Daily Papers

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.

Workspace learning requires AI agents to identify, reason over, exploit, and update explicit and implicit dependencies among heterogeneous files in a worker's workspace, enabling them to complete both routine and advanced tasks effectively. Despite its importance, existing relevant benchmarks largely evaluate agents on pre-specified or synthesized files with limited real-world dependencies, leaving workspace-level evaluation underexplored. To this end, we introduce Workspace-Bench, a benchmark for evaluating AI agents on Workspace Learning invOlving Large-Scale File Dependencies. We construct realistic workspaces with 5 worker profiles, 74 file types, 20,476 files (up to 20GB) and curate 388 tasks, each with its own file dependency graph, evaluated across 7,399 total rubrics that require cross-file retrieval, contextual reasoning, and adaptive decision-making. We further provide Workspace-Bench-Lite, a 100-task subset that preserves the benchmark distribution while reducing evaluation costs by about 70%. We evaluate 4 popular agent harnesses and 7 foundation models. Experimental results show that current agents remain far from reliable workspace learning, where the best reaches only 68.7%, substantially below the human result of 80.7%, and the average performance across agents is only 47.4%.

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.

LLM-based code review agents promise scalable, always-on review, yet current systems suffer from two intertwined weaknesses: (1) non-determinism--unbounded tool use makes review outcomes unstable, and (2) context locality--the reviewer's access remains bounded to the diff, capping discoverable issue depth. Both give rise to three challenges: misaligned context retrieval, a coherence-efficiency trade-off in multi-file pull requests, and hallucinated comments that erode trust. To address these, we introduce OpenCodeReview, built on deterministic engineering for uncertain agents: rather than granting maximal freedom, we inject determinism at three deliberate pipeline points. Rule-Guided Dispatch uses a multi-layer rule system to deterministically select files and review criteria, eliminating variability of agent-driven triage. Grounded File Review replaces free-form exploration with a curated tool set exposed through a ReAct loop, while file-level parallel SubAgents balance context coherence against efficiency and recover cross-file dependencies on demand. Independent Reflection introduces a falsification-first filter under an asymmetric information boundary--the reflector sees only the diff, not the agent's tool-augmented exploration--removing hallucinated comments without self-reinforcing bias, improving precision while preserving recall. On AACR-Bench (200 real-world PRs, 10 languages, 1,505 expert-verified comments), OpenCodeReview outperforms mainstream coding agents (e.g., Claude Code and Codex) across six LLM backends, achieving up to 2.17x higher SEM-F1 (25.10% vs. 11.57%) while consuming 5-15x fewer tokens. We open-source OpenCodeReview at https://github.com/alibaba/open-code-review.

Front-end development accumulates change after change at the repository level, weaving complex cross-file dependencies that current LLM coding agents tuned for single-shot tasks cannot reliably track across multiple iterations, leading to functional regressions and code that resists maintenance. We argue the missing piece is design knowledge: architectural principles, module responsibilities, and structural constraints that developers lean on to keep code readable, maintainable, and evolvable as a system scales. To operationalize this, we propose WebDesignIter, a framework built around a persistent knowledge graph (WebAppArchKG) that fuses repository structure with design knowledge and keeps both in sync across development cycles. WebDesignIter works in two stages: design-informed planning pulls historical context and architectural overviews from WebAppArchKG to produce an implementation plan with corresponding test scripts, and design-aware generation executes that plan through targeted diff-based patches, validated by sandbox execution and automatic syntax repair. On Web-Bench, WebDesignIter delivers an average Pass@2 gain of 9.55 percentage points across nine foundation models over existing baselines. More importantly, WebDesignIter outperforms every general-purpose coding agent Claude Code, OpenHands, SWE-Agent, Codex CLI on every model configuration, posting the highest Pass@1 and Pass@2 while consuming 2530 fewer input tokens. Ablation singles out design knowledge as the most impactful component: stripping it drops Pass@1 by 11.40 percentage points, a degradation far larger than removing code-graph retrieval, patch-based generation, or sandbox verification, confirming that design knowledge provides a fundamentally more efficient and reliable path to repository-level code generation.

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.

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

Recent advances in coding agents suggest rapid progress toward autonomous software development, yet existing benchmarks fail to rigorously evaluate the long-horizon capabilities required to build complete software systems. Most prior evaluations focus on localized code generation, scaffolded completion, or short-term repair tasks, leaving open the question of whether agents can sustain coherent reasoning, planning, and execution over the extended horizons demanded by real-world repository construction. To address this gap, we present NL2Repo Bench, a benchmark explicitly designed to evaluate the long-horizon repository generation ability of coding agents. Given only a single natural-language requirements document and an empty workspace, agents must autonomously design the architecture, manage dependencies, implement multi-module logic, and produce a fully installable Python library. Our experiments across state-of-the-art open- and closed-source models reveal that long-horizon repository generation remains largely unsolved: even the strongest agents achieve below 40% average test pass rates and rarely complete an entire repository correctly. Detailed analysis uncovers fundamental long-horizon failure modes, including premature termination, loss of global coherence, fragile cross-file dependencies, and inadequate planning over hundreds of interaction steps. NL2Repo Bench establishes a rigorous, verifiable testbed for measuring sustained agentic competence and highlights long-horizon reasoning as a central bottleneck for the next generation of autonomous coding agents.

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

Large language models have achieved striking results in interactive theorem proving, particularly in Lean. However, most benchmarks for LLM-based proof automation are drawn from mathematics in the Mathlib ecosystem, whereas proofs in software verification are developed inside definition-rich codebases with substantial project-specific libraries. We introduce VeriSoftBench, a benchmark of 500 Lean 4 proof obligations drawn from open-source formal-methods developments and packaged to preserve realistic repository context and cross-file dependencies. Our evaluation of frontier LLMs and specialized provers yields three observations. First, provers tuned for Mathlib-style mathematics transfer poorly to this repository-centric setting. Second, success is strongly correlated with transitive repository dependence: tasks whose proofs draw on large, multi-hop dependency closures are less likely to be solved. Third, providing curated context restricted to a proof's dependency closure improves performance relative to exposing the full repository, but nevertheless leaves substantial room for improvement. Our benchmark and evaluation suite are released at https://github.com/utopia-group/VeriSoftBench.

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.

Existing binary corpora typically capture only one or two axes of binary variation: they either provide cross-compiler builds without a temporal axis, or CVE labels for single-build binaries. None combine cross-build diversity, cross-version history, and CVE labels into a queryable structure. We present ASSEMBLAGE-DEEPHISTORY, which consolidates these dimensions into a unified framework where every binary's compilation context, source code, vulnerable functions, and package version are stored as first-class metadata. ASSEMBLAGE-DEEPHISTORY comprises 73,610 binaries spanning 248 open-source projects, compiled across GCC, Clang, and MSVC at multiple optimization levels on Linux and Windows, with multi-year historical builds. Each binary is indexed in a database that links it to its source code, functions, debug info, variant builds, historical versions, and vulnerable functions. Three analyses demonstrate this structure's value: (1) a three-stage LLM benchmark (recognition, strategy-guided detection, and cross-build transfer) to test whether LLMs reason about binary vulnerabilities or pattern-match on build-specific artifacts; (2) a comparison of MalConv embeddings, jTrans function embeddings, and TLSH fuzzy hashes quantifying how same-package versions cluster in each space; and (3) a Bayesian regression decomposing binary similarity into contributions from temporal distance, file changes, and commits.

Modern LLM training pipelines increasingly rely on other models to generate data, filter corpora, judge outputs, and guide development decisions. These dependencies are recursive: a model may depend on an upstream artifact whose own dependencies are documented only in separate releases and artifacts. As a result, the full dependency structure is fragmented across heterogeneous public artifacts, with complexity and recursive depth far outpacing humans' ability to trace. We introduce ModSleuth, an agentic system that recursively reconstructs LLM dependency graphs from public artifacts with source-grounded evidence. We find that the primary challenge is no longer information extraction, but defining what constitutes a dependency and reconciling artifact references across inconsistent documentation. We address these challenges through a formalization that distinguishes direct and indirect dependencies, represents heterogeneous pipeline roles through operation-centered relationships, and resolves artifact identities across names, versions, and repositories. Applying ModSleuth to four public-artifact-rich LLM releases, we recover 1,060 source-verified dependencies and construct large-scale dependency graphs of modern LLM development. These graphs reveal multi-hop license obligations, train-evaluation coupling, discrepancies between released and training-time artifacts, and documentation inconsistencies that would otherwise be difficult to uncover. We release ModSleuth and the resulting dependency graphs to support transparent analysis of the increasingly complex ecosystems underlying modern LLMs.

Open-source libraries and tools are widely reused, but compatibility maintenance is expensive. Once maintainers leave, useful repositories can stop working as runtimes and dependencies evolve. We study whether LLM agents can adapt old repositories to modern environments, a task we call compatibility rescue. Unlike bug repair, compatibility rescue starts from a repository that worked in its original environment but fails after ecosystem drift. RepoRescue gives agents only the repository and its failing modern environment; the agent must diagnose the failure, locate affected code, and produce a source-code rescue that restores the historical test suite. We build RepoRescue from 193 Python and 122 Java repositories, each verified to pass historically and fail after modernization. We evaluate five deployed agent systems on Python and three on Java. Beyond full-patch pass rate, we rerun patches after removing test-file edits to measure source-only repair, add a runtime-enforced regime that blocks test edits, and validate practical use for repositories whose suites pass after rescue. We find that Claude Code systems sometimes edit failing tests even when prompted not to; with runtime blocking, Kimi still rescues 41.5% of repositories. Systems are complementary: their union reaches 62.7%, exceeding the best single system by 10.9 points. Difficulty concentrates in cross-file coordination: on 14 repositories requiring coordinated whole-codebase changes, GPT-5.2 through Codex passes all 14, while every Claude Code system passes at most two. Finally, a passing suite is only an initial signal: among 34 unmaintained Python candidates whose suites pass after rescue, 22 work in realistic scenarios and 12 pass bug-hunt with patches that address the compatibility failure. RepoRescue benchmarks compatibility rescue with source-only auditing, runtime enforcement, practical validation, and reasoning labels.

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.

Application Programming Interfaces (APIs) facilitate the integration of third-party dependencies within the code of client applications. However, changes to an API, such as deprecation, modification of parameter names or types, or complete replacement with a new API, can break existing client code. These changes are called breaking dependency updates; It is often tedious for API users to identify the cause of these breaks and update their code accordingly. In this paper, we explore the use of Large Language Models (LLMs) to automate client code updates in response to breaking dependency updates. We evaluate our approach on the BUMP dataset, a benchmark for breaking dependency updates in Java projects. Our approach leverages LLMs with advanced prompts, including information from the build process and from the breaking dependency analysis. We assess effectiveness at three granularity levels: at the build level, the file level, and the individual compilation error level. We experiment with five LLMs: Google Gemini-2.0 Flash, OpenAI GPT4o-mini, OpenAI o3-mini, Alibaba Qwen2.5-32b-instruct, and DeepSeek V3. Our results show that LLMs can automatically repair breaking updates. Among the considered models, OpenAI's o3-mini is the best, able to completely fix 27% of the builds when using prompts that include contextual information such as the buggy line, API differences, error messages, and step-by-step reasoning instructions. Also, it fixes 78% of the individual compilation errors. Overall, our findings demonstrate the potential for LLMs to fix compilation errors due to breaking dependency updates, supporting developers in their efforts to stay up-to-date with changes in their dependencies.

Pre-trained models (PTMs) are machine learning models that have been trained in advance, often on large-scale data, and can be reused for new tasks, thereby reducing the need for costly training from scratch. Their widespread adoption introduces a new class of software dependency, which we term Software Dependencies 2.0, extending beyond conventional libraries to learned behaviors embodied in trained models and their associated artifacts. The integration of PTMs as software dependencies in real projects remains unclear, potentially threatening maintainability and reliability of modern software systems that increasingly rely on them. Objective: In this study, we investigate Software Dependencies 2.0 in open-source software (OSS) projects by examining the reuse of PTMs, with a focus on how developers manage and integrate these models. Specifically, we seek to understand: (1) how OSS projects structure and document their PTM dependencies; (2) what stages and organizational patterns emerge in the reuse pipelines of PTMs within these projects; and (3) the interactions among PTMs and other learned components across pipeline stages. We conduct a mixed-methods analysis of a statistically significant random sample of 401 GitHub repositories from the PeaTMOSS dataset (28,575 repositories reusing PTMs from Hugging Face and PyTorch Hub). We quantitatively examine PTM reuse by identifying patterns and qualitatively investigate how developers integrate and manage these models in practice.

Package dependencies are a critical control point in modern software supply chains. Dependency changes can substantially alter a project's security posture. As AI coding agents increasingly modify software via pull requests, it is unclear whether their dependency decisions introduce distinct security risks. We study 117,062 dependency changes from agent- and human-authored pull requests across seven ecosystems. Agents select known-vulnerable versions more often than humans (2.46% vs. 1.64%), and their vulnerable selections are more disruptive to remediate, with 36.8% requiring major-version upgrades compared to 12.9% for humans, despite patched alternatives existing in most cases. At the aggregate level, agent-driven dependency work yields a net vulnerability increase of 98, whereas human-authored work yields a net reduction of 1,316. These findings motivate pull-request-time vulnerability screening and registry-aware guardrails to make agent-driven dependency updates safer.

Large Language Models (LLMs) are increasingly integrated into software systems, giving rise to a new class of systems referred to as LLMware. Beyond traditional source-code components, LLMware embeds or interacts with LLMs that depend on other models and datasets, forming complex supply chains across open-source software (OSS), models, and datasets. However, licensing issues emerging from these intertwined dependencies remain largely unexplored. Leveraging GitHub and Hugging Face, we curate a large-scale dataset capturing LLMware supply chains, including 12,180 OSS repositories, 3,988 LLMs, and 708 datasets. Our analysis reveals that license distributions in LLMware differ substantially from traditional OSS ecosystems. We further examine license-related discussions and find that license selection and maintenance are the dominant concerns, accounting for 84% of cases. To understand incompatibility risks, we analyze license conflicts along supply chains and evaluate state-of-the-art detection approaches, which achieve only 58% and 76% F1 scores in this setting. Motivated by these limitations, we propose LiAgent, an LLM-based agent framework for ecosystem-level license compatibility analysis. LiAgent achieves an F1 score of 87%, improving performance by 14 percentage points over prior methods. We reported 60 incompatibility issues detected by LiAgent, 11 of which have been confirmed by developers. Notably, two conflicted LLMs have over 107 million and 5 million downloads on Hugging Face, respectively, indicating potentially widespread downstream impact. We conclude with implications and recommendations to support the sustainable growth of the LLMware ecosystem.

Modern software projects depend on third-party libraries that evolve continuously, introducing breaking API changes that prevent client code from compiling after a dependency update. When the same library update breaks multiple projects, existing repair approaches generate project-specific patches that cannot be reused, requiring each affected project to be repaired independently. We present BigBag, an agentic framework that generates fixing transformations: structured, executable programs that encode the repair logic at the API level and transfer to any client broken by the same update. We evaluate BigBag on 157 compilation failure breaking dependency updates from the BUMP benchmark, across eight configurations combining four large language models and two AST transformation engines (Spoon and JavaParser). The best configuration achieves a compilable transformation rate of 94.3% and a fix rate of 78.6%. Generated transformations transfer across projects, achieving a cross-project fix rate of 33.3% overall and 80% or above for breaking updates where all clients invoke the affected API element uniformly. These results show that agentic generation of reusable fixing transformations is a viable approach to scalable repair of breaking updates.

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.

Universal Dependencies is an open community effort to create cross-linguistically consistent treebank annotation for many languages within a dependency-based lexicalist framework. The annotation consists in a linguistically motivated word segmentation; a morphological layer comprising lemmas, universal part-of-speech tags, and standardized morphological features; and a syntactic layer focusing on syntactic relations between predicates, arguments and modifiers. In this paper, we describe version 2 of the guidelines (UD v2), discuss the major changes from UD v1 to UD v2, and give an overview of the currently available treebanks for 90 languages.

Numeric format proliferation in machine learning hardware -- FP8 (E4M3 and E5M2), BF16, MXFP4, microscaling block formats, and dozens of research variants -- has outpaced the availability of vendor-neutral, bit-exact reference material. Engineers porting models across accelerators encounter silent divergences that are difficult to diagnose without a shared ruler. This paper describes a catalog of 84 numeric formats spanning 13 families, a suite of six bit-exact conformance packs covering GF16, MXFP4 element, BF16, FP8 E4M3, FP8 E5M2, and E8M0 block scale, and an IEEE P3109 v3.2.0 cross-walk that maps each pack to its corresponding standards-track configured format. Each pack is a self-contained JSON document with a SHA-256 fingerprint, a shared row schema, and an anchor vector that encodes 3.0 -- the identity phi^2 + 1/phi^2 = 3 -- as a cross-pack sanity check. Packs are cross-validated against ml_dtypes 0.5.4 (Google/JAX); any divergence is documented explicitly and interpreted as a spec-permitted interpretation gap rather than hidden. The work is framed as registry filling: it does not propose new formats, make model-accuracy claims, or assert superiority over any vendor's implementation. All artifacts are publicly available at https://github.com/gHashTag/t27 under an open license.

Many modern software projects evolve rapidly to incorporate new features and security patches. It is important for users to update their dependencies to safer versions, but many still use older, vulnerable package versions because upgrading can be difficult and may break their existing codebase. Software developers can mitigate this problem by backporting security patches to older releases. However, manually backporting is time-consuming and error-prone. The effectiveness of existing automated backporting techniques on general software remains unclear since they typically target only code-hunk or function-level patch porting scenarios and are evaluated with imperfect metrics. To facilitate the development and evaluation of automated backporting techniques, we introduce BackportBench, the first comprehensive benchmark suite for patch backporting problem. BackportBench is a multilingual benchmark that contains 202 patch backporting problems from PyPI, Maven, and npm, each with executable Docker environments and relevant test cases. We evaluated existing patch porting methods and LLM-based techniques that have the potential to adapt to this task using BackportBench. The results show that the agentic method has outperformed traditional patch porting methods, especially on cases that require logical and structural changes. However, the performance varies across different programming languages. Based on the findings, we draw several implications for researchers and software practitioners in future work on automated backporting.

Model merging has shown that multitask models can be created by directly combining the parameters of different models that are each specialized on tasks of interest. However, models trained independently on distinct tasks often exhibit interference that degrades the merged model's performance. To solve this problem, we formally define the notion of Cross-Task Interference as the drift in the representation of the merged model relative to its constituent models. Reducing cross-task interference is key to improving merging performance. To address this issue, we propose our method, Resolving Interference (RI), a light-weight adaptation framework which disentangles expert models to be functionally orthogonal to the space of other tasks, thereby reducing cross-task interference. RI does this whilst using only unlabeled auxiliary data as input (i.e., no task-data is needed), allowing it to be applied in data-scarce scenarios. RI consistently improves the performance of state-of-the-art merging methods by up to 3.8% and generalization to unseen domains by up to 2.3%. We also find RI to be robust to the source of auxiliary input while being significantly less sensitive to tuning of merging hyperparameters. Our codebase is available at: https://github.com/pramesh39/resolving_interference

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

Open-Source Software (OSS) vulnerabilities bring great challenges to the software security and pose potential risks to our society. Enormous efforts have been devoted into automated vulnerability detection, among which deep learning (DL)-based approaches have proven to be the most effective. However, the current labeled data present the following limitations: (1) Tangled Patches: Developers may submit code changes unrelated to vulnerability fixes within patches, leading to tangled patches. (2) Lacking Inter-procedural Vulnerabilities: The existing vulnerability datasets typically contain function-level and file-level vulnerabilities, ignoring the relations between functions, thus rendering the approaches unable to detect the inter-procedural vulnerabilities. (3) Outdated Patches: The existing datasets usually contain outdated patches, which may bias the model during training. To address the above limitations, in this paper, we propose an automated data collection framework and construct the first repository-level high-quality vulnerability dataset named ReposVul. The proposed framework mainly contains three modules: (1) A vulnerability untangling module, aiming at distinguishing vulnerability-fixing related code changes from tangled patches, in which the Large Language Models (LLMs) and static analysis tools are jointly employed. (2) A multi-granularity dependency extraction module, aiming at capturing the inter-procedural call relationships of vulnerabilities, in which we construct multiple-granularity information for each vulnerability patch, including repository-level, file-level, function-level, and line-level. (3) A trace-based filtering module, aiming at filtering the outdated patches, which leverages the file path trace-based filter and commit time trace-based filter to construct an up-to-date dataset.

C-to-Rust transpilation is essential for modernizing legacy C code while enhancing safety and interoperability with modern Rust ecosystems. However, no dataset currently exists for evaluating whether a system can transpile C into safe Rust that passes a set of test cases. We introduce CRUST-Bench, a dataset of 100 C repositories, each paired with manually-written interfaces in safe Rust as well as test cases that can be used to validate correctness of the transpilation. By considering entire repositories rather than isolated functions, CRUST-Bench captures the challenges of translating complex projects with dependencies across multiple files. The provided Rust interfaces provide explicit specifications that ensure adherence to idiomatic, memory-safe Rust patterns, while the accompanying test cases enforce functional correctness. We evaluate state-of-the-art large language models (LLMs) on this task and find that safe and idiomatic Rust generation is still a challenging problem for various state-of-the-art methods and techniques. We also provide insights into the errors LLMs usually make in transpiling code from C to safe Rust. The best performing model, OpenAI o1, is able to solve only 15 tasks in a single-shot setting. Improvements on CRUST-Bench would lead to improved transpilation systems that can reason about complex scenarios and help in migrating legacy codebases from C into languages like Rust that ensure memory safety. You can find the dataset and code at https://github.com/anirudhkhatry/CRUST-bench.

As Large Language Models (LLMs) are increasingly integrated into software development workflows, their trustworthiness has become a critical concern. However, in dependency recommendation scenarios, the reliability of LLMs is undermined by widespread package hallucinations, where models often recommend hallucinated packages. Recent studies have proposed a range of approaches to mitigate this issue. Nevertheless, existing approaches typically merely reduce hallucination rates rather than eliminate them, leaving persistent software security risks. In this work, we argue that package hallucinations are theoretically preventable based on the key insight that package validity is decidable through finite and enumerable authoritative package lists. Building on this, we propose PackMonitor, the first approach capable of fundamentally eliminating package hallucinations by continuously monitoring the model's decoding process and intervening when necessary. To implement this in practice, PackMonitor addresses three key challenges: (1) determining when to trigger intervention via a Context-Aware Parser that continuously monitors model outputs and selectively activates intervening only during installation command generation; (2) resolving how to intervene by employing a Package-Name Intervenor that strictly limits the decoding space to an authoritative package list; and (3) ensuring monitoring efficiency through a DFA-Caching Mechanism that enables scalability to millions of packages with negligible overhead. Extensive experiments on five widely used LLMs demonstrate that PackMonitor is a training-free, plug-and-play solution that consistently reduces package hallucination rates to zero while maintaining low-latency inference and preserving original model capabilities.

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.

Parallel coding agents can independently produce locally valid changes while still interfering at integration time, expanding beyond planned scope, or relying on premises invalidated by concurrent work. Existing responses emphasize communication, isolated workspaces, late merge-time repair, continuous supervision, or post-hoc runtime recovery. This paper presents Claim Plane, a model-agnostic coordination architecture that treats concurrent software change as a pre-write admission problem. Before implementation, each worker declares a versioned ChangeIntent containing an exact base commit, typed resources, dependencies, and operations marked as committed or contingent. A deterministic control plane atomically admits compatible intents, constrains same-file parallelism to declared regions, serializes unresolved overlap, tracks dependency invalidation, and fails closed on ambiguous authority. During execution, a contingent mutation does not reserve write ownership initially; the first attempted mutation triggers atomic scope promotion and re-admission against the current active set. Brokered execution binds capabilities to intent versions, leases, OS-level worktree locks, monotonic fencing tokens, and Git-tree provenance, while integration verifies immutable patches and evidence. A preliminary six-pair CooperBench mechanism check is reported only as feasibility evidence: static Claim Plane achieved 6/6 pair passes with full serialization, while dynamic scope retained parallel admission on half of the pairs, performed seven successful scope promotions, and failed closed on two undeclared mutations. The sample is intentionally too small for comparative claims. We argue that separating probabilistic planning from deterministic authority provides a foundation for a future learned semantic-dependency model and frontier-model escalation only on unresolved cases.

Model diffing, the process of comparing models' internal representations to identify their differences, is a promising approach for uncovering safety-critical behaviors in new models. However, its application has so far been primarily focused on comparing a base model with its finetune. Since new LLM releases are often novel architectures, cross-architecture methods are essential to make model diffing widely applicable. Crosscoders are one solution capable of cross-architecture model diffing but have only ever been applied to base vs finetune comparisons. We provide the first application of crosscoders to cross-architecture model diffing and introduce Dedicated Feature Crosscoders (DFCs), an architectural modification designed to better isolate features unique to one model. Using this technique, we find in an unsupervised fashion features including Chinese Communist Party alignment in Qwen3-8B and Deepseek-R1-0528-Qwen3-8B, American exceptionalism in Llama3.1-8B-Instruct, and a copyright refusal mechanism in GPT-OSS-20B. Together, our results work towards establishing cross-architecture crosscoder model diffing as an effective method for identifying meaningful behavioral differences between AI models.

Developers today use significant amounts of open source code, surfacing the need for ways to automatically audit and upgrade library dependencies, and giving rise to the subfield of Software Composition Analysis (SCA). SCA products are concerned with three tasks: discovering dependencies, checking the reachability of vulnerable code for false positive elimination, and automated remediation. The latter two tasks rely on call graphs of application and library code to check whether vulnerability-specific sinks identified in libraries are used by applications. However, statically-constructed call graphs introduce both false positives and false negatives on real-world projects. In this paper, we develop a novel, modular means of combining call graphs derived from both static and dynamic analysis to improve the performance of false positive elimination. Our experiments indicate significant performance improvements.

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

Automatically compiling open-source software (OSS) projects is a vital, labor-intensive, and complex task, which makes it a good challenge for LLM Agents. Existing methods rely on manually curated rules and workflows, which cannot adapt to OSS that requires customized configuration or environment setup. Recent attempts using Large Language Models (LLMs) used selective evaluation on a subset of highly rated OSS, a practice that underestimates the realistic challenges of OSS compilation. In practice, compilation instructions are often absent, dependencies are undocumented, and successful builds may even require patching source files or modifying build scripts. We propose a more challenging and realistic benchmark, BUILD-BENCH, comprising OSS that are more diverse in quality, scale, and characteristics. Furthermore, we propose a strong baseline LLM-based agent, OSS-BUILD-AGENT, an effective system with enhanced build instruction retrieval module that achieves state-of-the-art performance on BUILD-BENCH and is adaptable to heterogeneous OSS characteristics. We also provide detailed analysis regarding different compilation method design choices and their influence to the whole task, offering insights to guide future advances. We believe performance on BUILD-BENCH can faithfully reflect an agent's ability to tackle compilation as a complex software engineering tasks, and, as such, our benchmark will spur innovation with a significant impact on downstream applications in the fields of software development and software security.

Modern coding agents expose multiple tool surfaces -- IDE primitives, bash, and Model Context Protocol (MCP) code-execution -- and the field has shipped three contradictory claims about which one matters. We run the missing crossed comparison: an integrity-clean three-arm ablation (baseline / bash_only / code_only) on synthetic computation tasks and SWE-bench Mini modification tasks, holding model, harness, and prompts fixed, with two agents (Claude Code, OpenAI Codex CLI) so the comparison spans both regime and agent-design axes. Across the four resulting (regime, agent) cells, restricting the agent to a single execute_code MCP tool is cheaper than -- or statistically tied with -- its cheapest tool-rich rival in three cells (significantly on Artifact/Claude and SWE-bench/Codex; directionally on Artifact/Codex), with pass rates statistically tied within each cell. The lone exception is SWE-bench/Claude, where code_only is directionally costlier (+14.4%, not significant); a conditional-cost analysis localizes that gap to failure-cost on doomed-run trajectories, not a per-edit tax on successful runs. Two implications: the cheapest tool surface is jointly determined by task regime and agent design rather than by either axis alone, and the headline cost signal lives in cache-adjusted cost -- not pass rate, which is invariant across surfaces at the model sizes we evaluate. The benchmark harness, task suite, and analysis code are available at https://github.com/hyang0129/onlycodes.

Organizations often develop and maintain portfolios of related applications: independently deployable codebases that share substantial domain logic, interface patterns, or operational conventions. As LLM coding agents are increasingly used to generate and maintain such software, a naive application-by-application workflow duplicates shared logic across codebases and allows prolonged agentic maintenance to accumulate verbosity, dead code, and structural erosion. We introduce the Super Library Agent problem, where an agent sequentially generates a portfolio of N related applications while maintaining a shared Super Library of reusable cross-application components. A minimal sequential scaffold can in principle extract shared code and migrate applications to the evolving library, but in practice suffers from low extraction recall and fragile dependency migration. We address these failures with candidate-guided extraction over code chunk summaries, pre-extraction codebase consolidation, and context-aware migration using extraction traces and call-graph information. Across WebGen-Bench and PaperBench, our method preserves application functionality while significantly reducing redundancy and token footprint (verbosity, token length) over zero-shot, and avoiding the structural erosion introduced by naive library construction, with additional reductions in LOC and MDL. Our code is available at https://github.com/sbigstar0310/super-library-agent.

Cross-capability transfer is a key challenge in large language model (LLM) research, with applications in multi-task integration, model compression, and continual learning. Recent works like FuseLLM and FuseChat have demonstrated the potential of transferring multiple model capabilities to lightweight models, enhancing adaptability and efficiency, which motivates our investigation into more efficient cross-capability transfer methods. However, existing approaches primarily focus on small, homogeneous models, limiting their applicability. For large, heterogeneous models, knowledge distillation with full-parameter fine-tuning often overlooks the student model's intrinsic capacity and risks catastrophic forgetting, while PEFT methods struggle to effectively absorb knowledge from source LLMs. To address these issues, we introduce GraftLLM, a novel method that stores source model capabilities in a target model with SkillPack format. This approach preserves general capabilities, reduces parameter conflicts, and supports forget-free continual learning and model fusion. We employ a module-aware adaptive compression strategy to compress parameter updates, ensuring efficient storage while maintaining task-specific knowledge. The resulting SkillPack serves as a compact and transferable knowledge carrier, ideal for heterogeneous model fusion and continual learning. Experiments across various scenarios demonstrate that GraftLLM outperforms existing techniques in knowledge transfer, knowledge fusion, and forget-free learning, providing a scalable and efficient solution for cross-capability transfer. The code is publicly available at: https://github.com/duguodong7/GraftLLM.

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

Trusted Execution Environments (TEEs) provide hardware-based isolation to protect sensitive data and computations from potentially compromised operating systems (OS). However, TEE applications inevitably interact with the untrusted OS through SDK interfaces, and improper partitioning can introduce severe vulnerabilities such as data leakage and code injection. While prior work has proposed static analysis tools to detect such issues, automated repair remains largely unexplored. This problem is particularly challenging due to three TEE-specific factors: the lack of standardized secure development guidelines, the difficulty of extracting semantic information from low-level C code, and the absence of mature testing and validation methods. In this work, we present TEERepair, a framework for automatically repairing bad partitioning issues in TEE applications. Our approach tackles the above challenges by introducing a domain-specific language (DSL) to encode repair rules that express and capture common TEE security patterns, which are instantiated as patch templates with placeholders for context-specific variables. We then leverage large language models (LLMs) to reason about code semantics and synthesize context-aware patches, and further generate test clients to validate the repairs. We evaluate TEERepair on the TEE Partitioning Errors Benchmark (PartitioningE-Bench), achieving a significantly higher repair success rate of 87.6% compared to baselines. Furthermore, applying TEERepair to real-world TEE projects, we submitted 5 repair pull requests, 2 of which have been confirmed and merged by project maintainers.

Open-source scientific software is a major driver of scientific progress, yet its development and reuse remain difficult in collaborative settings. Researchers repeatedly face four recurring challenges: discovering and reproducing existing routines, adapting them for new use cases, sharing and scaling them across collaborators, and stabilizing them with reproducible execution environments. We present Album, an open-source framework for packaging and sharing scientific routines as executable artifacts through two minimal primitives: (i) the solution, a Python-native executable entry point that combines machine-readable metadata, arguments, environment specifications, and lifecycle hooks; and (ii) the catalog, a decentralized, git-native distribution mechanism with indexed search and optional web rendering for discovery, provenance, and governance. Album uses a two-context execution model in which a host controller evaluates manifests and prepares per-solution environments, while lifecycle hooks execute inside isolated solution environments. This design supports reproducible execution, post-environment setup, and the composition of routines with incompatible dependencies. Album can be used in conjunction with LLM agents: solutions can be drafted and revised with LLM assistance, and a MCP interface exposes cataloged solutions as callable tools for tool-grounded discovery and orchestration. We evaluate Album through four realworld imaging deployments spanning interactive visualization of electron microscopy data, integration of multiple segmentation methods, the orchestration of cryo-electron tomography competition workflows, and mineral quantification pipelines. Overall, Album complements package managers, workflow systems, and container runtimes by making scientific routines executable, shareable artifacts. Documentation and examples are available at https://album.solutions.

AI coding agents set up projects by reading documentation and installing the dependencies it lists, without verifying their names, sources, or known vulnerabilities. By editing only a README, requirements file, or Makefile, an attacker can redirect the agent to an untrusted registry, a known-vulnerable version, or a wrong-but-plausible name: documentation becomes a vector for code execution. We present the first systematic evaluation of package-install-time supply-chain attacks delivered through ordinary project-setup documentation across production coding-agent harnesses, probing frontier models on twelve scenarios in five attack classes, grounded in documented incidents. The same model catches an attack through one harness and installs it through another: install-time security rests on the harness-model combination, not the model alone. Agents catch blatant typosquats reliably, but plausible separator-confusion names (azurecore for azure-core) slip through, and how often depends on the harness-model pairing. Source-based attacks like registry redirection are missed almost everywhere. The source blind spot recurs on npm and Cargo, where nearly every model installs the untrusted dependency; name detection carries over less consistently across ecosystems. Security-oriented prompts recover part of the gap but only for the dimension they name; a deterministic pre-install check that verifies names, sources, and versions before any code runs closes most of it.

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.

Automatically generating formal specifications could reduce the effort needed to improve program correctness, but in practice, this is still challenging. Many developers avoid writing contracts by hand, which limits the use of automated verification tools. Recent large language models (LLMs) can generate specifications from code, but these specifications often fail in terms of verification. The reason is syntax errors, overly strict constraints, or mismatches with program behavior. We present SpecPylot, a Python tool that synthesizes executable specifications for Python programs as icontract annotations and checks them using crosshair's symbolic execution. The tool relies on LLMs to propose candidate contracts and uses crosshair to validate them. When crosshair finds a concrete counterexample, SpecPylot updates only the generated contracts and leaves the program itself untouched. In addition, the tool can produce coverage-driven pytest stubs and keep detailed execution artifacts that are useful during debugging. Overall, the evaluation indicates that SpecPylot is able to generate crosshair-compatible contracts for most programs, but it also highlights the practical limits introduced by bounded symbolic exploration and differences in LLM behavior.

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.

While third-party libraries are extensively reused to enhance productivity during software development, they can also introduce potential security risks such as vulnerability propagation. Software composition analysis, proposed to identify reused TPLs for reducing such risks, has become an essential procedure within modern DevSecOps. As one of the mainstream SCA techniques, binary-to-source SCA identifies the third-party source projects contained in binary files via binary source code matching, which is a major challenge in reverse engineering since binary and source code exhibit substantial disparities after compilation. The existing binary-to-source SCA techniques leverage basic syntactic features that suffer from redundancy and lack robustness in the large-scale TPL dataset, leading to inevitable false positives and compromised recall. To mitigate these limitations, we introduce BinaryAI, a novel binary-to-source SCA technique with two-phase binary source code matching to capture both syntactic and semantic code features. First, BinaryAI trains a transformer-based model to produce function-level embeddings and obtain similar source functions for each binary function accordingly. Then by applying the link-time locality to facilitate function matching, BinaryAI detects the reused TPLs based on the ratio of matched source functions. Our experimental results demonstrate the superior performance of BinaryAI in terms of binary source code matching and the downstream SCA task. Specifically, our embedding model outperforms the state-of-the-art model CodeCMR, i.e., achieving 22.54% recall@1 and 0.34 MRR compared with 10.75% and 0.17 respectively. Additionally, BinaryAI outperforms all existing binary-to-source SCA tools in TPL detection, increasing the precision from 73.36% to 85.84% and recall from 59.81% to 64.98% compared with the well-recognized commercial SCA product.

GCC and LLVM underpin much of modern software infrastructure, relying on distinct Intermediate Representations (IRs) to drive optimizations and code generation. However, the semantic and structural differences between these IRs create significant barriers for cross-toolchain interaction, limiting the reuse of compiler frontends, backends, and optimization pipelines across programming languages and compilation ecosystems. Traditional rule-based translators have attempted to bridge this gap, but their complexity and maintenance cost have hindered practical adoption. In this context, Large Language Models (LLMs) appear to be an emerging technology that offers a data-driven alternative, capable of learning complex mappings between heterogeneous compiler IRs directly from sufficiently representative examples. To explore this approach, this paper presents IRIS-14B, a 14-billion-parameter transformer model fine-tuned to translate GIMPLE (as emitted by GCC) to LLVM IR (as emitted by LLVM). The model is trained on paired IRs extracted from C sources and evaluated on the GIMPLE-to-LLVM IR transformation applied to IRs derived from real-world C code and competitive programming problems. To the best of our knowledge, IRIS-14B is the first model trained explicitly for IR-to-IR translation. It outperforms the accuracy of widely used models, including the largest state-of-the-art open models available today, ranging from 13 to 1,000 billion parameters, by up to 44 percentage points. The proposed transformation supports the integration of LLMs as complementary components within hybrid neuro-symbolic compiler architectures, where models such as IRIS-14B act as interoperability layers enabling cross-toolchain workflows without modifying existing compiler passes, while traditional compiler infrastructure continues to perform deterministic compilation and optimization.

In the rapidly evolving software development landscape, Python stands out for its simplicity, versatility, and extensive ecosystem. Python packages, as units of organization, reusability, and distribution, have become a pressing concern, highlighted by the considerable number of vulnerability reports. As a scripting language, Python often cooperates with other languages for performance or interoperability. This adds complexity to the vulnerabilities inherent to Python packages, and the effectiveness of current vulnerability detection tools remains underexplored. This paper addresses these gaps by introducing PyVul, the first comprehensive benchmark suite of Python-package vulnerabilities. PyVul includes 1,157 publicly reported, developer-verified vulnerabilities, each linked to its affected packages. To accommodate diverse detection techniques, it provides annotations at both commit and function levels. An LLM-assisted data cleansing method is incorporated to improve label accuracy, achieving 100% commit-level and 94% function-level accuracy, establishing PyVul as the most precise large-scale Python vulnerability benchmark. We further carry out a distribution analysis of PyVul, which demonstrates that vulnerabilities in Python packages involve multiple programming languages and exhibit a wide variety of types. Moreover, our analysis reveals that multi-lingual Python packages are potentially more susceptible to vulnerabilities. Evaluation of state-of-the-art detectors using this benchmark reveals a significant discrepancy between the capabilities of existing tools and the demands of effectively identifying real-world security issues in Python packages. Additionally, we conduct an empirical review of the top-ranked CWEs observed in Python packages, to diagnose the fine-grained limitations of current detection tools and highlight the necessity for future advancements in the field.

Coding agents are becoming increasingly capable of completing end-to-end software engineering workflows that previously required a human developer, including raising pull requests (PRs) to propose their changes. However, we still know little about how these agents use libraries when generating code, a core part of real-world software development. To fill this gap, we study 26,760 agent-authored PRs from the AIDev dataset to examine three questions: how often do agents import libraries, how often do they introduce new dependencies (and with what versioning), and which specific libraries do they choose? We find that agents often import libraries (29.5% of PRs) but rarely add new dependencies (1.3% of PRs); and when they do, they follow strong versioning practices (75.0% specify a version), an improvement on direct LLM usage where versions are rarely mentioned. Generally, agents draw from a surprisingly diverse set of external libraries, contrasting with the limited "library preferences" seen in prior non-agentic LLM studies. Our results offer an early empirical view into how AI coding agents interact with today's software ecosystems.

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/.

Accurate project localization (e.g., files and functions) for issue resolution is a critical first step in software maintenance. However, existing benchmarks for issue localization, such as SWE-Bench and LocBench, are limited. They focus predominantly on pull-request issues and code locations, ignoring other evidence and non-code files such as commits, comments, configurations, and documentation. To address this gap, we introduce MULocBench, a comprehensive dataset of 1,100 issues from 46 popular GitHub Python projects. Comparing with existing benchmarks, MULocBench offers greater diversity in issue types, root causes, location scopes, and file types, providing a more realistic testbed for evaluation. Using this benchmark, we assess the performance of state-of-the-art localization methods and five LLM-based prompting strategies. Our results reveal significant limitations in current techniques: even at the file level, performance metrics (Acc@5, F1) remain below 40%. This underscores the challenge of generalizing to realistic, multi-faceted issue resolution. To enable future research on project localization for issue resolution, we publicly release MULocBench at https://huggingface.co/datasets/somethingone/MULocBench.

Progress in software-engineering agents is increasingly constrained by the scarcity of executable, scalable, and realistic data for training and evaluation. This scarcity stems from three fundamental challenges in existing pipelines: environments are brittle and difficult to reproduce across languages; synthesizing realistic, system-level bugs at scale is computationally expensive; and existing data predominantly consists of short-horizon repairs, failing to capture long-horizon competencies like architectural consistency. We introduce SWE-Hub, an end-to-end system that operationalizes the data factory abstraction by unifying environment automation, scalable synthesis, and diverse task generation into a coherent production stack. At its foundation, the Env Agent establishes a shared execution substrate by automatically converting raw repository snapshots into reproducible, multi-language container environments with standardized interfaces. Built upon this substrate, SWE-Scale engine addresses the need for high-throughput generation, combining cross-language code analysis with cluster-scale validation to synthesize massive volumes of localized bug-fix instances. Bug Agent generates high-fidelity repair tasks by synthesizing system-level regressions involving cross-module dependencies, paired with user-like issue reports that describe observable symptoms rather than root causes. Finally, SWE-Architect expands the task scope from repair to creation by translating natural-language requirements into repository-scale build-a-repo tasks. By integrating these components, SWE-Hub establishes a unified production pipeline capable of continuously delivering executable tasks across the entire software engineering lifecycle.

Package confusion attacks such as typosquatting threaten software supply chains. Attackers make packages with names that syntactically or semantically resemble legitimate ones, tricking engineers into installing malware. While prior work has developed defenses against package confusions in some software package registries, notably NPM, PyPI, and RubyGems, gaps remain: high false-positive rates; generalization to more software package ecosystems; and insights from real-world deployment. In this work, we introduce ConfuGuard, a solution designed to address the challenges posed by package confusion threats. We begin by presenting the first empirical analysis of benign signals derived from prior package confusion data, uncovering their threat patterns, engineering practices, and measurable attributes. We observed that 13.3% of real package confusion attacks are initially stealthy, so we take that into consideration and refined the definitions. Building on state-of-the-art approaches, we extend support from three to six software package registries, and leverage package metadata to distinguish benign packages. Our approach significantly reduces 64% false-positive (from 77% to 13%), with acceptable additional overhead to filter out benign packages by analyzing the package metadata. ConfuGuard is in production at our industry partner, whose analysts have already confirmed 301 packages detected by ConfuGuard as real attacks. We share lessons learned from production and provide insights to researchers.

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

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

Multilingual proficiency presents a significant challenge for large language models (LLMs). English-centric models are usually suboptimal in other languages, particularly those that are linguistically distant from English. This performance discrepancy mainly stems from the imbalanced distribution of training data across languages during pre-training and instruction tuning stages. To address this problem, we propose a novel approach called CrossIn, which utilizes a mixed composition of cross-lingual instruction tuning data. Our method leverages the compressed representation shared by various languages to efficiently enhance the model's task-solving capabilities and multilingual proficiency within a single process. In addition, we introduce a multi-task and multi-faceted benchmark to evaluate the effectiveness of CrossIn. Experimental results demonstrate that our method substantially improves performance across tasks and languages, and we provide extensive insights into the impact of cross-lingual data volume and the integration of translation data on enhancing multilingual consistency and accuracy.

The SZZ algorithm is the dominant technique for identifying bug-inducing commits and underpins many software engineering tasks, such as defect prediction and vulnerability analysis. Despite numerous variants, including recent LLM-based approaches, performance remains limited on developer-annotated datasets (e.g., recall of 0.552 on the Linux kernel). A key limitation is the reliance on git blame, which traces line-level changes within the same file, failing in common scenarios such as ghost and cross-file cases-making nearly one-quarter of bug-inducing commits inherently untraceable. Moreover, current approaches follow fixed pipelines that restrict iterative reasoning and exploration, unlike developers who investigate bugs through an interactive, multi-tool process. To address these challenges, we propose AgentSZZ, an agent-based framework that leverages LLM-driven agents to explore repositories and identify bug-inducing commits. Unlike prior methods, AgentSZZ integrates task-specific tools, domain knowledge, and a ReAct-style loop to enable adaptive and causal tracing of bugs. A structured compression module further improves efficiency by reducing redundant context while preserving key evidence. Extensive experiments on three widely used datasets show that AgentSZZ consistently outperforms state-of-the-art SZZ algorithms across all settings, achieving F1-score gains of up to 27.2% over prior LLM-based approaches. The improvements are especially pronounced in challenging scenarios such as cross-file and ghost commits, with recall gains of up to 300% and 60%, respectively. Ablation studies show that task-specific tools and domain knowledge are critical, while compression tool outputs reduce token consumption by over 30% with negligible impact. The replication package is available.

Large language models for code generation often need to use APIs that are absent from their pretraining data. This requires more than recalling a function name: models must coordinate signatures, module paths, input-output contracts, semantics, and executable usage patterns. Existing novel-API benchmarks are typically static, rely on coarse pass/fail metrics, or use synthetic APIs that may not reflect real library evolution. We introduce NovelAPIBench, a fully automated dynamic benchmark that, for any base model and target library, discovers novel APIs, extracts decomposed knowledge bundles, generates executable coding tasks, and assigns failed samples to six diagnostic categories. Across about 1.9K tasks, four base models, and five domains, we compare knowledge injected through retrieval with knowledge internalized through parametric adaptation. We find that knowledge components are not interchangeable: usage examples are the strongest standalone signal, while the best two-component setting pairs signatures with either mechanisms or examples depending on the domain and backbone. Adding more context, especially source code, can hurt by increasing import-path errors. Parametric adaptation also does not replace retrieval once external knowledge is removed; rather, fine-tuning mainly teaches models how to use provided bundles, and this ability transfers to held-out libraries. These results suggest that retrieval and tuning play complementary roles: retrieval supplies volatile API content, while tuning improves procedural integration.

Code Agents have achieved remarkable advances in recent years, exhibiting strong capabilities across a wide range of software engineering tasks. However, their misuse often produces bloated and disorganized code that impairing readability, extensibility, and robustness. Despite this risk, existing benchmarks largely evaluate functional correctness rather than long-term maintainability of code agents. In this paper, we propose SmellBench, an extensible code refactoring benchmark that proactively injects code smells into clean code snippets from real-world repositories. This design enables the generation of controlled, high-quality, and diverse refactoring cases with human-written ground truth. Specifically, it contains 294 cases spanning 7 popular smell types, 3 difficulty levels, 2 instruction settings across 7 real-world repositories. We further design 3 evaluation aspects covering functional correctness, localization ability, and refactoring quality assessment. Experiments with 2 popular agents and 6 large langauge models (LLMs) show that the best combination - Qwen Code + Claude Sonnet 4.5 - achieved only a 50.34 score of smell elimination. Further analysis reveals that this gap arises from a focus on local code smells and a lack of cross-file understanding, which hinders comprehensive smell elimination.

We present CodeReef - an open platform to share all the components necessary to enable cross-platform MLOps (MLSysOps), i.e. automating the deployment of ML models across diverse systems in the most efficient way. We also introduce the CodeReef solution - a way to package and share models as non-virtualized, portable, customizable and reproducible archive files. Such ML packages include JSON meta description of models with all dependencies, Python APIs, CLI actions and portable workflows necessary to automatically build, benchmark, test and customize models across diverse platforms, AI frameworks, libraries, compilers and datasets. We demonstrate several CodeReef solutions to automatically build, run and measure object detection based on SSD-Mobilenets, TensorFlow and COCO dataset from the latest MLPerf inference benchmark across a wide range of platforms from Raspberry Pi, Android phones and IoT devices to data centers. Our long-term goal is to help researchers share their new techniques as production-ready packages along with research papers to participate in collaborative and reproducible benchmarking, compare the different ML/software/hardware stacks and select the most efficient ones on a Pareto frontier using online CodeReef dashboards.

You have an environment, a model, and a reinforcement learning library that are designed to work together but don't. PufferLib makes them play nice. The library provides one-line environment wrappers that eliminate common compatibility problems and fast vectorization to accelerate training. With PufferLib, you can use familiar libraries like CleanRL and SB3 to scale from classic benchmarks like Atari and Procgen to complex simulators like NetHack and Neural MMO. We release pip packages and prebuilt images with dependencies for dozens of environments. All of our code is free and open-source software under the MIT license, complete with baselines, documentation, and support at pufferai.github.io.

Current learning-based Automated Vulnerability Repair (AVR) approaches, while promising, often fail to generalize effectively in real-world scenarios. Our diagnostic analysis reveals three fundamental weaknesses in state-of-the-art AVR approaches: (1) limited cross-repository generalization, with performance drops on unseen codebases; (2) inability to capture long-range dependencies, causing a performance degradation on complex, multi-hunk repairs; and (3) over-reliance on superficial lexical patterns, leading to significant performance drops on vulnerabilities with minor syntactic variations like variable renaming. To address these limitations, we propose SeCuRepair, a semantics-aligned, curriculum-driven, and reasoning-enhanced framework for vulnerability repair. At its core, SeCuRepair adopts a reason-then-edit paradigm, requiring the model to articulate why and how a vulnerability should be fixed before generating the patch. This explicit reasoning enforces a genuine understanding of repair logic rather than superficial memorization of lexical patterns. SeCuRepair also moves beyond traditional supervised fine-tuning and employs semantics-aware reinforcement learning, rewarding patches for their syntactic and semantic alignment with the oracle patch rather than mere token overlap. Complementing this, a difficulty-aware curriculum progressively trains the model, starting with simple fixes and advancing to complex, multi-hunk coordinated edits. We evaluate SeCuRepair on strict, repository-level splits of BigVul and newly crafted PrimeVul_AVR datasets. SeCuRepair significantly outperforms all baselines, surpassing the best-performing baselines by 34.52% on BigVul and 31.52% on PrimeVulAVR in terms of CodeBLEU, respectively. Comprehensive ablation studies further confirm that each component of our framework contributes to its final performance.