Daily Papers

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.

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.

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

Assisting non-expert users to develop complex interactive websites has become a popular task for LLM-powered code agents. However, existing code agents tend to only generate frontend web pages, masking the lack of real full-stack data processing and storage with fancy visual effects. Notably, constructing production-level full-stack web applications is far more challenging than only generating frontend web pages, demanding careful control of data flow, comprehensive understanding of constantly updating packages and dependencies, and accurate localization of obscure bugs in the codebase. To address these difficulties, we introduce FullStack-Agent, a unified agent system for full-stack agentic coding that consists of three parts: (1) FullStack-Dev, a multi-agent framework with strong planning, code editing, codebase navigation, and bug localization abilities. (2) FullStack-Learn, an innovative data-scaling and self-improving method that back-translates crawled and synthesized website repositories to improve the backbone LLM of FullStack-Dev. (3) FullStack-Bench, a comprehensive benchmark that systematically tests the frontend, backend and database functionalities of the generated website. Our FullStack-Dev outperforms the previous state-of-the-art method by 8.7%, 38.2%, and 15.9% on the frontend, backend, and database test cases respectively. Additionally, FullStack-Learn raises the performance of a 30B model by 9.7%, 9.5%, and 2.8% on the three sets of test cases through self-improvement, demonstrating the effectiveness of our approach. The code is released at https://github.com/mnluzimu/FullStack-Agent.

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

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.

Large Language Models (LLMs) are advancing at an amazing speed and have become indispensable across academia, industry, and daily applications. To keep pace with the status quo, this survey probes the core challenges that the rise of LLMs poses for evaluation. We identify and analyze two pivotal transitions: (i) from task-specific to capability-based evaluation, which reorganizes benchmarks around core competencies such as knowledge, reasoning, instruction following, multi-modal understanding, and safety; and (ii) from manual to automated evaluation, encompassing dynamic dataset curation and "LLM-as-a-judge" scoring. Yet, even with these transitions, a crucial obstacle persists: the evaluation generalization issue. Bounded test sets cannot scale alongside models whose abilities grow seemingly without limit. We will dissect this issue, along with the core challenges of the above two transitions, from the perspectives of methods, datasets, evaluators, and metrics. Due to the fast evolving of this field, we will maintain a living GitHub repository (links are in each section) to crowd-source updates and corrections, and warmly invite contributors and collaborators.

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.

Academic output is produced across a fragmented toolchain: literature discovery in one application, reference management in another, writing in a LaTeX editor, formatting against venue templates by hand, and submission through yet another portal. Each boundary between tools forces a context switch, a format conversion, or a manual copy-paste step, and the cumulative cost dominates the time researchers spend on activities that are not research. We present Bibby AI, an editor-native platform that collapses this toolchain into a single Research-Write-Publish pipeline built around a cloud LaTeX editor. Unlike assistants that attach to an existing editor through a browser extension, Bibby AI owns the full document state, compilation pipeline, and revision history, which allows its agents to perform retrieval-grounded citation insertion, structural edits, and template-compliant reformatting as first-class, verifiable operations rather than text suggestions. The platform integrates (i) ingestion pipelines that convert PDF, DOCX, and handwritten mathematics into clean LaTeX; (ii) a retrieval layer over scholarly metadata enriched with patent-to-paper citation signals derived from USPTO PatentsView and the Marx-Fuegi citation corpus, surfacing the translational impact of candidate references; and (iii) task-scoped agents for literature triage, drafting, revision, and venue formatting that operate directly on the document's abstract syntax representation. Bibby AI is deployed in production and serves more than 5,000 active researchers across more than 50 subscribing universities. We describe the architecture, the design decisions that editor-nativeness makes possible, and the workflow-level time-savings framework we use to evaluate the platform against fragmented baselines.

Issue-commit linking, which connects issues with commits that fix them, is crucial for software maintenance. Existing approaches have shown promise in automatically recovering these links. Evaluations of these techniques assess their ability to identify genuine links from plausible but false links. However, these evaluations overlook the fact that, in reality, when a repository has more commits, the presence of more plausible yet unrelated commits may interfere with the tool in differentiating the correct fix commits. To address this, we propose the Realistic Distribution Setting (RDS) and use it to construct a more realistic evaluation dataset that includes 20 open-source projects. By evaluating tools on this dataset, we observe that the performance of the state-of-the-art deep learning-based approach drops by more than half, while the traditional Information Retrieval method, VSM, outperforms it. Inspired by these observations, we propose EasyLink, which utilizes a vector database as a modern Information Retrieval technique. To address the long-standing problem of the semantic gap between issues and commits, EasyLink leverages a large language model to rerank the commits retrieved from the database. Under our evaluation, EasyLink achieves an average Precision@1 of 75.03\%, improving over the state-of-the-art by over four times. Additionally, this paper provides practical guidelines for advancing research in issue-commit link recovery.

Repository-level code editing requires models to understand complex dependencies and execute precise multi-file modifications across a large codebase. While recent gains on SWE-bench rely heavily on complex agent scaffolding, it remains unclear how much of this capability can be internalised via high-quality training signals. To address this, we propose Clean Pull Request (Clean-PR), a mid-training paradigm that leverages real-world GitHub pull requests as a training signal for repository-level editing. We introduce a scalable pipeline that converts noisy pull request diffs into Search/Replace edit blocks through reconstruction and validation, resulting in the largest publicly available corpus of 2 million pull requests spanning 12 programming languages. Using this training signal, we perform a mid-training stage followed by an agentless-aligned supervised fine-tuning process with error-driven data augmentation. On SWE-bench, our model significantly outperforms the instruction-tuned baseline, achieving absolute improvements of 13.6% on SWE-bench Lite and 12.3% on SWE-bench Verified. These results demonstrate that repository-level code understanding and editing capabilities can be effectively internalised into model weights under a simplified, agentless protocol, without relying on heavy inference-time scaffolding.

Faithfully translating research papers into repository-level implementations remains challenging because papers often describe methods at a high level, leave implementation assumptions implicit, and require generated repositories to preserve method logic, evaluation protocols, and cross-file consistency. Despite recent advances in paper-to-code agents, their intermediate outputs are often presented as free-form plans or summaries that downstream coding agents may ignore, reinterpret, or compress, leading to algorithmic simplification and inconsistent repository structure. To address these challenges, we introduce PaperCompiler, a paper-to-code generation framework that compiles paper-grounded evidence into explicit repository-level implementation specifications. PaperCompiler grounds implementation-relevant evidence while preserving source provenance and distinguishing paper-supported, inferred, externally delegated, and unresolved information. The resulting specifications encode non-degradation requirements, ownership assignments, cross-file dependencies, and file-level constraints. Repository generation proceeds under these compiled specifications while retaining flexibility over local engineering choices not fixed by the paper. PaperCompiler outperforms strong baselines on Paper2CodeBench, achieving a 13.8% relative improvement in reference-based fidelity (from 3.64 to 4.15) and reducing high-severity evaluator critiques (from 13.2% to 6.1%).

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.

Revising scientific papers based on peer feedback is a challenging task that requires not only deep scientific knowledge and reasoning, but also the ability to recognize the implicit requests in high-level feedback and to choose the best of many possible ways to update the manuscript in response. We introduce this task for large language models and release ARIES, a dataset of review comments and their corresponding paper edits, to enable training and evaluating models. We study two versions of the task: comment-edit alignment and edit generation, and evaluate several baselines, including GPT-4. We find that models struggle even to identify the edits that correspond to a comment, especially in cases where the comment is phrased in an indirect way or where the edit addresses the spirit of a comment but not the precise request. When tasked with generating edits, GPT-4 often succeeds in addressing comments on a surface level, but it rigidly follows the wording of the feedback rather than the underlying intent, and includes fewer technical details than human-written edits. We hope that our formalization, dataset, and analysis will form a foundation for future work in this area.

Textual knowledge bases such as Wikipedia require considerable effort to keep up to date and consistent. While automated writing assistants could potentially ease this burden, the problem of suggesting edits grounded in external knowledge has been under-explored. In this paper, we introduce the novel generation task of *faithfully reflecting updated information in text* (FRUIT) where the goal is to update an existing article given new evidence. We release the FRUIT-WIKI dataset, a collection of over 170K distantly supervised data produced from pairs of Wikipedia snapshots, along with our data generation pipeline and a gold evaluation set of 914 instances whose edits are guaranteed to be supported by the evidence. We provide benchmark results for popular generation systems as well as EDIT5 -- a T5-based approach tailored to editing we introduce that establishes the state of the art. Our analysis shows that developing models that can update articles faithfully requires new capabilities for neural generation models, and opens doors to many new applications.

Revision is an essential part of the human writing process. It tends to be strategic, adaptive, and, more importantly, iterative in nature. Despite the success of large language models on text revision tasks, they are limited to non-iterative, one-shot revisions. Examining and evaluating the capability of large language models for making continuous revisions and collaborating with human writers is a critical step towards building effective writing assistants. In this work, we present a human-in-the-loop iterative text revision system, Read, Revise, Repeat (R3), which aims at achieving high quality text revisions with minimal human efforts by reading model-generated revisions and user feedbacks, revising documents, and repeating human-machine interactions. In R3, a text revision model provides text editing suggestions for human writers, who can accept or reject the suggested edits. The accepted edits are then incorporated into the model for the next iteration of document revision. Writers can therefore revise documents iteratively by interacting with the system and simply accepting/rejecting its suggested edits until the text revision model stops making further revisions or reaches a predefined maximum number of revisions. Empirical experiments show that R3 can generate revisions with comparable acceptance rate to human writers at early revision depths, and the human-machine interaction can get higher quality revisions with fewer iterations and edits. The collected human-model interaction dataset and system code are available at https://github.com/vipulraheja/IteraTeR. Our system demonstration is available at https://youtu.be/lK08tIpEoaE.

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.

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.

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.

Document editing has become a pervasive component of the production of information, with version control systems enabling edits to be efficiently stored and applied. In light of this, the task of learning distributed representations of edits has been recently proposed. With this in mind, we propose a novel approach that employs variational inference to learn a continuous latent space of vector representations to capture the underlying semantic information with regard to the document editing process. We achieve this by introducing a latent variable to explicitly model the aforementioned features. This latent variable is then combined with a document representation to guide the generation of an edited version of this document. Additionally, to facilitate standardized automatic evaluation of edit representations, which has heavily relied on direct human input thus far, we also propose a suite of downstream tasks, PEER, specifically designed to measure the quality of edit representations in the context of natural language processing.

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.

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.

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.

Scientific publications are the primary means to communicate research discoveries, where the writing quality is of crucial importance. However, prior work studying the human editing process in this domain mainly focused on the abstract or introduction sections, resulting in an incomplete picture. In this work, we provide a complete computational framework for studying text revision in scientific writing. We first introduce arXivEdits, a new annotated corpus of 751 full papers from arXiv with gold sentence alignment across their multiple versions of revision, as well as fine-grained span-level edits and their underlying intentions for 1,000 sentence pairs. It supports our data-driven analysis to unveil the common strategies practiced by researchers for revising their papers. To scale up the analysis, we also develop automatic methods to extract revision at document-, sentence-, and word-levels. A neural CRF sentence alignment model trained on our corpus achieves 93.8 F1, enabling the reliable matching of sentences between different versions. We formulate the edit extraction task as a span alignment problem, and our proposed method extracts more fine-grained and explainable edits, compared to the commonly used diff algorithm. An intention classifier trained on our dataset achieves 78.9 F1 on the fine-grained intent classification task. Our data and system are released at tiny.one/arxivedits.

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.

The integration of Large Language Models (LLMs) into software engineering has shifted the focus from function-level generation to repository-scale assistance. However, existing benchmarks largely rely on bug reports from GitHub Issues, which often allow models to bypass genuine understanding via pattern matching on error logs. This misalignment under-measures Edit Bias, which refers to premature generation, where models prematurely propose code modifications instead of understanding the existing repository architecture. Furthermore, current LLM-as-a-Judge scalar scoring suffers from high variance and low interpretability. This work introduces RepoProbe, a novel benchmark for evaluating repository-level code understanding through open-ended Q&A using GitHub Discussions, which focuses on open-ended architectural inquiries rather than defect reporting. To ensure rigorous evaluation, we propose a Checklist-Based Verification Protocol that decomposes answers into atomic, verifiable facts, thereby replacing subjective ratings with objective verification. Our evaluation of state-of-the-art (SOTA) LLMs reveals a persistent gap between high clarity and evidencegrounded technical correctness. It also quantitatively confirms the prevalence of edit bias, in which models prioritize code generation instead of architectural analysis. Finally, we demonstrate that our verification protocol significantly improves evaluation reliability compared to traditional evaluations with scalar scoring.

Scientists increasingly rely on open-source tools to support their research workflows, yet discovering relevant software among over 600 million GitHub repositories remains challenging. Existing code search benchmarks focus on general software engineering tasks and fail to capture the domain-specific vocabulary and needs of scientific computing. We present a curated corpus of 5,264 high-quality, domain-classified scientific repositories spanning five NASA Science Mission Directorate divisions -- Earth Science, Astrophysics, Planetary Science, Heliophysics, and Biological & Physical Sciences -- enriched with cleaned READMEs, extracted topics, and additional context from crawled links. Building on this corpus, we introduce two novel information retrieval benchmarks: (1) a repository search benchmark with 219 expert-curated queries designed by domain scientists, and (2) a large-scale code snippet retrieval benchmark containing 117,950 code snippets and 119,720 queries across seven programming languages. Baseline evaluations on repository search reveal significant performance variation across scientific domains. Code snippet retrieval proves equally challenging, with substantial variation driven by differing documentation practices, coding standards, and programming language conventions across scientific communities. All datasets and benchmarks are publicly released on HuggingFace to support research on scientific tool discovery.

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

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.

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

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.

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.

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

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.

Iterative text revision improves text quality by fixing grammatical errors, rephrasing for better readability or contextual appropriateness, or reorganizing sentence structures throughout a document. Most recent research has focused on understanding and classifying different types of edits in the iterative revision process from human-written text instead of building accurate and robust systems for iterative text revision. In this work, we aim to build an end-to-end text revision system that can iteratively generate helpful edits by explicitly detecting editable spans (where-to-edit) with their corresponding edit intents and then instructing a revision model to revise the detected edit spans. Leveraging datasets from other related text editing NLP tasks, combined with the specification of editable spans, leads our system to more accurately model the process of iterative text refinement, as evidenced by empirical results and human evaluations. Our system significantly outperforms previous baselines on our text revision tasks and other standard text revision tasks, including grammatical error correction, text simplification, sentence fusion, and style transfer. Through extensive qualitative and quantitative analysis, we make vital connections between edit intentions and writing quality, and better computational modeling of iterative text revisions.

Writing is, by nature, a strategic, adaptive, and more importantly, an iterative process. A crucial part of writing is editing and revising the text. Previous works on text revision have focused on defining edit intention taxonomies within a single domain or developing computational models with a single level of edit granularity, such as sentence-level edits, which differ from human's revision cycles. This work describes IteraTeR: the first large-scale, multi-domain, edit-intention annotated corpus of iteratively revised text. In particular, IteraTeR is collected based on a new framework to comprehensively model the iterative text revisions that generalize to various domains of formal writing, edit intentions, revision depths, and granularities. When we incorporate our annotated edit intentions, both generative and edit-based text revision models significantly improve automatic evaluations. Through our work, we better understand the text revision process, making vital connections between edit intentions and writing quality, enabling the creation of diverse corpora to support computational modeling of iterative text revisions.

Fine-tuning large language models for code editing has typically relied on mining commits and pull requests. The working hypothesis has been that commit messages describe human intent in natural language, and patches to code describe the changes that implement that intent. However, much of the previously collected data is noisy: commit messages are terse, human-written commits commingle several unrelated edits, and many commits come from simple, rule-based bots. The recent adoption of software engineering agents changes this landscape. Code changes co-authored by humans and agents tend to be more narrowly scoped and focused on clearer goals. Their commit messages, generated by LLMs, articulate intent and rationale in much greater detail. Moreover, when these changes land in public repositories, they are implicitly filtered by humans: maintainers discard low-quality commits to their projects. We present AgentPack, a corpus of 1.3M code edits co-authored by Claude Code, OpenAI Codex, and Cursor Agent across public GitHub projects up to mid-August 2025. We describe the identification and curation pipeline, quantify adoption trends of these agents, and analyze the structural properties of the edits. Finally, we show that models fine-tuned on AgentPack can outperform models trained on prior human-only commit corpora, highlighting the potential of using public data from software engineering agents to train future code-editing models.

LLMs hold great promise for healthcare applications, but the rapid evolution of medical knowledge and errors in training data often cause them to generate outdated or inaccurate information, limiting their applicability in high-stakes clinical practice. Model editing has emerged as a potential remedy without full retraining. While parameter-based editing often compromises locality and is thus ill-suited for the medical domain, retrieval-based editing offers a more viable alternative. However, it still faces two critical challenges: (1) representation overlap within the medical knowledge space often causes inaccurate retrieval and reduces editing accuracy; (2) existing methods are restricted to single-sample edits, while batch-editing remains largely unexplored despite its importance for real-world medical applications. To address these challenges, we first construct MedVersa, an enhanced benchmark with broader coverage of medical subjects, designed to evaluate both single and batch edits under strict locality constraints. We then propose MedREK, a retrieval-based editing framework that integrates a shared query-key module for precise matching with an attention-based prompt encoder for informative guidance. Experimental results on various medical benchmarks demonstrate that our MedREK achieves superior performance across different core metrics and provides the first validated solution for batch-editing in medical LLMs. Our code and dataset are available at https://github.com/mylittleriver/MedREK.

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.

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.

Large Language Models (LLMs) have significantly advanced natural language processing, demonstrating strong capabilities in tasks such as text generation, summarization, and reasoning. Recently, their potential for automating precise text editing tasks across specialized domains, such as programming code, LaTeX, and structured database languages, has gained attention. However, current state-of-the-art LLMs still struggle with executing precise, instruction-driven edits, particularly when structural accuracy and strict adherence to domain conventions are required. To address these challenges, we introduce InstrEditBench, an automated benchmark dataset comprising over 30,000 structured editing tasks spanning diverse domains, including Wikipedia articles, LaTeX documents, source code, and database languages. Using this benchmark, we develop FineEdit, a specialized editing model explicitly trained for accurate, context-aware text modifications. Experimental evaluations demonstrate that FineEdit outperforms state-of-the-art models, achieving improvements of approximately 10% over Gemini models on single-turn edits, up to 30% over Llama-3.2-3B, and exceeding Mistral-7B-OpenOrca performance by over 40% on direct editing tasks. FineEdit also effectively generalizes to realistic multi-turn editing scenarios, highlighting its practical applicability.

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.

General-purpose automated software engineering (ASE) includes tasks such as code completion, retrieval, repair, QA, and summarization. These tasks require a code retrieval system that can handle specific queries about code entities, or code entity queries (for example, locating a specific class or retrieving the dependencies of a function), as well as general queries without explicit code entities, or natural language queries (for example, describing a task and retrieving the corresponding code). We present RANGER, a repository-level code retrieval agent designed to address both query types, filling a gap in recent works that have focused primarily on code-entity queries. We first present a tool that constructs a comprehensive knowledge graph of the entire repository, capturing hierarchical and cross-file dependencies down to the variable level, and augments graph nodes with textual descriptions and embeddings to bridge the gap between code and natural language. RANGER then operates on this graph through a dual-stage retrieval pipeline. Entity-based queries are answered through fast Cypher lookups, while natural language queries are handled by MCTS-guided graph exploration. We evaluate RANGER across four diverse benchmarks that represent core ASE tasks including code search, question answering, cross-file dependency retrieval, and repository-level code completion. On CodeSearchNet and RepoQA it outperforms retrieval baselines that use embeddings from strong models such as Qwen3-8B. On RepoBench, it achieves superior cross-file dependency retrieval over baselines, and on CrossCodeEval, pairing RANGER with BM25 delivers the highest exact match rate in code completion compared to other RAG methods.

Large language model (LLM)-based coding agents achieve impressive results on controlled benchmarks yet routinely produce pull requests that real maintainers reject. The root cause is not functional incorrectness but a lack of organicity: generated code ignores project-specific conventions, duplicates functionality already provided by internal APIs, and violates implicit architectural constraints accumulated over years of development. Simply exposing an agent to the latest repository snapshot is not enough: the snapshot reveals the final state of the codebase, but not the repository-specific change patterns by which that state was reached. We introduce Learning to Commit, a framework that closes this gap through Online Repository Memory. Given a repository with a strict chronological split, the agent performs supervised contrastive reflection on earlier commits: it blindly attempts to resolve each historical issue, compares its prediction against the oracle diff, and distils the gap into a continuously growing set of skills-reusable patterns capturing coding style, internal API usage, and architectural invariants. When a new PR description arrives, the agent conditions its generation on these accumulated skills, producing changes grounded in the project's own evolution rather than generic pretraining priors. Evaluation is conducted on genuinely future, merged pull requests that could not have been seen during the skill-building phase, and spans multiple dimensions including functional correctness, code-style consistency, internal API reuse rate, and modified-region plausibility. Experiments on an expert-maintained repository with rich commit history show that Online Repository Memory effectively improves organicity scores on held-out future tasks.

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.

While large language models have been dominating the research landscape recently, small language models remain highly relevant across various domains; yet, they receive far less attention. In this study, we investigate how smaller language models perform during the generation stage within a Retrieval-Augmented Generation (RAG) system. To benchmark these models effectively, we utilised both open-source and proprietary datasets covering diverse subject areas and question types. Our findings demonstrate that a RAG system with small language models can be executed directly on-device without requiring any GPU hardware within a reasonable time. The experimental code and links to the supplementary materials can be accessed through the GitHub repository: https://github.com/SibNN/SLM-RAG-EVAL.

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

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

We present the Mellum models family, open-weight code completion models designed for interactive use in JetBrains IDEs. Mellums have 4B parameters, adopt a Llama-style architecture, and are pre-trained on ~4T tokens of permissively licensed, multi-language code. Our studies show that (i) careful data curation and staged training significantly improve the model's quality, (ii) editor-critical capabilities such as context packing are necessary for high-quality suggestions, and (iii) a compact, task-focused model can meet the cost and latency constraints of interactive completion. In the paper, we describe an end-to-end industrial pipeline for producing contextualized in-editor completion: disciplined data governance, multi-stage training that includes fill-in-the-middle and project context via supervised fine-tuning, and alignment via direct preference optimization using feedback from real-world scenarios. Our quality evaluations include both large-scale offline benchmarks and online telemetry from production deployments in JetBrains IDEs. Mellums are released under the Apache-2.0 license on HuggingFace, with a public model card providing a reproducible reference for practitioners. Our experience offers a pragmatic blueprint for taking a focused, open model from a research prototype to at scale production for hundreds of thousands of users.

Keeping large language models factually up-to-date is crucial for deployment, yet costly retraining remains a challenge. Knowledge editing offers a promising alternative, but methods are only tested on small-scale or synthetic edit benchmarks. In this work, we aim to bridge research into lifelong knowledge editing to real-world edits at practically relevant scale. We first introduce WikiBigEdit; a large-scale benchmark of real-world Wikidata edits, built to automatically extend lifelong for future-proof benchmarking. In its first instance, it includes over 500K question-answer pairs for knowledge editing alongside a comprehensive evaluation pipeline. Finally, we use WikiBigEdit to study existing knowledge editing techniques' ability to incorporate large volumes of real-world facts and contrast their capabilities to generic modification techniques such as retrieval augmentation and continual finetuning to acquire a complete picture of the practical extent of current lifelong knowledge editing.

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.

Despite the growing adoption of large language models (LLMs) in academic workflows, their capabilities remain limited when it comes to supporting high-quality scientific writing. Most existing systems are designed for general-purpose scientific text generation and fail to meet the sophisticated demands of research communication beyond surface-level polishing, such as conceptual coherence across sections. Furthermore, academic writing is inherently iterative and revision-driven, a process not well supported by direct prompting-based paradigms. To address these scenarios, we propose a human-AI collaboration framework for academic paper revision. We first introduce a comprehensive dataset of 7,040 research papers from top-tier venues annotated with over 140,000 instruction-response pairs that reflect realistic, section-level scientific revisions. Building on the dataset, we develop XtraGPT, the first suite of open-source LLMs, designed to provide context-aware, instruction-guided writing assistance, ranging from 1.5B to 14B parameters. Extensive experiments validate that XtraGPT significantly outperforms same-scale baselines and approaches the quality of proprietary systems. Both automated preference assessments and human evaluations confirm the effectiveness of our models in improving scientific drafts.

Wikipedia plays a key role in shaping public understanding of science, and its openly accessible revision history is a unique record of how scientific knowledge evolves over time. Yet scientifically meaningful revisions are obscured by the sheer volume of routine edits, leaving each article's scientific history hidden. We present WikiSTAR (Scientific Tracking of Article Revisions), an interactive system for exploring scientifically meaningful changes across an article's revision history. Using an LLM classifier with an expert-designed multi-label taxonomy, WikiSTAR first tags edit types such as the addition of technical terms, new research findings, and changes in scientific narrative. Then, through interactive views, an article's full revision history can be traced at any granularity - from aggregate trends that reveal when and in which sections scientific content was added or refined, down to individual edits - showing how scientific knowledge develops at a scale previously impossible. In a user study, experts from three domains found that WikiSTAR surfaced new patterns and research questions and enabled previously impractical analyses. We release our system, code and a human-annotated benchmark.

Benchmarks like SWE-bench have standardized the evaluation of Large Language Models (LLMs) on repository-level software engineering tasks. However, these efforts remain limited by manual curation, static datasets, and a focus on Python-based bug fixes. We introduce SWE-Bench++, an automated framework that generates repository-level coding tasks from open-source GitHub projects. Unlike synthetic approaches, our pipeline harvests live pull requests to cover both bug fixes and feature requests across 11 languages. SWE-Bench++ turns GitHub pull requests (PRs) into reproducible, execution-based tasks via four stages: programmatic sourcing, environment synthesis, test oracle extraction, and quality assurance. A final hint-guided trajectory synthesis step converts instances that strong models fail on into training trajectories. Our initial benchmark consists of 11,133 instances from 3,971 repositories across 11 languages. On a subset of 1,782 instances of this benchmark, today's strongest models perform as follows: claude-sonnet-4.5 achieves 36.20% pass@10, gpt-5-2025-08-07 34.57%, gemini/gemini-2.5-pro 24.92%, and gpt-4o 16.89%. We further demonstrate the utility of our dataset by showing that fine-tuning on SWE-Bench++ instances yields measurable improvements on the SWE-bench Multilingual benchmark. SWE-Bench++ provides a scalable, multilingual benchmark for evaluating and improving repository-level code generation.

This technical report details a novel approach to combining reasoning and retrieval augmented generation (RAG) within a single, lean language model architecture. While existing RAG systems typically rely on large-scale models and external APIs, our work addresses the increasing demand for performant and privacy-preserving solutions deployable in resource-constrained or secure environments. Building on recent developments in test-time scaling and small-scale reasoning models, we develop a retrieval augmented conversational agent capable of interpreting complex, domain-specific queries using a lightweight backbone model. Our system integrates a dense retriever with fine-tuned Qwen2.5-Instruct models, using synthetic query generation and reasoning traces derived from frontier models (e.g., DeepSeek-R1) over a curated corpus, in this case, the NHS A-to-Z condition pages. We explore the impact of summarisation-based document compression, synthetic data design, and reasoning-aware fine-tuning on model performance. Evaluation against both non-reasoning and general-purpose lean models demonstrates that our domain-specific fine-tuning approach yields substantial gains in answer accuracy and consistency, approaching frontier-level performance while remaining feasible for local deployment. All implementation details and code are publicly released to support reproducibility and adaptation across domains.

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

Large Language Models (LLMs) have demonstrated remarkable proficiency across a variety of complex tasks. One significant application of LLMs is in tackling software engineering challenges, particularly in resolving real-world tasks on GitHub by fixing code based on the issues reported by the users. However, many current approaches rely on proprietary LLMs, which limits reproducibility, accessibility, and transparency. The critical components of LLMs for addressing software engineering issues and how their capabilities can be effectively enhanced remain unclear. To address these challenges, we introduce SWE-Fixer, a novel open-source LLM designed to effectively and efficiently resolve GitHub issues. SWE-Fixer comprises two essential modules: a code file retrieval module and a code editing module. The retrieval module employs BM25 along with a lightweight LLM model to achieve coarse-to-fine file retrieval. Subsequently, the code editing module utilizes the other LLM model to generate patches for the identified files. Then, to mitigate the lack of publicly available datasets, we compile an extensive dataset that includes 110K GitHub issues along with their corresponding patches, and train the two modules of SWE-Fixer separately. We assess our approach on the SWE-Bench Lite and Verified benchmarks, achieving state-of-the-art performance among open-source models with scores of 23.3% and 30.2%, respectively. These outcomes highlight the efficacy of our approach. We will make our model, dataset, and code publicly available at https://github.com/InternLM/SWE-Fixer.

Evaluation of text generation to date has primarily focused on content created sequentially, rather than improvements on a piece of text. Writing, however, is naturally an iterative and incremental process that requires expertise in different modular skills such as fixing outdated information or making the style more consistent. Even so, comprehensive evaluation of a model's capacity to perform these skills and the ability to edit remains sparse. This work presents EditEval: An instruction-based, benchmark and evaluation suite that leverages high-quality existing and new datasets for automatic evaluation of editing capabilities such as making text more cohesive and paraphrasing. We evaluate several pre-trained models, which shows that InstructGPT and PEER perform the best, but that most baselines fall below the supervised SOTA, particularly when neutralizing and updating information. Our analysis also shows that commonly used metrics for editing tasks do not always correlate well, and that optimization for prompts with the highest performance does not necessarily entail the strongest robustness to different models. Through the release of this benchmark and a publicly available leaderboard challenge, we hope to unlock future research in developing models capable of iterative and more controllable editing.

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.

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.

Model editing has become an increasingly popular alternative for efficiently updating knowledge within language models. Current methods mainly focus on reliability, generalization, and locality, with many methods excelling across these criteria. Some recent works disclose the pitfalls of these editing methods such as knowledge distortion or conflict. However, the general abilities of post-edited language models remain unexplored. In this paper, we perform a comprehensive evaluation on various editing methods and different language models, and have following findings. (1) Existing editing methods lead to inevitable performance deterioration on general benchmarks, indicating that existing editing methods maintain the general abilities of the model within only a few dozen edits. When the number of edits is slightly large, the intrinsic knowledge structure of the model is disrupted or even completely damaged. (2) Instruction-tuned models are more robust to editing, showing less performance drop on general knowledge after editing. (3) Language model with large scale is more resistant to editing compared to small model. (4) The safety of the edited model, is significantly weakened, even for those safety-aligned models. Our findings indicate that current editing methods are only suitable for small-scale knowledge updates within language models, which motivates further research on more practical and reliable editing methods. The details of code and reproduction can be found in https://github.com/lqinfdim/EditingEvaluation.

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.

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.

Coding agents repeatedly search, navigate, and retain context from evolving repositories, but disconnected indexes, language servers, and task-local histories force repeated discovery and obscure lifecycle costs. CodeNib builds reusable lexical, dense, and structural views per repository commit, maps outputs to repository-relative source ranges, maintains selected views across edits, and serves ranked search, symbol navigation, and bounded context through one runtime. Across 100 snapshots, we map quality-cost frontiers across the repository-context lifecycle. When outputs match an independent rebuild, graph and vector updates are 8.7times and 25.4times faster at the median. On the static-navigation subset matching normalized live-server locations (63% of 1,000 requests), the median per-request live/static latency ratio is 4.7times. Across five models, selected context policies preserve localization with 50--87% fewer trajectory tokens than paired grep/read. Together, these results support multi-view repository-context serving with explicit, operation-specific validity boundaries.

Revision is a crucial step in scientific writing, where authors refine their work to improve clarity, structure, and academic quality. Existing approaches to automated writing assistance often focus on sentence-level revisions, which fail to capture the broader context needed for effective modification. In this paper, we explore the impact of shifting from sentence-level to paragraph-level scope for the task of scientific text revision. The paragraph level definition of the task allows for more meaningful changes, and is guided by detailed revision instructions rather than general ones. To support this task, we introduce ParaRev, the first dataset of revised scientific paragraphs with an evaluation subset manually annotated with revision instructions. Our experiments demonstrate that using detailed instructions significantly improves the quality of automated revisions compared to general approaches, no matter the model or the metric considered.

Retrieval, re-ranking, and retrieval-augmented generation (RAG) are critical components of modern applications in information retrieval, question answering, or knowledge-based text generation. However, existing solutions are often fragmented, lacking a unified framework that easily integrates these essential processes. The absence of a standardized implementation, coupled with the complexity of retrieval and re-ranking workflows, makes it challenging for researchers to compare and evaluate different approaches in a consistent environment. While existing toolkits such as Rerankers and RankLLM provide general-purpose reranking pipelines, they often lack the flexibility required for fine-grained experimentation and benchmarking. In response to these challenges, we introduce Rankify, a powerful and modular open-source toolkit designed to unify retrieval, re-ranking, and RAG within a cohesive framework. Rankify supports a wide range of retrieval techniques, including dense and sparse retrievers, while incorporating state-of-the-art re-ranking models to enhance retrieval quality. Additionally, Rankify includes a collection of pre-retrieved datasets to facilitate benchmarking, available at Huggingface (https://huggingface.co/datasets/abdoelsayed/reranking-datasets-light). To encourage adoption and ease of integration, we provide comprehensive documentation (http://rankify.readthedocs.io/), an open-source implementation on GitHub (https://github.com/DataScienceUIBK/rankify), and a PyPI package for easy installation (https://pypi.org/project/rankify/). As a unified and lightweight framework, Rankify allows researchers and practitioners to advance retrieval and re-ranking methodologies while ensuring consistency, scalability, and ease of use.

Wikipedia can easily be justified as a behemoth, considering the sheer volume of content that is added or removed every minute to its several projects. This creates an immense scope, in the field of natural language processing towards developing automated tools for content moderation and review. In this paper we propose Self Attentive Revision Encoder (StRE) which leverages orthographic similarity of lexical units toward predicting the quality of new edits. In contrast to existing propositions which primarily employ features like page reputation, editor activity or rule based heuristics, we utilize the textual content of the edits which, we believe contains superior signatures of their quality. More specifically, we deploy deep encoders to generate representations of the edits from its text content, which we then leverage to infer quality. We further contribute a novel dataset containing 21M revisions across 32K Wikipedia pages and demonstrate that StRE outperforms existing methods by a significant margin at least 17% and at most 103%. Our pretrained model achieves such result after retraining on a set as small as 20% of the edits in a wikipage. This, to the best of our knowledge, is also the first attempt towards employing deep language models to the enormous domain of automated content moderation and review in Wikipedia.

Text editing or revision is an essential function of the human writing process. Understanding the capabilities of LLMs for making high-quality revisions and collaborating with human writers is a critical step toward building effective writing assistants. With the prior success of LLMs and instruction tuning, we leverage instruction-tuned LLMs for text revision to improve the quality of user-generated text and improve the efficiency of the process. We introduce CoEdIT, a state-of-the-art text editing model for writing assistance. CoEdIT takes instructions from the user specifying the attributes of the desired text, such as "Make the sentence simpler" or "Write it in a more neutral style," and outputs the edited text. We present a large language model fine-tuned on a diverse collection of task-specific instructions for text editing (a total of 82K instructions). Our model (1) achieves state-of-the-art performance on various text editing benchmarks, (2) is competitive with publicly available largest-sized LLMs trained on instructions while being sim60x smaller, (3) is capable of generalizing to unseen edit instructions, and (4) exhibits compositional comprehension abilities to generalize to instructions containing different combinations of edit actions. Through extensive qualitative and quantitative analysis, we show that writers prefer the edits suggested by CoEdIT, relative to other state-of-the-art text editing models. Our code and dataset are publicly available.

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.

Text editing is a crucial task that involves modifying text to better align with user intents. However, existing text editing benchmark datasets have limitations in providing only coarse-grained instructions. Consequently, although the edited output may seem reasonable, it often deviates from the intended changes outlined in the gold reference, resulting in low evaluation scores. To comprehensively investigate the text editing capabilities of large language models, this paper introduces XATU, the first benchmark specifically designed for fine-grained instruction-based explainable text editing. XATU covers a wide range of topics and text types, incorporating lexical, syntactic, semantic, and knowledge-intensive edits. To enhance interpretability, we leverage high-quality data sources and human annotation, resulting in a benchmark that includes fine-grained instructions and gold-standard edit explanations. By evaluating existing open and closed large language models against our benchmark, we demonstrate the effectiveness of instruction tuning and the impact of underlying architecture across various editing tasks. Furthermore, extensive experimentation reveals the significant role of explanations in fine-tuning language models for text editing tasks. The benchmark will be open-sourced to support reproduction and facilitate future research.

Large language models are increasingly integrated into academic writing workflows; however, the most widely used \LaTeX\ editors remain AI-peripheral -- offering compilation and collaboration, but no native intelligence. This separation forces researchers to leave their editing environment for AI assistance, fragmenting document context and interrupting writing flow. We present Bibby AI (trybibby.com), a native, AI-first \LaTeX\ editor that unifies the complete research writing lifecycle within a single interface. Bibby embeds an AI writing assistant, smart citation search, AI table and equation generation, an AI paper reviewer, abstract generator, literature review drafting, a deep research assistant, and real-time \LaTeX\ error detection and auto-fix -- all natively, without plugins or copy-paste workflows. We introduce LaTeXBench-500, a benchmark of 500 real-world compilation errors across six categories. Bibby achieves 91.4\% detection accuracy and 83.7\% one-click fix accuracy, outperforming Overleaf's native diagnostics (61.2\%) and OpenAI Prism (78.3 / 64.1\%) by large margins. Bibby demonstrates that a privacy-preserving, research-first AI editor can meaningfully accelerate every stage of academic manuscript preparation. We found that Bibby AI is a far superior alternative to overleaf latex and better than OpenAI Prism functionalities and AI.

Large Language Models provide significant new opportunities for the generation of high-quality written works. However, their employment in the research community is inhibited by their tendency to hallucinate invalid sources and lack of direct access to a knowledge base of relevant scientific articles. In this work, we present Citegeist: An application pipeline using dynamic Retrieval Augmented Generation (RAG) on the arXiv Corpus to generate a related work section and other citation-backed outputs. For this purpose, we employ a mixture of embedding-based similarity matching, summarization, and multi-stage filtering. To adapt to the continuous growth of the document base, we also present an optimized way of incorporating new and modified papers. To enable easy utilization in the scientific community, we release both, a website (https://citegeist.org), as well as an implementation harness that works with several different LLM implementations.

This study examined code issue detection and revision automation by integrating Large Language Models (LLMs) such as OpenAI's GPT-3.5 Turbo and GPT-4o into software development workflows. A static code analysis framework detects issues such as bugs, vulnerabilities, and code smells within a large-scale software project. Detailed information on each issue was extracted and organized to facilitate automated code revision using LLMs. An iterative prompt engineering process is applied to ensure that prompts are structured to produce accurate and organized outputs aligned with the project requirements. Retrieval-augmented generation (RAG) is implemented to enhance the relevance and precision of the revisions, enabling LLM to access and integrate real-time external knowledge. The issue of LLM hallucinations - where the model generates plausible but incorrect outputs - is addressed by a custom-built "Code Comparison App," which identifies and corrects erroneous changes before applying them to the codebase. Subsequent scans using the static code analysis framework revealed a significant reduction in code issues, demonstrating the effectiveness of combining LLMs, static analysis, and RAG to improve code quality, streamline the software development process, and reduce time and resource expenditure.

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.

Large language models have shown strong fluency in scientific writing, yet the evaluation of related work generation (RWG) remains limited. Existing RWG evaluations largely inherit summarization-oriented metrics, using lexical or semantic similarity to reference sections as proxies for quality. However, related work writing is fundamentally a citation-level scholarly positioning task: it requires selecting, organizing, and framing prior work to clarify how a target paper relates to, differs from, and contributes beyond existing research.As a result, models may generate coherent and semantically-relevant text while exhibiting academically critical failures, such as inappropriate citation selection or misplaced references, that conventional metrics do not capture.To this end, we introduce RWGBench, a benchmark that evaluates RWG from the perspective of citation decision-making rather than text similarity. RWGBench is constructed from a large-scale collection of 40,108 computer science papers and a retrieval corpus of 1.09 million documents, with a carefully curated test set comprising 100 papers and their corresponding published related work sections.We propose a multi-dimensional evaluation framework that assesses citation selection, contextual appropriateness, organization, and discourse structure.Experiments reveal systematic limitations in current systems that are obscured by standard evaluations, while Oracle studies further disentangle retrieval-level and generation-level bottlenecks. Human evaluation further shows that our citation-centric metrics align substantially better with expert judgment than surface-level text metrics. RWGBench offers a citation-centric testbed for developing and evaluating related work generation systems that are better aligned with scholarly writing practices.

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.

Conducting literature reviews for scientific papers is essential for understanding research, its limitations, and building on existing work. It is a tedious task which makes an automatic literature review generator appealing. Unfortunately, many existing works that generate such reviews using Large Language Models (LLMs) have significant limitations. They tend to hallucinate-generate non-factual information-and ignore the latest research they have not been trained on. To address these limitations, we propose a toolkit that operates on Retrieval Augmented Generation (RAG) principles, specialized prompting and instructing techniques with the help of LLMs. Our system first initiates a web search to retrieve relevant papers by summarizing user-provided abstracts into keywords using an off-the-shelf LLM. Authors can enhance the search by supplementing it with relevant papers or keywords, contributing to a tailored retrieval process. Second, the system re-ranks the retrieved papers based on the user-provided abstract. Finally, the related work section is generated based on the re-ranked results and the abstract. There is a substantial reduction in time and effort for literature review compared to traditional methods, establishing our toolkit as an efficient alternative. Our project page including the demo and toolkit can be accessed here: https://litllm.github.io

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%.

Cybersecurity literature reviews require a reproducible denominator: the set of papers that a protocol includes before screening and synthesis begin. Today, that denominator is often reconstructed from publisher portals, bibliographic indices, and scholarly application programming interfaces (APIs) whose coverage, formats, and query semantics change over time. This paper presents TopVenues, an open-source system that materializes corpus construction as a versioned research artifact. TopVenues declares a venue and year scope, uses DBLP Computer Science Bibliography (DBLP) as the metadata spine, enriches records with abstracts and BibTeX entries via open scholarly APIs and publisher-specific extractors, and stores the results in a monotonic SQLite snapshot, accessible via a command-line interface (CLI), a web interface, and export paths for review workflows. The May 2026 snapshot contains 9,925 papers from 11 cybersecurity sources over 2017 to 2026, with 99.86% abstract coverage and 99.99% BibTeX coverage; keyword search over the full corpus completes in under 31 ms, and a 250-test suite validates the data-integrity invariants. The fixed denominator also enables repeatable measurement: 29.2% of 2024 to 2025 papers from the four top-ranked security conferences in our scope appear as arXiv preprints, with a median of five months before publication, and a prior-author-track-record filter yields a 16.5x precision gain at 90% recall for triaging preprints that later appear in the same venue set. TopVenues links corpus construction to auditable cybersecurity measurement by making the corpus itself executable, inspectable, and citable. The artifact is available at https://github.com/sidneibarbieri/topVenues.

Reproducing research results from papers and released code is central to scientific progress. Existing works have introduced benchmarks to evaluate whether LLM agents can assist with reproducibility, but they are difficult to scale due to their reliance on substantial manual effort for data curation and evaluation. We introduce ReproRepo, a scalable framework for reproducibility evaluation that leverages human-raised GitHub issues as naturally occurring supervision on realistic reproduction blockers. We instantiate ReproRepo on 1,149 recent machine learning papers from major conferences and evaluate four frontier model-agent configurations. Our results show that LLM agents, even without executing code, can identify many real-world reproducibility problems from paper-repository pairs: the best agent in our study, namely Codex with GPT-5.5, surfaces at least one semantically related human-reported blocker for ~90% of papers in the study. Further analysis shows that agents are particularly effective for surfacing visible failures and identifying the right semantic region, but may still be insufficient in exact localization. ReproRepo can serve as a reusable, scalable framework for future evaluations of LLM agents on real-world reproducibility auditing. Our code is released at https://github.com/LithiumDA/ReproRepo.

An edit summary is a succinct comment written by a Wikipedia editor explaining the nature of, and reasons for, an edit to a Wikipedia page. Edit summaries are crucial for maintaining the encyclopedia: they are the first thing seen by content moderators and help them decide whether to accept or reject an edit. Additionally, edit summaries constitute a valuable data source for researchers. Unfortunately, as we show, for many edits, summaries are either missing or incomplete. To overcome this problem and help editors write useful edit summaries, we propose a model for recommending edit summaries generated by a language model trained to produce good edit summaries given the representation of an edit diff. This is a challenging task for multiple reasons, including mixed-quality training data, the need to understand not only what was changed in the article but also why it was changed, and efficiency requirements imposed by the scale of Wikipedia. We address these challenges by curating a mix of human and synthetically generated training data and fine-tuning a generative language model sufficiently small to be used on Wikipedia at scale. Our model performs on par with human editors. Commercial large language models are able to solve this task better than human editors, but would be too expensive to run on Wikipedia at scale. More broadly, this paper showcases how language modeling technology can be used to support humans in maintaining one of the largest and most visible projects on the Web.

This paper presents rerankers, a Python library which provides an easy-to-use interface to the most commonly used re-ranking approaches. Re-ranking is an integral component of many retrieval pipelines; however, there exist numerous approaches to it, relying on different implementation methods. rerankers unifies these methods into a single user-friendly interface, allowing practitioners and researchers alike to explore different methods while only changing a single line of Python code. Moreover ,rerankers ensures that its implementations are done with the fewest dependencies possible, and re-uses the original implementation whenever possible, guaranteeing that our simplified interface results in no performance degradation compared to more complex ones. The full source code and list of supported models are updated regularly and available at https://github.com/answerdotai/rerankers.

Artificial Intelligence systems, which benefit from the availability of large-scale datasets and increasing computational power, have become effective solutions to various critical tasks, such as natural language understanding, speech recognition, and image processing. The advancement of these AI systems is inseparable from open-source software (OSS). This paper presents an empirical study that investigates the issues in the repositories of open-source AI repositories to assist developers in understanding problems during the process of employing AI systems. We collect 576 repositories from the PapersWithCode platform. Among these repositories, we find 24,953 issues by utilizing GitHub REST APIs. Our empirical study includes three phases. First, we manually analyze these issues to categorize the problems that developers are likely to encounter in open-source AI repositories. Specifically, we provide a taxonomy of 13 categories related to AI systems. The two most common issues are runtime errors (23.18%) and unclear instructions (19.53%). Second, we see that 67.5% of issues are closed. We also find that half of these issues resolve within four days. Moreover, issue management features, e.g., label and assign, are not widely adopted in open-source AI repositories. In particular, only 7.81% and 5.9% of repositories label issues and assign these issues to assignees, respectively. Finally, we empirically show that employing GitHub issue management features and writing issues with detailed descriptions facilitate the resolution of issues. Based on our findings, we make recommendations for developers to help better manage the issues of open-source AI repositories and improve their quality.

There are a few prominent practices for conducting reviews of academic literature, including searching for specific keywords on Google Scholar or checking citations from some initial seed paper(s). These approaches serve a critical purpose for academic literature reviews, yet there remain challenges in identifying relevant literature when similar work may utilize different terminology (e.g., mixed-initiative visual analytics papers may not use the same terminology as papers on model-steering, yet the two topics are relevant to one another). In this paper, we introduce a system, VitaLITy, intended to complement existing practices. In particular, VitaLITy promotes serendipitous discovery of relevant literature using transformer language models, allowing users to find semantically similar papers in a word embedding space given (1) a list of input paper(s) or (2) a working abstract. VitaLITy visualizes this document-level embedding space in an interactive 2-D scatterplot using dimension reduction. VitaLITy also summarizes meta information about the document corpus or search query, including keywords and co-authors, and allows users to save and export papers for use in a literature review. We present qualitative findings from an evaluation of VitaLITy, suggesting it can be a promising complementary technique for conducting academic literature reviews. Furthermore, we contribute data from 38 popular data visualization publication venues in VitaLITy, and we provide scrapers for the open-source community to continue to grow the list of supported venues.

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 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

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.

Large language models (LLMs) often exhibit hallucinations due to incorrect or outdated knowledge. Hence, model editing methods have emerged to enable targeted knowledge updates. To achieve this, a prevailing paradigm is the locating-then-editing approach, which first locates influential parameters and then edits them by introducing a perturbation. While effective, current studies have demonstrated that this perturbation inevitably disrupt the originally preserved knowledge within LLMs, especially in sequential editing scenarios. To address this, we introduce AlphaEdit, a novel solution that projects perturbation onto the null space of the preserved knowledge before applying it to the parameters. We theoretically prove that this projection ensures the output of post-edited LLMs remains unchanged when queried about the preserved knowledge, thereby mitigating the issue of disruption. Extensive experiments on various LLMs, including LLaMA3, GPT2-XL, and GPT-J, show that AlphaEdit boosts the performance of most locating-then-editing methods by an average of 36.4% with a single line of additional code for projection solely. Our code is available at: https://github.com/jianghoucheng/AlphaEdit.

We introduce KAPSO, a modular framework for autonomous program synthesis and optimization. Given a natural language goal and an evaluation method, KAPSO iteratively performs ideation, code synthesis and editing, execution, evaluation, and learning to improve a runnable artifact toward measurable objectives. Rather than treating synthesis as the endpoint, KAPSO uses synthesis as an operator within a long-horizon optimization loop, where progress is defined by evaluator outcomes. KAPSO targets long-horizon failures common in coding agents, including lost experimental state, brittle debugging, and weak reuse of domain expertise, by integrating three tightly coupled components. First, a git-native experimentation engine isolates each attempt as a branch, producing reproducible artifacts and preserving provenance across iterations. Second, a knowledge system ingests heterogeneous sources, including repositories, internal playbooks, and curated external resources such as documentation, scientific papers, and web search results, and organizes them into a structured representation that supports retrieval over workflows, implementations, and environment constraints. Third, a cognitive memory layer coordinates retrieval and maintains an episodic store of reusable lessons distilled from experiment traces (run logs, diffs, and evaluator feedback), reducing repeated error modes and accelerating convergence. We evaluated KAPSO on MLE-Bench (Kaggle-style ML competitions) and ALE-Bench (AtCoder heuristic optimization), and report end-to-end performance. Code Available at: https://github.com/Leeroo-AI/kapso

Academic literature reviews have traditionally relied on techniques such as keyword searches and accumulation of relevant back-references, using databases like Google Scholar or IEEEXplore. However, both the precision and accuracy of these search techniques is limited by the presence or absence of specific keywords, making literature review akin to searching for needles in a haystack. We present vitaLITy 2, a solution that uses a Large Language Model or LLM-based approach to identify semantically relevant literature in a textual embedding space. We include a corpus of 66,692 papers from 1970-2023 which are searchable through text embeddings created by three language models. vitaLITy 2 contributes a novel Retrieval Augmented Generation (RAG) architecture and can be interacted with through an LLM with augmented prompts, including summarization of a collection of papers. vitaLITy 2 also provides a chat interface that allow users to perform complex queries without learning any new programming language. This also enables users to take advantage of the knowledge captured in the LLM from its enormous training corpus. Finally, we demonstrate the applicability of vitaLITy 2 through two usage scenarios. vitaLITy 2 is available as open-source software at https://vitality-vis.github.io.

Generating a review for an academic research paper is a complex task that requires a deep understanding of the document's content and the interdependencies between its sections. It demands not only insight into technical details but also an appreciation of the paper's overall coherence and structure. Recent methods have predominantly focused on fine-tuning large language models (LLMs) to address this challenge. However, they often overlook the computational and performance limitations imposed by long input token lengths. To address this, we introduce AutoRev, an Automatic Peer Review System for Academic Research Papers. Our novel framework represents an academic document as a graph, enabling the extraction of the most critical passages that contribute significantly to the review. This graph-based approach demonstrates effectiveness for review generation and is potentially adaptable to various downstream tasks, such as question answering, summarization, and document representation. When applied to review generation, our method outperforms SOTA baselines by an average of 58.72% across all evaluation metrics. We hope that our work will stimulate further research in applying graph-based extraction techniques to other downstream tasks in NLP. We plan to make our code public upon acceptance.

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

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

This paper introduces a scholarly Question Answering (QA) system on top of the NFDI4DataScience Gateway, employing a Retrieval Augmented Generation-based (RAG) approach. The NFDI4DS Gateway, as a foundational framework, offers a unified and intuitive interface for querying various scientific databases using federated search. The RAG-based scholarly QA, powered by a Large Language Model (LLM), facilitates dynamic interaction with search results, enhancing filtering capabilities and fostering a conversational engagement with the Gateway search. The effectiveness of both the Gateway and the scholarly QA system is demonstrated through experimental analysis.

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.

Large Language Models (LLMs) have greatly advanced code auto-completion systems, with a potential for substantial productivity enhancements for developers. However, current benchmarks mainly focus on single-file tasks, leaving an assessment gap for more complex, real-world, multi-file programming scenarios. To fill this gap, we introduce RepoBench, a new benchmark specifically designed for evaluating repository-level code auto-completion systems. RepoBench consists of three interconnected evaluation tasks: RepoBench-R (Retrieval), RepoBench-C (Code Completion), and RepoBench-P (Pipeline). Each task respectively measures the system's ability to retrieve the most relevant code snippets from other files as cross-file context, predict the next line of code with cross-file and in-file context, and handle complex tasks that require a combination of both retrieval and next-line prediction. RepoBench aims to facilitate a more complete comparison of performance and encouraging continuous improvement in auto-completion systems. RepoBench is publicly available at https://github.com/Leolty/repobench.

Expository documents are vital resources for conveying complex information to readers. Despite their usefulness, writing expository text by hand is a challenging process that requires careful content planning, obtaining facts from multiple sources, and the ability to clearly synthesize these facts. To ease these burdens, we propose the task of expository text generation, which seeks to automatically generate an accurate and stylistically consistent expository text for a topic by intelligently searching a knowledge source. We solve our task by developing IRP, a framework that overcomes the limitations of retrieval-augmented models and iteratively performs content planning, fact retrieval, and rephrasing. Through experiments on three diverse, newly-collected datasets, we show that IRP produces factual and organized expository texts that accurately inform readers.

Knowledge editing techniques, aiming to efficiently modify a minor proportion of knowledge in large language models (LLMs) without negatively impacting performance across other inputs, have garnered widespread attention. However, existing methods predominantly rely on memorizing the updated knowledge, impeding LLMs from effectively combining the new knowledge with their inherent knowledge when answering questions. To this end, we propose a Learning to Edit (LTE) framework, focusing on teaching LLMs to apply updated knowledge into input questions, inspired by the philosophy of "Teach a man to fish." LTE features a two-phase process: (i) the Alignment Phase, which fine-tunes LLMs on a meticulously curated parallel dataset to make reliable, in-scope edits while preserving out-of-scope information and linguistic proficiency; and (ii) the Inference Phase, which employs a retrieval-based mechanism for real-time and mass knowledge editing. By comparing our approach with seven advanced baselines across four popular knowledge editing benchmarks and two LLM architectures, we demonstrate LTE's superiority in knowledge editing performance, robustness in both batch and sequential editing, minimal interference on general tasks, and rapid editing speeds. The data and code are available at https://github.com/YJiangcm/LTE.

Natural language to repository generation (NL2Repo) requires a system to construct an entire software repository from a natural-language requirements document. Compared with function-level code generation, this task demands longer planning horizons, stable interfaces across files, and iterative debugging of cross-file inconsistencies. To address these challenges, we propose CodeTeam, an LLM-based multi-agent framework that separates planning, decision making, and implementation into distinct, coordinated stages. In the planning stage, multiple Architect agents draft competing software design sketches (SDS), optionally grounded by retrieved design references. A CTO agent then evaluates, selects, and normalizes the most promising SDS into a machine-checkable contract that specifies file ownership, public interfaces, and dependency constraints. In the implementation stage, Developer agents generate code under a dependency-aware scheduler with bounded context and lightweight Git-based coordination, while a QA agent runs tests and drives iterative repairs. On the synthesis-based SketchEval benchmark, we explicitly compare CodeTeam's prompt-engineering (PE) and supervised fine-tuning (SFT) variants with the corresponding CodeS variants, where CodeTeam improves the overall SketchBLEU by 4.1 and 2.9 absolute points, respectively. On the execution-based NL2Repo-Bench benchmark, used as an external validation protocol, CodeTeam achieves the highest average test pass rate in both settings (34.6% PE, 42.3% SFT), confirming that the sketch-improvements extend to functional correctness under upstream test suites. Ablation results show that project-specific developer allocation and retrieval-augmented planning each contribute substantially to the SketchBLEU improvement (9.9% and 8.1% relative, respectively). CodeTeam and the experimental results are available at https://github.com/WhitenWhiten/CodeTeam

Document structure editing involves manipulating localized textual, visual, and layout components in document images based on the user's requests. Past works have shown that multimodal grounding of user requests in the document image and identifying the accurate structural components and their associated attributes remain key challenges for this task. To address these, we introduce the DocEdit-v2, a novel framework that performs end-to-end document editing by leveraging Large Multimodal Models (LMMs). It consists of three novel components: (1) Doc2Command, which simultaneously localizes edit regions of interest (RoI) and disambiguates user edit requests into edit commands; (2) LLM-based Command Reformulation prompting to tailor edit commands originally intended for specialized software into edit instructions suitable for generalist LMMs. (3) Moreover, DocEdit-v2 processes these outputs via Large Multimodal Models like GPT-4V and Gemini, to parse the document layout, execute edits on grounded Region of Interest (RoI), and generate the edited document image. Extensive experiments on the DocEdit dataset show that DocEdit-v2 significantly outperforms strong baselines on edit command generation (2-33%), RoI bounding box detection (12-31%), and overall document editing (1-12\%) tasks.

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.

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.

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

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.

Large Language Models (LLMs) excel at code generation but struggle with complex problems. Retrieval-Augmented Generation (RAG) mitigates this issue by integrating external knowledge, yet retrieval models often miss relevant context, and generation models hallucinate with irrelevant data. We propose Programming Knowledge Graph (PKG) for semantic representation and fine-grained retrieval of code and text. Our approach enhances retrieval precision through tree pruning and mitigates hallucinations via a re-ranking mechanism that integrates non-RAG solutions. Structuring external data into finer-grained nodes improves retrieval granularity. Evaluations on HumanEval and MBPP show up to 20% pass@1 accuracy gains and a 34% improvement over baselines on MBPP. Our findings demonstrate that our proposed PKG approach along with re-ranker effectively address complex problems while maintaining minimal negative impact on solutions that are already correct without RAG. The replication package is published at https://github.com/iamshahd/ProgrammingKnowledgeGraph

Tool-augmented large language models have advanced from single-turn question answering to deep research workflows that iteratively plan queries, invoke external tools, and synthesize information to address complex information needs. Evaluating such workflows presents a fundamental challenge: reliance on live APIs introduces non-determinism, as tool invocations may yield different results across runs due to temporal drift, rate limiting, and evolving backend states. This variance undermines reproducibility and invalidates cross-system comparisons. We present ScholarGym, a simulation environment for reproducible evaluation of deep research workflows on academic literature. The environment decouples workflow components into query planning, tool invocation, and relevance assessment, enabling fine-grained analysis of each stage under controlled conditions. Built on a static corpus of 570K papers with deterministic retrieval, ScholarGym provides 2,536 queries with expert-annotated ground truth. Experiments across diverse backbone models reveal how reasoning capabilities, planning strategies, and selection mechanisms interact over iterative refinement.

Large language models are increasingly embedded into academic writing workflows, yet existing assistants remain external to the editor, preventing deep interaction with document state, structure, and revision history. This separation makes it impossible to support agentic, context-aware operations directly within LaTeX editors such as Overleaf. We present PaperDebugger, an in-editor, multi-agent, and plugin-based academic writing assistant that brings LLM-driven reasoning directly into the writing environment. Enabling such in-editor interaction is technically non-trivial: it requires reliable bidirectional synchronization with the editor, fine-grained version control and patching, secure state management, multi-agent scheduling, and extensible communication with external tools. PaperDebugger addresses these challenges through a Chrome-approved extension, a Kubernetes-native orchestration layer, and a Model Context Protocol (MCP) toolchain that integrates literature search, reference lookup, document scoring, and revision pipelines. Our demo showcases a fully integrated workflow, including localized edits, structured reviews, parallel agent execution, and diff-based updates, encapsulated within a minimal-intrusion user interface (UI). Early aggregated analytics demonstrate active user engagement and validate the practicality of an editor-native, agentic writing assistant. More details about this demo and video could be found at https://github.com/PaperDebugger/PaperDebugger.

Large Language Models (LLMs) have revolutionized Natural Language Processing (NLP) but pose risks of inadvertently exposing copyrighted or proprietary data, especially when such data is used for training but not intended for distribution. Traditional methods address these leaks only after content is generated, which can lead to the exposure of sensitive information. This study introduces a proactive approach: examining LLMs' internal states before text generation to detect potential leaks. By using a curated dataset of copyrighted materials, we trained a neural network classifier to identify risks, allowing for early intervention by stopping the generation process or altering outputs to prevent disclosure. Integrated with a Retrieval-Augmented Generation (RAG) system, this framework ensures adherence to copyright and licensing requirements while enhancing data privacy and ethical standards. Our results show that analyzing internal states effectively mitigates the risk of copyrighted data leakage, offering a scalable solution that fits smoothly into AI workflows, ensuring compliance with copyright regulations while maintaining high-quality text generation. The implementation is available on GitHub.https://github.com/changhu73/Internal_states_leakage

This paper presents UltraEdit, a large-scale (approximately 4 million editing samples), automatically generated dataset for instruction-based image editing. Our key idea is to address the drawbacks in existing image editing datasets like InstructPix2Pix and MagicBrush, and provide a systematic approach to producing massive and high-quality image editing samples. UltraEdit offers several distinct advantages: 1) It features a broader range of editing instructions by leveraging the creativity of large language models (LLMs) alongside in-context editing examples from human raters; 2) Its data sources are based on real images, including photographs and artworks, which provide greater diversity and reduced bias compared to datasets solely generated by text-to-image models; 3) It also supports region-based editing, enhanced by high-quality, automatically produced region annotations. Our experiments show that canonical diffusion-based editing baselines trained on UltraEdit set new records on MagicBrush and Emu-Edit benchmarks. Our analysis further confirms the crucial role of real image anchors and region-based editing data. The dataset, code, and models can be found in https://ultra-editing.github.io.

Autonomous research systems are often evaluated as one-shot paper generators: given a topic, they produce a manuscript and a small set of experiment logs. This framing hides the operational problem that makes such systems difficult to trust: research is long-running, branching, failure-prone, and dependent on auditable handoffs between agents and humans. XScientist is a git-like research protocol and operating system for this setting. It orchestrates idea generation, experiment execution, manuscript drafting, self-review, repair, quality gating, daemon scheduling, and reproducibility artifacts as one continuously observable pipeline. The central design choice is to treat each run as a portable research artifact rather than only as a PDF. XScientist exports an Agent-Native Research Artifact (ARA), a protocol that records an exploration DAG, per-node code and outputs, claim-to-evidence anchors, content hashes, provenance, and re-execution hooks. This makes each generated paper inspectable as a science exploration tree: failed branches, repaired experiments, ablations, and manuscript claims remain connected to the nodes that produced them. The system also includes deterministic integrity forensics, sample gates, truth contracts, reviewer-oriented repair loops, and long-running daemon controls. This paper describes the current XScientist architecture, the ARA protocol surface, and the practical safeguards needed to move autonomous science from single-run demos toward reproducible, reviewable, and forkable research infrastructure. The implementation and manuscript source are maintained in the public GitHub repository at https://github.com/smileformylove/XScientist.

Language Models [LMs] are now playing an increasingly large role in information generation and synthesis; the representation of scientific knowledge in these systems needs to be highly accurate. A prime challenge is hallucination; that is, generating apparently plausible but actually false information, including invented citations and nonexistent research papers. This kind of inaccuracy is dangerous in all the domains that require high levels of factual correctness, such as academia and education. This work presents a pipeline for evaluating the frequency with which language models hallucinate in generating responses in the scientific literature. We propose ArxEval, an evaluation pipeline with two tasks using ArXiv as a repository: Jumbled Titles and Mixed Titles. Our evaluation includes fifteen widely used language models and provides comparative insights into their reliability in handling scientific literature.

Retrieval-Augmented Generation (RAG) has advanced significantly in recent years. The complexity of RAG systems, which involve multiple components-such as indexing, retrieval, and generation-along with numerous other parameters, poses substantial challenges for systematic evaluation and quality enhancement. Previous research highlights that evaluating RAG systems is essential for documenting advancements, comparing configurations, and identifying effective approaches for domain-specific applications. This study systematically reviews 63 academic articles to provide a comprehensive overview of state-of-the-art RAG evaluation methodologies, focusing on four key areas: datasets, retrievers, indexing and databases, and the generator component. We observe the feasibility of an automated evaluation approach for each component of a RAG system, leveraging an LLM capable of both generating evaluation datasets and conducting evaluations. In addition, we found that further practical research is essential to provide companies with clear guidance on the do's and don'ts of implementing and evaluating RAG systems. By synthesizing evaluation approaches for key RAG components and emphasizing the creation and adaptation of domain-specific datasets for benchmarking, we contribute to the advancement of systematic evaluation methods and the improvement of evaluation rigor for RAG systems. Furthermore, by examining the interplay between automated approaches leveraging LLMs and human judgment, we contribute to the ongoing discourse on balancing automation and human input, clarifying their respective contributions, limitations, and challenges in achieving robust and reliable evaluations.

Dynamic retrieval augmented generation (RAG) paradigm actively decides when and what to retrieve during the text generation process of Large Language Models (LLMs). There are two key elements of this paradigm: identifying the optimal moment to activate the retrieval module (deciding when to retrieve) and crafting the appropriate query once retrieval is triggered (determining what to retrieve). However, current dynamic RAG methods fall short in both aspects. Firstly, the strategies for deciding when to retrieve often rely on static rules. Moreover, the strategies for deciding what to retrieve typically limit themselves to the LLM's most recent sentence or the last few tokens, while the LLM's real-time information needs may span across the entire context. To overcome these limitations, we introduce a new framework, DRAGIN, i.e., Dynamic Retrieval Augmented Generation based on the real-time Information Needs of LLMs. Our framework is specifically designed to make decisions on when and what to retrieve based on the LLM's real-time information needs during the text generation process. We evaluate DRAGIN along with existing methods comprehensively over 4 knowledge-intensive generation datasets. Experimental results show that DRAGIN achieves superior performance on all tasks, demonstrating the effectiveness of our method. We have open-sourced all the code, data, and models in GitHub: https://github.com/oneal2000/DRAGIN/tree/main

Many LLM-based open-ended search systems freeze the foundation model that proposes improvements to existing solutions, which may bottleneck long-run progress. Recent work has explored updating the proposal model at test time [arXiv:2511.23473], but the update strategy is still typically hand-specified. Therefore, this study investigated whether an LLM can use task feedback to decide how it should update its weights. For tractability, we focused on the simpler case where there is only one round of self-improvement, and restricted the update operator to self-supervised next token prediction (NTP), leaving the model freedom in choosing its training data and key NTP hyperparameters. Using the Self-Adapting Language Models (SEAL) [arXiv:2506.10943] framework as a testbed, we relaxed its fixed human template constraint and allowed the model to generate its own self-edit templates, thereby giving it more control over its training data and hyperparameters. Two variants were studied, differing in whether template generation was conditioned on a lightweight archive of past templates. In SEAL's Single-Passage Knowledge Incorporation setting with Qwen3-8B on SQuAD [arXiv:1606.05250], the no-archive variant performed comparably to the weaker "Implications" baseline, while the archive variant outperformed "Implications" and approached the strongest human-designed "Rewrite" baseline without surpassing it. Further analysis of collapse in the model's exploration revealed that a naive archive can confer some short-term robustness but can also accelerate homogenization, suggesting that explicit novelty pressure may be required to consistently advance beyond carefully optimized human strategies. Our code is available at https://github.com/cheongalc/search-self-edit-strategies .

Transforming static research papers into dynamic media such as posters, slides, and videos is essential for effective dissemination but remains a labor-intensive challenge. Existing automated approaches often treat these formats in isolation and consequently fail to maintain semantic consistency across the entire presentation suite. We address this fragmentation by formalizing the task of unified presentation suite generation and proposing OmniPresent to orchestrate the creation of coherent deliverables. Our framework adopts a renderable HTML representation to enable centralized content planning and a self-correcting verify-and-repair loop that actively resolves conflicts across modalities. We further facilitate scalable research in this domain by releasing OmniPreBench, a comprehensive dataset comprising over one thousand papers with paired artifacts, and establishing a rigorous VLM-based evaluation protocol. Empirical results confirm that our method generates high-quality and faithful presentation suites that significantly surpass strong baselines in both accuracy and visual appeal.

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

Despite the ability to train capable LLMs, the methodology for maintaining their relevancy and rectifying errors remains elusive. To this end, the past few years have witnessed a surge in techniques for editing LLMs, the objective of which is to efficiently alter the behavior of LLMs within a specific domain without negatively impacting performance across other inputs. This paper embarks on a deep exploration of the problems, methods, and opportunities related to model editing for LLMs. In particular, we provide an exhaustive overview of the task definition and challenges associated with model editing, along with an in-depth empirical analysis of the most progressive methods currently at our disposal. We also build a new benchmark dataset to facilitate a more robust evaluation and pinpoint enduring issues intrinsic to existing techniques. Our objective is to provide valuable insights into the effectiveness and feasibility of each editing technique, thereby assisting the community in making informed decisions on the selection of the most appropriate method for a specific task or context. Code and datasets are available at https://github.com/zjunlp/EasyEdit.

Retrieval-Augmented Generation (RAG) significantly enhances the performance of large language models (LLMs) in downstream tasks by integrating external knowledge. To facilitate researchers in deploying RAG systems, various RAG toolkits have been introduced. However, many existing RAG toolkits lack support for knowledge adaptation tailored to specific application scenarios. To address this limitation, we propose UltraRAG, a RAG toolkit that automates knowledge adaptation throughout the entire workflow, from data construction and training to evaluation, while ensuring ease of use. UltraRAG features a user-friendly WebUI that streamlines the RAG process, allowing users to build and optimize systems without coding expertise. It supports multimodal input and provides comprehensive tools for managing the knowledge base. With its highly modular architecture, UltraRAG delivers an end-to-end development solution, enabling seamless knowledge adaptation across diverse user scenarios. The code, demonstration videos, and installable package for UltraRAG are publicly available at https://github.com/OpenBMB/UltraRAG.