Software Engineering Benchmarks

Overview

Software engineering benchmarks measure whether AI systems can perform tasks such as fixing repository-level bugs, writing tests, reviewing code, and building or evolving applications. They commonly use real repositories, executable environments, hidden tests, and simulated user interactions, with newer evaluations also examining agent trajectories, tool use, and coordination. The field is moving beyond one-shot code generation toward long-running workflows and broader measures of quality, including performance, security, design constraints, and maintainability. A central challenge is making results reliable and representative: tests can miss valid solutions or accept flawed ones, and scores can depend heavily on task selection, evaluation rules, and agent setup.

Latest papers

157 papers32 papers in the last four weeks, up 113% on the four weeks before. 0.2% of all new papers.

Apr 17, 2026

Neurosymbolic Repo-level Code Localization

Code localization is a cornerstone of autonomous software engineering. Recent advancements have achieved impressive performance on real-world issue benchmarks. However, we identify a critical yet overlooked bias: these benchmarks are saturated with keyword references (e.g. file paths, function names), encouraging models to rely on superficial lexical matching rather than genuine structural reasoning. We term this phenomenon the Keyword Shortcut. To address this, we formalize the challenge of Keyword-Agnostic Logical Code Localization (KA-LCL) and introduce KA-LogicQuery, a diagnostic benchmark requiring structural reasoning without any naming hints. Our evaluation reveals a catastrophic performance drop of state-of-the-art approaches on KA-LogicQuery, exposing their lack of deterministic reasoning capabilities. We propose LogicLoc, a novel agentic framework that combines large language models with the rigorous logical reasoning of Datalog for precise localization. LogicLoc extracts program facts from the codebase and leverages an LLM to synthesize Datalog programs, with parser-gated validation and mutation-based intermediate-rule diagnostic feedback to ensure correctness and efficiency. The validated programs are executed by a high-performance inference engine, enabling accurate and verifiable localization in a fully automated, closed-loop workflow. Experimental results demonstrate that LogicLoc significantly outperforms SOTA methods on KA-LogicQuery while maintaining competitive performance on popular issue-driven benchmarks. Notably, LogicLoc attains superior performance with significantly lower token consumption and faster execution by offloading structural traversal to a deterministic engine, reducing the overhead of iterative LLM inference.
Apr 16, 2026

Benchmarks for Trajectory Safety Evaluation and Diagnosis in OpenClaw and Codex: ATBench-Claw and ATBench-Codex

As agent systems move into increasingly diverse execution settings, trajectory-level safety evaluation and diagnosis require benchmarks that evolve with them. ATBench is a diverse and realistic agent trajectory benchmark for safety evaluation and diagnosis. This report presents ATBench-Claw and ATBench-Codex, two domain-customized extensions that carry ATBench into the OpenClaw and OpenAI Codex / Codex-runtime settings. The key adaptation mechanism is to analyze each new setting, customize the three-dimensional Safety Taxonomy over risk source, failure mode, and real-world harm, and then use that customized taxonomy to define the benchmark specification consumed by the shared ATBench construction pipeline. This extensibility matters because agent frameworks remain relatively stable at the architectural level even as their concrete execution settings, tool ecosystems, and product capabilities evolve quickly. Concretely, ATBench-Claw targets OpenClaw-sensitive execution chains over tools, skills, sessions, and external actions, while ATBench-Codex targets trajectories in the OpenAI Codex / Codex-runtime setting over repositories, shells, patches, dependencies, approvals, and runtime policy boundaries. Our emphasis therefore falls on taxonomy customization, domain-specific risk coverage, and benchmark design under a shared ATBench generation framework.
Apr 15, 2026

LLMs taking shortcuts in test generation: A study with SAP HANA and LevelDB

Large Language Models (LLMs) have achieved impressive results on public benchmarks, often leading to claims of advanced reasoning and understanding. However, recent research in cognitive science reveals that these models sometimes rely on shallow heuristics and memorization, taking shortcuts rather than demonstrating genuine cognitive abilities. This paper investigates LLM behavior in automated test generation for software, contrasting performance on an open-source system (LevelDB) with SAP HANA, one of the most widely deployed commercial database systems worldwide, whose proprietary codebase is guaranteed to be absent from training data. We combine cognitive evaluation principles, drawing on Mitchell's mechanism-focused assessment methodology, with empirical software testing, employing mutation score and iterative compiler-feedback repair loops to assess both accuracy and underlying reasoning strategies. Results show that LLMs excel on familiar, open-source benchmarks but struggle with unseen, complex domains, often prioritizing compilability over semantic effectiveness. These findings provide independent software engineering evidence for the broader claim that current LLMs lack robust reasoning, and highlight the need for evaluation frameworks that penalize trivial shortcuts and reward true generalization.
Apr 14, 2026

LogicEval: A Systematic Framework for Evaluating Automated Repair Techniques for Logical Vulnerabilities in Real-World Software

Logical vulnerabilities in software stem from flaws in program logic rather than memory safety, which can lead to critical security failures. Although existing automated program repair techniques primarily focus on repairing memory corruption vulnerabilities, they struggle with logical vulnerabilities because of their limited semantic understanding of the vulnerable code and its expected behavior. On the other hand, recent successes of large language models (LLMs) in understanding and repairing code are promising. However, no framework currently exists to analyze the capabilities and limitations of such techniques for logical vulnerabilities. We aim to systematically evaluate both traditional and LLM based repair approaches for addressing real world logical vulnerabilities. To facilitate our assessment, we created the first ever dataset, LogicDS, comprising 122 logical vulnerabilities that reflect tangible security impact. We also developed a systematic framework, LogicEval, to evaluate patches for logical vulnerabilities. Evaluations suggest that compilation and testing failures are primarily driven by prompt sensitivity, loss of code context, and difficulty in patch localization.
Apr 14, 2026

CodeSpecBench: Benchmarking LLMs for Executable Behavioral Specification Generation

Large language models (LLMs) can generate code from natural language, but the extent to which they capture intended program behavior remains unclear. Executable behavioral specifications, defined via preconditions and postconditions, provide a concrete means to assess such understanding. However, existing work on specification generation is constrained in evaluation methodology, task settings, and specification expressiveness. We introduce CodeSpecBench, a benchmark for executable behavioral specification generation under an execution-based evaluation protocol. CodeSpecBench supports both function-level and repository-level tasks and encodes specifications as executable Python functions. Constructed from diverse real-world codebases, it enables a realistic assessment of both correctness (accepting valid behaviors) and completeness (rejecting invalid behaviors). Evaluating 15 state-of-the-art LLMs on CodeSpecBench, we observe a sharp performance degradation on repository-level tasks, where the best model attains only a 20.2% pass rate. We further find that specification generation is substantially more challenging than code generation, indicating that strong coding performance does not necessarily reflect deep understanding of intended program semantics. Our data and code are available at https://github.com/SparksofAGI/CodeSpecBench.
Apr 12, 2026

ReFEree: Reference-Free and Fine-Grained Method for Evaluating Factual Consistency in Real-World Code Summarization

As Large Language Models (LLMs) have become capable of generating long and descriptive code summaries, accurate and reliable evaluation of factual consistency has become a critical challenge. However, previous evaluation methods are primarily designed for short summaries of isolated code snippets. Consequently, they struggle to provide fine-grained evaluation of multi-sentence functionalities and fail to accurately assess dependency context commonly found in real-world code summaries. To address this, we propose ReFEree, a reference-free and fine-grained method for evaluating factual consistency in real-world code summaries. We define factual inconsistency criteria specific to code summaries and evaluate them at the segment level using these criteria along with dependency information. These segment-level results are then aggregated into a fine-grained score. We construct a code summarization benchmark with human-annotated factual consistency labels. The evaluation results demonstrate that ReFEree achieves the highest correlation with human judgment among 13 baselines, improving 15-18% over the previous state-of-the-art. Our code and data are available at https://github.com/bsy99615/ReFEree.git.
Apr 9, 2026

ORACLE-SWE: Quantifying the Contribution of Critical Information Signals on SWE Agents

Recent advances in Language Model (LM) agents have increasingly focused on repository-level software engineering (SWE) tasks, leading to various agentic workflows, training methods and failure analysis. Interestingly, rather than directly generating or evaluating edit patches, these approaches first examine and improve intermediate information signals collected during agent exploration, including Reproduction Test, Regression Test, Edit Location, Execution Context, and API Usage. Although different studies examine different subsets of these signals, no work has systematically compared their relative effectiveness in improving final task success or measured the remaining space for improvement in each signal. To address this gap, this work quantifies the contributions of both oracle and agent-extracted signals to final task success and measures the gap between current agent-found signals and their oracle counterparts. We hope our findings could suggest future research emphasis in SWE agents. We release our source code and oracle-signal dataset as a reusable methodology to benefit future signal analysis of SWE agents.
Apr 8, 2026

Evaluating Repository-level Software Documentation via Question Answering and Feature-Driven Development

Software documentation is crucial for repository comprehension. While Large Language Models (LLMs) advance documentation generation from code snippets to entire repositories, existing benchmarks have two key limitations: (1) they lack a holistic, repository-level assessment, and (2) they rely on unreliable evaluation strategies, such as LLM-as-a-judge, which suffers from vague criteria and limited repository-level knowledge. To address these issues, we introduce SWD-Bench, a novel benchmark for evaluating repository-level software documentation. Inspired by documentation-driven development, our strategy evaluates documentation quality by assessing an LLM's ability to understand and implement functionalities using the documentation, rather than by directly scoring it. This is measured through function-driven Question Answering (QA) tasks. SWD-Bench comprises three interconnected QA tasks: (1) Functionality Detection, to determine if a functionality is described; (2) Functionality Localization, to evaluate the accuracy of locating related files; and (3) Functionality Completion, to measure the comprehensiveness of implementation details. We construct the benchmark, containing 4,170 entries, by mining high-quality Pull Requests and enriching them with repository-level context. Experiments reveal limitations in current documentation generation methods and show that source code provides complementary value. Notably, documentation from the best-performing method improves the issue-solving rate of SWE-Agent by 20.00%, which demonstrates the practical value of high-quality documentation in supporting documentation-driven development.
Apr 7, 2026

Does Pass Rate Tell the Whole Story? Evaluating Design Constraint Compliance in LLM-based Issue Resolution

Repository-level issue resolution benchmarks have become a standard testbed for evaluating LLM-based agents, yet success is still predominantly measured by test pass rates. In practice, however, acceptable patches must also comply with project-specific design constraints, such as architectural conventions, error-handling policies, and maintainability requirements, which are rarely encoded in tests and are often documented only implicitly in code review discussions. This paper introduces design-aware issue resolution and presents \bench{}, a benchmark that makes such implicit design constraints explicit and measurable. \bench{} is constructed by mining and validating design constraints from real-world pull requests, linking them to issue instances, and automatically checking patch compliance using an LLM-based verifier, yielding 495 issues and 1,787 validated constraints across six repositories, aligned with SWE-bench-Verified and SWE-bench-Pro. Experiments with state-of-the-art agents show that test-based correctness substantially overestimates patch quality: fewer than half of resolved issues are fully design-satisfying, design violations are widespread, and functional correctness exhibits negligible statistical association with design satisfaction. While providing issue-specific design guidance reduces violations, substantial non-compliance remains, highlighting a fundamental gap in current agent capabilities and motivating design-aware evaluation beyond functional correctness.
Apr 6, 2026

Edit, But Verify: An Empirical Audit of Instructed Code-Editing Benchmarks

Instructed code editing, where an LLM modifies existing code based on a natural language instruction, accounts for roughly 19% of real-world coding assistant interactions. Yet very few benchmarks directly evaluate this capability. From a survey of over 150 code-related benchmarks, we find that only two, CanItEdit and EDIT-Bench, target instructed code editing with human-authored instructions and test-based evaluation. We audit both by comparing their programming languages, edit intents, and application domains against distributions observed in the wild (Copilot Arena, AIDev, GitHub Octoverse), and by measuring test counts, statement coverage, and test scope across all 213 problems. Both benchmarks concentrate over 90% of evaluation on Python while TypeScript, GitHub's most-used language, is absent. Backend and frontend development, which together constitute 46% of real-world editing activity, are largely missing, and documentation, testing, and maintenance edits (31.4% of human PRs) have zero representation. Both benchmarks have modest test counts (CanItEdit median 13, EDIT-Bench median 4), though CanItEdit compensates with near-complete whole-file coverage and fail-before/pass-after validation. 59% of EDIT-Bench's low-coverage suites would not detect modifications outside the edit region. EDIT-Bench has 15 problems that are not solved by any of 40 LLMs and 11 of these problems trace failures to poor benchmark artifacts rather than model limitations. Further, 29% of EDIT-Bench problems and 6% of CanItEdit problems share a codebase with at least one other problem within the benchmark. In summary, these benchmarks measure a narrower construct than deployment decisions require. We therefore propose six empirically grounded desiderata and release all audit artifacts so the community can build instructed code-editing benchmarks whose scores reliably reflect real-world editing capability.
Apr 5, 2026

SW-A2A^2-Bench: Benchmarking Autonomous Software Agent Generation for Agentic Web

The Agentic Web is emerging as a paradigm in which autonomous software agents interact with online resources and with each other to accomplish user goals. However, the capacity of Agentic Web is still limited by insufficient autonomous software agent population, which has become a crucial challenge for scaling Agentic Web. In order to alleviate this, we study the task of automatically converting existing code repositories into autonomous software agents via coding agents, decompose the process into critical stages, and identify key technical hurdles. To systematically evaluate this capability, we propose SoftWare Agent generation for Agentic Web Bench (SW-A2A^2-Bench), the first benchmark designed for software agent generation. SW-A2A^2-Bench evaluates not only whether software agents can be generated, but also whether generated software agents are faithful to the source repositories and interoperable with other agents in multi-agent workflows. Our experiments demonstrate that our approach effectively activates the functional capabilities of code repositories and enables interoperable multi-agent collaboration in Agentic Web. We believe that this work will provide a standardized evaluation for software agent generation and will contribute to the future of scaling the capacity of Agentic Web.
Apr 3, 2026

Beyond Isolated Tasks: A Framework for Evaluating Coding Agents on Sequential Software Evolution

Existing datasets for coding agents evaluate performance on isolated, single pull request (PR) tasks in a stateless manner, failing to capture the reality of real-world software development where code changes accumulate, technical debt accrues, and test suites grow over time. To bridge this gap, we introduce an automated coding task generation framework, which helps generate our dataset SWE-STEPS, that evaluates coding agents on long-horizon tasks through two realistic settings mirroring actual developer workflows: Conversational coding with iterative requests, and single-shot Project Requirement document (PRD)-based coding. Unlike existing datasets that evaluate agents on disjointed Pull Requests (PRs), our framework assesses performance across chains of dependent PRs, enabling evaluation of sequential execution, regression verification, and long-term repository health. We discover that widely used isolated PR evaluations yield inflated success rates, w.r.t. our settings - overshooting performance by as much as 20 percentage points - because they ignore the ``spillover'' effects of previous inefficient or buggy code. Furthermore, our analysis reveals that even when agents successfully resolve issues, they degrade repository health by generating code with higher cognitive complexity and technical debt compared to human developers, underscoring the necessity for multidimensional evaluation.
Apr 1, 2026

In harmony with gpt-oss

No one has independently reproduced OpenAI's published scores for gpt-oss-20b with tools, because the original paper discloses neither the tools nor the agent harness. We reverse-engineered the model's in-distribution tools: when prompted without tool definitions, gpt-oss still calls tools from its training distribution with high statistical confidence -- a strong prior, not a hallucination. We then built a native harmony agent harness (https://github.com/borislavmavrin/harmonyagent.git) that encodes messages in the model's native format, bypassing the lossy Chat Completions conversion. Together, these yield the first independent reproduction of OpenAI's published scores: 60.4% on SWE Verified HIGH (published 60.7%), 53.3% MEDIUM (53.2%), and 91.7% on AIME25 with tools (90.4%).
Mar 28, 2026

ComBench: A Repo-level Real-world Benchmark for Compilation Error Repair

Compilation errors pose pervasive and critical challenges in software development, significantly hindering productivity. Therefore, Automated Compilation Error Repair (ACER) techniques are proposed to mitigate these issues. Despite recent advancements in ACER, its real-world performance remains poorly evaluated. This can be largely attributed to the limitations of existing benchmarks, \ie decontextualized single-file data, lack of authentic source diversity, and biased local task modeling that ignores crucial repository-level complexities. To bridge this critical gap, we propose ComBench, the first repository-level, reproducible real-world benchmark for C/C++ compilation error repair. ComBench is constructed through a novel, automated framework that systematically mines real-world failures from the GitHub CI histories of large-scale open-source projects. Our framework contributes techniques for the high-precision identification of ground-truth repair patches from complex version histories and a high-fidelity mechanism for reproducing the original, ephemeral build environments. To ensure data quality, all samples in ComBench are execution-verified -- guaranteeing reproducible failures and build success with ground-truth patches. Using ComBench, we conduct a comprehensive evaluation of 12 modern LLMs under both direct and agent-based repair settings. Our experiments reveal a significant gap between a model's ability to achieve syntactic correctness (a 73% success rate for GPT-5) and its ability to ensure semantic correctness (only 41% of its patches are valid). We also find that different models exhibit distinct specializations for different error types. ComBench provides a robust and realistic platform to guide the future development of ACER techniques capable of addressing the complexities of modern software development.
Mar 27, 2026

Beyond Code Snippets: Benchmarking LLMs on Repository-Level Question Answering

Large Language Models (LLMs) have shown impressive capabilities across software engineering tasks, including question answering (QA). However, most studies and benchmarks focus on isolated functions or single-file snippets, overlooking the challenges of real-world program comprehension, which often spans multiple files and system-level dependencies. In this work, we introduce StackRepoQA, the first multi-project, repository-level question answering dataset constructed from 1,318 real developer questions and accepted answers across 134 open-source Java projects. Using this dataset, we systematically evaluate two widely used LLMs (Claude 3.5 Sonnet and GPT-4o) under both direct prompting and agentic configurations. We compare baseline performance with retrieval-augmented generation methods that leverage file-level retrieval and graph-based representations of structural dependencies. Our results show that LLMs achieve moderate accuracy at baseline, with performance improving when structural signals are incorporated. Nonetheless, overall accuracy remains limited for repository-scale comprehension. The analysis reveals that high scores often result from verbatim reproduction of Stack Overflow answers rather than genuine reasoning. To our knowledge, this is the first empirical study to provide such evidence in repository-level QA. We release StackRepoQA to encourage further research into benchmarks, evaluation protocols, and augmentation strategies that disentangle memorization from reasoning, advancing LLMs as reliable tool for repository-scale program comprehension.
Mar 27, 2026

ATime-Consistent Benchmark for Repository-Level Software Engineering Evaluation

Evaluation of repository-aware software engineering systems is often confounded by synthetic task design, prompt leakage, and temporal contamination between repository knowledge and future code changes. We present a time-consistent benchmark methodology that snapshots a repository at time T0, constructs repository-derived code knowledge using only artifacts available before T0, and evaluates on engineering tasks derived from pull requests merged in the future interval (T0, T1]. Each historical pull request is transformed into a natural-language task through an LLM-assisted prompt-generation pipeline, and the benchmark is formalized as a matched A/B comparison in which the same software engineering agent is evaluated with and without repository-derived code knowledge while all other variables are held constant. We also report a baseline characterization study on two open-source repositories, DragonFly and React, using three Claude-family models and four prompt granularities. Across both repositories, file-level F1 increases monotonically from minimal to guided prompts, reaching 0.8081 on DragonFly and 0.8078 on React for the strongest tested model. These results show that prompt construction is a first-order benchmark variable. More broadly, the benchmark highlights that temporal consistency and prompt control are core validity requirements for repository-aware software engineering evaluation.
Mar 26, 2026

MobileDev-Bench: A Benchmark for Issue Resolution in Mobile Application Development

Large language models (LLMs) have shown strong performance on automated software engineering tasks, yet existing benchmarks focus primarily on library-style repositories, leaving mobile application development largely unexplored despite its framework-specific build systems, heterogeneous artifact types, and coordinated multi-file fix requirements. We introduce MobileDev-Bench, a benchmark comprising 407 real-world issue-resolution tasks collected from 19 production mobile applications spanning Android Native (Java/Kotlin), React Native (TypeScript), and Flutter (Dart). Each task pairs a verified developer-reported issue with executable test patches, enabling fully automated validation of model-generated fixes within mobile build environments. The benchmark exhibits substantially greater patch complexity than prior benchmarks: fixes modify 12.9 files and 334.6 lines on average, and 41% of instances require coordinated changes across multiple artifact types, such as source, build configuration, and resource files. Evaluation of four frontier LLMs (Claude Sonnet 4.5, Qwen3-Coder, GPT-5.2, and Gemini 2.5 Flash) yields end-to-end resolution rates of only 3.23% - 4.23% under automated retrieval and at most 5.69% under oracle retrieval, well below resolution rates reported on existing benchmarks. We release MobileDev-Bench with task instances, an evaluation harness, and containerized environments to support reproducible research on AI-assisted mobile application development.
Mar 25, 2026

Composer 2 Technical Report

Composer 2 is a specialized model designed for agentic software engineering. The model demonstrates strong long-term planning and coding intelligence while maintaining the ability to efficiently solve problems for interactive use. The model is trained in two phases: first, continued pretraining to improve the model's knowledge and latent coding ability, followed by large-scale reinforcement learning to improve end-to-end coding performance through stronger reasoning, accurate multi-step execution, and coherence on long-horizon realistic coding problems. We develop infrastructure to support training in the same Cursor harness that is used by the deployed model, with equivalent tools and structure, and use environments that match real problems closely. To measure the ability of the model on increasingly difficult tasks, we introduce a benchmark derived from real software engineering problems in large codebases including our own. Composer 2 is a frontier-level coding model and demonstrates a process for training strong domain-specialized models. On our CursorBench evaluations the model achieves a major improvement in accuracy compared to previous Composer models (61.3). On public benchmarks the model scores 61.7 on Terminal-Bench and 73.7 on SWE-bench Multilingual in our harness, comparable to state-of-the-art systems.
Mar 25, 2026

Coherence Collapse: Diagnosing Why Code Agents Fail After Reaching the Right Code

Code agents resolve 65-70% of SWE-bench Verified issues, but Pass@1 cannot tell us why the rest fail, and, as we show, capable-model failures are systematically misdiagnosed without trajectory data. We introduce TRAJEVAL, a training-free decomposition of agent trajectories into reference-patch-aligned search, read, and edit stages, and apply it across 16,758 trajectories spanning three architectures and seven models. The dominant failure of capable models is not localization: 60-69% of failures on SWE-Agent and OpenHands reach and edit the correct functions yet still produce incorrect patches, and the pattern persists for most models on the bash-only LiveSWEAgent. Within this Edit-Quality residual, we identify Coherence Collapse, where the agent reaches correct code and then overwrites or thrashes it, as the largest theme, replicating across SWE-bench Verified and the multilingual PolyBench Verified. In 5 cases, the agent produces a patch bit-identical to the gold reference mid-trajectory and destroys it later; an edit-commit checkpoint recovers all 5 against the SWE-bench Docker harness. A reference-free consensus-driven variant yields a directional +3.0 pp Pass@1 measurement on GPT-5 (p=0.08).
Mar 24, 2026

Code Review Agent Benchmark

Software engineering agents have shown significant promise in writing code. As AI agents permeate code writing, and generate huge volumes of code automatically -- the matter of code quality comes front and centre. As the automatically generated code gets integrated into huge code-bases -- the issue of code review and broadly quality assurance becomes important. In this paper, we take a fresh look at the problem and curate a code review dataset for AI agents to work with. Our dataset called c-CRAB (pronounced see-crab) can evaluate agents for code review tasks. Specifically given a pull-request (which could be coming from code generation agents or humans), if a code review agent produces a review, our evaluation framework can asses the reviewing capability of the code review agents. Our evaluation framework is used to evaluate the state of the art today -- the open-source PR-agent, as well as commercial code review agents from Devin, Claude Code, and Codex. Our c-CRAB dataset is systematically constructed from human reviews -- given a human review of a pull request instance we generate corresponding tests to evaluate the code review agent generated reviews. Such a benchmark construction gives us several insights. Firstly, the existing review agents taken together can solve only around 40% of the c-CRAB tasks, indicating the potential to close this gap by future research. Secondly, we observe that the agent reviews often consider different aspects from the human reviews -- indicating the potential for human-agent collaboration for code review that could be deployed in future software teams. Last but not the least, the agent generated tests from our data-set act as a held out test-suite and hence quality gate for agent generated reviews. What this will mean for future collaboration of code generation agents, test generation agents and code review agents -- remains to be investigated.
Mar 23, 2026

Do Papers Tell the Whole Story? A Benchmark and Framework for Uncovering Hidden Implementation Gaps in Bioinformatics

As bioinformatics software is increasingly applied across a broader range of scenarios and the rapid development of large language models (LLMs) further lowers the barriers to software use and development, the composition of the bioinformatics research community is undergoing substantial change. Consequently, a growing number of researchers require a deeper understanding of methodological details and software behavior. In this context, systematically analyzing the relationship between paper descriptions and code implementations is emerging as an important new challenge in the field. To address this challenge, we introduce paper-code consistency analysis as a new research perspective and construct BioCon, the first benchmark dataset for paper-code consistency analysis in bioinformatics. Furthermore, we develop a unified cross-modal analysis framework to systematically investigate this problem from three perspectives: sentence-level detection, cross-modal retrieval, and project-level assessment. Experimental results demonstrate that the proposed framework can effectively model the semantic relationships between scientific publications and software implementations. Further case studies reveal that paper-code inconsistency is not a single phenomenon but arises from multiple underlying causes, among which Author-Perceived Non-Essential Details represents the most prevalent category. These findings suggest that paper-code consistency analysis is not merely a technical problem but also raises broader discussions regarding knowledge dissemination, the boundaries of code disclosure, and community norms. We hope that this work will encourage the bioinformatics community to re-examine the relationship between scientific publications and software implementations while providing a foundation for future research in paper-code consistency analysis.
Mar 23, 2026

Cross-Context Verification: Hierarchical Detection of Benchmark Contamination through Session-Isolated Analysis

LLM coding benchmarks face a credibility crisis: widespread solution leakage and test quality issues undermine SWE-bench Verified, while existing detection methods--paraphrase consistency, n-gram overlap, perplexity analysis--never directly observe whether a model reasons or recalls. Meanwhile, simply repeating verification degrades accuracy: multi-turn review generates false positives faster than it discovers true errors, suggesting that structural approaches are needed. We introduce Cross-Context Verification (CCV), a black-box method that solves the same benchmark problem in N independent sessions and measures solution diversity, combined with the Hierarchical Cross-Context Architecture (HCCA), a multi-agent analysis framework that prevents confirmation bias through intentional information restriction across specialized analytical roles. On 9 SWE-bench Verified problems (45 trials, Claude Opus 4.6, temperature 0), CCV achieves perfect separation between contaminated and genuine reasoning (Mann-Whitney U=0, p approx 0.012, r = 1.0). Key findings: (1) contamination is binary--models either recall perfectly or not at all; (2) reasoning absence is a perfect discriminator; (3) 33% of prior contamination labels are false positives; (4) HCCA's independent analysis structure discovers contamination-flaw composite cases that single-analyst approaches miss. A pilot experiment extending HCCA to multi-stage verification (Worker to Verifier to Director) yields a negative result--100% sycophantic confirmation--providing further evidence that information restriction, not structural complexity, is the key mechanism. We release all code and data.
Mar 17, 2026

SWE-QA-Pro: A Representative Benchmark and Scalable Training Recipe for Repository-Level Code Understanding

Agentic repository-level code understanding is essential for automating complex software engineering tasks, yet the field lacks reliable benchmarks. Existing evaluations often overlook the long tail topics and rely on popular repositories where Large Language Models (LLMs) can cheat via memorized knowledge. To address this, we introduce SWE-QA-Pro, a benchmark constructed from diverse, long-tail repositories with executable environments. We enforce topical balance via issue-driven clustering to cover under-represented task types and apply a rigorous difficulty calibration process: questions solvable by direct-answer baselines are filtered out. This results in a dataset where agentic workflows significantly outperform direct answering (e.g., a ~13-point gap for Claude Sonnet 4.5), confirming the necessity of agentic codebase exploration. Furthermore, to tackle the scarcity of training data for such complex behaviors, we propose a scalable synthetic data pipeline that powers a two-stage training recipe: Supervised Fine-Tuning (SFT) followed by Reinforcement Learning from AI Feedback (RLAIF). This approach allows small open models to learn efficient tool usage and reasoning. Empirically, a Qwen3-8B model trained with our recipe surpasses GPT-4o by 2.3 points on SWE-QA-Pro and substantially narrows the gap to state-of-the-art proprietary models, demonstrating both the validity of our evaluation and the effectiveness of our agentic training workflow.
Mar 16, 2026

SWE-Skills-Bench: Do Agent Skills Actually Help in Real-World Software Engineering?

Agent skills, structured procedural knowledge packages injected at inference time, are increasingly used to augment LLM agents on software engineering tasks. However, their real utility in end-to-end development settings remains unclear, and no standard procedure tests an individual skill before installation. We present swe-skills-bench, a skill-centric, requirement-driven benchmark that measures how much individual agent skills improve performance on real-world software engineering (SWE) tasks. We start from 98 public SWE skills, each paired with a real GitHub repository pinned at a fixed commit. For each skill, we derive repository-specific requirements, create executable verifiers, and build a reproducible environment. Under each of four agent-model configurations, we run every task once without the skill and once with it, yielding 3,920 paired evaluations. For each requirement, we compute a paired delta, i.e., the change in outcome when the skill is added. We then aggregate these deltas across a skill's ten requirements into a per-skill utility profile, and use a statistical test to classify each skill as Golden (significantly helpful), Ineffective (no significant effect), or Harmful (significantly detrimental). Our results show that skills provide limited benefits: 92 of 98 skills have no statistically significant effect, and adding skills raises the average pass ratio only from 76.6% to 76.9%. The few helpful skills supply procedures that the agent would otherwise omit (gains of up to +17.7+17.7 points). In contrast, harmful skills anchor the agent on their own templates and override the task's explicit instructions (losses of up to -17.0 points). Our code is available at https://github.com/ControllableModel/SWE-Skills-Bench.
Mar 13, 2026

daVinci-Env: Open SWE Environment Synthesis at Scale

Training capable software engineering (SWE) agents demands large-scale, executable, and verifiable environments that provide dynamic feedback loops for iterative code editing, test execution, and solution refinement. However, existing open-source datasets remain limited in scale and repository diversity, while industrial solutions are opaque with unreleased infrastructure, creating a prohibitive barrier for most academic research groups. We present OpenSWE, the largest fully transparent framework for SWE agent training in Python, comprising 45,320 executable Docker environments spanning over 12.8k repositories, with all Dockerfiles, evaluation scripts, and infrastructure fully open-sourced for reproducibility. OpenSWE is built through a multi-agent synthesis pipeline deployed across a 64-node distributed cluster, automating repository exploration, Dockerfile construction, evaluation script generation, and iterative test analysis. Beyond scale, we propose a quality-centric filtering pipeline that characterizes the inherent difficulty of each environment, filtering out instances that are either unsolvable or insufficiently challenging and retaining only those that maximize learning efficiency. With 891Kspentonenvironmentconstructionandanadditional891K spent on environment construction and an additional 576K on trajectory sampling and difficulty-aware curation, the entire project represents a total investment of approximately $1.47 million, yielding about 13,000 curated trajectories from roughly 9,000 quality guaranteed environments. Extensive experiments validate OpenSWE's effectiveness: OpenSWE-32B and OpenSWE-72B achieve 62.4% and 66.0% on SWE-bench Verified, establishing SOTA among Qwen2.5 series. Moreover, SWE-focused training yields substantial out-of-domain improvements, including up to 12 points on mathematical reasoning and 5 points on science benchmarks, without degrading factual recall.
Mar 13, 2026

SWE-Milestone: Evaluating AI Agents on Continuous Software Evolution

Real-world software must continuously evolve to meet ever-changing and open-ended requirements. AI agents, increasingly deployed as long-running systems, are now entrusted to drive this evolution. Yet, existing benchmarks evaluate agents on isolated, one-off coding tasks, neglecting the temporal dependencies and technical debt inherent in real-world software evolution. To bridge this gap, we introduce DeepCommit, an agentic pipeline that reconstructs verifiable Milestone DAGs from noisy commit logs, where milestones are defined as functionally cohesive development goals. These executable sequences enable SWE-Milestone, a benchmark that evaluates agents on streams of milestone-level tasks, requiring them to sustain system integrity and limit error accumulation, dimensions of long-term software evolution largely missing from current benchmarks. Our evaluation of 12 frontier models across 4 agent frameworks reveals a critical vulnerability: overall performance scores drop significantly from >80% on isolated tasks to 38.03% in continuous settings, exposing agents' profound struggle with long-term maintenance and error propagation.
Mar 4, 2026

SWE-CI: Evaluating Agent Capabilities in Maintaining Codebases via Continuous Integration

Large language model (LLM)-powered agents have demonstrated strong capabilities in automating software engineering tasks such as static bug fixing. However, in the real world, the development of mature software is typically predicated on complex requirement changes and long-term feature iterations -- a process that static, one-shot repair paradigms fail to capture. To bridge this gap, we propose SWE-CI, the first repository-level benchmark built upon the Continuous Integration loop, aiming to shift the evaluation paradigm for code generation from static, short-term functional correctness toward dynamic, long-term maintainability. The key insight is simple: Maintainability can be revealed by tracking how functional correctness changes over time. The benchmark comprises 100 tasks, each deriving from a real-world code repository with a development history spanning an average of 233 days and 71 consecutive commits. SWE-CI requires agents to systematically resolve these tasks through dozens of rounds of analysis and coding iterations. SWE-CI provides valuable insights into how well agents can sustain code quality throughout long-term evolution.
Mar 3, 2026

BeyondSWE: Can Current Code Agent Survive Beyond Single-Repo Bug Fixing?

Current code-agent benchmarks primarily evaluate localized issue resolution within a single target repository, leaving under-tested many software engineering tasks that require external knowledge or broader repository-level changes. We introduce BeyondSWE, a 500-instance benchmark drawn from 246 real-world GitHub repositories to evaluate code agents beyond single-repository bug fixing. BeyondSWE covers four representative settings: cross-repository issue resolution, domain-specific issue resolution, dependency-driven migration, and document-to-repository generation, spanning both broader knowledge scope and broader resolution scope. Our evaluation shows that BeyondSWE remains far from saturated: the best OpenHands-based agent reaches 46.12 average score, while the strongest Codex harness with GPT-5.4 (xhigh) reaches 56.65 under a search-aware prompt. To study whether external information access closes this gap, we use SearchSWE as a controlled diagnostic baseline for search-augmented coding. Search access improves most models and substantially helps some tasks, but the gains remain limited and uneven, showing that current agents still struggle to convert retrieved information into precise, version-compatible, and locally actionable code changes. These results suggest that deep search for coding remains an open problem: progress requires agents that can reliably combine external evidence with repository-local reasoning and execution-based verification.
Feb 28, 2026

SWE-Hub: A Unified Production System for Scalable, Executable Software Engineering Tasks

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.
Feb 27, 2026

SWE-rebench V2: Language-Agnostic SWE Task Collection at Scale

Software engineering agents (SWE) are improving rapidly, with recent gains largely driven by reinforcement learning (RL). However, RL training is constrained by the scarcity of large-scale task collections with reproducible execution environments and reliable test suites. Although a growing number of benchmarks have emerged, datasets suitable for training remain limited in scale and diversity or often target a limited set of high-resource language ecosystems. We introduce SWE-rebench V2, a language-agnostic automated pipeline for harvesting executable real-world SWE tasks and constructing RL training environments at scale. The pipeline synthesizes repository-specific installation and test procedures via an interactive setup agent, and filters unsound instances using an ensemble of LLM judges, validated against human-verified SWE-bench annotations. Using this pipeline, we construct a dataset of 32,079 tasks spanning 20 languages and 3,617 repositories, with pre-built images for reproducible execution. To further scale training data, we additionally release 120,000+ tasks with installation instructions, fail-to-pass tests and rich metadata, where the problem statement is generated based on the original pull request description. We validate the collected instances through a diagnostic study that covers a subset of tasks in five programming languages across seven popular models, and provide instance-level metadata that flags common confounders such as overly restrictive tests and underspecified descriptions. We release the datasets, the collection and execution code, and associated artifacts to enable large-scale training of SWE agents across diverse languages and repositories.