt proposals. The prompt proposals take context from the entire repository, thereby incorporating both the structure of the repository and the context from other relevant files (e.g. imports, parent class files). Our technique doesn't require any access to the weights of the LLM, making it applicable in cases where we only have black-box access to the LLM. We conduct experiments on the task of single-line code-autocompletion using code repositories taken from Google Code archives. We demonstrate that an oracle constructed from our prompt proposals gives a remarkably high relative improvement of 36% over Codex, showing the quality of these proposals. Further, we show that when we train a model to predict a prompt proposal, we can achieve significant performance gains over Codex and other baselines. We release our code, data, and trained checkpoints at: https://github.com/shrivastavadisha/repo_level_prompt_generation.

Text Retrieval (TR) involves finding and retrieving text-based content relevant to a user's query from a large repository, with applications in real-world scenarios such as legal document retrieval. While most existing studies focus on English, limited work addresses Japanese contexts. In this paper, we introduce a new dataset specifically designed for Japanese legal contexts and propose a novel two-phase pipeline tailored to this domain. In the first phase, the model learns a broad understanding of global contexts, enhancing its generalization and adaptability to diverse queries. In the second phase, the model is fine-tuned to address complex queries specific to legal scenarios. Extensive experiments are conducted to demonstrate the superior performance of our method, which outperforms existing baselines. Furthermore, our pipeline proves effective in English contexts, surpassing comparable baselines on the MS MARCO dataset. We have made our code publicly available on GitHub, and the model checkpoints are accessible via HuggingFace.

In this paper, we identify and characterize the emerging area of representation engineering (RepE), an approach to enhancing the transparency of AI systems that draws on insights from cognitive neuroscience. RepE places population-level representations, rather than neurons or circuits, at the center of analysis, equipping us with novel methods for monitoring and manipulating high-level cognitive phenomena in deep neural networks (DNNs). We provide baselines and an initial analysis of RepE techniques, showing that they offer simple yet effective solutions for improving our understanding and control of large language models. We showcase how these methods can provide traction on a wide range of safety-relevant problems, including honesty, harmlessness, power-seeking, and more, demonstrating the promise of top-down transparency research. We hope that this work catalyzes further exploration of RepE and fosters advancements in the transparency and safety of AI systems.

The widespread availability of open-source repositories has led to a vast collection of reusable software components, yet their utilization remains manual, error-prone, and disconnected. Developers must navigate documentation, understand APIs, and write integration code, creating significant barriers to efficient software reuse. To address this, we present EnvX, a framework that leverages Agentic AI to agentize GitHub repositories, transforming them into intelligent, autonomous agents capable of natural language interaction and inter-agent collaboration. Unlike existing approaches that treat repositories as static code resources, EnvX reimagines them as active agents through a three-phase process: (1) TODO-guided environment initialization, which sets up the necessary dependencies, data, and validation datasets; (2) human-aligned agentic automation, allowing repository-specific agents to autonomously perform real-world tasks; and (3) Agent-to-Agent (A2A) protocol, enabling multiple agents to collaborate. By combining large language model capabilities with structured tool integration, EnvX automates not just code generation, but the entire process of understanding, initializing, and operationalizing repository functionality. We evaluate EnvX on the GitTaskBench benchmark, using 18 repositories across domains such as image processing, speech recognition, document analysis, and video manipulation. Our results show that EnvX achieves a 74.07% execution completion rate and 51.85% task pass rate, outperforming existing frameworks. Case studies further demonstrate EnvX's ability to enable multi-repository collaboration via the A2A protocol. This work marks a shift from treating repositories as passive code resources to intelligent, interactive agents, fostering greater accessibility and collaboration within the open-source ecosystem.

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.

In Greek mythology, Pistis symbolized good faith, trust, and reliability, echoing the core principles of RAG in LLM systems. Pistis-RAG, a scalable multi-stage framework, effectively addresses the challenges of large-scale retrieval-augmented generation (RAG). Each stage plays a distinct role: matching refines the search space, pre-ranking prioritizes semantically relevant documents, and ranking aligns with the large language model's (LLM) preferences. The reasoning and aggregating stage supports the implementation of complex chain-of-thought (CoT) methods within this cascading structure. We argue that the lack of strong alignment between LLMs and the external knowledge ranking methods used in RAG tasks is relevant to the reliance on the model-centric paradigm in RAG frameworks. A content-centric approach would prioritize seamless integration between the LLMs and external information sources, optimizing the content transformation process for each specific task. Critically, our ranking stage deviates from traditional RAG approaches by recognizing that semantic relevance alone may not directly translate to improved generation. This is due to the sensitivity of the few-shot prompt order, as highlighted in prior work lu2021fantastically. Current RAG frameworks fail to account for this crucial factor. We introduce a novel ranking stage specifically designed for RAG systems. It adheres to information retrieval principles while considering the unique business scenario captured by LLM preferences and user feedback. Our approach integrates in-context learning (ICL) methods and reasoning steps to incorporate user feedback, ensuring efficient alignment. Experiments on the MMLU benchmark demonstrate a 9.3\% performance improvement. The model and code will be open-sourced on GitHub. Experiments on real-world, large-scale data validate our framework's scalability.

There is a compelling necessity from enterprises for fine tuning LLMs (Large Language Models) o get them trained on proprietary domain knowledge. The challenge is to imbibe the LLMs with domain specific knowledge using the most optimial resource and cost and in the best possible time. Many enterprises rely on RAG (Retrieval Augmented Generation) which does not need LLMs to be ine-tuned but they are limited by the quality of vector databases and their retrieval capabilities rather than the intrinsic capabilities of the LLMs themselves. In our current work we focus on fine tuning LLaMA, an open source LLM using proprietary documents and code from an enterprise repository and use the fine tuned models to evaluate the quality of responses. As part of this work, we aim to guide beginners on how to start with fine tuning an LLM for documentation and code by making educated guesses on size of GPU required and options that are available for formatting the data. We also propose pre processing recipes for both documentation and code to prepare dataset in different formats. The proposed methods of data preparation for document datasets are forming paragraph chunks, forming question and answer pairs and forming keyword and paragraph chunk pairs. For code dataset we propose forming summary and function pairs. Further, we qualitatively evaluate the results of the models for domain specific queries. Finally, we also propose practical guidelines and recommendations for fine tuning LLMs.

Large language models (LLMs) have recently achieved human-level performance on a range of professional and academic benchmarks. The accessibility of these models has lagged behind their performance. State-of-the-art LLMs require costly infrastructure; are only accessible via rate-limited, geo-locked, and censored web interfaces; and lack publicly available code and technical reports. In this paper, we tell the story of GPT4All, a popular open source repository that aims to democratize access to LLMs. We outline the technical details of the original GPT4All model family, as well as the evolution of the GPT4All project from a single model into a fully fledged open source ecosystem. It is our hope that this paper acts as both a technical overview of the original GPT4All models as well as a case study on the subsequent growth of the GPT4All open source ecosystem.

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.

Information extraction (IE) aims to extract structural knowledge (such as entities, relations, and events) from plain natural language texts. Recently, generative Large Language Models (LLMs) have demonstrated remarkable capabilities in text understanding and generation, allowing for generalization across various domains and tasks. As a result, numerous works have been proposed to harness abilities of LLMs and offer viable solutions for IE tasks based on a generative paradigm. To conduct a comprehensive systematic review and exploration of LLM efforts for IE tasks, in this study, we survey the most recent advancements in this field. We first present an extensive overview by categorizing these works in terms of various IE subtasks and learning paradigms, then we empirically analyze the most advanced methods and discover the emerging trend of IE tasks with LLMs. Based on thorough review conducted, we identify several insights in technique and promising research directions that deserve further exploration in future studies. We maintain a public repository and consistently update related resources at: https://github.com/quqxui/Awesome-LLM4IE-Papers.

Software engineers are increasingly adding semantic search capabilities to applications using a strategy known as Retrieval Augmented Generation (RAG). A RAG system involves finding documents that semantically match a query and then passing the documents to a large language model (LLM) such as ChatGPT to extract the right answer using an LLM. RAG systems aim to: a) reduce the problem of hallucinated responses from LLMs, b) link sources/references to generated responses, and c) remove the need for annotating documents with meta-data. However, RAG systems suffer from limitations inherent to information retrieval systems and from reliance on LLMs. In this paper, we present an experience report on the failure points of RAG systems from three case studies from separate domains: research, education, and biomedical. We share the lessons learned and present 7 failure points to consider when designing a RAG system. The two key takeaways arising from our work are: 1) validation of a RAG system is only feasible during operation, and 2) the robustness of a RAG system evolves rather than designed in at the start. We conclude with a list of potential research directions on RAG systems for the software engineering community.

Following the rise of large language models (LLMs), many studies have emerged in recent years focusing on exploring the adoption of LLM-based tools for software development by novice developers: computer science/software engineering students and early-career industry developers with two years or less of professional experience. These studies have sought to understand the perspectives of novice developers on using these tools, a critical aspect of the successful adoption of LLMs in software engineering. To systematically collect and summarise these studies, we conducted a systematic literature review (SLR) following the guidelines by Kitchenham et al. on 80 primary studies published between April 2022 and June 2025 to answer four research questions (RQs). In answering RQ1, we categorised the study motivations and methodological approaches. In RQ2, we identified the software development tasks for which novice developers use LLMs. In RQ3, we categorised the advantages, challenges, and recommendations discussed in the studies. Finally, we discuss the study limitations and future research needs suggested in the primary studies in answering RQ4. Throughout the paper, we also indicate directions for future work and implications for software engineering researchers, educators, and developers. Our research artifacts are publicly available at https://github.com/Samuellucas97/SupplementaryInfoPackage-SLR.

This survey presents an in-depth exploration of knowledge distillation (KD) techniques within the realm of Large Language Models (LLMs), spotlighting the pivotal role of KD in transferring sophisticated capabilities from proprietary giants such as GPT-4 to accessible, open-source models like LLaMA and Mistral. Amidst the evolving AI landscape, this work elucidates the critical disparities between proprietary and open-source LLMs, demonstrating how KD serves as an essential conduit for imbuing the latter with the former's advanced functionalities and nuanced understandings. Our survey is meticulously structured around three foundational pillars: algorithm, skill, and verticalization -- providing a comprehensive examination of KD mechanisms, the enhancement of specific cognitive abilities, and their practical implications across diverse fields. Crucially, the survey navigates the intricate interplay between data augmentation (DA) and KD, illustrating how DA emerges as a powerful paradigm within the KD framework to bolster LLMs' performance. By leveraging DA to generate context-rich, skill-specific training data, KD transcends traditional boundaries, enabling open-source models to approximate the contextual adeptness, ethical alignment, and deep semantic insights characteristic of their proprietary counterparts. This work aims to provide an insightful guide for researchers and practitioners, offering a detailed overview of current methodologies in knowledge distillation and proposing future research directions. By bridging the gap between proprietary and open-source LLMs, this survey underscores the potential for more accessible, efficient, and sustainable AI solutions, fostering a more inclusive and equitable landscape in AI advancements. An associated Github repository is available at https://github.com/Tebmer/Awesome-Knowledge-Distillation-of-LLMs.

Embeddings have become a pivotal means to represent complex, multi-faceted information about entities, concepts, and relationships in a condensed and useful format. Nevertheless, they often preclude direct interpretation. While downstream tasks make use of these compressed representations, meaningful interpretation usually requires visualization using dimensionality reduction or specialized machine learning interpretability methods. This paper addresses the challenge of making such embeddings more interpretable and broadly useful, by employing Large Language Models (LLMs) to directly interact with embeddings -- transforming abstract vectors into understandable narratives. By injecting embeddings into LLMs, we enable querying and exploration of complex embedding data. We demonstrate our approach on a variety of diverse tasks, including: enhancing concept activation vectors (CAVs), communicating novel embedded entities, and decoding user preferences in recommender systems. Our work couples the immense information potential of embeddings with the interpretative power of LLMs.

Recognizing software entities such as library names from free-form text is essential to enable many software engineering (SE) technologies, such as traceability link recovery, automated documentation, and API recommendation. While many approaches have been proposed to address this problem, they suffer from small entity vocabularies or noisy training data, hindering their ability to recognize software entities mentioned in sophisticated narratives. To address this challenge, we leverage the Wikipedia taxonomy to develop a comprehensive entity lexicon with 79K unique software entities in 12 fine-grained types, as well as a large labeled dataset of over 1.7M sentences. Then, we propose self-regularization, a noise-robust learning approach, to the training of our software entity recognition (SER) model by accounting for many dropouts. Results show that models trained with self-regularization outperform both their vanilla counterparts and state-of-the-art approaches on our Wikipedia benchmark and two Stack Overflow benchmarks. We release our models, data, and code for future research.

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.

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.

In this survey, we systematically analyze techniques used to adapt large multimodal models (LMMs) for low-resource (LR) languages, examining approaches ranging from visual enhancement and data creation to cross-modal transfer and fusion strategies. Through a comprehensive analysis of 106 studies across 75 LR languages, we identify key patterns in how researchers tackle the challenges of limited data and computational resources. We find that visual information often serves as a crucial bridge for improving model performance in LR settings, though significant challenges remain in areas such as hallucination mitigation and computational efficiency. We aim to provide researchers with a clear understanding of current approaches and remaining challenges in making LMMs more accessible to speakers of LR (understudied) languages. We complement our survey with an open-source repository available at: https://github.com/marianlupascu/LMM4LRL-Survey.

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.

Large language models (LLMs) have recently shown strong progress on scientific reasoning, yet two major bottlenecks remain. First, explicit retrieval fragments reasoning, imposing a hidden "tool tax" of extra tokens and steps. Second, multi-agent pipelines often dilute strong solutions by averaging across all candidates. We address these challenges with a unified framework that combines implicit retrieval and structured collaboration. At its foundation, a Monitor-based retrieval module operates at the token level, integrating external knowledge with minimal disruption to reasoning. On top of this substrate, Hierarchical Solution Refinement (HSR) iteratively designates each candidate as an anchor to be repaired by its peers, while Quality-Aware Iterative Reasoning (QAIR) adapts refinement to solution quality. On Humanity's Last Exam (HLE) Bio/Chem Gold, our framework achieves 48.3\% accuracy -- the highest reported to date, surpassing the strongest agent baseline by 13.4 points and leading frontier LLMs by up to 18.1 points, while simultaneously reducing token usage by 53.5\% and agent steps by 43.7\%. Results on SuperGPQA and TRQA confirm robustness across domains. Error analysis shows that reasoning failures and knowledge gaps co-occur in over 85\% of cases, while diversity analysis reveals a clear dichotomy: retrieval tasks benefit from solution variety, whereas reasoning tasks favor consensus. Together, these findings demonstrate how implicit augmentation and structured refinement overcome the inefficiencies of explicit tool use and uniform aggregation. Code is available at: https://github.com/tangxiangru/Eigen-1.

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.

The performance of Retrieval Augmented Generation (RAG) systems relies heavily on the retriever quality and the size of the retrieved context. A large enough context ensures that the relevant information is present in the input context for the LLM, but also incorporates irrelevant content that has been shown to confuse the models. On the other hand, a smaller context reduces the irrelevant information, but it often comes at the risk of losing important information necessary to answer the input question. This duality is especially challenging to manage for complex queries that contain little information to retrieve the relevant chunks from the full context. To address this, we present a novel framework, called FB-RAG, which enhances the RAG pipeline by relying on a combination of backward lookup (overlap with the query) and forward lookup (overlap with candidate reasons and answers) to retrieve specific context chunks that are the most relevant for answering the input query. Our evaluations on 9 datasets from two leading benchmarks show that FB-RAG consistently outperforms RAG and Long Context baselines developed recently for these benchmarks. We further show that FB-RAG can improve performance while reducing latency. We perform qualitative analysis of the strengths and shortcomings of our approach, providing specific insights to guide future work.

Given that Large Language Models (LLMs) have made significant progress in writing code, can they now be used to autonomously reproduce results from research repositories? Such a capability would be a boon to the research community, helping researchers validate, understand, and extend prior work. To advance towards this goal, we introduce SUPER, the first benchmark designed to evaluate the capability of LLMs in setting up and executing tasks from research repositories. SUPERaims to capture the realistic challenges faced by researchers working with Machine Learning (ML) and Natural Language Processing (NLP) research repositories. Our benchmark comprises three distinct problem sets: 45 end-to-end problems with annotated expert solutions, 152 sub problems derived from the expert set that focus on specific challenges (e.g., configuring a trainer), and 602 automatically generated problems for larger-scale development. We introduce various evaluation measures to assess both task success and progress, utilizing gold solutions when available or approximations otherwise. We show that state-of-the-art approaches struggle to solve these problems with the best model (GPT-4o) solving only 16.3% of the end-to-end set, and 46.1% of the scenarios. This illustrates the challenge of this task, and suggests that SUPER can serve as a valuable resource for the community to make and measure progress.

Interpretability is a key challenge in fostering trust for Large Language Models (LLMs), which stems from the complexity of extracting reasoning from model's parameters. We present the Frame Representation Hypothesis, a theoretically robust framework grounded in the Linear Representation Hypothesis (LRH) to interpret and control LLMs by modeling multi-token words. Prior research explored LRH to connect LLM representations with linguistic concepts, but was limited to single token analysis. As most words are composed of several tokens, we extend LRH to multi-token words, thereby enabling usage on any textual data with thousands of concepts. To this end, we propose words can be interpreted as frames, ordered sequences of vectors that better capture token-word relationships. Then, concepts can be represented as the average of word frames sharing a common concept. We showcase these tools through Top-k Concept-Guided Decoding, which can intuitively steer text generation using concepts of choice. We verify said ideas on Llama 3.1, Gemma 2, and Phi 3 families, demonstrating gender and language biases, exposing harmful content, but also potential to remediate them, leading to safer and more transparent LLMs. Code is available at https://github.com/phvv-me/frame-representation-hypothesis.git

DeepResearch agents represent a transformative AI paradigm, conducting expert-level research through sophisticated reasoning and multi-tool integration. However, evaluating these systems remains critically challenging due to open-ended research scenarios and existing benchmarks that focus on isolated capabilities rather than holistic performance. Unlike traditional LLM tasks, DeepResearch systems must synthesize diverse sources, generate insights, and present coherent findings, which are capabilities that resist simple verification. To address this gap, we introduce DeepResearch-ReportEval, a comprehensive framework designed to assess DeepResearch systems through their most representative outputs: research reports. Our approach systematically measures three dimensions: quality, redundancy, and factuality, using an innovative LLM-as-a-Judge methodology achieving strong expert concordance. We contribute a standardized benchmark of 100 curated queries spanning 12 real-world categories, enabling systematic capability comparison. Our evaluation of four leading commercial systems reveals distinct design philosophies and performance trade-offs, establishing foundational insights as DeepResearch evolves from information assistants toward intelligent research partners. Source code and data are available at: https://github.com/HKUDS/DeepResearch-Eval.

Recent advancements in Large Language Models (LLMs) have transformed code generation from natural language queries. However, despite their extensive knowledge and ability to produce high-quality code, LLMs often struggle with contextual accuracy, particularly in evolving codebases. Current code search and retrieval methods frequently lack robustness in both the quality and contextual relevance of retrieved results, leading to suboptimal code generation. This paper introduces a novel knowledge graph-based approach to improve code search and retrieval leading to better quality of code generation in the context of repository-level tasks. The proposed approach represents code repositories as graphs, capturing structural and relational information for enhanced context-aware code generation. Our framework employs a hybrid approach for code retrieval to improve contextual relevance, track inter-file modular dependencies, generate more robust code and ensure consistency with the existing codebase. We benchmark the proposed approach on the Evolutionary Code Benchmark (EvoCodeBench) dataset, a repository-level code generation benchmark, and demonstrate that our method significantly outperforms the baseline approach. These findings suggest that knowledge graph based code generation could advance robust, context-sensitive coding assistance tools.

Retrieval Augmented Generation (RAG) has emerged as a standard paradigm for enhancing the factual accuracy and contextual relevance of Large Language Models (LLMs) by integrating retrieval mechanisms. However, existing evaluation frameworks fail to provide a holistic black-box approach to assessing RAG systems, especially in real-world deployment scenarios. To address this gap, we introduce SCARF (System for Comprehensive Assessment of RAG Frameworks), a modular and flexible evaluation framework designed to benchmark deployed RAG applications systematically. SCARF provides an end-to-end, black-box evaluation methodology, enabling a limited-effort comparison across diverse RAG frameworks. Our framework supports multiple deployment configurations and facilitates automated testing across vector databases and LLM serving strategies, producing a detailed performance report. Moreover, SCARF integrates practical considerations such as response coherence, providing a scalable and adaptable solution for researchers and industry professionals evaluating RAG applications. Using the REST APIs interface, we demonstrate how SCARF can be applied to real-world scenarios, showcasing its flexibility in assessing different RAG frameworks and configurations. SCARF is available at GitHub repository.

Software engineering activities such as package migration, fixing errors reports from static analysis or testing, and adding type annotations or other specifications to a codebase, involve pervasively editing the entire repository of code. We formulate these activities as repository-level coding tasks. Recent tools like GitHub Copilot, which are powered by Large Language Models (LLMs), have succeeded in offering high-quality solutions to localized coding problems. Repository-level coding tasks are more involved and cannot be solved directly using LLMs, since code within a repository is inter-dependent and the entire repository may be too large to fit into the prompt. We frame repository-level coding as a planning problem and present a task-agnostic framework, called CodePlan to solve it. CodePlan synthesizes a multi-step chain of edits (plan), where each step results in a call to an LLM on a code location with context derived from the entire repository, previous code changes and task-specific instructions. CodePlan is based on a novel combination of an incremental dependency analysis, a change may-impact analysis and an adaptive planning algorithm. We evaluate the effectiveness of CodePlan on two repository-level tasks: package migration (C#) and temporal code edits (Python). Each task is evaluated on multiple code repositories, each of which requires inter-dependent changes to many files (between 2-97 files). Coding tasks of this level of complexity have not been automated using LLMs before. Our results show that CodePlan has better match with the ground truth compared to baselines. CodePlan is able to get 5/6 repositories to pass the validity checks (e.g., to build without errors and make correct code edits) whereas the baselines (without planning but with the same type of contextual information as CodePlan) cannot get any of the repositories to pass them.

The rapid evolution of Multimodal Large Language Models (MLLMs) has brought substantial advancements in artificial intelligence, significantly enhancing the capability to understand and generate multimodal content. While prior studies have largely concentrated on model architectures and training methodologies, a thorough analysis of the benchmarks used for evaluating these models remains underexplored. This survey addresses this gap by systematically reviewing 211 benchmarks that assess MLLMs across four core domains: understanding, reasoning, generation, and application. We provide a detailed analysis of task designs, evaluation metrics, and dataset constructions, across diverse modalities. We hope that this survey will contribute to the ongoing advancement of MLLM research by offering a comprehensive overview of benchmarking practices and identifying promising directions for future work. An associated GitHub repository collecting the latest papers is available.

Automated code review (CR) is a key application for Large Language Models (LLMs), but progress is hampered by a "reality gap": existing benchmarks evaluate models on isolated sub-tasks using simplified, context-poor data. This fails to reflect the holistic context-rich nature of real-world CR. To bridge this gap, we introduce CodeFuse-CR-Bench, the first comprehensiveness-aware benchmark for repository-level CR evaluation. CodeFuse-CR-Bench comprises 601 high-quality instances from 70 Python projects covering nine Pull-Request (PR) problem domains, where each instance provides rich, multi-faceted context including the associated issue, PR details, and repository state, enabling end-to-end evaluation. Beyond superficial metrics, we also propose a novel evaluation framework that combines rule-based checks for location and syntax with model-based judgments of review quality. We present the first large-scale assessment of state-of-the-art LLMs on this comprehensive CR task. Our results establish crucial baselines and reveal that (1) no single LLM dominates all aspects of CR; (2) Gemini 2.5 Pro achieves the highest comprehensive performance; and (3) different LLMs exhibit varying robustness to redundant context. These findings highlight the necessity of holistic, multi-dimensional evaluation and provide actionable insights for advancing truly intelligent yet practical CR assistants.

Large Language Models (LLMs) excel in stand-alone code tasks like HumanEval and MBPP, but struggle with handling entire code repositories. This challenge has prompted research on enhancing LLM-codebase interaction at a repository scale. Current solutions rely on similarity-based retrieval or manual tools and APIs, each with notable drawbacks. Similarity-based retrieval often has low recall in complex tasks, while manual tools and APIs are typically task-specific and require expert knowledge, reducing their generalizability across diverse code tasks and real-world applications. To mitigate these limitations, we introduce \framework, a system that integrates LLM agents with graph database interfaces extracted from code repositories. By leveraging the structural properties of graph databases and the flexibility of the graph query language, \framework enables the LLM agent to construct and execute queries, allowing for precise, code structure-aware context retrieval and code navigation. We assess \framework using three benchmarks: CrossCodeEval, SWE-bench, and EvoCodeBench. Additionally, we develop five real-world coding applications. With a unified graph database schema, \framework demonstrates competitive performance and potential in both academic and real-world environments, showcasing its versatility and efficacy in software engineering. Our application demo: https://github.com/modelscope/modelscope-agent/tree/master/apps/codexgraph_agent.

Retrieval-Augmented Generation (RAG) has emerged as a fundamental paradigm for expanding Large Language Models beyond their static training limitations. However, a critical misalignment exists between current RAG capabilities and real-world information environments. Modern knowledge repositories are inherently multimodal, containing rich combinations of textual content, visual elements, structured tables, and mathematical expressions. Yet existing RAG frameworks are limited to textual content, creating fundamental gaps when processing multimodal documents. We present RAG-Anything, a unified framework that enables comprehensive knowledge retrieval across all modalities. Our approach reconceptualizes multimodal content as interconnected knowledge entities rather than isolated data types. The framework introduces dual-graph construction to capture both cross-modal relationships and textual semantics within a unified representation. We develop cross-modal hybrid retrieval that combines structural knowledge navigation with semantic matching. This enables effective reasoning over heterogeneous content where relevant evidence spans multiple modalities. RAG-Anything demonstrates superior performance on challenging multimodal benchmarks, achieving significant improvements over state-of-the-art methods. Performance gains become particularly pronounced on long documents where traditional approaches fail. Our framework establishes a new paradigm for multimodal knowledge access, eliminating the architectural fragmentation that constrains current systems. Our framework is open-sourced at: https://github.com/HKUDS/RAG-Anything.

While language models (LMs) have proven remarkably adept at generating code, many programs are challenging for LMs to generate using their parametric knowledge alone. Providing external contexts such as library documentation can facilitate generating accurate and functional code. Despite the success of retrieval-augmented generation (RAG) in various text-oriented tasks, its potential for improving code generation remains under-explored. In this work, we conduct a systematic, large-scale analysis by asking: in what scenarios can retrieval benefit code generation models? and what challenges remain? We first curate a comprehensive evaluation benchmark, CodeRAG-Bench, encompassing three categories of code generation tasks, including basic programming, open-domain, and repository-level problems. We aggregate documents from five sources for models to retrieve contexts: competition solutions, online tutorials, library documentation, StackOverflow posts, and GitHub repositories. We examine top-performing models on CodeRAG-Bench by providing contexts retrieved from one or multiple sources. While notable gains are made in final code generation by retrieving high-quality contexts across various settings, our analysis reveals room for improvement -- current retrievers still struggle to fetch useful contexts especially with limited lexical overlap, and generators fail to improve with limited context lengths or abilities to integrate additional contexts. We hope CodeRAG-Bench serves as an effective testbed to encourage further development of advanced code-oriented RAG methods.

Information retrieval is a cornerstone of modern knowledge acquisition, enabling billions of queries each day across diverse domains. However, traditional keyword-based search engines are increasingly inadequate for handling complex, multi-step information needs. Our position is that Large Language Models (LLMs), endowed with reasoning and agentic capabilities, are ushering in a new paradigm termed Agentic Deep Research. These systems transcend conventional information search techniques by tightly integrating autonomous reasoning, iterative retrieval, and information synthesis into a dynamic feedback loop. We trace the evolution from static web search to interactive, agent-based systems that plan, explore, and learn. We also introduce a test-time scaling law to formalize the impact of computational depth on reasoning and search. Supported by benchmark results and the rise of open-source implementations, we demonstrate that Agentic Deep Research not only significantly outperforms existing approaches, but is also poised to become the dominant paradigm for future information seeking. All the related resources, including industry products, research papers, benchmark datasets, and open-source implementations, are collected for the community in https://github.com/DavidZWZ/Awesome-Deep-Research.

Replicating AI research is a crucial yet challenging task for large language model (LLM) agents. Existing approaches often struggle to generate executable code, primarily due to insufficient background knowledge and the limitations of retrieval-augmented generation (RAG) methods, which fail to capture latent technical details hidden in referenced papers. Furthermore, previous approaches tend to overlook valuable implementation-level code signals and lack structured knowledge representations that support multi-granular retrieval and reuse. To overcome these challenges, we propose Executable Knowledge Graphs (xKG), a modular and pluggable knowledge base that automatically integrates technical insights, code snippets, and domain-specific knowledge extracted from scientific literature. When integrated into three agent frameworks with two different LLMs, xKG shows substantial performance gains (10.9% with o3-mini) on PaperBench, demonstrating its effectiveness as a general and extensible solution for automated AI research replication. Code will released at https://github.com/zjunlp/xKG.

Retrieval-Augmented Generation (RAG) enhances large language models (LLMs) by integrating external knowledge, where the LLM's ability to generate responses based on the combination of a given query and retrieved documents is crucial. However, most benchmarks focus on overall RAG system performance, rarely assessing LLM-specific capabilities. Current benchmarks emphasize broad aspects such as noise robustness, but lack a systematic and granular evaluation framework on document utilization. To this end, we introduce Placeholder-RAG-Benchmark, a multi-level fine-grained benchmark, emphasizing the following progressive dimensions: (1) multi-level filtering abilities, (2) combination abilities, and (3) reference reasoning. To provide a more nuanced understanding of LLMs' roles in RAG systems, we formulate an innovative placeholder-based approach to decouple the contributions of the LLM's parametric knowledge and the external knowledge. Experiments demonstrate the limitations of representative LLMs in the RAG system's generation capabilities, particularly in error resilience and context faithfulness. Our benchmark provides a reproducible framework for developing more reliable and efficient RAG systems. Our code is available in https://github.com/Alipay-Med/PRGB.

Semantic role labeling (SRL) is a central natural language processing (NLP) task aiming to understand the semantic roles within texts, facilitating a wide range of downstream applications. While SRL has garnered extensive and enduring research, there is currently a lack of a comprehensive survey that thoroughly organizes and synthesizes the field. This paper aims to review the entire research trajectory of the SRL community over the past two decades. We begin by providing a complete definition of SRL. To offer a comprehensive taxonomy, we categorize SRL methodologies into four key perspectives: model architectures, syntax feature modeling, application scenarios, and multi-modal extensions. Further, we discuss SRL benchmarks, evaluation metrics, and paradigm modeling approaches, while also exploring practical applications across various domains. Finally, we analyze future research directions in SRL, addressing the evolving role of SRL in the age of large language models (LLMs) and its potential impact on the broader NLP landscape. We maintain a public repository and consistently update related resources at: https://github.com/DreamH1gh/Awesome-SRL

Retrieval-augmented systems are typically evaluated in settings where information required to answer the query can be found within a single source or the answer is short-form or factoid-based. However, many real-world applications demand the ability to integrate and summarize information scattered across multiple sources, where no single source is sufficient to respond to the user's question. In such settings, the retrieval component of a RAG pipeline must recognize a variety of relevance signals, and the generation component must connect and synthesize information across multiple sources. We present a scalable framework for constructing evaluation benchmarks that challenge RAG systems to integrate information across distinct sources and generate long-form responses. Using our framework, we build two new benchmarks on Multi-Source Retrieval and Synthesis: MSRS-Story and MSRS-Meet, representing narrative synthesis and summarization tasks, respectively, that require retrieval from large collections. Our extensive experiments with various RAG pipelines -- including sparse and dense retrievers combined with frontier LLMs -- reveal that generation quality is highly dependent on retrieval effectiveness, which varies greatly by task. While multi-source synthesis proves challenging even in an oracle retrieval setting, we find that reasoning models significantly outperform standard LLMs at this distinct step.

Retrieval-augmented generation (RAG) incorporates external knowledge into large language models (LLMs), improving their adaptability to downstream tasks and enabling information updates. Surprisingly, recent empirical evidence demonstrates that injecting noise into retrieved relevant documents paradoxically facilitates exploitation of external knowledge and improves generation quality. Although counterintuitive and challenging to apply in practice, this phenomenon enables granular control and rigorous analysis of how LLMs integrate external knowledge. Therefore, in this paper, we intervene on noise injection and establish a layer-specific functional demarcation within the LLM: shallow layers specialize in local context modeling, intermediate layers focus on integrating long-range external factual knowledge, and deeper layers primarily rely on parametric internal knowledge. Building on this insight, we propose Layer Fused Decoding (LFD), a simple decoding strategy that directly combines representations from an intermediate layer with final-layer decoding outputs to fully exploit the external factual knowledge. To identify the optimal intermediate layer, we introduce an internal knowledge score (IKS) criterion that selects the layer with the lowest IKS value in the latter half of layers. Experimental results across multiple benchmarks demonstrate that LFD helps RAG systems more effectively surface retrieved context knowledge with minimal cost.

Given a large and evolving codebase, the ability to automatically generate holistic, architecture-aware documentation that captures not only individual functions but also cross-file, cross-module, and system-level interactions remains an open challenge. Comprehensive documentation is essential for long-term software maintenance and collaboration, yet current automated approaches still fail to model the rich semantic dependencies and architectural structures that define real-world software systems. We present CodeWiki, a unified framework for automated repository-level documentation across seven programming languages. CodeWiki introduces three key innovations: (i) hierarchical decomposition that preserves architectural context across multiple levels of granularity, (ii) recursive multi-agent processing with dynamic task delegation for scalable generation, and (iii) multi-modal synthesis that integrates textual descriptions with visual artifacts such as architecture diagrams and data-flow representations. To enable rigorous evaluation, we introduce CodeWikiBench, a comprehensive benchmark featuring multi-dimensional rubrics and LLM-based assessment protocols. Experimental results show that CodeWiki achieves a 68.79\% quality score with proprietary models, outperforming the closed-source DeepWiki baseline (64.06\%) by 4.73\%, with particularly strong improvements on high-level scripting languages (+10.47\%). We open-source CodeWiki to foster future research and community adoption.

The GitHub issue resolution task aims to resolve issues reported in repositories automatically. With advances in large language models (LLMs), this task has gained increasing attention, and several benchmarks are proposed to evaluate the issue resolution ability of LLMs. However, existing benchmarks have three main limitations. First, current benchmarks focus on a single programming language, limiting the evaluation of issues from repositories across different languages. Second, they usually cover a narrow range of domains, which may fail to represent the diversity of real-world issues. Third, existing benchmarks rely solely on textual information in issue descriptions, overlooking multimodal information such as images in issues. In this paper, we propose OmniGIRL, a GitHub Issue ResoLution benchmark that is multilingual, multimodal, and multi-domain. OmniGIRL includes 959 task instances, which are collected from repositories across four programming languages (i.e., Python, JavaScript, TypeScript, and Java) and eight different domains. Our evaluation shows that current LLMs show limited performances on OmniGIRL. Notably, the best-performing model, GPT-4o, resolves only 8.6% of the issues. Besides, we find that current LLMs struggle to resolve issues requiring understanding images. The best performance is achieved by Claude-3.5-Sonnet, which resolves only 10.5% of the issues with image information. Finally, we analyze the reasons behind current LLMs' failure on OmniGIRL, providing insights for future improvements.

Generative models have demonstrated considerable potential in software engineering, particularly in tasks such as code generation and debugging. However, their utilization in the domain of code documentation generation remains underexplored. To this end, we introduce RepoAgent, a large language model powered open-source framework aimed at proactively generating, maintaining, and updating code documentation. Through both qualitative and quantitative evaluations, we have validated the effectiveness of our approach, showing that RepoAgent excels in generating high-quality repository-level documentation. The code and results are publicly accessible at https://github.com/OpenBMB/RepoAgent.

Recent advancements in NLP systems, particularly with the introduction of LLMs, have led to widespread adoption of these systems by a broad spectrum of users across various domains, impacting decision-making, the job market, society, and scientific research. This surge in usage has led to an explosion in NLP model interpretability and analysis research, accompanied by numerous technical surveys. Yet, these surveys often overlook the needs and perspectives of explanation stakeholders. In this paper, we address three fundamental questions: Why do we need interpretability, what are we interpreting, and how? By exploring these questions, we examine existing interpretability paradigms, their properties, and their relevance to different stakeholders. We further explore the practical implications of these paradigms by analyzing trends from the past decade across multiple research fields. To this end, we retrieved thousands of papers and employed an LLM to characterize them. Our analysis reveals significant disparities between NLP developers and non-developer users, as well as between research fields, underscoring the diverse needs of stakeholders. For example, explanations of internal model components are rarely used outside the NLP field. We hope this paper informs the future design, development, and application of methods that align with the objectives and requirements of various stakeholders.

Recent advances in LLM-based decompilers have been shown effective to convert low-level binaries into human-readable source code. However, there still lacks a comprehensive benchmark that provides large-scale binary-source function pairs, which is critical for advancing the LLM decompilation technology. Creating accurate binary-source mappings incurs severe issues caused by complex compilation settings and widespread function inlining that obscure the correspondence between binaries and their original source code. Previous efforts have either relied on used contest-style benchmarks, synthetic binary-source mappings that diverge significantly from the mappings in real world, or partially matched binaries with only code lines or variable names, compromising the effectiveness of analyzing the binary functionality. To alleviate these issues, we introduce Decompile-Bench, the first open-source dataset comprising two million binary-source function pairs condensed from 100 million collected function pairs, i.e., 450GB of binaries compiled from permissively licensed GitHub projects. For the evaluation purposes, we also developed a benchmark Decompile-Bench-Eval including manually crafted binaries from the well-established HumanEval and MBPP, alongside the compiled GitHub repositories released after 2025 to mitigate data leakage issues. We further explore commonly-used evaluation metrics to provide a thorough assessment of the studied LLM decompilers and find that fine-tuning with Decompile-Bench causes a 20% improvement over previous benchmarks in terms of the re-executability rate. Our code and data has been released in HuggingFace and Github. https://github.com/albertan017/LLM4Decompile

Large Language Models (LLMs) excel at many reasoning tasks but struggle with knowledge-intensive queries due to their inability to dynamically access up-to-date or domain-specific information. Retrieval-Augmented Generation (RAG) has emerged as a promising solution, enabling LLMs to ground their responses in external sources. However, existing RAG methods lack fine-grained control over both the query and source sides, often resulting in noisy retrieval and shallow reasoning. In this work, we introduce DeepSieve, an agentic RAG framework that incorporates information sieving via LLM-as-a-knowledge-router. DeepSieve decomposes complex queries into structured sub-questions and recursively routes each to the most suitable knowledge source, filtering irrelevant information through a multi-stage distillation process. Our design emphasizes modularity, transparency, and adaptability, leveraging recent advances in agentic system design. Experiments on multi-hop QA tasks across heterogeneous sources demonstrate improved reasoning depth, retrieval precision, and interpretability over conventional RAG approaches. Our codes are available at https://github.com/MinghoKwok/DeepSieve.

Retrieval-Augmented Generation (RAG) has quickly grown into a pivotal paradigm in the development of Large Language Models (LLMs). While much of the current research in this field focuses on performance optimization, particularly in terms of accuracy and efficiency, the trustworthiness of RAG systems remains an area still under exploration. From a positive perspective, RAG systems are promising to enhance LLMs by providing them with useful and up-to-date knowledge from vast external databases, thereby mitigating the long-standing problem of hallucination. While from a negative perspective, RAG systems are at the risk of generating undesirable contents if the retrieved information is either inappropriate or poorly utilized. To address these concerns, we propose a unified framework that assesses the trustworthiness of RAG systems across six key dimensions: factuality, robustness, fairness, transparency, accountability, and privacy. Within this framework, we thoroughly review the existing literature on each dimension. Additionally, we create the evaluation benchmark regarding the six dimensions and conduct comprehensive evaluations for a variety of proprietary and open-source models. Finally, we identify the potential challenges for future research based on our investigation results. Through this work, we aim to lay a structured foundation for future investigations and provide practical insights for enhancing the trustworthiness of RAG systems in real-world applications.

The increasing adoption of large language models (LLMs) in software engineering necessitates rigorous security evaluation of their generated code. However, existing benchmarks often lack relevance to real-world AI programming scenarios, making them inadequate for assessing the practical security risks associated with AI-generated code in production environments. To address this gap, we introduce A.S.E (AI Code Generation Security Evaluation), a repository-level evaluation benchmark designed to closely mirror real-world AI programming tasks, offering a comprehensive and reliable framework for assessing the security of AI-generated code. Our evaluation of leading LLMs on A.S.E reveals several key findings. In particular, current LLMs still struggle with secure coding. The complexity in repository-level scenarios presents challenges for LLMs that typically perform well on snippet-level tasks. Morever, a larger reasoning budget does not necessarily lead to better code generation. These observations offer valuable insights into the current state of AI code generation, assisting developers in selecting the most appropriate models for practical tasks, while laying the foundation for refining LLMs to generate secure and efficient code in real-world applications.

The improvement of LLMs' instruction-following capabilities depends critically on the availability of high-quality instruction-response pairs. While existing automatic data synthetic methods alleviate the burden of manual curation, they often rely heavily on either the quality of seed data or strong assumptions about the structure and content of web documents. To tackle these challenges, we propose Web Reconstruction (WebR), a fully automated framework for synthesizing high-quality instruction-tuning (IT) data directly from raw web documents with minimal assumptions. Leveraging the inherent diversity of raw web content, we conceptualize web reconstruction as an instruction-tuning data synthesis task via a novel dual-perspective paradigm--Web as Instruction and Web as Response--where each web document is designated as either an instruction or a response to trigger the reconstruction process. Comprehensive experiments show that datasets generated by WebR outperform state-of-the-art baselines by up to 16.65% across four instruction-following benchmarks. Notably, WebR demonstrates superior compatibility, data efficiency, and scalability, enabling enhanced domain adaptation with minimal effort. The data and code are publicly available at https://github.com/YJiangcm/WebR.

Retrieval-augmented generation (RAG) faces challenges related to factual correctness, source attribution, and response completeness. The LiveRAG Challenge hosted at SIGIR'25 aims to advance RAG research using a fixed corpus and a shared, open-source LLM. We propose a modular pipeline that operates on information nuggets-minimal, atomic units of relevant information extracted from retrieved documents. This multistage pipeline encompasses query rewriting, passage retrieval and reranking, nugget detection and clustering, cluster ranking and summarization, and response fluency enhancement. This design inherently promotes grounding in specific facts, facilitates source attribution, and ensures maximum information inclusion within length constraints. In this challenge, we extend our focus to also address the retrieval component of RAG, building upon our prior work on multi-faceted query rewriting. Furthermore, for augmented generation, we concentrate on improving context curation capabilities, maximizing the breadth of information covered in the response while ensuring pipeline efficiency. Our results show that combining original queries with a few sub-query rewrites boosts recall, while increasing the number of documents used for reranking and generation beyond a certain point reduces effectiveness, without improving response quality.

Despite notable advancements in Retrieval-Augmented Generation (RAG) systems that expand large language model (LLM) capabilities through external retrieval, these systems often struggle to meet the complex and diverse needs of real-world industrial applications. The reliance on retrieval alone proves insufficient for extracting deep, domain-specific knowledge performing in logical reasoning from specialized corpora. To address this, we introduce sPecIalized KnowledgE and Rationale Augmentation Generation (PIKE-RAG), focusing on extracting, understanding, and applying specialized knowledge, while constructing coherent rationale to incrementally steer LLMs toward accurate responses. Recognizing the diverse challenges of industrial tasks, we introduce a new paradigm that classifies tasks based on their complexity in knowledge extraction and application, allowing for a systematic evaluation of RAG systems' problem-solving capabilities. This strategic approach offers a roadmap for the phased development and enhancement of RAG systems, tailored to meet the evolving demands of industrial applications. Furthermore, we propose knowledge atomizing and knowledge-aware task decomposition to effectively extract multifaceted knowledge from the data chunks and iteratively construct the rationale based on original query and the accumulated knowledge, respectively, showcasing exceptional performance across various benchmarks.

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 .

The development and training of deep learning models have become increasingly costly and complex. Consequently, software engineers are adopting pre-trained models (PTMs) for their downstream applications. The dynamics of the PTM supply chain remain largely unexplored, signaling a clear need for structured datasets that document not only the metadata but also the subsequent applications of these models. Without such data, the MSR community cannot comprehensively understand the impact of PTM adoption and reuse. This paper presents the PeaTMOSS dataset, which comprises metadata for 281,638 PTMs and detailed snapshots for all PTMs with over 50 monthly downloads (14,296 PTMs), along with 28,575 open-source software repositories from GitHub that utilize these models. Additionally, the dataset includes 44,337 mappings from 15,129 downstream GitHub repositories to the 2,530 PTMs they use. To enhance the dataset's comprehensiveness, we developed prompts for a large language model to automatically extract model metadata, including the model's training datasets, parameters, and evaluation metrics. Our analysis of this dataset provides the first summary statistics for the PTM supply chain, showing the trend of PTM development and common shortcomings of PTM package documentation. Our example application reveals inconsistencies in software licenses across PTMs and their dependent projects. PeaTMOSS lays the foundation for future research, offering rich opportunities to investigate the PTM supply chain. We outline mining opportunities on PTMs, their downstream usage, and cross-cutting questions.

Retrieval-Augmented Generation (RAG) plays a crucial role in grounding Large Language Models by leveraging external knowledge, whereas the effectiveness is often compromised by the retrieval of contextually flawed or incomplete information. To address this, knowledge graph-based RAG methods have evolved towards hierarchical structures, organizing knowledge into multi-level summaries. However, these approaches still suffer from two critical, unaddressed challenges: high-level conceptual summaries exist as disconnected ``semantic islands'', lacking the explicit relations needed for cross-community reasoning; and the retrieval process itself remains structurally unaware, often degenerating into an inefficient flat search that fails to exploit the graph's rich topology. To overcome these limitations, we introduce LeanRAG, a framework that features a deeply collaborative design combining knowledge aggregation and retrieval strategies. LeanRAG first employs a novel semantic aggregation algorithm that forms entity clusters and constructs new explicit relations among aggregation-level summaries, creating a fully navigable semantic network. Then, a bottom-up, structure-guided retrieval strategy anchors queries to the most relevant fine-grained entities and then systematically traverses the graph's semantic pathways to gather concise yet contextually comprehensive evidence sets. The LeanRAG can mitigate the substantial overhead associated with path retrieval on graphs and minimizes redundant information retrieval. Extensive experiments on four challenging QA benchmarks with different domains demonstrate that LeanRAG significantly outperforming existing methods in response quality while reducing 46\% retrieval redundancy. Code is available at: https://github.com/RaZzzyz/LeanRAG

We consider the problem of translating high-level textual descriptions to formal representations in technical documentation as part of an effort to model the meaning of such documentation. We focus specifically on the problem of learning translational correspondences between text descriptions and grounded representations in the target documentation, such as formal representation of functions or code templates. Our approach exploits the parallel nature of such documentation, or the tight coupling between high-level text and the low-level representations we aim to learn. Data is collected by mining technical documents for such parallel text-representation pairs, which we use to train a simple semantic parsing model. We report new baseline results on sixteen novel datasets, including the standard library documentation for nine popular programming languages across seven natural languages, and a small collection of Unix utility manuals.

The instruction-following ability of Large Language Models (LLMs) has cultivated a class of LLM-based systems capable of approaching complex tasks such as making edits to large code repositories. Due to the high sensitivity and unpredictability of LLM behavior in response to changes in prompting, robust evaluation tools are needed to drive future iteration of these systems. We propose RES-Q, a natural language instruction-based benchmark for evaluating Repository Editing Systems, which consists of 100 repository editing tasks derived from real GitHub commits. Given an edit instruction and a code repository, RES-Q evaluates an LLM system's ability to gather information and construct an edit that satisfies the criteria set by the instruction. We argue that evaluating LLMs in this way addresses issues with traditional benchmarks and provides a more holistic assessment of a model's abilities. We evaluate various state-of-the-art LLMs as language agents in a repository-editing system built on Qurrent OS, our language agent development software. Despite their 1% pass@1 performance difference on HumanEval, we find Claude Sonnet 3.5 outperforms GPT-4o by 12% pass@1 on RES-Q, indicating RES-Q's capacity to differentiate model capability as traditional benchmarks approach saturation. We further investigate token efficiency, performance relationships with existing benchmarks, and interesting disparities between closed and open-source LLMs. Code and dataset are available at https://github.com/Qurrent-AI/RES-Q.

Retrieval-Augmented Generation (RAG) mitigates key limitations of Large Language Models (LLMs)-such as factual errors, outdated knowledge, and hallucinations-by dynamically retrieving external information. Recent work extends this paradigm through agentic RAG systems, where LLMs act as agents to iteratively plan, retrieve, and reason over complex queries. However, these systems still struggle with challenging multi-hop questions, and their intermediate reasoning capabilities remain underexplored. To address this, we propose RAGCap-Bench, a capability-oriented benchmark for fine-grained evaluation of intermediate tasks in agentic RAG workflows. We analyze outputs from state-of-the-art systems to identify common tasks and the core capabilities required for their execution, then construct a taxonomy of typical LLM errors to design targeted evaluation questions. Experiments show that "slow-thinking" models with stronger RAGCap performance achieve better end-to-end results, underscoring the benchmark's validity and the importance of enhancing these intermediate capabilities.

Retrieval-Augmented Generation (RAG) is a critical paradigm for building reliable, knowledge-intensive Large Language Model (LLM) applications. However, the multi-stage pipeline (retrieve, generate) and unique workload characteristics (e.g., knowledge dependency) of RAG systems pose significant challenges for serving performance optimization. Existing generic LLM inference traces fail to capture these RAG-specific dynamics, creating a significant performance gap between academic research and real-world deployment. To bridge this gap, this paper introduces RAGPulse, an open-source RAG workload trace dataset. This dataset was collected from an university-wide Q&A system serving that has served more than 40,000 students and faculties since April 2024. We detail RAGPulse's system architecture, its privacy-preserving hash-based data format, and provide an in-depth statistical analysis. Our analysis reveals that real-world RAG workloads exhibit significant temporal locality and a highly skewed hot document access pattern. RAGPulse provides a high-fidelity foundation for researchers to develop and validate novel optimization strategies for RAG systems, such as content-aware batching and retrieval caching, ultimately enhancing the efficiency and reliability of RAG services. The code is available at https://github.com/flashserve/RAGPulse.

Retrieval-augmented generation (RAG) has increasingly shown its power in extending large language models' (LLMs') capability beyond their pre-trained knowledge. Existing works have shown that RAG can help with software development tasks such as code generation, code update, and test generation. Yet, the effectiveness of adapting LLMs to fast-evolving or less common API libraries using RAG remains unknown. To bridge this gap, we take an initial step to study this unexplored yet practical setting - when developers code with a less common library, they often refer to its API documentation; likewise, when LLMs are allowed to look up API documentation via RAG, to what extent can LLMs be advanced? To mimic such a setting, we select four less common open-source Python libraries with a total of 1017 eligible APIs. We study the factors that affect the effectiveness of using the documentation of less common API libraries as additional knowledge for retrieval and generation. Our intensive study yields interesting findings: (1) RAG helps improve LLMs' performance by 83%-220%. (2) Example code contributes the most to advance LLMs, instead of the descriptive texts and parameter lists in the API documentation. (3) LLMs could sometimes tolerate mild noises (typos in description or incorrect parameters) by referencing their pre-trained knowledge or document context. Finally, we suggest that developers pay more attention to the quality and diversity of the code examples in the API documentation. The study sheds light on future low-code software development workflows.

In this paper, we champion the use of structured and semantic content representation of discourse-based scholarly communication, inspired by tools like Wikipedia infoboxes or structured Amazon product descriptions. These representations provide users with a concise overview, aiding scientists in navigating the dense academic landscape. Our novel automated approach leverages the robust text generation capabilities of LLMs to produce structured scholarly contribution summaries, offering both a practical solution and insights into LLMs' emergent abilities. For LLMs, the prime focus is on improving their general intelligence as conversational agents. We argue that these models can also be applied effectively in information extraction (IE), specifically in complex IE tasks within terse domains like Science. This paradigm shift replaces the traditional modular, pipelined machine learning approach with a simpler objective expressed through instructions. Our results show that finetuned FLAN-T5 with 1000x fewer parameters than the state-of-the-art GPT-davinci is competitive for the task.

Multiple-choice question (MCQ) datasets like Massive Multitask Language Understanding (MMLU) are widely used to evaluate the commonsense, understanding, and problem-solving abilities of large language models (LLMs). However, the open-source nature of these benchmarks and the broad sources of training data for LLMs have inevitably led to benchmark contamination, resulting in unreliable evaluation results. To alleviate this issue, we propose a contamination-free and more challenging MCQ benchmark called MMLU-CF. This benchmark reassesses LLMs' understanding of world knowledge by averting both unintentional and malicious data leakage. To avoid unintentional data leakage, we source data from a broader domain and design three decontamination rules. To prevent malicious data leakage, we divide the benchmark into validation and test sets with similar difficulty and subject distributions. The test set remains closed-source to ensure reliable results, while the validation set is publicly available to promote transparency and facilitate independent verification. Our evaluation of mainstream LLMs reveals that the powerful GPT-4o achieves merely a 5-shot score of 73.4% and a 0-shot score of 71.9% on the test set, which indicates the effectiveness of our approach in creating a more rigorous and contamination-free evaluation standard. The GitHub repository is available at https://github.com/microsoft/MMLU-CF and the dataset refers to https://huggingface.co/datasets/microsoft/MMLU-CF.

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}

Retrieval-Augmented Generation (RAG) based on Large Language Models (LLMs) is a powerful solution to understand and query the industry's closed-source documents. However, basic RAG often struggles with complex QA tasks in legal and regulatory domains, particularly when dealing with numerous government documents. The top-k strategy frequently misses golden chunks, leading to incomplete or inaccurate answers. To address these retrieval bottlenecks, we explore two strategies to improve evidence coverage and answer quality. The first is a One-SHOT retrieval method that adaptively selects chunks based on a token budget, allowing as much relevant content as possible to be included within the model's context window. Additionally, we design modules to further filter and refine the chunks. The second is an iterative retrieval strategy built on a Reasoning Agentic RAG framework, where a reasoning LLM dynamically issues search queries, evaluates retrieved results, and progressively refines the context over multiple turns. We identify query drift and retrieval laziness issues and further design two modules to tackle them. Through extensive experiments on a dataset of government documents, we aim to offer practical insights and guidance for real-world applications in legal and regulatory domains.

This paper presents a systematic review of benchmarks and approaches for explainability in Machine Reading Comprehension (MRC). We present how the representation and inference challenges evolved and the steps which were taken to tackle these challenges. We also present the evaluation methodologies to assess the performance of explainable systems. In addition, we identify persisting open research questions and highlight critical directions for future work.

Supervised Fine-Tuning (SFT) is essential for training large language models (LLMs), significantly enhancing critical capabilities such as instruction following and in-context learning. Nevertheless, creating suitable training datasets tailored for specific domains remains challenging due to unique domain constraints and data scarcity. In this paper, we propose SearchInstruct, an innovative method explicitly designed to construct high quality instruction datasets for SFT. Our approach begins with a limited set of domain specific, human generated questions, which are systematically expanded using a large language model. Subsequently, domain relevant resources are dynamically retrieved to generate accurate and contextually appropriate answers for each augmented question. Experimental evaluation demonstrates that SearchInstruct enhances both the diversity and quality of SFT datasets, leading to measurable improvements in LLM performance within specialized domains. Additionally, we show that beyond dataset generation, the proposed method can also effectively facilitate tasks such as model editing, enabling efficient updates to existing models. To facilitate reproducibility and community adoption, we provide full implementation details, the complete set of generated instruction response pairs, and the source code in a publicly accessible Git repository: [https://github.com/mostafaamiri/SearchInstruct](https://github.com/mostafaamiri/SearchInstruct)

Commit messages are natural language descriptions of code changes, which are important for program understanding and maintenance. However, writing commit messages manually is time-consuming and laborious, especially when the code is updated frequently. Various approaches utilizing generation or retrieval techniques have been proposed to automatically generate commit messages. To achieve a better understanding of how the existing approaches perform in solving this problem, this paper conducts a systematic and in-depth analysis of the state-of-the-art models and datasets. We find that: (1) Different variants of the BLEU metric are used in previous works, which affects the evaluation and understanding of existing methods. (2) Most existing datasets are crawled only from Java repositories while repositories in other programming languages are not sufficiently explored. (3) Dataset splitting strategies can influence the performance of existing models by a large margin. Some models show better performance when the datasets are split by commit, while other models perform better when the datasets are split by timestamp or by project. Based on our findings, we conduct a human evaluation and find the BLEU metric that best correlates with the human scores for the task. We also collect a large-scale, information-rich, and multi-language commit message dataset MCMD and evaluate existing models on this dataset. Furthermore, we conduct extensive experiments under different dataset splitting strategies and suggest the suitable models under different scenarios. Based on the experimental results and findings, we provide feasible suggestions for comprehensively evaluating commit message generation models and discuss possible future research directions. We believe this work can help practitioners and researchers better evaluate and select models for automatic commit message generation.

Implementing new features in repository-level codebases is a crucial application of code generation models. However, current benchmarks lack a dedicated evaluation framework for this capability. To fill this gap, we introduce FEA-Bench, a benchmark designed to assess the ability of large language models (LLMs) to perform incremental development within code repositories. We collect pull requests from 83 GitHub repositories and use rule-based and intent-based filtering to construct task instances focused on new feature development. Each task instance containing code changes is paired with relevant unit test files to ensure that the solution can be verified. The feature implementation requires LLMs to simultaneously possess code completion capabilities for new components and code editing abilities for other relevant parts in the code repository, providing a more comprehensive evaluation method of LLMs' automated software engineering capabilities. Experimental results show that LLMs perform significantly worse in the FEA-Bench, highlighting considerable challenges in such repository-level incremental code development.

Large Language Models (LLMs) have shown remarkable capabilities through two complementary paradigms: Retrieval-Augmented Generation (RAG), which enhances knowledge grounding, and Reinforcement Learning from Verifiable Rewards (RLVR), which optimizes complex reasoning abilities. However, these two capabilities are often developed in isolation, and existing efforts to unify them remain narrow in scope-typically limited to open-domain QA with fixed retrieval settings and task-specific assumptions. This lack of integration constrains generalization and limits the applicability of RAG-RL methods to broader domains. To bridge this gap, we propose UR2 (Unified RAG and Reasoning), a general framework that unifies retrieval and reasoning through reinforcement learning. UR2 introduces two key contributions: a difficulty-aware curriculum training that selectively invokes retrieval only for challenging problems, and a hybrid knowledge access strategy combining domain-specific offline corpora with LLM-generated summaries. These components are designed to enable dynamic coordination between retrieval and reasoning, improving adaptability across a diverse range of tasks. Experiments across open-domain QA, MMLU-Pro, medical, and mathematical reasoning tasks demonstrate that UR2 (built on Qwen2.5-3/7B and LLaMA-3.1-8B) significantly outperforms existing RAG and RL methods, achieving comparable performance to GPT-4o-mini and GPT-4.1-mini on several benchmarks. We have released all code, models, and data at https://github.com/Tsinghua-dhy/UR2.

Understanding and reasoning about code semantics is essential for enhancing code LLMs' abilities to solve real-world software engineering (SE) tasks. Although several code reasoning benchmarks exist, most rely on synthetic datasets or educational coding problems and focus on coarse-grained reasoning tasks such as input/output prediction, limiting their effectiveness in evaluating LLMs in practical SE contexts. To bridge this gap, we propose CodeSense, the first benchmark that makes available a spectrum of fine-grained code reasoning tasks concerned with the software engineering of real-world code. We collected Python, C and Java software projects from real-world repositories. We executed tests from these repositories, collected their execution traces, and constructed a ground truth dataset for fine-grained semantic reasoning tasks. We then performed comprehensive evaluations on state-of-the-art LLMs. Our results show a clear performance gap for the models to handle fine-grained reasoning tasks. Although prompting techniques such as chain-of-thought and in-context learning helped, the lack of code semantics in LLMs fundamentally limit models' capabilities of code reasoning. Besides dataset, benchmark and evaluation, our work produced an execution tracing framework and tool set that make it easy to collect ground truth for fine-grained SE reasoning tasks, offering a strong basis for future benchmark construction and model post training. Our code and data are located at https://codesense-bench.github.io/.

Large Language Models (LLMs) have been integrated into recommendation systems to enhance user behavior comprehension. The Retrieval Augmented Generation (RAG) technique is further incorporated into these systems to retrieve more relevant items and improve system performance. However, existing RAG methods rely primarily on textual semantics and often fail to incorporate the most relevant items, limiting the effectiveness of the systems. In this paper, we propose Representation learning for retrieval-Augmented Large Language model Recommendation (RALLRec). Specifically, we enhance textual semantics by prompting LLMs to generate more detailed item descriptions, followed by joint representation learning of textual and collaborative semantics, which are extracted by the LLM and recommendation models, respectively. Considering the potential time-varying characteristics of user interest, a simple yet effective reranking method is further introduced to capture the dynamics of user preference. We conducted extensive experiments on three real-world datasets, and the evaluation results validated the effectiveness of our method. Code is made public at https://github.com/JianXu95/RALLRec.

We present a new benchmark for evaluating Deep Search--a realistic and complex form of retrieval-augmented generation (RAG) that requires source-aware, multi-hop reasoning over diverse, sparsed, but related sources. These include documents, meeting transcripts, Slack messages, GitHub, and URLs, which vary in structure and often contain human-to-human interactions. We build it using a synthetic data pipeline that simulates business workflows across product planning, development, and support stages, generating interconnected content with realistic noise and multi-hop questions with guaranteed ground-truth answers. We release our benchmark with both answerable and unanswerable queries, and retrieval pool of 39,190 enterprise artifacts, enabling fine-grained evaluation of long-context LLM and RAG systems. Our experiments reveal that even the best-performing agentic RAG methods achieve an average performance score of 32.96 on our benchmark. With further analysis, we highlight retrieval as the main bottleneck: existing methods struggle to conduct deep searches and retrieve all necessary evidence. Consequently, they often reason over partial context, leading to significant performance degradation.

Medical open-domain question answering demands substantial access to specialized knowledge. Recent efforts have sought to decouple knowledge from model parameters, counteracting architectural scaling and allowing for training on common low-resource hardware. The retrieve-then-read paradigm has become ubiquitous, with model predictions grounded on relevant knowledge pieces from external repositories such as PubMed, textbooks, and UMLS. An alternative path, still under-explored but made possible by the advent of domain-specific large language models, entails constructing artificial contexts through prompting. As a result, "to generate or to retrieve" is the modern equivalent of Hamlet's dilemma. This paper presents MedGENIE, the first generate-then-read framework for multiple-choice question answering in medicine. We conduct extensive experiments on MedQA-USMLE, MedMCQA, and MMLU, incorporating a practical perspective by assuming a maximum of 24GB VRAM. MedGENIE sets a new state-of-the-art (SOTA) in the open-book setting of each testbed, even allowing a small-scale reader to outcompete zero-shot closed-book 175B baselines while using up to 706times fewer parameters. Overall, our findings reveal that generated passages are more effective than retrieved counterparts in attaining higher accuracy.

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

Retrieval-Augmented Generation allows to enhance Large Language Models with external knowledge. In response to the recent popularity of generative LLMs, many RAG approaches have been proposed, which involve an intricate number of different configurations such as evaluation datasets, collections, metrics, retrievers, and LLMs. Inconsistent benchmarking poses a major challenge in comparing approaches and understanding the impact of each component in the pipeline. In this work, we study best practices that lay the groundwork for a systematic evaluation of RAG and present BERGEN, an end-to-end library for reproducible research standardizing RAG experiments. In an extensive study focusing on QA, we benchmark different state-of-the-art retrievers, rerankers, and LLMs. Additionally, we analyze existing RAG metrics and datasets. Our open-source library BERGEN is available under https://github.com/naver/bergen.

The integration of external knowledge through Retrieval-Augmented Generation (RAG) has become foundational in enhancing large language models (LLMs) for knowledge-intensive tasks. However, existing RAG paradigms often overlook the cognitive step of applying knowledge, leaving a gap between retrieved facts and task-specific reasoning. In this work, we introduce RAG+, a principled and modular extension that explicitly incorporates application-aware reasoning into the RAG pipeline. RAG+ constructs a dual corpus consisting of knowledge and aligned application examples, created either manually or automatically, and retrieves both jointly during inference. This design enables LLMs not only to access relevant information but also to apply it within structured, goal-oriented reasoning processes. Experiments across mathematical, legal, and medical domains, conducted on multiple models, demonstrate that RAG+ consistently outperforms standard RAG variants, achieving average improvements of 3-5%, and peak gains up to 7.5% in complex scenarios. By bridging retrieval with actionable application, RAG+ advances a more cognitively grounded framework for knowledge integration, representing a step toward more interpretable and capable LLMs.

Large Language Models (LLMs) demonstrate human-level capabilities in dialogue, reasoning, and knowledge retention. However, even the most advanced LLMs face challenges such as hallucinations and real-time updating of their knowledge. Current research addresses this bottleneck by equipping LLMs with external knowledge, a technique known as Retrieval Augmented Generation (RAG). However, two key issues constrained the development of RAG. First, there is a growing lack of comprehensive and fair comparisons between novel RAG algorithms. Second, open-source tools such as LlamaIndex and LangChain employ high-level abstractions, which results in a lack of transparency and limits the ability to develop novel algorithms and evaluation metrics. To close this gap, we introduce RAGLAB, a modular and research-oriented open-source library. RAGLAB reproduces 6 existing algorithms and provides a comprehensive ecosystem for investigating RAG algorithms. Leveraging RAGLAB, we conduct a fair comparison of 6 RAG algorithms across 10 benchmarks. With RAGLAB, researchers can efficiently compare the performance of various algorithms and develop novel algorithms.

Large Language Models (LLMs) have demonstrated remarkable capabilities in important tasks such as natural language understanding, language generation, and complex reasoning and have the potential to make a substantial impact on our society. Such capabilities, however, come with the considerable resources they demand, highlighting the strong need to develop effective techniques for addressing their efficiency challenges. In this survey, we provide a systematic and comprehensive review of efficient LLMs research. We organize the literature in a taxonomy consisting of three main categories, covering distinct yet interconnected efficient LLMs topics from model-centric, data-centric, and framework-centric perspective, respectively. We have also created a GitHub repository where we compile the papers featured in this survey at https://github.com/AIoT-MLSys-Lab/EfficientLLMs, and will actively maintain this repository and incorporate new research as it emerges. We hope our survey can serve as a valuable resource to help researchers and practitioners gain a systematic understanding of the research developments in efficient LLMs and inspire them to contribute to this important and exciting field.

Recent advances in natural language processing, primarily propelled by Large Language Models (LLMs), have showcased their remarkable capabilities grounded in in-context learning. A promising avenue for guiding LLMs in intricate reasoning tasks involves the utilization of intermediate reasoning steps within the Chain-of-Thought (CoT) paradigm. Nevertheless, the central challenge lies in the effective selection of exemplars for facilitating in-context learning. In this study, we introduce a framework that leverages Dual Queries and Low-rank approximation Re-ranking (DQ-LoRe) to automatically select exemplars for in-context learning. Dual Queries first query LLM to obtain LLM-generated knowledge such as CoT, then query the retriever to obtain the final exemplars via both question and the knowledge. Moreover, for the second query, LoRe employs dimensionality reduction techniques to refine exemplar selection, ensuring close alignment with the input question's knowledge. Through extensive experiments, we demonstrate that DQ-LoRe significantly outperforms prior state-of-the-art methods in the automatic selection of exemplars for GPT-4, enhancing performance from 92.5% to 94.2%. Our comprehensive analysis further reveals that DQ-LoRe consistently outperforms retrieval-based approaches in terms of both performance and adaptability, especially in scenarios characterized by distribution shifts. DQ-LoRe pushes the boundary of in-context learning and opens up new avenues for addressing complex reasoning challenges. Our code is released at https://github.com/AI4fun/DQ-LoRe}{https://github.com/AI4fun/DQ-LoRe.

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.