Daily Papers

The proliferation of Large Language Models (LLMs) has created a significant integration challenge in the AI agent ecosystem, often called the "N times M problem," where N models require custom integrations for M tools. This fragmentation stifles innovation and creates substantial development overhead. While the Model Context Protocol (MCP) has emerged as a standard to resolve this, its adoption is hindered by the manual effort required to convert the vast universe of existing software into MCP-compliant services. This is especially true for the millions of open-source repositories on GitHub, the world's largest collection of functional code. This paper introduces Code2MCP, a highly automated, agentic framework designed to transform any GitHub repository into a functional MCP service with minimal human intervention. Our system employs a multi-stage workflow that automates the entire process, from code analysis and environment configuration to service generation and deployment. A key innovation of our framework is an LLM-driven, closed-loop "Run--Review--Fix" cycle, which enables the system to autonomously debug and repair the code it generates. Code2MCP produces not only deployable services but also comprehensive technical documentation, acting as a catalyst to accelerate the MCP ecosystem by systematically unlocking the world's largest open-source code repository and automating the critical last mile of tool integration. The code is open-sourced at https://github.com/DEFENSE-SEU/MCP-Github-Agent.

Foundation Large Language Models (LLMs) such as GPT-4 represent a revolution in AI due to their real-world applications though natural language processing. However, they also pose many significant risks such as the presence of biased, private, or harmful text, and the unauthorized inclusion of copyrighted material. We introduce h2oGPT, a suite of open-source code repositories for the creation and use of Large Language Models (LLMs) based on Generative Pretrained Transformers (GPTs). The goal of this project is to create the world's best truly open-source alternative to closed-source GPTs. In collaboration with and as part of the incredible and unstoppable open-source community, we open-source several fine-tuned h2oGPT models from 7 to 40 Billion parameters, ready for commercial use under fully permissive Apache 2.0 licenses. Included in our release is 100% private document search using natural language. Open-source language models help boost AI development and make it more accessible and trustworthy. They lower entry hurdles, allowing people and groups to tailor these models to their needs. This openness increases innovation, transparency, and fairness. An open-source strategy is needed to share AI benefits fairly, and H2O.ai will continue to democratize AI and LLMs.

Physics-based numerical models have been the bedrock of atmospheric sciences for decades, offering robust solutions but often at the cost of significant computational resources. Deep learning (DL) models have emerged as powerful tools in meteorology, capable of analyzing complex weather and climate data by learning intricate dependencies and providing rapid predictions once trained. While these models demonstrate promising performance in weather prediction, often surpassing traditional physics-based methods, they still face critical challenges. This paper presents a comprehensive survey of recent deep learning and foundation models for weather prediction. We propose a taxonomy to classify existing models based on their training paradigms: deterministic predictive learning, probabilistic generative learning, and pre-training and fine-tuning. For each paradigm, we delve into the underlying model architectures, address major challenges, offer key insights, and propose targeted directions for future research. Furthermore, we explore real-world applications of these methods and provide a curated summary of open-source code repositories and widely used datasets, aiming to bridge research advancements with practical implementations while fostering open and trustworthy scientific practices in adopting cutting-edge artificial intelligence for weather prediction. The related sources are available at https://github.com/JimengShi/ DL-Foundation-Models-Weather.

Automated program repair (APR) aims to fix software bugs automatically and plays a crucial role in software development and maintenance. With the recent advances in deep learning (DL), an increasing number of APR techniques have been proposed to leverage neural networks to learn bug-fixing patterns from massive open-source code repositories. Such learning-based techniques usually treat APR as a neural machine translation (NMT) task, where buggy code snippets (i.e., source language) are translated into fixed code snippets (i.e., target language) automatically. Benefiting from the powerful capability of DL to learn hidden relationships from previous bug-fixing datasets, learning-based APR techniques have achieved remarkable performance. In this paper, we provide a systematic survey to summarize the current state-of-the-art research in the learning-based APR community. We illustrate the general workflow of learning-based APR techniques and detail the crucial components, including fault localization, patch generation, patch ranking, patch validation, and patch correctness phases. We then discuss the widely-adopted datasets and evaluation metrics and outline existing empirical studies. We discuss several critical aspects of learning-based APR techniques, such as repair domains, industrial deployment, and the open science issue. We highlight several practical guidelines on applying DL techniques for future APR studies, such as exploring explainable patch generation and utilizing code features. Overall, our paper can help researchers gain a comprehensive understanding about the achievements of the existing learning-based APR techniques and promote the practical application of these techniques. Our artifacts are publicly available at https://github.com/QuanjunZhang/AwesomeLearningAPR.

Millions of open-source projects with numerous bug fixes are available in code repositories. This proliferation of software development histories can be leveraged to learn how to fix common programming bugs. To explore such a potential, we perform an empirical study to assess the feasibility of using Neural Machine Translation techniques for learning bug-fixing patches for real defects. First, we mine millions of bug-fixes from the change histories of projects hosted on GitHub, in order to extract meaningful examples of such bug-fixes. Next, we abstract the buggy and corresponding fixed code, and use them to train an Encoder-Decoder model able to translate buggy code into its fixed version. In our empirical investigation we found that such a model is able to fix thousands of unique buggy methods in the wild. Overall, this model is capable of predicting fixed patches generated by developers in 9-50% of the cases, depending on the number of candidate patches we allow it to generate. Also, the model is able to emulate a variety of different Abstract Syntax Tree operations and generate candidate patches in a split second.

Data scientists today search large data lakes to discover and integrate datasets. In order to bring together disparate data sources, dataset discovery methods rely on some form of schema matching: the process of establishing correspondences between datasets. Traditionally, schema matching has been used to find matching pairs of columns between a source and a target schema. However, the use of schema matching in dataset discovery methods differs from its original use. Nowadays schema matching serves as a building block for indicating and ranking inter-dataset relationships. Surprisingly, although a discovery method's success relies highly on the quality of the underlying matching algorithms, the latest discovery methods employ existing schema matching algorithms in an ad-hoc fashion due to the lack of openly-available datasets with ground truth, reference method implementations, and evaluation metrics. In this paper, we aim to rectify the problem of evaluating the effectiveness and efficiency of schema matching methods for the specific needs of dataset discovery. To this end, we propose Valentine, an extensible open-source experiment suite to execute and organize large-scale automated matching experiments on tabular data. Valentine includes implementations of seminal schema matching methods that we either implemented from scratch (due to absence of open source code) or imported from open repositories. The contributions of Valentine are: i) the definition of four schema matching scenarios as encountered in dataset discovery methods, ii) a principled dataset fabrication process tailored to the scope of dataset discovery methods and iii) the most comprehensive evaluation of schema matching techniques to date, offering insight on the strengths and weaknesses of existing techniques, that can serve as a guide for employing schema matching in future dataset discovery methods.

In Open Source Software, the source code and any other resources available in a project can be viewed or reused by anyone subject to often permissive licensing restrictions. In contrast to some studies of dependency-based reuse supported via package managers, no studies of OSS-wide copy-based reuse exist. This dataset seeks to encourage the studies of OSS-wide copy-based reuse by providing copying activity data that captures whole-file reuse in nearly all OSS. To accomplish that, we develop approaches to detect copy-based reuse by developing an efficient algorithm that exploits World of Code infrastructure: a curated and cross referenced collection of nearly all open source repositories. We expect this data to enable future research and tool development that support such reuse and minimize associated risks.

Data-driven research on the automated discovery and repair of security vulnerabilities in source code requires comprehensive datasets of real-life vulnerable code and their fixes. To assist in such research, we propose a method to automatically collect and curate a comprehensive vulnerability dataset from Common Vulnerabilities and Exposures (CVE) records in the public National Vulnerability Database (NVD). We implement our approach in a fully automated dataset collection tool and share an initial release of the resulting vulnerability dataset named CVEfixes. The CVEfixes collection tool automatically fetches all available CVE records from the NVD, gathers the vulnerable code and corresponding fixes from associated open-source repositories, and organizes the collected information in a relational database. Moreover, the dataset is enriched with meta-data such as programming language, and detailed code and security metrics at five levels of abstraction. The collection can easily be repeated to keep up-to-date with newly discovered or patched vulnerabilities. The initial release of CVEfixes spans all published CVEs up to 9 June 2021, covering 5365 CVE records for 1754 open-source projects that were addressed in a total of 5495 vulnerability fixing commits. CVEfixes supports various types of data-driven software security research, such as vulnerability prediction, vulnerability classification, vulnerability severity prediction, analysis of vulnerability-related code changes, and automated vulnerability repair.

As an essential part of modern hardware design, manually writing Register Transfer Level (RTL) code such as Verilog is often labor-intensive. Following the tremendous success of large language models (LLMs), researchers have begun to explore utilizing LLMs for generating RTL code. However, current studies primarily focus on generating simple single modules, which can not meet the demands in real world. In fact, due to challenges in managing long-context RTL code and complex cross-file dependencies, existing solutions cannot handle large-scale Verilog repositories in practical hardware development. As the first endeavor to exclusively adapt LLMs for large-scale RTL development, we propose RTLRepoCoder, a groundbreaking solution that incorporates specific fine-tuning and Retrieval-Augmented Generation (RAG) for repository-level Verilog code completion. Open-source Verilog repositories from the real world, along with an extended context size, are used for domain-specific fine-tuning. The optimized RAG system improves the information density of the input context by retrieving relevant code snippets. Tailored optimizations for RAG are carried out, including the embedding model, the cross-file context splitting strategy, and the chunk size. Our solution achieves state-of-the-art performance on public benchmark, significantly surpassing GPT-4 and advanced domain-specific LLMs on Edit Similarity and Exact Match rate. Comprehensive experiments demonstrate the remarkable effectiveness of our approach and offer insights for future work.

Recent advances in machine learning have significantly improved the understanding of source code data and achieved good performance on a number of downstream tasks. Open source repositories like GitHub enable this process with rich unlabeled code data. However, the lack of high quality labeled data has largely hindered the progress of several code related tasks, such as program translation, summarization, synthesis, and code search. This paper introduces XLCoST, Cross-Lingual Code SnippeT dataset, a new benchmark dataset for cross-lingual code intelligence. Our dataset contains fine-grained parallel data from 8 languages (7 commonly used programming languages and English), and supports 10 cross-lingual code tasks. To the best of our knowledge, it is the largest parallel dataset for source code both in terms of size and the number of languages. We also provide the performance of several state-of-the-art baseline models for each task. We believe this new dataset can be a valuable asset for the research community and facilitate the development and validation of new methods for cross-lingual code intelligence.

Large language models (LLMs) often struggle with visualization tasks like plotting diagrams, charts, where success depends on both code correctness and visual semantics. Existing instruction-tuning datasets lack execution-grounded supervision and offer limited support for iterative code correction, resulting in fragile and unreliable plot generation. We present VisCode-200K, a large-scale instruction tuning dataset for Python-based visualization and self-correction. It contains over 200K examples from two sources: (1) validated plotting code from open-source repositories, paired with natural language instructions and rendered plots; and (2) 45K multi-turn correction dialogues from Code-Feedback, enabling models to revise faulty code using runtime feedback. We fine-tune Qwen2.5-Coder-Instruct on VisCode-200K to create VisCoder, and evaluate it on PandasPlotBench. VisCoder significantly outperforms strong open-source baselines and approaches the performance of proprietary models like GPT-4o-mini. We further adopt a self-debug evaluation protocol to assess iterative repair, demonstrating the benefits of feedback-driven learning for executable, visually accurate code generation.

Large language models (LLMs) have brought significant advancements to code generation and code repair, benefiting both novice and experienced developers. However, their training using unsanitized data from open-source repositories, like GitHub, raises the risk of inadvertently propagating security vulnerabilities. Despite numerous studies investigating the safety of code LLMs, there remains a gap in comprehensively addressing their security features. In this work, we aim to present a comprehensive study aimed at precisely evaluating and enhancing the security aspects of code LLMs. To support our research, we introduce CodeSecEval, a meticulously curated dataset designed to address 44 critical vulnerability types with 180 distinct samples. CodeSecEval serves as the foundation for the automatic evaluation of code models in two crucial tasks: code generation and code repair, with a strong emphasis on security. Our experimental results reveal that current models frequently overlook security issues during both code generation and repair processes, resulting in the creation of vulnerable code. In response, we propose different strategies that leverage vulnerability-aware information and insecure code explanations to mitigate these security vulnerabilities. Furthermore, our findings highlight that certain vulnerability types particularly challenge model performance, influencing their effectiveness in real-world applications. Based on these findings, we believe our study will have a positive impact on the software engineering community, inspiring the development of improved methods for training and utilizing LLMs, thereby leading to safer and more trustworthy model deployment.

Large language models (LLMs) have brought significant advancements to code generation, benefiting both novice and experienced developers. However, their training using unsanitized data from open-source repositories, like GitHub, introduces the risk of inadvertently propagating security vulnerabilities. To effectively mitigate this concern, this paper presents a comprehensive study focused on evaluating and enhancing code LLMs from a software security perspective. We introduce SecuCoGenSecuCoGen has been uploaded as supplemental material and will be made publicly available after publication., a meticulously curated dataset targeting 21 critical vulnerability types. SecuCoGen comprises 180 samples and serves as the foundation for conducting experiments on three crucial code-related tasks: code generation, code repair and vulnerability classification, with a strong emphasis on security. Our experimental results reveal that existing models often overlook security concerns during code generation, leading to the generation of vulnerable code. To address this, we propose effective approaches to mitigate the security vulnerabilities and enhance the overall robustness of code generated by LLMs. Moreover, our study identifies weaknesses in existing models' ability to repair vulnerable code, even when provided with vulnerability information. Additionally, certain vulnerability types pose challenges for the models, hindering their performance in vulnerability classification. Based on these findings, we believe our study will have a positive impact on the software engineering community, inspiring the development of improved methods for training and utilizing LLMs, thereby leading to safer and more trustworthy model deployment.

Automated program repair (APR) aims to help developers improve software reliability by generating patches for buggy programs. Although many code language models (CLM) are developed and effective in many software tasks such as code completion, there has been little comprehensive, in-depth work to evaluate CLMs' fixing capabilities and to fine-tune CLMs for the APR task. Firstly, this work is the first to evaluate ten CLMs on four APR benchmarks, which shows that surprisingly, the best CLM, as is, fixes 72% more bugs than the state-of-the-art deep-learning (DL)-based APR techniques. Secondly, one of the four APR benchmarks was created by us in this paper to avoid data leaking for a fair evaluation. Thirdly, it is the first work to fine-tune CLMs with APR training data, which shows that fine-tuning brings 31%-1,267% improvement to CLMs and enables them to fix 46%-164% more bugs than existing DL-based APR techniques. Fourthly, this work studies the impact of buggy lines, showing that CLMs, as is, cannot make good use of the buggy lines to fix bugs, yet fine-tuned CLMs could potentially over-rely on buggy lines. Lastly, this work analyzes the size, time, and memory efficiency of different CLMs. This work shows promising directions for the APR domain, such as fine-tuning CLMs with APR-specific designs, and also raises awareness of fair and comprehensive evaluations of CLMs and calls for more transparent reporting of open-source repositories used in the pre-training data to address the data leaking problem.

Recent advances in language model (LM) agents and function calling have enabled autonomous, feedback-driven systems to solve problems across various digital domains. To better understand the unique limitations of LM agents, we introduce RefactorBench, a benchmark consisting of 100 large handcrafted multi-file refactoring tasks in popular open-source repositories. Solving tasks within RefactorBench requires thorough exploration of dependencies across multiple files and strong adherence to relevant instructions. Every task is defined by 3 natural language instructions of varying specificity and is mutually exclusive, allowing for the creation of longer combined tasks on the same repository. Baselines on RefactorBench reveal that current LM agents struggle with simple compositional tasks, solving only 22% of tasks with base instructions, in contrast to a human developer with short time constraints solving 87%. Through trajectory analysis, we identify various unique failure modes of LM agents, and further explore the failure mode of tracking past actions. By adapting a baseline agent to condition on representations of state, we achieve a 43.9% improvement in solving RefactorBench tasks. We further extend our state-aware approach to encompass entire digital environments and outline potential directions for future research. RefactorBench aims to support the study of LM agents by providing a set of real-world, multi-hop tasks within the realm of code.

Language models (LMs) have exhibited impressive abilities in generating code from natural language requirements. In this work, we highlight the diversity of code generated by LMs as a critical criterion for evaluating their code generation capabilities. There is a lack of studies focused on assessing the diversity of generated code, which overlooks its importance in code LMs. Therefore, we propose a systematic approach to evaluate code diversity, introducing various metrics with inter-code similarity. Specifically, we introduce code clustering methods that leverages LMs' capabilities in code understanding and reasoning, resulting in a set of metrics that represent the number of algorithms in model-generated solutions. We extensively investigate the property of model-generated solutions by contrasting them with human-written ones and quantifying the impact of various factors on code diversity: model size, temperature, instruction tuning, and problem complexity. Our analysis demonstrates that model-generated solutions exhibit low algorithmic diversity, which was neglected by the research community. Moreover, we explore methods to increase code diversity by combining solutions from different models and increasing sampling temperatures. Our findings highlight that code diversity can be enhanced with the help of heterogeneous models and setting temperature beyond 1.0 that has not been fully explored due to the functional correctness degradation. To facilitate our research direction, we publicly share our code and datasets through open-source repositories.

AI-powered coding assistants such as GitHub Copilot and OpenAI ChatGPT have achieved notable success in automating code generation. However, these tools rely on pre-trained Large Language Models (LLMs) that are typically trained on human-written code sourced from open-source project hosting sites like GitHub, which often contains inherent security vulnerabilities. These vulnerabilities may then be mirrored in the code generated by these LLMs, a critical risk revealed and highlighted by recent empirical studies. In this work, we present an exploratory study on whether fine-tuning pre-trained LLMs on datasets of vulnerability-fixing commits can promote secure code generation. We explored two parameter-efficient fine-tuning techniques (LoRa and IA3) on two pre-trained LLMs for code generation. We crawled a fine-tuning dataset (14,622 C and C++ files) for secure code generation by collecting code fixes of confirmed vulnerabilities from open-source repositories. Our evaluation dataset comprises 52 vulnerability scenarios designed to cover the top most dangerous C and C++ Common Weakness Enumerations (CWEs). Each scenario is a prompt that may induce LLMs to generate vulnerable code. Our exploration reveals that fine-tuning LLMs can improve secure code generation by 6.4% in C language and 5.4% in C++ language. We further experimented with fine-tuning LLMs using different versions of the collected secure code dataset (block, function, and line). We found that fine-tuning with function-level and block-level datasets achieves the best secure code generation performance, compared to the alternatives (file-level and line-level).

Motivated by recent work on lifelong learning applications for language models (LMs) of code, we introduce CodeLL, a lifelong learning dataset focused on code changes. Our contribution addresses a notable research gap marked by the absence of a long-term temporal dimension in existing code change datasets, limiting their suitability in lifelong learning scenarios. In contrast, our dataset aims to comprehensively capture code changes across the entire release history of open-source software repositories. In this work, we introduce an initial version of CodeLL, comprising 71 machine-learning-based projects mined from Software Heritage. This dataset enables the extraction and in-depth analysis of code changes spanning 2,483 releases at both the method and API levels. CodeLL enables researchers studying the behaviour of LMs in lifelong fine-tuning settings for learning code changes. Additionally, the dataset can help studying data distribution shifts within software repositories and the evolution of API usages over time.

This work presents a new dataset for the Martian digital elevation model prediction task, ready for machine learning applications called MCTED. The dataset has been generated using a comprehensive pipeline designed to process high-resolution Mars orthoimage and DEM pairs from Day et al., yielding a dataset consisting of 80,898 data samples. The source images are data gathered by the Mars Reconnaissance Orbiter using the CTX instrument, providing a very diverse and comprehensive coverage of the Martian surface. Given the complexity of the processing pipelines used in large-scale DEMs, there are often artefacts and missing data points in the original data, for which we developed tools to solve or mitigate their impact. We divide the processed samples into training and validation splits, ensuring samples in both splits cover no mutual areas to avoid data leakage. Every sample in the dataset is represented by the optical image patch, DEM patch, and two mask patches, indicating values that were originally missing or were altered by us. This allows future users of the dataset to handle altered elevation regions as they please. We provide statistical insights of the generated dataset, including the spatial distribution of samples, the distributions of elevation values, slopes and more. Finally, we train a small U-Net architecture on the MCTED dataset and compare its performance to a monocular depth estimation foundation model, DepthAnythingV2, on the task of elevation prediction. We find that even a very small architecture trained on this dataset specifically, beats a zero-shot performance of a depth estimation foundation model like DepthAnythingV2. We make the dataset and code used for its generation completely open source in public repositories.

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.

Multimodal agents for computer use rely exclusively on primitive actions (click, type, scroll) that require accurate visual grounding and lengthy execution chains, leading to cascading failures and performance bottlenecks. While other agents leverage rich programmatic interfaces (APIs, MCP servers, tools), computer-use agents (CUAs) remain isolated from these capabilities. We present UltraCUA, a foundation model that bridges this gap through hybrid action -- seamlessly integrating GUI primitives with high-level programmatic tool calls. To achieve this, our approach comprises four key components: (1) an automated pipeline that scales programmatic tools from software documentation, open-source repositories, and code generation; (2) a synthetic data engine producing over 17,000 verifiable tasks spanning real-world computer-use scenarios; (3) a large-scale high-quality hybrid action trajectory collection with both low-level GUI actions and high-level programmatic tool calls; and (4) a two-stage training pipeline combining supervised fine-tuning with online reinforcement learning, enabling strategic alternation between low-level and high-level actions. Experiments with our 7B and 32B models demonstrate substantial improvements over state-of-the-art agents. On OSWorld, UltraCUA models achieve an average 22% relative improvement over base models, while being 11% faster in terms of steps. Out-of-domain evaluation on WindowsAgentArena shows our model reaches 21.7% success rate, outperforming baselines trained on Windows data. The hybrid action mechanism proves critical, reducing error propagation while maintaining execution efficiency.

Code completion models have made significant progress in recent years, yet current popular evaluation datasets, such as HumanEval and MBPP, predominantly focus on code completion tasks within a single file. This over-simplified setting falls short of representing the real-world software development scenario where repositories span multiple files with numerous cross-file dependencies, and accessing and understanding cross-file context is often required to complete the code correctly. To fill in this gap, we propose CrossCodeEval, a diverse and multilingual code completion benchmark that necessitates an in-depth cross-file contextual understanding to complete the code accurately. CrossCodeEval is built on a diverse set of real-world, open-sourced, permissively-licensed repositories in four popular programming languages: Python, Java, TypeScript, and C#. To create examples that strictly require cross-file context for accurate completion, we propose a straightforward yet efficient static-analysis-based approach to pinpoint the use of cross-file context within the current file. Extensive experiments on state-of-the-art code language models like CodeGen and StarCoder demonstrate that CrossCodeEval is extremely challenging when the relevant cross-file context is absent, and we see clear improvements when adding these context into the prompt. However, despite such improvements, the pinnacle of performance remains notably unattained even with the highest-performing model, indicating that CrossCodeEval is also capable of assessing model's capability in leveraging extensive context to make better code completion. Finally, we benchmarked various methods in retrieving cross-file context, and show that CrossCodeEval can also be used to measure the capability of code retrievers.

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

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

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.

Open Source Software (OSS) is forming the spines of technology infrastructures, attracting millions of talents to contribute. Notably, it is challenging and critical to consider both the developers' interests and the semantic features of the project code to recommend appropriate development tasks to OSS developers. In this paper, we formulate the novel problem of code recommendation, whose purpose is to predict the future contribution behaviors of developers given their interaction history, the semantic features of source code, and the hierarchical file structures of projects. Considering the complex interactions among multiple parties within the system, we propose CODER, a novel graph-based code recommendation framework for open source software developers. CODER jointly models microscopic user-code interactions and macroscopic user-project interactions via a heterogeneous graph and further bridges the two levels of information through aggregation on file-structure graphs that reflect the project hierarchy. Moreover, due to the lack of reliable benchmarks, we construct three large-scale datasets to facilitate future research in this direction. Extensive experiments show that our CODER framework achieves superior performance under various experimental settings, including intra-project, cross-project, and cold-start recommendation. We will release all the datasets, code, and utilities for data retrieval upon the acceptance of this work.

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.

Implementing Retrieval-Augmented Generation (RAG) systems is inherently complex, requiring deep understanding of data, use cases, and intricate design decisions. Additionally, evaluating these systems presents significant challenges, necessitating assessment of both retrieval accuracy and generative quality through a multi-faceted approach. We introduce RAG Foundry, an open-source framework for augmenting large language models for RAG use cases. RAG Foundry integrates data creation, training, inference and evaluation into a single workflow, facilitating the creation of data-augmented datasets for training and evaluating large language models in RAG settings. This integration enables rapid prototyping and experimentation with various RAG techniques, allowing users to easily generate datasets and train RAG models using internal or specialized knowledge sources. We demonstrate the framework effectiveness by augmenting and fine-tuning Llama-3 and Phi-3 models with diverse RAG configurations, showcasing consistent improvements across three knowledge-intensive datasets. Code is released as open-source in https://github.com/IntelLabs/RAGFoundry.

The proliferation of open-source scientific software for science and research presents opportunities and challenges. In this paper, we introduce the SciCat dataset -- a comprehensive collection of Free-Libre Open Source Software (FLOSS) projects, designed to address the need for a curated repository of scientific and research software. This collection is crucial for understanding the creation of scientific software and aiding in its development. To ensure extensive coverage, our approach involves selecting projects from a pool of 131 million deforked repositories from the World of Code data source. Subsequently, we analyze README.md files using OpenAI's advanced language models. Our classification focuses on software designed for scientific purposes, research-related projects, and research support software. The SciCat dataset aims to become an invaluable tool for researching science-related software, shedding light on emerging trends, prevalent practices, and challenges in the field of scientific software development. Furthermore, it includes data that can be linked to the World of Code, GitHub, and other platforms, providing a solid foundation for conducting comparative studies between scientific and non-scientific software.

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.

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

Repository-level code 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.

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%.

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

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

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.

Large Language Models (LLMs) have shown promise in automated code generation but typically excel only in simpler tasks such as generating standalone code units. Real-world software development, however, often involves complex code repositories (named repo) with complex dependencies and extensive documentation. To fill this gap, our research pivots towards evaluating LLMs in a more realistic setting -- real-world repo-level code generation. We introduce CodeAgentBench, a manually curated benchmark for repo-level code generation. This benchmark comprises five high-quality Python projects, encompassing a total of 101 samples. We assess nine leading LLMs on repo-level tasks and observe a decline in their performance. To tackle this, we present CodeAgent, a novel LLM-based agent framework that employs external tools for effective repo-level code generation. CodeAgent integrates five programming tools, enabling interaction with software artifacts for information retrieval, code symbol navigation, and code testing. We implement four agent strategies to optimize these tools' usage. Our experiments on CodeAgentBench show that CodeAgent enhances LLM performance significantly, with improvements ranging from 18.1\% to 250\%. Further tests on the HumanEval benchmark confirm CodeAgent's adaptability and efficacy across various code generation tasks. Notably, CodeAgent outperforms commercial products like Github Copilot, showcasing superior accuracy and efficiency. These results demonstrate CodeAgent's robust capabilities in code generation, highlighting its potential for real-world repo-level coding challenges.

A package's source code repository records the development history of the package, providing indispensable information for the use and risk monitoring of the package. However, a package release often misses its source code repository due to the separation of the package's development platform from its distribution platform. Existing tools retrieve the release's repository information from its metadata, which suffers from two limitations: the metadata may not contain or contain wrong information. Our analysis shows that existing tools can only retrieve repository information for up to 70.5% of PyPI releases. To address the limitations, this paper proposes PyRadar, a novel framework that utilizes the metadata and source distribution to retrieve and validate the repository information for PyPI releases. We start with an empirical study to compare four existing tools on 4,227,425 PyPI releases and analyze phantom files (files appearing in the release's distribution but not in the release's repository) in 14,375 correct package-repository links and 2,064 incorrect links. Based on the findings, we design PyRadar with three components, i.e., Metadata-based Retriever, Source Code Repository Validator, and Source Code-based Retriever. In particular, the Metadata-based Retriever combines best practices of existing tools and successfully retrieves repository information from the metadata for 72.1% of PyPI releases. The Source Code Repository Validator applies common machine learning algorithms on six crafted features and achieves an AUC of up to 0.995. The Source Code-based Retriever queries World of Code with the SHA-1 hashes of all Python files in the release's source distribution and retrieves repository information for 90.2% of packages in our dataset with an accuracy of 0.970. Both practitioners and researchers can employ the PyRadar to better use PyPI packages.

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

The ability of CodeLLMs to generate executable and functionally correct code at the repository-level scale remains largely unexplored. We introduce RepoExec, a novel benchmark for evaluating code generation at the repository-level scale. RepoExec focuses on three main aspects: executability, functional correctness through automated test case generation with high coverage rate, and carefully crafted cross-file contexts to accurately generate code. Our work explores a controlled scenario where developers specify necessary code dependencies, challenging the model to integrate these accurately. Experiments show that while pretrained LLMs outperform instruction-tuned models in correctness, the latter excel in utilizing provided dependencies and demonstrating debugging capabilities. We also introduce a new instruction-tuned dataset that focuses on code dependencies and demonstrate that CodeLLMs fine-tuned on our dataset have a better capability to leverage these dependencies effectively. RepoExec aims to provide a comprehensive evaluation of code functionality and alignment with developer intent, paving the way for more reliable and applicable CodeLLMs in real-world scenarios. The dataset and source code can be found at~https://github.com/FSoft-AI4Code/RepoExec.

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.

A critical part of creating code suggestion systems is the pre-training of Large Language Models on vast amounts of source code and natural language text, often of questionable origin or quality. This may contribute to the presence of bugs and vulnerabilities in code generated by LLMs. While efforts to identify bugs at or after code generation exist, it is preferable to pre-train or fine-tune LLMs on curated, high-quality, and compliant datasets. The need for vast amounts of training data necessitates that such curation be automated, minimizing human intervention. We propose an automated source code autocuration technique that leverages the complete version history of open-source software projects to improve the quality of training data. This approach leverages the version history of all OSS projects to identify training data samples that have been modified or have undergone changes in at least one OSS project, and pinpoint a subset of samples that include fixes for bugs or vulnerabilities. We evaluate this method using The Stack v2 dataset, and find that 17% of the code versions in the dataset have newer versions, with 17% of those representing bug fixes, including 2.36% addressing known CVEs. The deduplicated version of Stack v2 still includes blobs vulnerable to 6,947 known CVEs. Furthermore, 58% of the blobs in the dataset were never modified after creation, suggesting they likely represent software with minimal or no use. Misidentified blob origins present an additional challenge, as they lead to the inclusion of non-permissively licensed code, raising serious compliance concerns. By addressing these issues, the training of new models can avoid perpetuating buggy code patterns or license violations. We expect our results to inspire process improvements for automated data curation, with the potential to enhance the reliability of outputs generated by AI tools.

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

Large Language Models (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.

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

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.

Code auditing is the process of reviewing code with the aim of identifying bugs. Large Language Models (LLMs) have demonstrated promising capabilities for this task without requiring compilation, while also supporting user-friendly customization. However, auditing a code repository with LLMs poses significant challenges: limited context windows and hallucinations can degrade the quality of bug reports, and analyzing large-scale repositories incurs substantial time and token costs, hindering efficiency and scalability. This work introduces an LLM-based agent, RepoAudit, designed to perform autonomous repository-level code auditing. Equipped with agent memory, RepoAudit explores the codebase on demand by analyzing data-flow facts along feasible program paths within individual functions. It further incorporates a validator module to mitigate hallucinations by verifying data-flow facts and checking the satisfiability of path conditions associated with potential bugs, thereby reducing false positives. RepoAudit detects 40 true bugs across 15 real-world benchmark projects with a precision of 78.43%, requiring on average only 0.44 hours and $2.54 per project. Also, it detects 185 new bugs in high-profile projects, among which 174 have been confirmed or fixed. We have open-sourced RepoAudit at https://github.com/PurCL/RepoAudit.

We present RepoST, a scalable method to construct environments that provide execution feedback for repository-level code generation for both training and evaluation. Unlike existing works that aim to build entire repositories for execution, which is challenging for both human and LLMs, we provide execution feedback with sandbox testing, which isolates a given target function and its dependencies to a separate script for testing. Sandbox testing reduces the complexity of external dependencies and enables constructing environments at a large scale. We use our method to construct RepoST-Train, a large-scale train set with 7,415 functions from 832 repositories. Training with the execution feedback provided by RepoST-Train leads to a performance gain of 5.5% Pass@1 on HumanEval and 3.5% Pass@1 on RepoEval. We also build an evaluation dataset, RepoST-Eval, and benchmark 12 code generation models.

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.

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.

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

The introduction of large language models has significantly advanced code generation. However, open-source models often lack the execution capabilities and iterative refinement of advanced systems like the GPT-4 Code Interpreter. To address this, we introduce OpenCodeInterpreter, a family of open-source code systems designed for generating, executing, and iteratively refining code. Supported by Code-Feedback, a dataset featuring 68K multi-turn interactions, OpenCodeInterpreter integrates execution and human feedback for dynamic code refinement. Our comprehensive evaluation of OpenCodeInterpreter across key benchmarks such as HumanEval, MBPP, and their enhanced versions from EvalPlus reveals its exceptional performance. Notably, OpenCodeInterpreter-33B achieves an accuracy of 83.2 (76.4) on the average (and plus versions) of HumanEval and MBPP, closely rivaling GPT-4's 84.2 (76.2) and further elevates to 91.6 (84.6) with synthesized human feedback from GPT-4. OpenCodeInterpreter brings the gap between open-source code generation models and proprietary systems like GPT-4 Code Interpreter.

Large language models (LLMs) for code have become indispensable in various domains, including code generation, reasoning tasks and agent systems.While open-access code LLMs are increasingly approaching the performance levels of proprietary models, high-quality code LLMs suitable for rigorous scientific investigation, particularly those with reproducible data processing pipelines and transparent training protocols, remain limited. The scarcity is due to various challenges, including resource constraints, ethical considerations, and the competitive advantages of keeping models advanced. To address the gap, we introduce OpenCoder, a top-tier code LLM that not only achieves performance comparable to leading models but also serves as an ``open cookbook'' for the research community. Unlike most prior efforts, we release not only model weights and inference code, but also the reproducible training data, complete data processing pipeline, rigorous experimental ablation results, and detailed training protocols for open scientific research. Through this comprehensive release, we identify the key ingredients for building a top-tier code LLM: (1) code optimized heuristic rules for data cleaning and methods for data deduplication, (2) recall of text corpus related to code and (3) high-quality synthetic data in both annealing and supervised fine-tuning stages. By offering this level of openness, we aim to broaden access to all aspects of a top-tier code LLM, with OpenCoder serving as both a powerful model and an open foundation to accelerate research, and enable reproducible advancements in code AI.

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.

Large language models (LLMs) are increasingly being integrated into software development processes. The ability to generate code and submit pull requests with minimal human intervention, through the use of autonomous AI agents, is poised to become a standard practice. However, little is known about the practical usefulness of these pull requests and the extent to which their contributions are accepted in real-world projects. In this paper, we empirically study 567 GitHub pull requests (PRs) generated using Claude Code, an agentic coding tool, across 157 diverse open-source projects. Our analysis reveals that developers tend to rely on agents for tasks such as refactoring, documentation, and testing. The results indicate that 83.8% of these agent-assisted PRs are eventually accepted and merged by project maintainers, with 54.9% of the merged PRs are integrated without further modification. The remaining 45.1% require additional changes benefit from human revisions, especially for bug fixes, documentation, and adherence to project-specific standards. These findings suggest that while agent-assisted PRs are largely acceptable, they still benefit from human oversight and refinement.

Data catalogs play a crucial role in modern data-driven organizations by facilitating the discovery, understanding, and utilization of diverse data assets. However, ensuring their quality and reliability is complex, especially in open and large-scale data environments. This paper proposes a framework to automatically determine the quality of open data catalogs, addressing the need for efficient and reliable quality assessment mechanisms. Our framework can analyze various core quality dimensions, such as accuracy, completeness, consistency, scalability, and timeliness, offer several alternatives for the assessment of compatibility and similarity across such catalogs as well as the implementation of a set of non-core quality dimensions such as provenance, readability, and licensing. The goal is to empower data-driven organizations to make informed decisions based on trustworthy and well-curated data assets. The source code that illustrates our approach can be downloaded from https://www.github.com/jorge-martinez-gil/dataq/.

Beyond scratch coding, exploiting large-scale code repositories (e.g., GitHub) for practical tasks is vital in real-world software development, yet current benchmarks rarely evaluate code agents in such authentic, workflow-driven scenarios. To bridge this gap, we introduce GitTaskBench, a benchmark designed to systematically assess this capability via 54 realistic tasks across 7 modalities and 7 domains. Each task pairs a relevant repository with an automated, human-curated evaluation harness specifying practical success criteria. Beyond measuring execution and task success, we also propose the alpha-value metric to quantify the economic benefit of agent performance, which integrates task success rates, token cost, and average developer salaries. Experiments across three state-of-the-art agent frameworks with multiple advanced LLMs show that leveraging code repositories for complex task solving remains challenging: even the best-performing system, OpenHands+Claude 3.7, solves only 48.15% of tasks. Error analysis attributes over half of failures to seemingly mundane yet critical steps like environment setup and dependency resolution, highlighting the need for more robust workflow management and increased timeout preparedness. By releasing GitTaskBench, we aim to drive progress and attention toward repository-aware code reasoning, execution, and deployment -- moving agents closer to solving complex, end-to-end real-world tasks. The benchmark and code are open-sourced at https://github.com/QuantaAlpha/GitTaskBench.

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.

How to evaluate the coding abilities of Large Language Models (LLMs) remains an open question. We find that existing benchmarks are poorly aligned with real-world code repositories and are insufficient to evaluate the coding abilities of LLMs. To address the knowledge gap, we propose a new benchmark named DevEval, which has three advances. (1) DevEval aligns with real-world repositories in multiple dimensions, e.g., code distributions and dependency distributions. (2) DevEval is annotated by 13 developers and contains comprehensive annotations (e.g., requirements, original repositories, reference code, and reference dependencies). (3) DevEval comprises 1,874 testing samples from 117 repositories, covering 10 popular domains (e.g., Internet, Database). Based on DevEval, we propose repository-level code generation and evaluate 8 popular LLMs on DevEval (e.g., gpt-4, gpt-3.5, StarCoder 2, DeepSeek Coder, CodeLLaMa). Our experiments reveal these LLMs' coding abilities in real-world code repositories. For example, in our experiments, the highest Pass@1 of gpt-4-turbo is only 53.04%. We also analyze LLMs' failed cases and summarize their shortcomings. We hope DevEval can facilitate the development of LLMs in real code repositories. DevEval, prompts, and LLMs' predictions have been released.

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.

We present CodeNav, an LLM agent that navigates and leverages previously unseen code repositories to solve user queries. In contrast to tool-use LLM agents that require ``registration'' of all relevant tools via manual descriptions within the LLM context, CodeNav automatically indexes and searches over code blocks in the target codebase, finds relevant code snippets, imports them, and uses them to iteratively generate a solution with execution feedback. To highlight the core-capabilities of CodeNav, we first showcase three case studies where we use CodeNav for solving complex user queries using three diverse codebases. Next, on three benchmarks, we quantitatively compare the effectiveness of code-use (which only has access to the target codebase) to tool-use (which has privileged access to all tool names and descriptions). Finally, we study the effect of varying kinds of tool and library descriptions on code-use performance, as well as investigate the advantage of the agent seeing source code as opposed to natural descriptions of code. All code will be made open source under a permissive license.

We present HaPy-Bug, a curated dataset of 793 Python source code commits associated with bug fixes, with each line of code annotated by three domain experts. The annotations offer insights into the purpose of modified files, changes at the line level, and reviewers' confidence levels. We analyze HaPy-Bug to examine the distribution of file purposes, types of modifications, and tangled changes. Additionally, we explore its potential applications in bug tracking, the analysis of bug-fixing practices, and the development of repository analysis tools. HaPy-Bug serves as a valuable resource for advancing research in software maintenance and security.

Large language models (LLMs) have shown remarkable ability in code generation with more than 90 pass@1 in solving Python coding problems in HumanEval and MBPP. Such high accuracy leads to the question: can LLMs replace human programmers? Existing manual crafted, simple, or single-line code generation benchmarks cannot answer this question due to their gap with real-world software development. To answer this question, we propose REPOCOD, a code generation benchmark with 980 problems collected from 11 popular real-world projects, with more than 58% of them requiring file-level or repository-level context information. In addition, REPOCOD has the longest average canonical solution length (331.6 tokens) and the highest average cyclomatic complexity (9.00) compared to existing benchmarks. In our evaluations on ten LLMs, none of the models can achieve more than 30 pass@1 on REPOCOD, disclosing the necessity of building stronger LLMs that can help developers in real-world software development.

The dream to create AI assistants as capable and versatile as the fictional J.A.R.V.I.S from Iron Man has long captivated imaginations. With the evolution of (multi-modal) large language models ((M)LLMs), this dream is closer to reality, as (M)LLM-based Agents using computing devices (e.g., computers and mobile phones) by operating within the environments and interfaces (e.g., Graphical User Interface (GUI)) provided by operating systems (OS) to automate tasks have significantly advanced. This paper presents a comprehensive survey of these advanced agents, designated as OS Agents. We begin by elucidating the fundamentals of OS Agents, exploring their key components including the environment, observation space, and action space, and outlining essential capabilities such as understanding, planning, and grounding. We then examine methodologies for constructing OS Agents, focusing on domain-specific foundation models and agent frameworks. A detailed review of evaluation protocols and benchmarks highlights how OS Agents are assessed across diverse tasks. Finally, we discuss current challenges and identify promising directions for future research, including safety and privacy, personalization and self-evolution. This survey aims to consolidate the state of OS Agents research, providing insights to guide both academic inquiry and industrial development. An open-source GitHub repository is maintained as a dynamic resource to foster further innovation in this field. We present a 9-page version of our work, accepted by ACL 2025, to provide a concise overview to the domain.

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

Finetuning large language models (LLMs) on instructions leads to vast performance improvements on natural language tasks. We apply instruction tuning using code, leveraging the natural structure of Git commits, which pair code changes with human instructions. We compile CommitPack: 4 terabytes of Git commits across 350 programming languages. We benchmark CommitPack against other natural and synthetic code instructions (xP3x, Self-Instruct, OASST) on the 16B parameter StarCoder model, and achieve state-of-the-art performance among models not trained on OpenAI outputs, on the HumanEval Python benchmark (46.2% pass@1). We further introduce HumanEvalPack, expanding the HumanEval benchmark to a total of 3 coding tasks (Code Repair, Code Explanation, Code Synthesis) across 6 languages (Python, JavaScript, Java, Go, C++, Rust). Our models, OctoCoder and OctoGeeX, achieve the best performance across HumanEvalPack among all permissive models, demonstrating CommitPack's benefits in generalizing to a wider set of languages and natural coding tasks. Code, models and data are freely available at https://github.com/bigcode-project/octopack.

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

Large language models 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.

In software development, resolving the emergent issues within GitHub repositories is a complex challenge that involves not only the incorporation of new code but also the maintenance of existing code. Large Language Models (LLMs) have shown promise in code generation but face difficulties in resolving Github issues, particularly at the repository level. To overcome this challenge, we empirically study the reason why LLMs fail to resolve GitHub issues and analyze the major factors. Motivated by the empirical findings, we propose a novel LLM-based Multi-Agent framework for GitHub Issue reSolution, MAGIS, consisting of four agents customized for software evolution: Manager, Repository Custodian, Developer, and Quality Assurance Engineer agents. This framework leverages the collaboration of various agents in the planning and coding process to unlock the potential of LLMs to resolve GitHub issues. In experiments, we employ the SWE-bench benchmark to compare MAGIS with popular LLMs, including GPT-3.5, GPT-4, and Claude-2. MAGIS can resolve 13.94% GitHub issues, significantly outperforming the baselines. Specifically, MAGIS achieves an eight-fold increase in resolved ratio over the direct application of GPT-4, the advanced LLM.

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.

In today's digital landscape, the importance of timely and accurate vulnerability detection has significantly increased. This paper presents a novel approach that leverages transformer-based models and machine learning techniques to automate the identification of software vulnerabilities by analyzing GitHub issues. We introduce a new dataset specifically designed for classifying GitHub issues relevant to vulnerability detection. We then examine various classification techniques to determine their effectiveness. The results demonstrate the potential of this approach for real-world application in early vulnerability detection, which could substantially reduce the window of exploitation for software vulnerabilities. This research makes a key contribution to the field by providing a scalable and computationally efficient framework for automated detection, enabling the prevention of compromised software usage before official notifications. This work has the potential to enhance the security of open-source software ecosystems.

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.

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.

In this technical report, we introduce OpenR, an open-source framework designed to integrate key components for enhancing the reasoning capabilities of large language models (LLMs). OpenR unifies data acquisition, reinforcement learning training (both online and offline), and non-autoregressive decoding into a cohesive software platform. Our goal is to establish an open-source platform and community to accelerate the development of LLM reasoning. Inspired by the success of OpenAI's o1 model, which demonstrated improved reasoning abilities through step-by-step reasoning and reinforcement learning, OpenR integrates test-time compute, reinforcement learning, and process supervision to improve reasoning in LLMs. Our work is the first to provide an open-source framework that explores the core techniques of OpenAI's o1 model with reinforcement learning, achieving advanced reasoning capabilities beyond traditional autoregressive methods. We demonstrate the efficacy of OpenR by evaluating it on the MATH dataset, utilising publicly available data and search methods. Our initial experiments confirm substantial gains, with relative improvements in reasoning and performance driven by test-time computation and reinforcement learning through process reward models. The OpenR framework, including code, models, and datasets, is accessible at https://openreasoner.github.io.

Code completion has become an essential tool for daily software development. Existing evaluation benchmarks often employ static methods that do not fully capture the dynamic nature of real-world coding environments and face significant challenges, including limited context length, reliance on superficial evaluation metrics, and potential overfitting to training datasets. In this work, we introduce a novel framework for enhancing code completion in software development through the creation of a repository-level benchmark ExecRepoBench and the instruction corpora Repo-Instruct, aim at improving the functionality of open-source large language models (LLMs) in real-world coding scenarios that involve complex interdependencies across multiple files. ExecRepoBench includes 1.2K samples from active Python repositories. Plus, we present a multi-level grammar-based completion methodology conditioned on the abstract syntax tree to mask code fragments at various logical units (e.g. statements, expressions, and functions). Then, we fine-tune the open-source LLM with 7B parameters on Repo-Instruct to produce a strong code completion baseline model Qwen2.5-Coder-Instruct-C based on the open-source model. Qwen2.5-Coder-Instruct-C is rigorously evaluated against existing benchmarks, including MultiPL-E and ExecRepoBench, which consistently outperforms prior baselines across all programming languages. The deployment of can be used as a high-performance, local service for programming development\url{https://execrepobench.github.io/}.

Recent advancements in Large Language Models (LLMs) and their utilization in code generation tasks have significantly reshaped the field of software development. Despite the remarkable efficacy of code completion solutions in mainstream programming languages, their performance lags when applied to less ubiquitous formats such as OpenAPI definitions. This study evaluates the OpenAPI completion performance of GitHub Copilot, a prevalent commercial code completion tool, and proposes a set of task-specific optimizations leveraging Meta's open-source model Code Llama. A semantics-aware OpenAPI completion benchmark proposed in this research is used to perform a series of experiments through which the impact of various prompt-engineering and fine-tuning techniques on the Code Llama model's performance is analyzed. The fine-tuned Code Llama model reaches a peak correctness improvement of 55.2% over GitHub Copilot despite utilizing 25 times fewer parameters than the commercial solution's underlying Codex model. Additionally, this research proposes an enhancement to a widely used code infilling training technique, addressing the issue of underperformance when the model is prompted with context sizes smaller than those used during training. The dataset, the benchmark, and the model fine-tuning code are made publicly available.

In software development, the predominant emphasis on functionality often supersedes security concerns, a trend gaining momentum with AI-driven automation tools like GitHub Copilot. These tools significantly improve developers' efficiency in functional code development. Nevertheless, it remains a notable concern that such tools are also responsible for creating insecure code, predominantly because of pre-training on publicly available repositories with vulnerable code. Moreover, developers are called the "weakest link in the chain" since they have very minimal knowledge of code security. Although existing solutions provide a reasonable solution to vulnerable code, they must adequately describe and educate the developers on code security to ensure that the security issues are not repeated. Therefore we introduce a multipurpose code vulnerability analysis system SecRepair, powered by a large language model, CodeGen2 assisting the developer in identifying and generating fixed code along with a complete description of the vulnerability with a code comment. Our innovative methodology uses a reinforcement learning paradigm to generate code comments augmented by a semantic reward mechanism. Inspired by how humans fix code issues, we propose an instruction-based dataset suitable for vulnerability analysis with LLMs. We further identify zero-day and N-day vulnerabilities in 6 Open Source IoT Operating Systems on GitHub. Our findings underscore that incorporating reinforcement learning coupled with semantic reward augments our model's performance, thereby fortifying its capacity to address code vulnerabilities with improved efficacy.

Reinforcement Learning (RL) offers a versatile framework for achieving long-term goals. Its generality allows us to formalize a wide range of problems that real-world intelligent systems encounter, such as dealing with delayed rewards, handling partial observability, addressing the exploration and exploitation dilemma, utilizing offline data to improve online performance, and ensuring safety constraints are met. Despite considerable progress made by the RL research community in addressing these issues, existing open-source RL libraries tend to focus on a narrow portion of the RL solution pipeline, leaving other aspects largely unattended. This paper introduces Pearl, a Production-ready RL agent software package explicitly designed to embrace these challenges in a modular fashion. In addition to presenting preliminary benchmark results, this paper highlights Pearl's industry adoptions to demonstrate its readiness for production usage. Pearl is open sourced on Github at github.com/facebookresearch/pearl and its official website is located at pearlagent.github.io.

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

Ensuring the correctness of code generated by Large Language Models (LLMs) presents a significant challenge in AI-driven software development. Existing approaches predominantly rely on black-box (closed-box) approaches that evaluate correctness post-generation, failing to utilize the rich insights embedded in the LLMs' internal states during code generation. In this paper, we introduce OPENIA, a novel white-box (open-box) framework that leverages these internal representations to assess the correctness of LLM-generated code. OPENIA systematically analyzes the intermediate states of representative open-source LLMs specialized for code, including DeepSeek-Coder, CodeLlama, and MagicCoder, across diverse code generation benchmarks. Our empirical analysis reveals that these internal representations encode latent information, which strongly correlates with the correctness of the generated code. Building on these insights, OPENIA uses a white-box/open-box approach to make informed predictions about code correctness, offering significant advantages in adaptability and robustness over traditional classification-based methods and zero-shot approaches. Experimental results demonstrate that OPENIA consistently outperforms baseline models, achieving higher accuracy, precision, recall, and F1-Scores with up to a 2X improvement in standalone code generation and a 46% enhancement in repository-specific scenarios. By unlocking the potential of in-process signals, OPENIA paves the way for more proactive and efficient quality assurance mechanisms in LLM-assisted code generation.

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

Large Language Models (LLMs) have transformed software development by enabling code generation, automated debugging, and complex reasoning. However, their continued advancement is constrained by the scarcity of high-quality, publicly available supervised fine-tuning (SFT) datasets tailored for coding tasks. To bridge this gap, we introduce OpenCodeInstruct, the largest open-access instruction tuning dataset, comprising 5 million diverse samples. Each sample includes a programming question, solution, test cases, execution feedback, and LLM-generated quality assessments. We fine-tune various base models, including LLaMA and Qwen, across multiple scales (1B+, 3B+, and 7B+) using our dataset. Comprehensive evaluations on popular benchmarks (HumanEval, MBPP, LiveCodeBench, and BigCodeBench) demonstrate substantial performance improvements achieved by SFT with OpenCodeInstruct. We also present a detailed methodology encompassing seed data curation, synthetic instruction and solution generation, and filtering.

Effective code retrieval plays a crucial role in advancing code generation, bug fixing, and software maintenance, particularly as software systems increase in complexity. While current code embedding models have demonstrated promise in retrieving code snippets for small-scale, well-defined tasks, they often underperform in more demanding real-world applications such as bug localization within GitHub repositories. We hypothesize that a key issue is their reliance on noisy and inconsistent datasets for training, which impedes their ability to generalize to more complex retrieval scenarios. To address these limitations, we introduce CoRNStack, a large-scale, high-quality contrastive training dataset for code that spans multiple programming languages. This dataset is curated using consistency filtering to eliminate noisy positives and is further enriched with mined hard negatives, thereby facilitating more effective learning. We demonstrate that contrastive training of embedding models using CoRNStack leads to state-of-the-art performance across a variety of code retrieval tasks. Furthermore, the dataset can be leveraged for training code reranking models, a largely underexplored area compared to text reranking. Our finetuned code reranking model significantly improves the ranking quality over the retrieved results. Finally, by employing our code retriever and reranker together, we demonstrate significant improvements in function localization for GitHub issues, an important component of real-world software development.

The BigCode project, an open-scientific collaboration focused on the responsible development of Large Language Models for Code (Code LLMs), introduces StarCoder2. In partnership with Software Heritage (SWH), we build The Stack v2 on top of the digital commons of their source code archive. Alongside the SWH repositories spanning 619 programming languages, we carefully select other high-quality data sources, such as GitHub pull requests, Kaggle notebooks, and code documentation. This results in a training set that is 4x larger than the first StarCoder dataset. We train StarCoder2 models with 3B, 7B, and 15B parameters on 3.3 to 4.3 trillion tokens and thoroughly evaluate them on a comprehensive set of Code LLM benchmarks. We find that our small model, StarCoder2-3B, outperforms other Code LLMs of similar size on most benchmarks, and also outperforms StarCoderBase-15B. Our large model, StarCoder2- 15B, significantly outperforms other models of comparable size. In addition, it matches or outperforms CodeLlama-34B, a model more than twice its size. Although DeepSeekCoder- 33B is the best-performing model at code completion for high-resource languages, we find that StarCoder2-15B outperforms it on math and code reasoning benchmarks, as well as several low-resource languages. We make the model weights available under an OpenRAIL license and ensure full transparency regarding the training data by releasing the SoftWare Heritage persistent IDentifiers (SWHIDs) of the source code data.

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

The BigCode community, an open-scientific collaboration working on the responsible development of Large Language Models for Code (Code LLMs), introduces StarCoder and StarCoderBase: 15.5B parameter models with 8K context length, infilling capabilities and fast large-batch inference enabled by multi-query attention. StarCoderBase is trained on 1 trillion tokens sourced from The Stack, a large collection of permissively licensed GitHub repositories with inspection tools and an opt-out process. We fine-tuned StarCoderBase on 35B Python tokens, resulting in the creation of StarCoder. We perform the most comprehensive evaluation of Code LLMs to date and show that StarCoderBase outperforms every open Code LLM that supports multiple programming languages and matches or outperforms the OpenAI code-cushman-001 model. Furthermore, StarCoder outperforms every model that is fine-tuned on Python, can be prompted to achieve 40\% pass@1 on HumanEval, and still retains its performance on other programming languages. We take several important steps towards a safe open-access model release, including an improved PII redaction pipeline and a novel attribution tracing tool, and make the StarCoder models publicly available under a more commercially viable version of the Open Responsible AI Model license.

The increasingly popular adoption of deep learning models in many critical source code tasks motivates the development of data augmentation (DA) techniques to enhance training data and improve various capabilities (e.g., robustness and generalizability) of these models. Although a series of DA methods have been proposed and tailored for source code models, there lacks a comprehensive survey and examination to understand their effectiveness and implications. This paper fills this gap by conducting a comprehensive and integrative survey of data augmentation for source code, wherein we systematically compile and encapsulate existing literature to provide a comprehensive overview of the field. We start with an introduction of data augmentation in source code and then provide a discussion on major representative approaches. Next, we highlight the general strategies and techniques to optimize the DA quality. Subsequently, we underscore techniques useful in real-world source code scenarios and downstream tasks. Finally, we outline the prevailing challenges and potential opportunities for future research. In essence, we aim to demystify the corpus of existing literature on source code DA for deep learning, and foster further exploration in this sphere. Complementing this, we present a continually updated GitHub repository that hosts a list of update-to-date papers on DA for source code modeling, accessible at https://github.com/terryyz/DataAug4Code.

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

We present SuperCoder2.0, an advanced autonomous system designed to enhance software development through artificial intelligence. The system combines an AI-native development approach with intelligent agents to enable fully autonomous coding. Key focus areas include a retry mechanism with error output traceback, comprehensive code rewriting and replacement using Abstract Syntax Tree (ast) parsing to minimize linting issues, code embedding technique for retrieval-augmented generation, and a focus on localizing methods for problem-solving rather than identifying specific line numbers. The methodology employs a three-step hierarchical search space reduction approach for code base navigation and bug localization:utilizing Retrieval Augmented Generation (RAG) and a Repository File Level Map to identify candidate files, (2) narrowing down to the most relevant files using a File Level Schematic Map, and (3) extracting 'relevant locations' within these files. Code editing is performed through a two-part module comprising CodeGeneration and CodeEditing, which generates multiple solutions at different temperature values and replaces entire methods or classes to maintain code integrity. A feedback loop executes repository-level test cases to validate and refine solutions. Experiments conducted on the SWE-bench Lite dataset demonstrate SuperCoder2.0's effectiveness, achieving correct file localization in 84.33% of cases within the top 5 candidates and successfully resolving 34% of test instances. This performance places SuperCoder2.0 fourth globally on the SWE-bench leaderboard. The system's ability to handle diverse repositories and problem types highlights its potential as a versatile tool for autonomous software development. Future work will focus on refining the code editing process and exploring advanced embedding models for improved natural language to code mapping.

The increasing complexity of computer science research projects demands more effective tools for deploying code repositories. Large Language Models (LLMs), such as Anthropic Claude and Meta Llama, have demonstrated significant advancements across various fields of computer science research, including the automation of diverse software engineering tasks. To evaluate the effectiveness of LLMs in handling complex code development tasks of research projects, particularly for NLP/CV/AI/ML/DM topics, we introduce CSR-Bench, a benchmark for Computer Science Research projects. This benchmark assesses LLMs from various aspects including accuracy, efficiency, and deployment script quality, aiming to explore their potential in conducting computer science research autonomously. We also introduce a novel framework, CSR-Agents, that utilizes multiple LLM agents to automate the deployment of GitHub code repositories of computer science research projects. Specifically, by checking instructions from markdown files and interpreting repository structures, the model generates and iteratively improves bash commands that set up the experimental environments and deploy the code to conduct research tasks. Preliminary results from CSR-Bench indicate that LLM agents can significantly enhance the workflow of repository deployment, thereby boosting developer productivity and improving the management of developmental workflows.

The maintenance risks of open source software (OSS) projects pose significant threats to the quality, security, and resilience of modern software supply chains. While prior research has proposed diverse approaches for predicting OSS maintenance risk -- leveraging signals ranging from surface features (e.g., stars, commits) to social network analyses and behavioral patterns -- existing methods often suffer from ambiguous operational definitions, limited interpretability, and datasets of insufficient scale or generalizability. In this work, we introduce ``maintenance cessation'', grounded in both explicit archival status and rigorous semantic analysis of project documentation. Building on this foundation, we curate a large-scale, longitudinal dataset of 115,466 GitHub repositories -- encompassing 57,733 confirmed cessation events -- complemented by comprehensive, timeline-based behavioral features. We propose an integrated, multi-perspective feature framework for predicting maintenance cessation, systematically combining user-centric features, maintainer-centric features and project evolution features. AFT survival analysis demonstrates a high C-index (0.846), substantially outperforming models relying only on surface features. Feature ablation and SHAP analysis further confirm the effectiveness and interpretability of our approach. Finally, we demonstrate real-world applicability by deploying a GBSA classifier in the openEuler ecosystem for proactive package risk screening. Our work establishes a scalable, interpretable foundation for maintenance-risk prediction, enabling reproducible risk management across large-scale open source ecosystems.

Modern software systems like the Linux kernel are among the world's largest and most intricate codebases, continually evolving with new features and increasing complexity. Understanding these systems poses significant challenges due to their scale and the unstructured nature of development artifacts such as commits and mailing list discussions. We introduce Code-Survey, the first LLM-driven methodology designed to systematically explore and analyze large-scale codebases. The central principle behind Code-Survey is to treat LLMs as human participants, acknowledging that software development is also a social activity and thereby enabling the application of established social science techniques. By carefully designing surveys, Code-Survey transforms unstructured data, such as commits, emails, into organized, structured, and analyzable datasets. This enables quantitative analysis of complex software evolution and uncovers valuable insights related to design, implementation, maintenance, reliability, and security. To demonstrate the effectiveness of Code-Survey, we apply it to the Linux kernel's eBPF subsystem. We construct the Linux-bpf dataset, comprising over 670 features and 16,000 commits from the Linux community. Our quantitative analysis uncovers important insights into the evolution of eBPF, such as development patterns, feature interdependencies, and areas requiring attention for reliability and security. The insights have been initially validated by eBPF experts. Furthermore, Code-Survey can be directly applied to other subsystems within Linux and to other large-scale software projects. By providing a versatile tool for systematic analysis, Code-Survey facilitates a deeper understanding of complex software systems, enabling improvements across a variety of domains and supporting a wide range of empirical studies. The code and dataset is open-sourced.

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

Developers often dedicate significant time to maintaining and refactoring existing code. However, most prior work on generative models for code focuses solely on creating new code, overlooking the distinctive needs of editing existing code. In this work, we explore a multi-round code auto-editing setting, aiming to predict edits to a code region based on recent changes within the same codebase. Our model, Coeditor, is a fine-tuned language model specifically designed for code editing tasks. We represent code changes using a line diff format and employ static analysis to form large customized model contexts, ensuring the availability of appropriate information for prediction. We collect a code editing dataset from the commit histories of 1650 open-source Python projects for training and evaluation. In a simplified single-round, single-edit task, Coeditor significantly outperforms GPT-3.5 and SOTA open-source code completion models (bringing exact-match accuracy from 34.7 up to 60.4), demonstrating the benefits of incorporating editing history for code completion. In a multi-round, multi-edit setting, we observe substantial gains by iteratively conditioning on additional user edits. We have open-sourced our code, data, and model weights to encourage future research and have released a VSCode extension powered by our model for interactive IDE usage.

Open source code is considered a common practice in modern software development. However, reusing other code allows bad actors to access a wide developers' community, hence the products that rely on it. Those attacks are categorized as supply chain attacks. Recent years saw a growing number of supply chain attacks that leverage open source during software development, relaying the download and installation procedures, whether automatic or manual. Over the years, many approaches have been invented for detecting vulnerable packages. However, it is uncommon to detect malicious code within packages. Those detection approaches can be broadly categorized as analyzes that use (dynamic) and do not use (static) code execution. Here, we introduce Malicious Source code Detection using Transformers (MSDT) algorithm. MSDT is a novel static analysis based on a deep learning method that detects real-world code injection cases to source code packages. In this study, we used MSDT and a dataset with over 600,000 different functions to embed various functions and applied a clustering algorithm to the resulting vectors, detecting the malicious functions by detecting the outliers. We evaluated MSDT's performance by conducting extensive experiments and demonstrated that our algorithm is capable of detecting functions that were injected with malicious code with precision@k values of up to 0.909.

Code performance optimization is paramount in real-world software engineering and critical for production-level systems. While Large Language Models (LLMs) have demonstrated impressive capabilities in code generation and bug fixing, their proficiency in enhancing code performance at the repository level remains largely unexplored. To address this gap, we introduce SWE-Perf, the first benchmark specifically designed to systematically evaluate LLMs on code performance optimization tasks within authentic repository contexts. SWE-Perf comprises 140 carefully curated instances, each derived from performance-improving pull requests from popular GitHub repositories. Each benchmark instance includes the relevant codebase, target functions, performance-related tests, expert-authored patches, and executable environments. Through a comprehensive evaluation of representative methods that span file-level and repo-level approaches (e.g., Agentless and OpenHands), we reveal a substantial capability gap between existing LLMs and expert-level optimization performance, highlighting critical research opportunities in this emerging field.

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

Large language models have shown promising performance in code generation benchmarks. However, a considerable divide exists between these benchmark achievements and their practical applicability, primarily attributed to real-world programming's reliance on pre-existing libraries. Instead of evaluating LLMs to code from scratch, this work aims to propose a new evaluation setup where LLMs use open-source libraries to finish machine learning tasks. Therefore, we propose ML-Bench, an expansive benchmark developed to assess the effectiveness of LLMs in leveraging existing functions in open-source libraries. Consisting of 10044 samples spanning 130 tasks over 14 notable machine learning GitHub repositories. In this setting, given a specific machine learning task instruction and the accompanying README in a codebase, an LLM is tasked to generate code to accomplish the task. This necessitates the comprehension of long and language-code interleaved documents, as well as the understanding of complex cross-file code structures, introducing new challenges. Notably, while GPT-4 exhibits remarkable improvement over other LLMs, it manages to accomplish only 39.73\% of the tasks, leaving a huge space for improvement. We address these challenges by proposing ML-Agent, designed to effectively navigate the codebase, locate documentation, retrieve code, and generate executable code. Empirical results demonstrate that ML-Agent, built upon GPT-4, results in further improvements. Code, data, and models are available at https://ml-bench.github.io/.

Automatically generating source code from natural language descriptions has been a growing field of research in recent years. However, current large-scale code generation models often encounter difficulties when selecting appropriate APIs for specific contexts. These models may generate APIs that do not meet requirements or refer to non-existent APIs in third-party libraries, especially for lesser-known or private libraries. Inspired by the process of human developers using tools to search APIs, we propose ToolCoder, a novel approach that integrates API search tools with existing models to assist in code generation and API selection. To teach our model to use tools, we introduce an automated data annotation method using ChatGPT to add tool usage information into the source code data and fine-tune code generation models. During inference, we integrate API search tools into the generation process so that our model can automatically use the search tool to get suggestions when selecting an API. Our experimental results demonstrate that ToolCoder exhibits excellent performance and generalization across five public and private library code generation benchmarks, with at least 6.21\% improvement on average pass@1 metrics and 9.64\% improvement on average pass@10 metrics compared to state-of-the-art methods. Furthermore, we show that our relatively small ToolCoder model is comparable to one of the current best models, GPT-3.5, highlighting the potential of incorporating programming tools into the code generation process.

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

Recent decisions by leading AI labs to either open-source their models or to restrict access to their models has sparked debate about whether, and how, increasingly capable AI models should be shared. Open-sourcing in AI typically refers to making model architecture and weights freely and publicly accessible for anyone to modify, study, build on, and use. This offers advantages such as enabling external oversight, accelerating progress, and decentralizing control over AI development and use. However, it also presents a growing potential for misuse and unintended consequences. This paper offers an examination of the risks and benefits of open-sourcing highly capable foundation models. While open-sourcing has historically provided substantial net benefits for most software and AI development processes, we argue that for some highly capable foundation models likely to be developed in the near future, open-sourcing may pose sufficiently extreme risks to outweigh the benefits. In such a case, highly capable foundation models should not be open-sourced, at least not initially. Alternative strategies, including non-open-source model sharing options, are explored. The paper concludes with recommendations for developers, standard-setting bodies, and governments for establishing safe and responsible model sharing practices and preserving open-source benefits where safe.

Language model (LM) agents, such as SWE-agent and OpenHands, have made progress toward automated issue resolution. However, existing approaches are often limited to Python-only issues and rely on pre-constructed containers in SWE-bench with reproduced issues, restricting their applicability to real-world and work for multi-language repositories. We present Prometheus, designed to resolve real-world issues beyond benchmark settings. Prometheus is a multi-agent system that transforms an entire code repository into a unified knowledge graph to guide context retrieval for issue resolution. Prometheus encodes files, abstract syntax trees, and natural language text into a graph of typed nodes and five general edge types to support multiple programming languages. Prometheus uses Neo4j for graph persistence, enabling scalable and structured reasoning over large codebases. Integrated by the DeepSeek-V3 model, Prometheus resolves 28.67% and 13.7% of issues on SWE-bench Lite and SWE-bench Multilingual, respectively, with an average API cost of 0.23 and 0.38 per issue. Prometheus resolves 10 unique issues not addressed by prior work and is the first to demonstrate effectiveness across seven programming languages. Moreover, it shows the ability to resolve real-world GitHub issues in the LangChain and OpenHands repositories. We have open-sourced Prometheus at: https://github.com/Pantheon-temple/Prometheus

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

Recently, an increasing number of AI-driven programming assistants powered by code LLMs have been integrated into various real-world software development environments, significantly boosting developer productivity. However, existing code generation benchmarks primarily focus on general-purpose scenarios, leaving the code generation performance of LLMs for specific application domains largely unknown. In this paper, we introduce a new benchmark, MultiCodeBench, to fill this gap. MultiCodeBench comprises 2,400 programming tasks, covering 12 popular software development domains and 15 programming languages. Specifically, we perform in-depth research to identify these 12 application domains. Given that each domain may involve multiple technical frameworks, and that different frameworks present distinct challenges in the coding process, we categorize the commonly used frameworks and platforms within each domain. We then sample programming problems from GitHub repositories related to these subdomains. To ensure the quality of the tasks and mitigate data leakage issues, we invite annotators to rewrite the docstrings for each task in MultiCodeBench. Additionally, we build a static analysis-based dependency parsing tool to extract the dependencies in the ground truth for each task, enabling deeper performance analysis. Through extensive experiments on MultiCodeBench with eleven representative mainstream LLMs, we reveal the code generation performance of the LLMs across different application domains, providing practical insights for developers in downstream fields when selecting LLMs. Furthermore, we analyze the reasons behind the models' failures in completing software application development tasks, offering guidance for model developers to enhance domain-specific code generation capabilities.

Code embeddings are essential for semantic code search; however, current approaches often struggle to capture the precise syntactic and contextual nuances inherent in code. Open-source models such as CodeBERT and UniXcoder exhibit limitations in scalability and efficiency, while high-performing proprietary systems impose substantial computational costs. We introduce a parameter-efficient fine-tuning method based on Low-Rank Adaptation (LoRA) to construct task-specific adapters for code retrieval. Our approach reduces the number of trainable parameters to less than two percent of the base model, enabling rapid fine-tuning on extensive code corpora (2 million samples in 25 minutes on two H100 GPUs). Experiments demonstrate an increase of up to 9.1% in Mean Reciprocal Rank (MRR) for Code2Code search, and up to 86.69% for Text2Code search tasks across multiple programming languages. Distinction in task-wise and language-wise adaptation helps explore the sensitivity of code retrieval for syntactical and linguistic variations.

Decompilation aims to restore compiled code to human-readable source code, but struggles with details like names and structure. Large language models (LLMs) show promise for programming tasks, motivating their application to decompilation. However, there does not exist any open-source LLM for decompilation. Moreover, existing decompilation evaluation systems mainly consider token-level accuracy and largely ignore code executability, which is the most important feature of any program. Therefore, we release the first open-access decompilation LLMs ranging from 1B to 33B pre-trained on 4 billion tokens of C source code and the corresponding assembly code. The open-source LLMs can serve as baselines for further development in the field. To ensure practical program evaluation, we introduce Decompile-Eval, the first dataset that considers re-compilability and re-executability for decompilation. The benchmark emphasizes the importance of evaluating the decompilation model from the perspective of program semantics. Experiments indicate that our LLM4Decompile has demonstrated the capability to accurately decompile 21% of the assembly code, which achieves a 50% improvement over GPT-4. Our code, dataset, and models are released at https://github.com/albertan017/LLM4Decompile

Large language models that exhibit instruction-following behaviour represent one of the biggest recent upheavals in conversational interfaces, a trend in large part fuelled by the release of OpenAI's ChatGPT, a proprietary large language model for text generation fine-tuned through reinforcement learning from human feedback (LLM+RLHF). We review the risks of relying on proprietary software and survey the first crop of open-source projects of comparable architecture and functionality. The main contribution of this paper is to show that openness is differentiated, and to offer scientific documentation of degrees of openness in this fast-moving field. We evaluate projects in terms of openness of code, training data, model weights, RLHF data, licensing, scientific documentation, and access methods. We find that while there is a fast-growing list of projects billing themselves as 'open source', many inherit undocumented data of dubious legality, few share the all-important instruction-tuning (a key site where human annotation labour is involved), and careful scientific documentation is exceedingly rare. Degrees of openness are relevant to fairness and accountability at all points, from data collection and curation to model architecture, and from training and fine-tuning to release and deployment.

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.

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

This paper introduces SecRepoBench, a benchmark to evaluate code agents on secure code completion in real-world repositories. SecRepoBench has 318 code completion tasks in 27 C/C++ repositories, covering 15 CWEs. We evaluate 28 standalone LLMs and 13 code agents across 3 state-of-the-art agent frameworks using our benchmark. We find that state-of-the-art LLMs struggle with generating correct and secure code completions. However, code agents significantly outperform standalone LLMs. We show that SecRepoBench is more difficult than the prior state-of-the-art benchmark. Finally, our comprehensive analysis provides insights into potential directions for enhancing the ability of code agents to write correct and secure code in real-world repositories.

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

The BigCode project is an open-scientific collaboration working on the responsible development of large language models for code. This tech report describes the progress of the collaboration until December 2022, outlining the current state of the Personally Identifiable Information (PII) redaction pipeline, the experiments conducted to de-risk the model architecture, and the experiments investigating better preprocessing methods for the training data. We train 1.1B parameter models on the Java, JavaScript, and Python subsets of The Stack and evaluate them on the MultiPL-E text-to-code benchmark. We find that more aggressive filtering of near-duplicates can further boost performance and, surprisingly, that selecting files from repositories with 5+ GitHub stars deteriorates performance significantly. Our best model outperforms previous open-source multilingual code generation models (InCoder-6.7B and CodeGen-Multi-2.7B) in both left-to-right generation and infilling on the Java, JavaScript, and Python portions of MultiPL-E, despite being a substantially smaller model. All models are released under an OpenRAIL license at https://hf.co/bigcode.

We present Open-CD, a change detection toolbox that contains a rich set of change detection methods as well as related components and modules. The toolbox started from a series of open source general vision task tools, including OpenMMLab Toolkits, PyTorch Image Models, etc. It gradually evolves into a unified platform that covers many popular change detection methods and contemporary modules. It not only includes training and inference codes, but also provides some useful scripts for data analysis. We believe this toolbox is by far the most complete change detection toolbox. In this report, we introduce the various features, supported methods and applications of Open-CD. In addition, we also conduct a benchmarking study on different methods and components. We wish that the toolbox and benchmark could serve the growing research community by providing a flexible toolkit to reimplement existing methods and develop their own new change detectors. Code and models are available at https://github.com/likyoo/open-cd. Pioneeringly, this report also includes brief descriptions of the algorithms supported in Open-CD, mainly contributed by their authors. We sincerely encourage researchers in this field to participate in this project and work together to create a more open community. This toolkit and report will be kept updated.

Large Language Models (LLMs) have garnered remarkable advancements across diverse code-related tasks, known as Code LLMs, particularly in code generation that generates source code with LLM from natural language descriptions. This burgeoning field has captured significant interest from both academic researchers and industry professionals due to its practical significance in software development, e.g., GitHub Copilot. Despite the active exploration of LLMs for a variety of code tasks, either from the perspective of natural language processing (NLP) or software engineering (SE) or both, there is a noticeable absence of a comprehensive and up-to-date literature review dedicated to LLM for code generation. In this survey, we aim to bridge this gap by providing a systematic literature review that serves as a valuable reference for researchers investigating the cutting-edge progress in LLMs for code generation. We introduce a taxonomy to categorize and discuss the recent developments in LLMs for code generation, covering aspects such as data curation, latest advances, performance evaluation, and real-world applications. In addition, we present a historical overview of the evolution of LLMs for code generation and offer an empirical comparison using the widely recognized HumanEval and MBPP benchmarks to highlight the progressive enhancements in LLM capabilities for code generation. We identify critical challenges and promising opportunities regarding the gap between academia and practical development. Furthermore, we have established a dedicated resource website (https://codellm.github.io) to continuously document and disseminate the most recent advances in the field.

Code Language Models have been trained to generate accurate solutions, typically with no regard for runtime. On the other hand, previous works that explored execution optimisation have observed corresponding drops in functional correctness. To that end, we introduce Code-Optimise, a framework that incorporates both correctness (passed, failed) and runtime (quick, slow) as learning signals via self-generated preference data. Our framework is both lightweight and robust as it dynamically selects solutions to reduce overfitting while avoiding a reliance on larger models for learning signals. Code-Optimise achieves significant improvements in pass@k while decreasing the competitive baseline runtimes by an additional 6% for in-domain data and up to 3% for out-of-domain data. As a byproduct, the average length of the generated solutions is reduced by up to 48% on MBPP and 23% on HumanEval, resulting in faster and cheaper inference. The generated data and codebase will be open-sourced at www.open-source.link.

Background: Leaking sensitive information, such as API keys, tokens, and credentials, in source code remains a persistent security threat. Traditional regex and entropy-based tools often generate high false positives due to limited contextual understanding. Aims: This work aims to enhance secret detection in source code using large language models (LLMs), reducing false positives while maintaining high recall. We also evaluate the feasibility of using fine-tuned, smaller models for local deployment. Method: We propose a hybrid approach combining regex-based candidate extraction with LLM-based classification. We evaluate pre-trained and fine-tuned variants of various Large Language Models on a benchmark dataset from 818 GitHub repositories. Various prompting strategies and efficient fine-tuning methods are employed for both binary and multiclass classification. Results: The fine-tuned LLaMA-3.1 8B model achieved an F1-score of 0.9852 in binary classification, outperforming regex-only baselines. For multiclass classification, Mistral-7B reached 0.982 accuracy. Fine-tuning significantly improved performance across all models. Conclusions: Fine-tuned LLMs offer an effective and scalable solution for secret detection, greatly reducing false positives. Open-source models provide a practical alternative to commercial APIs, enabling secure and cost-efficient deployment in development workflows.

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

In the dynamic landscape of open source software (OSS) development, understanding and addressing incivility within issue discussions is crucial for fostering healthy and productive collaborations. This paper presents a curated dataset of 404 locked GitHub issue discussion threads and 5961 individual comments, collected from 213 OSS projects. We annotated the comments with various categories of incivility using Tone Bearing Discussion Features (TBDFs), and, for each issue thread, we annotated the triggers, targets, and consequences of incivility. We observed that Bitter frustration, Impatience, and Mocking are the most prevalent TBDFs exhibited in our dataset. The most common triggers, targets, and consequences of incivility include Failed use of tool/code or error messages, People, and Discontinued further discussion, respectively. This dataset can serve as a valuable resource for analyzing incivility in OSS and improving automated tools to detect and mitigate such behavior.

We introduce EvoGit, a decentralized multi-agent framework for collaborative software development driven by autonomous code evolution. EvoGit deploys a population of independent coding agents, each proposing edits to a shared codebase without centralized coordination, explicit message passing, or shared memory. Instead, all coordination emerges through a Git-based phylogenetic graph that tracks the full version lineage and enables agents to asynchronously read from and write to the evolving code repository. This graph-based structure supports fine-grained branching, implicit concurrency, and scalable agent interaction while preserving a consistent historical record. Human involvement is minimal but strategic: users define high-level goals, periodically review the graph, and provide lightweight feedback to promote promising directions or prune unproductive ones. Experiments demonstrate EvoGit's ability to autonomously produce functional and modular software artifacts across two real-world tasks: (1) building a web application from scratch using modern frameworks, and (2) constructing a meta-level system that evolves its own language-model-guided solver for the bin-packing optimization problem. Our results underscore EvoGit's potential to establish a new paradigm for decentralized, automated, and continual software development. EvoGit is open-sourced at https://github.com/BillHuang2001/evogit.

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