Daily Papers

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.

The open-source software (OSS) ecosystem suffers from security threats caused by malware.However, OSS malware research has three limitations: a lack of high-quality datasets, a lack of malware diversity, and a lack of attack campaign contexts. In this paper, we first build the largest dataset of 24,356 malicious packages from online sources, then propose a knowledge graph to represent the OSS malware corpus and conduct malware analysis in the wild.Our main findings include (1) it is essential to collect malicious packages from various online sources because their data overlapping degrees are small;(2) despite the sheer volume of malicious packages, many reuse similar code, leading to a low diversity of malware;(3) only 28 malicious packages were repeatedly hidden via dependency libraries of 1,354 malicious packages, and dependency-hidden malware has a shorter active time;(4) security reports are the only reliable source for disclosing the malware-based context. Index Terms: Malicious Packages, Software Analysis

In this study, we aim to offer linguistically motivated solutions to resolve the issues of the lack of representation of null morphemes, highly productive derivational processes, and syncretic morphemes of Turkish in the BOUN Treebank without diverging from the Universal Dependencies framework. In order to tackle these issues, new annotation conventions were introduced by splitting certain lemmas and employing the MISC (miscellaneous) tab in the UD framework to denote derivation. Representational capabilities of the re-annotated treebank were tested on a LSTM-based dependency parser and an updated version of the BoAT Tool is introduced.

The development of generative language models that can create long and coherent textual outputs via autoregression has lead to a proliferation of uses and a corresponding sweep of analyses as researches work to determine the limitations of this new paradigm. Unlike humans, these 'Large Language Models' (LLMs) are highly sensitive to small changes in their inputs, leading to unwanted inconsistency in their behavior. One problematic inconsistency when LLMs are used to answer multiple-choice questions or analyze multiple inputs is order dependency: the output of an LLM can (and often does) change significantly when sub-sequences are swapped, despite both orderings being semantically identical. In this paper we present , a technique that guarantees the output of an LLM will not have order dependence on a specified set of sub-sequences. We show that this method provably eliminates order dependency, and that it can be applied to any transformer-based LLM to enable text generation that is unaffected by re-orderings. Delving into the implications of our method, we show that, despite our inputs being out of distribution, the impact on expected accuracy is small, where the expectation is over the order of uniformly chosen shuffling of the candidate responses, and usually significantly less in practice. Thus, can be used as a 'dropped-in' method on fully trained models. Finally, we discuss how our method's success suggests that other strong guarantees can be obtained on LLM performance via modifying the input representations.

In this research paper, I will elaborate on a method to evaluate machine translation models based on their performance on underlying syntactical phenomena between English and Arabic languages. This method is especially important as such "neural" and "machine learning" are hard to fine-tune and change. Thus, finding a way to evaluate them easily and diversely would greatly help the task of bettering them.

Deep research tasks require agents to navigate large knowledge spaces, synthesize evidence across many sources, and adapt their plans as findings emerge. Directed acyclic graph (DAG)-based multi-agent systems suit this setting because they support parallel execution and isolate each sub-task within a focused dependency context. Yet existing DAG-based agents instantiate a task-level plan before execution and repair the graph only after failures or missing evidence are observed. This Plan-then-Patch strategy is brittle for deep research: the system commits most strongly when its evidence is weakest, and later revisions waste computation on branches that should not have been planned. We propose DAGent, a DAG-based multi-agent framework with Evaluate-then-Grow incremental planning: an Orchestrator grows the task graph one batch at a time, conditioning each expansion on confidence and uncertainty signals from completed nodes. A hierarchical context layer propagates compact QueryDocs by default while preserving full execution traces for on-demand recall. The recorded DAG topology admits structural RL signals that outcome-only recipes cannot define; DAGRPO, a GRPO adaptation, injects topology-conditioned credit on Executor rollouts and a structural compliance regularization on Orchestrator plans. Across BrowseComp-Plus, GAIA, and xbench-DeepSearch, DAGent surpasses the strongest open-source baseline by 5.3 / 5.8 / 2.0 points at the Qwen3-235B-A22B scale, and the lead replicates across four open-source backbones and extends to GPT-5 at 327K context. At the Qwen3-8B scale, DAGRPO improves over a same-budget outcome-only GRPO baseline by 3.0 average Pass@1 points. A same-architecture comparison shows that evidence-conditioned planning reaches higher accuracy at lower per-task token, tool-call, and step footprints than its Plan-then-Patch counterpart. Code: https://github.com/hanwenliu6825/DAGent

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.

Social media data such as Twitter messages ("tweets") pose a particular challenge to NLP systems because of their short, noisy, and colloquial nature. Tasks such as Named Entity Recognition (NER) and syntactic parsing require highly domain-matched training data for good performance. To date, there is no complete training corpus for both NER and syntactic analysis (e.g., part of speech tagging, dependency parsing) of tweets. While there are some publicly available annotated NLP datasets of tweets, they are only designed for individual tasks. In this study, we aim to create Tweebank-NER, an English NER corpus based on Tweebank V2 (TB2), train state-of-the-art (SOTA) Tweet NLP models on TB2, and release an NLP pipeline called Twitter-Stanza. We annotate named entities in TB2 using Amazon Mechanical Turk and measure the quality of our annotations. We train the Stanza pipeline on TB2 and compare with alternative NLP frameworks (e.g., FLAIR, spaCy) and transformer-based models. The Stanza tokenizer and lemmatizer achieve SOTA performance on TB2, while the Stanza NER tagger, part-of-speech (POS) tagger, and dependency parser achieve competitive performance against non-transformer models. The transformer-based models establish a strong baseline in Tweebank-NER and achieve the new SOTA performance in POS tagging and dependency parsing on TB2. We release the dataset and make both the Stanza pipeline and BERTweet-based models available "off-the-shelf" for use in future Tweet NLP research. Our source code, data, and pre-trained models are available at: https://github.com/social-machines/TweebankNLP.

Reinforcement learning (RL) has become a key paradigm for training software engineering (SWE) agents, but existing pipelines typically rely on per-task containers for isolation. At scale, pre-built container images incur substantial storage overhead, slow environment setup, and require container-management privileges. We propose SWE-MiniSandbox, a lightweight, container-free method that enables scalable RL training of SWE agents without sacrificing isolation. Instead of relying on per-instance containers, SWE-MiniSandbox executes each task in an isolated workspace backed by kernel-level mechanisms, substantially reducing system overhead. It leverages lightweight environment pre-caching techniques to eliminate the need for bulky container images. As a result, our approach lowers disk usage to approximately 5\% of that required by container-based pipelines and reduces environment preparation time to about 25\% of the container baseline. Empirical results demonstrate that SWE-MiniSandbox achieves evaluation performance comparable to standard container-based pipelines. By removing the dependency on heavy container infrastructure, SWE-MiniSandbox offers a practical and accessible foundation for scaling RL-based SWE agents, particularly in resource-constrained research environments.

Autonomous agents powered by large language models (LLMs) have the potential to significantly enhance human productivity by reasoning, using tools, and executing complex tasks in diverse environments. However, current approaches to developing such agents remain costly and inefficient, as they typically require manually constructed task datasets and reinforcement learning (RL) pipelines with extensive random exploration. These limitations lead to prohibitively high data-construction costs, low exploration efficiency, and poor sample utilization. To address these challenges, we present AgentEvolver, a self-evolving agent system that leverages the semantic understanding and reasoning capabilities of LLMs to drive autonomous agent learning. AgentEvolver introduces three synergistic mechanisms: (i) self-questioning, which enables curiosity-driven task generation in novel environments, reducing dependence on handcrafted datasets; (ii) self-navigating, which improves exploration efficiency through experience reuse and hybrid policy guidance; and (iii) self-attributing, which enhances sample efficiency by assigning differentiated rewards to trajectory states and actions based on their contribution. By integrating these mechanisms into a unified framework, AgentEvolver enables scalable, cost-effective, and continual improvement of agent capabilities. Preliminary experiments indicate that AgentEvolver achieves more efficient exploration, better sample utilization, and faster adaptation compared to traditional RL-based baselines.

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.

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.

Deep Neural Networks (DNNs) are being adopted as components in software systems. Creating and specializing DNNs from scratch has grown increasingly difficult as state-of-the-art architectures grow more complex. Following the path of traditional software engineering, machine learning engineers have begun to reuse large-scale pre-trained models (PTMs) and fine-tune these models for downstream tasks. Prior works have studied reuse practices for traditional software packages to guide software engineers towards better package maintenance and dependency management. We lack a similar foundation of knowledge to guide behaviors in pre-trained model ecosystems. In this work, we present the first empirical investigation of PTM reuse. We interviewed 12 practitioners from the most popular PTM ecosystem, Hugging Face, to learn the practices and challenges of PTM reuse. From this data, we model the decision-making process for PTM reuse. Based on the identified practices, we describe useful attributes for model reuse, including provenance, reproducibility, and portability. Three challenges for PTM reuse are missing attributes, discrepancies between claimed and actual performance, and model risks. We substantiate these identified challenges with systematic measurements in the Hugging Face ecosystem. Our work informs future directions on optimizing deep learning ecosystems by automated measuring useful attributes and potential attacks, and envision future research on infrastructure and standardization for model registries.

Large language models (LLMs) are increasingly used to complete complex tasks by selecting and coordinating external tools across multiple steps. This requires aligning tool choices with subtask intent while satisfying directional execution dependencies among tools. To do this, existing methods model these dependencies as tool graphs and incorporate the graphs with LLMs through retrieval, serialization, or prompt-level injection. However, these external graph-use strategies all follow a matching paradigm, which often fails to align tool choices with the underlying subtask structure, producing semantically plausible plans that violate graph constraints. This issue is further exacerbated by error accumulation, where an early incorrect tool selection shifts the plan into an invalid graph state and causes subsequent predictions to drift away from the valid execution path. To address these challenges, we propose GRAFT, a graph-tokenized language model framework for dependency-aware tool planning. GRAFT internalizes the tool graph by mapping each tool node to a dedicated special token and learning directed tool dependencies within the representation space. It further introduces on-policy tool context distillation, training the model on its own sampled trajectories while distilling stepwise planning signals. Experiments show that GRAFT achieves state-of-the-art performance in exact sequence matching and dependency legality, supporting more reliable LLM tool planning in complex workflows.

LLMs have demonstrated significant potential in code generation tasks, achieving promising results at the function or statement level across various benchmarks. However, the complexities associated with creating code artifacts like classes, particularly within the context of real-world software repositories, remain underexplored. Prior research treats class-level generation as an isolated task, neglecting the intricate dependencies & interactions that characterize real-world software environments. To address this gap, we introduce RepoClassBench, a comprehensive benchmark designed to rigorously evaluate LLMs in generating complex, class-level code within real-world repositories. RepoClassBench includes "Natural Language to Class generation" tasks across Java, Python & C# from a selection of repositories. We ensure that each class in our dataset not only has cross-file dependencies within the repository but also includes corresponding test cases to verify its functionality. We find that current models struggle with the realistic challenges posed by our benchmark, primarily due to their limited exposure to relevant repository contexts. To address this shortcoming, we introduce Retrieve-Repotools-Reflect (RRR), a novel approach that equips LLMs with static analysis tools to iteratively navigate & reason about repository-level context in an agent-based framework. Our experiments demonstrate that RRR significantly outperforms existing baselines on RepoClassBench, showcasing its effectiveness across programming languages & under various settings. Our findings emphasize the critical need for code-generation benchmarks to incorporate repo-level dependencies to more accurately reflect the complexities of software development. Our work shows the benefits of leveraging specialized tools to enhance LLMs' understanding of repository context. We plan to make our dataset & evaluation harness public.

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

Code generation models based on the pre-training and fine-tuning paradigm have been increasingly attempted by both academia and industry, resulting in well-known industrial models such as Codex, CodeGen, and PanGu-Coder. To evaluate the effectiveness of these models, multiple existing benchmarks are proposed, including only cases of generating a standalone function, i.e., a function that may invoke or access only built-in functions and standard libraries. However, non-standalone functions, which typically are not included in the existing benchmarks, constitute more than 70% of the functions in popular open-source projects, and evaluating models' effectiveness on standalone functions cannot reflect these models' effectiveness on pragmatic code generation scenarios. To help bridge the preceding gap, in this paper, we propose a benchmark named CoderEval, consisting of 230 Python and 230 Java code generation tasks carefully curated from popular real-world open-source projects and a self-contained execution platform to automatically assess the functional correctness of generated code. CoderEval supports code generation tasks from six levels of context dependency, where context refers to code elements such as types, APIs, variables, and consts defined outside the function under generation but within the dependent third-party libraries, current class, file, or project. CoderEval can be used to evaluate the effectiveness of models in generating code beyond only standalone functions. By evaluating three code generation models on CoderEval, we find that the effectiveness of these models in generating standalone functions is substantially higher than that in generating non-standalone functions. Our analysis highlights the current progress and pinpoints future directions to further improve a model's effectiveness by leveraging contextual information for pragmatic code generation.

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.

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.

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.

Independently authored skills can impose incompatible requirements, competing preferences, and redundant instructions when jointly loaded by an LLM agent. We propose SkillFusion, an offline compiler that reconciles these interactions into a reusable merged skill. Its central idea is to make composition decisions explicit through typed, scoped constraints linked to their source directives. A type-scope gate selects candidate interactions, while selective fallback revisits pairs potentially missed by structural pruning. A classifier identifies interaction types, and an adversarial verifier re-examines uncertain judgments. The resolver applies conditional routing or explicit priorities to hard conflicts, verified abstraction to soft conflicts, and deduplication to redundant instructions. Source-linked checks guide synthesis and compression, and metadata synthesis supports discovery of the merged skill. The resulting artifact retains associated scripts and resources and can be reused across tasks and executor models. SkillFusion achieves the highest mean Success among evaluated non-oracle methods on all three agent benchmarks and on both transfer benchmarks across three executor models. At the largest tested instruction configurations, it achieves over 2.5 times the Success of unresolved multi-skill loading, highlighting the growing value of reconciliation as composition becomes more demanding. The code will be open-sourced after the review process concludes.

Large software projects often depend on older versions of libraries, even as APIs continue to evolve across releases. This creates a challenge for LLMs: they must maintain knowledge of multiple API versions, not merely the latest or most common one. However, current LLMs are trained on temporally mixed corpora and lack explicit mechanisms for such version-specific reasoning, leading to anachronistic errors - calling APIs as they exist in a different library version. To systematically evaluate this phenomenon, we introduce LibEvoBench, a multi-task benchmark spanning multiple versions of widely used Python libraries, along with a new metric, the Software Evolution Understanding Score (SEUS), to measure models' consistency when working with evolving APIs. Our results show that state-of-the-art models are largely version-oblivious: performance degrades for evolving APIs, while for stable APIs it remains the same across versions. Moreover, simply specifying the target version provides no benefit, while relevant documentation significantly boosts models' accuracy. These findings highlight a systematic limitation of current training paradigms and motivate new approaches for temporally grounded knowledge in code generation.

Repository-level coding benchmarks have become the standard for evaluating coding agents, yet they inherently suffer from data leakage because they are built upon popular open-source repositories repeatedly used for training. Consequently, strong performance may reflect memorization of canonical repository cues rather than robust repository reasoning. We propose SchrodingerRepo (Schrödinger's Repository), an evaluation framework for testing coding agents under dynamically instantiated repository representations. Instead of repeatedly using a static representation of the test repository, SchrodingerRepo treats the test repository as an evaluation-time latent variable that is dynamically instantiated only when the agent enters the evaluation environment. The instantiated repository preserves the original executable behavior while eroding familiar cues such as naming conventions, file layouts, and implementation patterns through four transformation levels: problem statement reconstruction, namespace remapping, intra-file layout reordering, and functionality-preserving code rewriting. We evaluate popular LLMs on SWE-bench Verified and SWE-QA. Results show that removing familiar repository cues consistently degrades agent performance and substantially increases interaction costs across models. Further analysis reveals that the additional cost is primarily caused by increased difficulty in repository exploration and localization. These findings suggest that current coding agents may partially rely on memorized repository-side cues, highlighting the need for evaluation under dynamically instantiated repository representations.

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

Large Language Models (LLMs) can interact with the real world by connecting with versatile external APIs, resulting in better problem-solving and task automation capabilities. Previous research primarily focuses on APIs with limited arguments from a single source or overlooks the complex dependency relationship between different APIs. However, it is essential to utilize multiple APIs collaboratively from various sources (e.g., different Apps in the iPhone), especially for complex user instructions. In this paper, we introduce AppBench, the first benchmark to evaluate LLMs' ability to plan and execute multiple APIs from various sources in order to complete the user's task. Specifically, we consider two significant challenges in multiple APIs: 1) graph structures: some APIs can be executed independently while others need to be executed one by one, resulting in graph-like execution order; and 2) permission constraints: which source is authorized to execute the API call. We have experimental results on 9 distinct LLMs; e.g., GPT-4o achieves only a 2.0\% success rate at the most complex instruction, revealing that the existing state-of-the-art LLMs still cannot perform well in this situation even with the help of in-context learning and finetuning. Our code and data are publicly available at https://github.com/ruleGreen/AppBench.

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.

While large language models (LLMs) are increasingly being used for program synthesis, they lack the global view needed to develop useful abstractions; they generally predict programs one at a time, often repeating the same functionality. Generating redundant code from scratch is both inefficient and error-prone. To address this, we propose Refactoring for Generalizable Abstraction Learning (ReGAL), a gradient-free method for learning a library of reusable functions via code refactorization, i.e. restructuring code without changing its execution output. ReGAL learns from a small set of existing programs, iteratively verifying and refining its abstractions via execution. We find that the shared function libraries discovered by ReGAL make programs easier to predict across diverse domains. On three datasets (LOGO graphics generation, Date reasoning, and TextCraft, a Minecraft-based text game), both open-source and proprietary LLMs improve in accuracy when predicting programs with ReGAL functions. For CodeLlama-13B, ReGAL results in absolute accuracy increases of 11.5% on graphics, 26.1% on date understanding, and 8.1% on TextCraft, outperforming GPT-3.5 in two of three domains. Our analysis reveals ReGAL's abstractions encapsulate frequently-used subroutines as well as environment dynamics.

Looped language models have shown promising results on reasoning benchmarks, yet their potential for agentic tool use remains largely unexplored. We study this question in compositional tool-calling settings, where models must coordinate multiple API calls, maintain intermediate state, and preserve dependencies across tool interactions. We evaluate native and retrofitted looped language models on API-Bank, BFCL, and NESTful, comparing looped and non-looped models trained under matched supervised fine-tuning recipes and varying recurrent depth at inference time. In controlled experiments, recurrent computation generally benefits compositional and dependency-aware tool use, while providing smaller and more model-dependent gains on isolated API invocation. Accuracy on multi-step tool use generally increases with recurrent depth; adaptive inference, however, achieves a more favorable compute-performance trade-off by allocating additional computation only when needed. Our results suggest that looped language models are a promising architecture for agentic systems that require reliable planning, coordination, and execution of compositional tool use workflows.

The availability of vast amounts of publicly accessible data of source code and the advances in modern language models, coupled with increasing computational resources, have led to a remarkable surge in the development of large language models for code (LLM4Code, for short). The interaction between code datasets and models gives rise to a complex ecosystem characterized by intricate dependencies that are worth studying. This paper introduces a pioneering analysis of the code model ecosystem. Utilizing Hugging Face -- the premier hub for transformer-based models -- as our primary source, we curate a list of datasets and models that are manually confirmed to be relevant to software engineering. By analyzing the ecosystem, we first identify the popular and influential datasets, models, and contributors. The popularity is quantified by various metrics, including the number of downloads, the number of likes, the number of reuses, etc. The ecosystem follows a power-law distribution, indicating that users prefer widely recognized models and datasets. Then, we manually categorize how models in the ecosystem are reused into nine categories, analyzing prevalent model reuse practices. The top 3 most popular reuse types are fine-tuning, architecture sharing, and quantization. We also explore the practices surrounding the publication of LLM4Code, specifically focusing on documentation practice and license selection. We find that the documentation in the ecosystem contains less information than that in general artificial intelligence (AI)-related repositories hosted on GitHub. Additionally, the license usage is also different from other software repositories. Models in the ecosystem adopt some AI-specific licenses, e.g., RAIL (Responsible AI Licenses) and AI model license agreement.

With the availability of various instruction datasets, a pivotal challenge is how to effectively select and integrate these instructions to fine-tune large language models (LLMs). Previous research mainly focuses on selecting individual high-quality instructions. However, these works overlooked the joint interactions and dependencies between different categories of instructions, leading to suboptimal selection strategies. Moreover, the nature of these interaction patterns remains largely unexplored, let alone optimize the instruction set with regard to them. To fill these gaps, in this paper, we: (1) systemically investigate interaction and dependency patterns between different categories of instructions, (2) manage to optimize the instruction set concerning the interaction patterns using a linear programming-based method, and optimize the learning schema of SFT using an instruction dependency taxonomy guided curriculum learning. Experimental results across different LLMs demonstrate improved performance over strong baselines on widely adopted benchmarks.

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.

Large language models excel at function- and file-level code generation, yet generating complete repositories from scratch remains a fundamental challenge. This process demands coherent and reliable planning across proposal- and implementation-level stages, while natural language, due to its ambiguity and verbosity, is ill-suited for faithfully representing complex software structures. To address this, we introduce the Repository Planning Graph (RPG), a persistent representation that unifies proposal- and implementation-level planning by encoding capabilities, file structures, data flows, and functions in one graph. RPG replaces ambiguous natural language with an explicit blueprint, enabling long-horizon planning and scalable repository generation. Building on RPG, we develop ZeroRepo, a graph-driven framework for repository generation from scratch. It operates in three stages: proposal-level planning and implementation-level refinement to construct the graph, followed by graph-guided code generation with test validation. To evaluate this setting, we construct RepoCraft, a benchmark of six real-world projects with 1,052 tasks. On RepoCraft, ZeroRepo produces repositories averaging nearly 36K LOC, roughly 3.9times the strongest baseline (Claude Code) and about 64times other baselines. It attains 81.5% functional coverage and a 69.7% pass rate, exceeding Claude Code by 27.3 and 35.8 percentage points, respectively. Further analysis shows that RPG models complex dependencies, enables progressively more sophisticated planning through near-linear scaling, and enhances LLM understanding of repositories, thereby accelerating agent localization.

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

Non-prefix KV cache reuse is a promising approach for improving inference efficiency in multi-agent systems as agents share the same context blocks. However, when agents have conflicting tasks, directly reusing non-prefix KV caches across agents can severely degrade model performance, causing up to a 90% drop. Existing remedies, including selective recomputation and offset-based calibration, recover a limited fraction of this loss. We argue that the problem lies not only in contaminated KV representations but also in the agent's difficulty interpreting reused context under its own instructions. To this end, we introduce LatentRemedy, which uses a few task-conditioned latent tokens to help the target agent leverage reused context without recomputing the shared block. Specifically, we use an MLP to map the last hidden state of the target prefix into a small number of latent tokens, which are placed after the reused KV block to interact with the shared context. To guide subsequent predictions toward the target task, we train the MLP through full-prefill distillation. Experiments show that LatentRemedy consistently outperforms existing reuse baselines on conflicting tasks while maintaining TTFT close to direct reuse as cache size grows. Code and data are available at https://github.com/chenzhwsysu57/kvreuse.

Recent code large language models (LLMs) have shown promising performance in generating standalone functions but face limitations in repository-level code generation due to their lack of awareness of repository-level dependencies (e.g., user-defined attributes), resulting in dependency errors such as undefined-variable and no-member errors. In this work, we introduce ToolGen, an approach that integrates autocompletion tools into the code LLM generation process to address these dependencies. ToolGen comprises two main phases: Trigger Insertion and Model Fine-tuning (Offline), and Tool-integrated Code Generation (Online). During the offline phase, ToolGen augments functions within a given code corpus with a special mark token, indicating positions to trigger autocompletion tools. These augmented functions, along with their corresponding docstrings, are then used to fine-tune a selected code LLM. In the online phase, ToolGen iteratively generates functions by predicting tokens step-by-step using the fine-tuned LLM. Whenever a mark token is encountered, ToolGen invokes the autocompletion tool to suggest code completions and selects the most appropriate one. We conduct comprehensive experiments to evaluate ToolGen's effectiveness in repository-level code generation. To facilitate this evaluation, we create a benchmark comprising 680 real-world code repositories and introduce two new repository-level metrics: Dependency Coverage and Static Validity Rate. The results demonstrate that ToolGen significantly improves Dependency Coverage by 15.2% to 45.8% and Static Validity Rate by 10.9% to 42.2% across three distinct code LLMs, while maintaining competitive performance in widely-recognized similarity metrics. Furthermore, our generalizability evaluation confirms ToolGen's consistent performance when applied to diverse code LLMs, including various model architectures and scales.

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

Continual Learning is an important and challenging problem in machine learning, where models must adapt to a continuous stream of new data without forgetting previously acquired knowledge. While existing frameworks are built on PyTorch, the rising popularity of JAX might lead to divergent codebases, ultimately hindering reproducibility and progress. To address this problem, we introduce SequeL, a flexible and extensible library for Continual Learning that supports both PyTorch and JAX frameworks. SequeL provides a unified interface for a wide range of Continual Learning algorithms, including regularization-based approaches, replay-based approaches, and hybrid approaches. The library is designed towards modularity and simplicity, making the API suitable for both researchers and practitioners. We release SequeL\url{https://github.com/nik-dim/sequel} as an open-source library, enabling researchers and developers to easily experiment and extend the library for their own purposes.

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

Large language models (LLMs) equipped with terminal access have demonstrated strong capabilities in automating software engineering tasks. However, existing agents remain brittle on long-horizon workflows, where they must repeatedly reconstruct program state scattered across source files, configurations, tests, dependencies, and runtime behavior, leading to increasingly long interaction histories, context explosion, and semantic drift. Large repositories further complicate the identification of task-relevant components. To address these challenges, we introduce Dev-Primitives (Development Primitives), a modular and executable abstraction that transforms repository components from passive software artifacts into active participants in software engineering. Each Dev-Primitive pairs a repository artifact with a resident LLM, which gives the artifact an agent-native interface grounded in its own implementation and dependencies, enabling natural-language reasoning, inter-component communication, and localized self-modification. Building on Dev-Primitives, we propose HERMES, a Harness Engineering framework for software engineeRing via Modular Executable Dev-PrimitiveS, which instantiates these primitives at repository scale through a dependency-aware dynamic activation mechanism and a bug diagnosis mechanism that maps execution evidence back to the components that must be revised. Extensive experiments on four software engineering benchmarks demonstrate that HERMES outperforms matched baseline harnesses by 12.4\% on average. Moreover, when paired with strong activation and diagnosis models, HERMES, even with Qwen3-8B Dev-Primitives, remains within 4.5\% of the homogeneous GPT-5.6 Sol configuration across all four benchmarks, while reducing inference cost by 26.2\% on Terminal-Bench 4.0, highlighting the importance of harness design in software engineering agents.

We propose a new shared task for tactical data-to-text generation in the domain of source code libraries. Specifically, we focus on text generation of function descriptions from example software projects. Data is drawn from existing resources used for studying the related problem of semantic parser induction (Richardson and Kuhn, 2017b; Richardson and Kuhn, 2017a), and spans a wide variety of both natural languages and programming languages. In this paper, we describe these existing resources, which will serve as training and development data for the task, and discuss plans for building new independent test sets.

Large Language Models (LLMs) often help users generate artifacts through iterative cycles of generation and revision in conversation. A challenge here is that, when users specify only a local change during revision, LLMs must instead identify the relevant dependencies and propagate the revision to all affected parts of the artifact. This paper studies this ability of LLMs on conversationally generated artifacts, where the artifact context and its dependencies may be embedded in the conversation history. Toward practical use, we also explore cost-effective test-time compute for this new setting. Specifically, we introduce a new benchmark for this setting, and evaluate nine revision methods, including sequential reflection and parallel sampling variants, using gpt-oss-20b/120b, gpt-5.4-mini, and qwen3.5-9b/27b/122b on the benchmark. The results show that baselines achieve accuracies of 68.3--93%, and the most cost-effective method is selecting from three parallel samples using either LLM-based or medoid selection, which improves accuracy by 2.2--9.7%. Our code and dataset are available at https://github.com/ntt-dkiku/llm-revision-propagation.

Large language models are increasingly used as programming agents for repository level software engineering tasks. While recent benchmarks evaluate correctness in realistic codebases, they largely treat tasks as independent and do not assess whether agents can reuse experience across related problems. As a result, the ability of agents to accumulate, retrieve, and apply prior experience, as well as the efficiency gains from such reuse, remains difficult to measure. We introduce SWE-ContextBench, a benchmark designed to explicitly evaluate experience reuse in programming agents. Built on SWE-Bench Lite, SWE-ContextBench augments 300 base tasks with 99 related tasks derived from real dependency and reference relationships among GitHub issues and pull requests, forming task sequences with shared context. The benchmark evaluates agents along three complementary dimensions: prediction accuracy, time efficiency, and cost efficiency. Using SWE-ContextBench, we study multiple experience reuse settings, including oracle guided and autonomous retrieval, as well as full execution trajectories and compact summaries. Our results show that correctly selected summarized experience improves resolution accuracy and substantially reduces runtime and token cost, particularly on harder tasks. In contrast, unfiltered or incorrectly selected experience provides limited or negative benefits. These findings highlight the importance of experience representation and retrieval quality, and position SWE-ContextBench as a principled benchmark for studying experience reuse in programming agents.

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

JEV models make multimodal decisions by directly scoring candidates. Although the common context is encoded once, candidate evaluation can still repeat matching token histories, duplicate inference states, and execute the full backbone. In this paper, we study these sources of redundancy and present FastJEV for compact candidate evaluation. We jointly organize history reuse and state storage, since sharing computation requires preserving states for later branches. We first introduce shared context anchoring to reuse recurrent initial states and omit unused final recurrent caches. We extend this reuse through candidate prefix sharing, retaining the intermediate states needed by subsequent branches. To further reduce the depth of these paths, we apply decision guided pruning based on relative score changes measured on a small unlabeled set. Our method retains full context encoding and all candidates without additional training. We evaluate FastJEV across three OmniJev model sizes on five public benchmarks and reconstructed LIBERO-10 offline questions. At the selected pruning budgets, the complete method reduces candidate depth by 43.75% to 45.83%, while retaining 93.66% to 97.52% of the original task scores on average across the six evaluation sets. Through controlled experiments, we show how candidate overlap and branching structure affect the execution cost of history reuse. In our implementation, candidate prefix sharing can reduce repeated computation while increasing latency. These findings motivate designing sharing granularity and execution schedules together for efficient JEV inference.

Large language models rely on KV caching to reduce repeated prefill computation in long context and interactive applications. As lightweight adapters evolve, cached states reflect earlier versions, so stale reuse distorts current model outputs, while complete affected suffix recomputation restores fidelity at substantial cost. We seek minimal recomputation that recovers current adapter behavior. Existing systems track token, context, or stable adapter identity, but neither represent caches from earlier adapter versions nor distinguish update propagation from the recomputation required for behavioral recovery. To address these gaps, we introduce CacheReforge, which represents stale KV caches as layerwise mixed-version objects. It combines per-layer adapter anchors, calibrated sensitivity, accumulated drift, and executable restart boundaries to select direct reuse, bounded recomputation, or complete affected-suffix recovery. We distinguish dependency depth from the functional recomputation horizon and use cumulative tail influence to characterize when bounded recovery preserves current-model behavior. We evaluate CacheReforge on Qwen2.5-1.5B and Qwen2.5-7B with continual LoRA updates, including 16K HotpotQA and 2WikiMQA workloads. CacheReforge reduces mean KL divergence by 92.4% relative to stale reuse, while recomputing only 5.44% of layers and reducing cache-maintenance time by 93.2% relative to fresh full prefill. These results show that version-aware recovery preserves model fidelity and most KV caching gains.

Large Language Models (LLMs) exhibit remarkable code generation capabilities but falter when adapting to frequent updates in external library APIs. This critical limitation, stemming from reliance on outdated API knowledge from their training data, even with access to current documentation, impedes reliable code generation in dynamic environments. To tackle this issue, we propose ReCode (rule-based Reinforcement learning for Code Update), a novel framework that mimics human programmer adaptation to API changes. Specifically, we construct a dataset of approximately 2,000 data entries to train the LLMs to perform version migration based on updated information. Then, we introduce a modified string similarity metric for code evaluation as the reward for reinforcement learning. Our experiments demonstrate that ReCode substantially boosts LLMs' code generation performance in dynamic API scenarios, especially on the unseen CodeUpdateArena task. Crucially, compared to supervised fine-tuning, ReCode has less impact on LLMs' general code generation abilities. We apply ReCode on various LLMs and reinforcement learning algorithms (GRPO and DAPO), all achieving consistent improvements. Notably, after training, Qwen2.5-Coder-7B outperforms that of the 32B parameter code instruction-tuned model and the reasoning model with the same architecture. Code is available at https://github.com/zjunlp/ReCode.

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.

Recovering accurate architecture from large-scale legacy software is hindered by architectural drift, missing relations, and the limited context of Large Language Models (LLMs). We present ArchAgent, a scalable agent-based framework that combines static analysis, adaptive code segmentation, and LLM-powered synthesis to reconstruct multiview, business-aligned architectures from cross-repository codebases. ArchAgent introduces scalable diagram generation with contextual pruning and integrates cross-repository data to identify business-critical modules. Evaluations of typical large-scale GitHub projects show significant improvements over existing benchmarks. An ablation study confirms that dependency context improves the accuracy of generated architectures of production-level repositories, and a real-world case study demonstrates effective recovery of critical business logics from legacy projects. The dataset is available at https://github.com/panrusheng/arch-eval-benchmark.

The Chain-of-Thought (CoT) paradigm has become a pivotal method for solving complex problems with large language models (LLMs). However, its application to domain-specific tasks remains challenging, as LLMs often fail to decompose tasks accurately or execute subtasks effectively. This paper introduces the Re-TASK framework, a novel theoretical model that revisits LLM tasks from capability, skill, and knowledge perspectives, drawing on the principles of Bloom's Taxonomy and Knowledge Space Theory. While CoT provides a workflow-centric perspective on tasks, Re-TASK introduces a Chain-of-Learning (CoL) paradigm that highlights task dependencies on specific capability items, further broken down into their constituent knowledge and skill components. To address CoT failures, we propose a Re-TASK prompting strategy, which strengthens task-relevant capabilities through targeted knowledge injection and skill adaptation. Experiments across diverse domains demonstrate the effectiveness of Re-TASK. In particular, we achieve improvements of 45.00% on Yi-1.5-9B and 24.50% on Llama3-Chinese-8B for legal tasks. These results highlight the potential of Re-TASK to significantly enhance LLM performance and its applicability in specialized domains. We release our code and data at https://github.com/Uylee/Re-TASK.

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.

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.

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

The harness surrounding a language model is a central determinant of agent performance. Recent methods optimize harnesses by searching over complete programs, where individual mechanisms are difficult to isolate and reuse. We introduce PluginRSI, which represents a harness as a composition of atomized plugins and organizes harness evolution around these plugins. Individual plugins are improved independently and accumulated in a shared library, then recombined into new harnesses at each iteration. PluginRSI improves over existing harness optimization methods across software engineering, command-line interaction, and question-answering tasks. The resulting harnesses retain their advantage when transferred to other solver models without further optimization. The evolved plugin library accelerates subsequent optimization from the initial harness, which helps faster and higher convergence on unseen tasks. These results show that accumulating reusable mechanisms provides an effective basis for continued harness improvement.

Large Language Models (LLMs) have already become quite proficient at solving simpler programming tasks like those in HumanEval or MBPP benchmarks. However, solving more complex and competitive programming tasks is still quite challenging for these models - possibly due to their tendency to generate solutions as monolithic code blocks instead of decomposing them into logical sub-tasks and sub-modules. On the other hand, experienced programmers instinctively write modularized code with abstraction for solving complex tasks, often reusing previously developed modules. To address this gap, we propose CodeChain, a novel framework for inference that elicits modularized code generation through a chain of self-revisions, each being guided by some representative sub-modules generated in previous iterations. Concretely, CodeChain first instructs the LLM to generate modularized codes through chain-of-thought prompting. Then it applies a chain of self-revisions by iterating the two steps: 1) extracting and clustering the generated sub-modules and selecting the cluster representatives as the more generic and re-usable implementations, and 2) augmenting the original chain-of-thought prompt with these selected module-implementations and instructing the LLM to re-generate new modularized solutions. We find that by naturally encouraging the LLM to reuse the previously developed and verified sub-modules, CodeChain can significantly boost both modularity as well as correctness of the generated solutions, achieving relative pass@1 improvements of 35% on APPS and 76% on CodeContests. It is shown to be effective on both OpenAI LLMs as well as open-sourced LLMs like WizardCoder. We also conduct comprehensive ablation studies with different methods of prompting, number of clusters, model sizes, program qualities, etc., to provide useful insights that underpin CodeChain's success.

Language models of code (LMs) work well when the surrounding code in the vicinity of generation provides sufficient context. This is not true when it becomes necessary to use types or functionality defined in another module or library, especially those not seen during training. LMs suffer from limited awareness of such global context and end up hallucinating, e.g., using types defined in other files incorrectly. Recent work tries to overcome this issue by retrieving global information to augment the local context. However, this bloats the prompt or requires architecture modifications and additional training. Integrated development environments (IDEs) assist developers by bringing the global context at their fingertips using static analysis. We extend this assistance, enjoyed by developers, to the LMs. We propose a notion of monitors that use static analysis in the background to guide the decoding. Unlike a priori retrieval, static analysis is invoked iteratively during the entire decoding process, providing the most relevant suggestions on demand. We demonstrate the usefulness of our proposal by monitoring for type-consistent use of identifiers whenever an LM generates code for object dereference. To evaluate our approach, we curate PragmaticCode, a dataset of open-source projects with their development environments. On models of varying parameter scale, we show that monitor-guided decoding consistently improves the ability of an LM to not only generate identifiers that match the ground truth but also improves compilation rates and agreement with ground truth. We find that LMs with fewer parameters, when guided with our monitor, can outperform larger LMs. With monitor-guided decoding, SantaCoder-1.1B achieves better compilation rate and next-identifier match than the much larger text-davinci-003 model. The datasets and code will be released at https://aka.ms/monitors4codegen .

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.

With the advent of neural language models, the performance of code generation has been significantly boosted. However, the problem of repetitions during the generation process continues to linger. Previous work has primarily focused on content repetition, which is merely a fraction of the broader repetition problem in code generation. A more prevalent and challenging problem is structural repetition. In structural repetition, the repeated code appears in various patterns but possesses a fixed structure, which can be inherently reflected in grammar. In this paper, we formally define structural repetition and propose an efficient decoding approach called RPG, which stands for Repetition Penalization based on Grammar, to alleviate the repetition problems in code generation for LLMs. Specifically, RPG first leverages grammar rules to identify repetition problems during code generation, and then strategically decays the likelihood of critical tokens that contribute to repetitions, thereby mitigating them in code generation. To facilitate this study, we construct a new dataset CodeRepetEval to comprehensively evaluate approaches for mitigating the repetition problems in code generation. Extensive experimental results demonstrate that RPG substantially outperforms the best-performing baselines on CodeRepetEval dataset as well as HumanEval and MBPP benchmarks, effectively reducing repetitions and enhancing the quality of generated code.

LLM-based agents have shown strong potential for solving complex multi-step tasks, yet existing performance improvements often rely on either scaling to larger backbone models or task-specific fine-tuning. The former incurs substantial computational costs, while the latter typically generalizes poorly across different tasks. Although prompt-based control is training-free and broadly applicable, existing methods still leave input-output dependencies between subtasks implicit in textual trajectories, making verified intermediate results difficult to reuse. To address these limitations, we propose Atomic Task Graph (ATG), a unified control framework for planning and execution. Specifically, ATG maintains an explicit graph to expose dependencies and support reuse. During planning, it recursively decomposes a high-level task into subtasks, forming a sequence of directed acyclic graphs (DAGs) whose evolution can be traced. During execution, the dependencies exposed by ATG allow independent branches to be executed in parallel, thereby improving execution efficiency. When failures are detected, ATG leverages the graph evolution history to localize the error source and repair only the affected region, preserving validated regions unchanged. Experiments show that ATG consistently outperforms strong baselines in success rate and execution efficiency across three interactive benchmarks using only 7B-8B backbones.

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%).

Tool agents--LLM-based systems that interact with external APIs--offer a way to execute real-world tasks. However, as tasks become increasingly complex, these agents struggle to identify and call the correct APIs in the proper order. To tackle this problem, we investigate converting API documentation into a structured API graph that captures API dependencies and leveraging it for multi-tool queries that require compositional API calls. To support this, we introduce In-N-Out, the first expert-annotated dataset of API graphs built from two real-world API benchmarks and their documentation. Using In-N-Out significantly improves performance on both tool retrieval and multi-tool query generation, nearly doubling that of LLMs using documentation alone. Moreover, graphs generated by models fine-tuned on In-N-Out close 90% of this gap, showing that our dataset helps models learn to comprehend API documentation and parameter relationships. Our findings highlight the promise of using explicit API graphs for tool agents and the utility of In-N-Out as a valuable resource. We release our dataset and code at https://github.com/holi-lab/In-N-Out-API-Graph.

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

Multi-agent coding has emerged as an increasingly active direction in software engineering, where complex development tasks are decomposed across multiple specialized agents working on different parts of the problem. Despite the shift from individual problem solving to distributed collaboration, multi-agent systems still lack a direct measure of collaboration and are largely evaluated through task-level outcomes inherited from single-agent coding, conflating individual coding capability with cross-agent coordination. We introduce AsynCodeBench, a dependency-centric benchmark for asynchronous multi-agent software engineering that represents each task with an explicit dependency graph and executable Dependency Checkers. Through this dependency-tracking process, we propose two complementary measures: Asynchronous Dependency Pass Rate (ADPR), which measures how many cross-agent dependencies are ultimately satisfied, and Dependency Resolution Step (DRS), which measures when each dependency first becomes satisfied during execution. AsynCodeBench comprises 19 tasks from real-world repositories, exposing 52 directed dependencies as explicit units for evaluating cross-agent collaboration. Experiments across model families, scales, and generations reveal a clear gap between coding and collaboration capability: improvements in coding performance do not necessarily translate into stronger collaboration, and task-level metrics can diverge substantially from dependency-level collaboration measures. Dependency-trajectory analysis further reveals that successful coordination often emerges not gradually, but through concentrated bursts in which many dependencies become resolved over a short portion of the execution trajectory, a pattern we term a hopping window.

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

Retrieval-augmented generation (RAG) is an umbrella of different components, design decisions, and domain-specific adaptations to enhance the capabilities of large language models and counter their limitations regarding hallucination and outdated and missing knowledge. Since it is unclear which design decisions lead to a satisfactory performance, developing RAG systems is often experimental and needs to follow a systematic and sound methodology to gain sound and reliable results. However, there is currently no generally accepted methodology for RAG evaluation despite a growing interest in this technology. In this paper, we propose a first blueprint of a methodology for a sound and reliable evaluation of RAG systems and demonstrate its applicability on a real-world software engineering research task: the validation of configuration dependencies across software technologies. In summary, we make two novel contributions: (i) A novel, reusable methodological design for evaluating RAG systems, including a demonstration that represents a guideline, and (ii) a RAG system, which has been developed following this methodology, that achieves the highest accuracy in the field of dependency validation. For the blueprint's demonstration, the key insights are the crucial role of choosing appropriate baselines and metrics, the necessity for systematic RAG refinements derived from qualitative failure analysis, as well as the reporting practices of key design decision to foster replication and evaluation.

We introduce Adapters, an open-source library that unifies parameter-efficient and modular transfer learning in large language models. By integrating 10 diverse adapter methods into a unified interface, Adapters offers ease of use and flexible configuration. Our library allows researchers and practitioners to leverage adapter modularity through composition blocks, enabling the design of complex adapter setups. We demonstrate the library's efficacy by evaluating its performance against full fine-tuning on various NLP tasks. Adapters provides a powerful tool for addressing the challenges of conventional fine-tuning paradigms and promoting more efficient and modular transfer learning. The library is available via https://adapterhub.ml/adapters.

Library learning compresses a given corpus of programs by extracting common structure from the corpus into reusable library functions. Prior work on library learning suffers from two limitations that prevent it from scaling to larger, more complex inputs. First, it explores too many candidate library functions that are not useful for compression. Second, it is not robust to syntactic variation in the input. We propose library learning modulo theory (LLMT), a new library learning algorithm that additionally takes as input an equational theory for a given problem domain. LLMT uses e-graphs and equality saturation to compactly represent the space of programs equivalent modulo the theory, and uses a novel e-graph anti-unification technique to find common patterns in the corpus more directly and efficiently. We implemented LLMT in a tool named BABBLE. Our evaluation shows that BABBLE achieves better compression orders of magnitude faster than the state of the art. We also provide a qualitative evaluation showing that BABBLE learns reusable functions on inputs previously out of reach for library learning.

Reusing and invoking existing code remains costly and unreliable, as most practical tools are embedded in heterogeneous code repositories and lack standardized, executable interfaces. Although large language models (LLMs) and Model Context Protocol (MCP)-based tool invocation frameworks enable natural language task execution, current approaches rely heavily on manual tool curation and standardization, which fundamentally limits scalability. In this paper, we propose ToolRosetta, a unified framework that automatically translates open-source code repositories and APIs into MCP-compatible tools that can be reliably invoked by LLMs. Given a user task, ToolRosetta autonomously plans toolchains, identifies relevant codebases, and converts them into executable MCP services, enabling end-to-end task completion with minimal human intervention. In addition, ToolRosetta incorporates a security inspection layer to mitigate risks inherent in executing arbitrary code. Extensive experiments across diverse scientific domains demonstrate that ToolRosetta can automatically standardize a large number of open-source tools and reduce the human effort required for code reproduction and deployment. Notably, by seamlessly leveraging specialized open-source tools, ToolRosetta-powered agents consistently improve task completion performance compared to commercial LLMs and existing agent systems.

Large language models (LLMs) have been widely adopted across diverse software engineering domains, such as code generation, program repair, and vulnerability detection. These applications require understanding beyond surface-level code patterns: value propagation, control flow, and interdependence between program elements. However, existing benchmarks primarily evaluate end-to-end outcomes, such as whether code is correctly repaired or generated, leaving the models ability for program semantic reasoning underexplored. This work presents CoRe, a high-quality, human-verified benchmark designed to evaluate LLMs on fundamental static analysis tasks. CoRe includes 12,553 task instances spanning data dependency, control dependency, and information flow across programs written in C/C++, Java, and Python. To ensure semantic diversity and reasoning complexity, we propose a semantics-aware diverse sampling strategy that selects targets and task instances based on structural coverage and dependency depth. We evaluate 10 mainstream LLMs and show that, while they perform well at identifying dependencies, models still struggle with tasks that require deeper semantic understanding and multi-step reasoning. We further conduct qualitative analyses to uncover key challenges, such as complex control structures and backward dependency patterns, offering insights into improving LLMs code reasoning capabilities.

Modern software -- from plugin systems to self-evolving agent harnesses -- increasingly requires dynamic composition, yet its formal foundations remain underdeveloped. We identify two orthogonal dimensions of the problem: temporal composability, the ability to completely revert a component's side effects upon removal, and spatial composability, the ability to declare and reactively manage inter-component dependencies. We address the two dimensions by lifting classical effect and coeffect concepts to runtime mechanisms. In particular, we formalize revertible effects, in which every context transformation carries an inverse that the runtime holds, establishing temporal composability local to one component. We formalize reactive coeffects, in which every context change is classified against a component's coeffect specification to drive its activation and deactivation, establishing spatial composability local to one component. We then unify the effect context and the coeffect context into a single context type and mediate every effect and coeffect through it, yielding a discipline we call the context paradigm; the mediation induces an observational equivalence up to which the effects of distinct components interleave without disturbing one another. Combining these mechanisms into the notion of a component, we give a calculus of dynamic composition whose metatheory carries spatiotemporal composability from a single component to a whole system of interleaved components. We implement these ideas in Cordis, a meta-framework of spatiotemporal composability that provides a core library with effect tracking and coeffect resolution, as well as a declarative component loader with configuration reconciliation and hot module replacement.

Tool calling has greatly expanded the practical utility of large language models (LLMs) by enabling them to interact with external applications. As LLM capabilities advance, effective tool use increasingly involves multi-step, multi-turn interactions to solve complex tasks. However, the resulting growth in tool interactions incurs substantial latency, posing a key challenge for real-time LLM serving. Through empirical analysis, we find that tool-calling traces are highly structured, conform to constrained schemas, and often exhibit recurring invocation patterns. Motivated by this, we propose ToolSpec, a schema-aware, retrieval-augmented speculative decoding method for accelerating tool calling. ToolSpec exploits predefined tool schemas to generate accurate drafts, using a finite-state machine to alternate between deterministic schema token filling and speculative generation for variable fields. In addition, ToolSpec retrieves similar historical tool invocations and reuses them as drafts to further improve efficiency. ToolSpec presents a plug-and-play solution that can be seamlessly integrated into existing LLM workflows. Experiments across multiple benchmarks demonstrate that ToolSpec achieves up to a 4.2x speedup, substantially outperforming existing training-free speculative decoding methods.

Long-context inference is central to modern large language model (LLM) applications such as retrieval-augmented generation and multi-document reasoning. To mitigate the growing inference cost, recent work has explored key-value (KV) cache reuse to reduce redundant prefill computation. However, existing reuse methods primarily focus on computation savings and overlook a critical bottleneck in long-context LLM serving: the cost of storing and accessing large KV caches. While KV compression appears to be a natural complement, naively combining compression with non-prefix KV reuse often leads to severe accuracy degradation. In this work, we propose C^2KV, a unified framework for non-prefix KV reuse that jointly optimizes KV extraction and inference-time concatenation. C^2KV learns a composable and compressed KV cache manifold that is explicitly designed to be position-agnostic. Our approach introduces a lightweight sidecar Extractor with learnable compression tokens and a structured attention flow, enabling modular KV representations that can be flexibly reused and concatenated without modifying the frozen base model. We further employ a compression-concatenation co-training strategy to align extraction-time representations with their downstream reuse behavior. Extensive experiments across multiple long-context benchmarks and model families demonstrate that C^2KV significantly reduces KV cache storage and transfer costs, achieving up to 17times inference speedup under long contexts, while preserving generation quality.

While Large Language Models (LLMs) have achieved remarkable success in code generation, they often struggle with the deep, long-horizon reasoning required for complex software engineering. We attribute this limitation to the nature of standard pre-training data: static software repositories represent only the terminal state of an intricate intellectual process, abstracting away the intermediate planning, debugging, and iterative refinement. To bridge this gap, we propose a novel paradigm: understanding via reconstruction. We hypothesize that reverse-engineering the latent agentic trajectories -- the planning, reasoning, and debugging steps -- behind static repositories provides a far richer supervision signal than raw code alone. To operationalize this, we introduce a framework that synthesizes these trajectories using a multi-agent simulation. This process is grounded in the structural realities of the source repositories (e.g., dependency graphs and file hierarchies) to ensure fidelity. Furthermore, to guarantee the logical rigor of the synthetic data, we employ a search-based optimization technique that iteratively refines the Chain-of-Thought (CoT) reasoning to maximize the likelihood of the ground-truth code. Empirical results demonstrate that continuous pre-training on these reconstructed trajectories significantly enhances Llama-3-8B's performance across diverse benchmarks, including long-context understanding, coding proficiency, and agentic capabilities.

Web application development often proceeds through successive requests that extend an existing implementation. Yet web-generation benchmarks primarily evaluate development toward fixed specifications. We introduce EvoWeb, a novel benchmark comprising 320 cumulative requests over 32 web applications, grounded in real-world product features and structured by functional dependency graphs. Agents iteratively modify a persistent codebase, while a multimodal web agent tests each intermediate application in a live browser, assessing newly requested functionality, cross-request integration, and previously requested functionality. To characterize reliability throughout development, we integrate trajectory performance across user-tolerance thresholds rather than impose a fixed stopping criterion. Experiments across open- and closed-source frontier models show that EvoWeb reveals clear performance differences between models, with cross-request integration emerging as a key challenge. Further analysis shows that later requests with deeper or more numerous dependencies are solved less accurately, while runtime errors become more frequent over successive requests. EvoWeb provides a testbed for evaluating and improving coding agents in long-horizon, multi-request development.

Large Language Models (LLMs) currently struggle with tool invocation and chaining, as they often hallucinate or miss essential steps in a sequence. We propose RE-GAINS and EnChAnT, two novel frameworks that empower LLMs to tackle complex user queries by making API calls to external tools based on tool descriptions and argument lists. Tools are chained based on the expected output, without receiving the actual results from each individual call. EnChAnT, an open-source solution, leverages an LLM format enforcer, OpenChat 3.5 (an LLM), and ToolBench's API Retriever. RE-GAINS utilizes OpenAI models and embeddings with a specialized prompt based on the Reasoning via Planning (RAP) framework. Both frameworks are low cost (0.01\$ per query). Our key contribution is enabling LLMs for tool invocation and chaining using modifiable, externally described tools.

Large language models store all learned knowledge in a single, fixed weight vector. Teaching a model new capabilities requires modifying those same weights, inevitably degrading previously acquired knowledge. This fundamental limitation, known as catastrophic forgetting, has resisted principled solutions for decades. Existing approaches treat weights as immutable artifacts that must be protected through techniques like regularization heuristics, replay buffers, or isolated adapter modules. The problem is none of these provide a structural guarantee against forgetting. In this work, we propose Non-Interfering Weight Fields (NIWF), a framework that replaces the fixed weight paradigm with a learned function that generates weight configurations on demand from a continuous capability coordinate space. After training on a task, we commit the occupied coordinate region by snapshotting the fields outputs on anchor points to enforce a functional lock during all future training. We validate NIWF on sequential instructionfollowing and code generation tasks using Mistral-7B, demonstrating zero forgetting on committed tasks with competitive perplexity on new tasks. The framework introduces the notion of software-like versioning for neural network intelligence, where capabilities can be committed, extended, composed, and rolled back without retraining.

Large-scale formalization of advanced mathematics requires more than translating individual statements: it must reconstruct a coherent theory distributed across heterogeneous sources. This process raises four challenges: discovering implicit dependencies, correcting source defects, preserving semantic fidelity, and reconciling cross-source misalignments. We present FormaTheoria, an end-to-end, AI-assisted workflow that coordinates source acquisition, formalization, proof construction, recursive dependency discovery, independent review, and reconciliation, while preserving provenance and protecting approved declarations. A shared agent framework supports long-horizon execution through tool use, context compaction, review-gated termination, section-level source context, and dependency-aware batch parallelization. Applying FormaTheoria to major components of the Classification of Finite Simple Groups (CFSG), we construct a machine-checked Lean development extending through the Bender--Suzuki theorem and encompassing the Feit--Thompson Odd Order Theorem, Glauberman's Z^* theorem, and the Brauer--Suzuki theorem. This development verifies an extensive body of deeply interdependent finite-group theory while providing a foundation for continuing the CFSG formalization. An empirical analysis of the code and recorded construction process supports the practical relevance of the identified challenges and illustrates the roles of the corresponding workflow components. Together, these results demonstrate how AI-assisted workflows can reconstruct mathematically significant formal theories from distributed literature by combining language-model agents with formal verification, structured review, and explicit dependency management.

Large language models (LLMs) are increasingly used for complex tasks requiring multiple chained generation calls, advanced prompting techniques, control flow, and interaction with external environments. However, efficient systems for programming and executing these applications are lacking. To bridge this gap, we introduce SGLang, a Structured Generation Language for LLMs. SGLang is designed for the efficient programming of LLMs and incorporates primitives for common LLM programming patterns. We have implemented SGLang as a domain-specific language embedded in Python, and we developed an interpreter, a compiler, and a high-performance runtime for SGLang. These components work together to enable optimizations such as parallelism, batching, caching, sharing, and other compilation techniques. Additionally, we propose RadixAttention, a novel technique that maintains a Least Recently Used (LRU) cache of the Key-Value (KV) cache for all requests in a radix tree, enabling automatic KV cache reuse across multiple generation calls at runtime. SGLang simplifies the writing of LLM programs and boosts execution efficiency. Our experiments demonstrate that SGLang can speed up common LLM tasks by up to 5x, while reducing code complexity and enhancing control.

Due to their black-box nature, LLMs suffer from limited explain- ability and a lack of determinism. Their usage cost can also rise, particularly with repetitive tasks on large codebases. To mitigate this, we conduct a novel empirical study targeting three domain- specific languages for transformation rules, namely Comby, GritQL, and Ast-Grep. We evaluate three LLMs (GPT-5.4, GPT-oss-120B, and Llama3.1-8B) on six diverse datasets covering four software- evolution tasks: API misuse correction, program repair, API migra- tion, and language version migration. Our results provide evidence that transformation rule synthesis moves beyond proof-of-concept with strong frontier models. GPT-5.4 achieves consistently high rule applicability rates and produces transformations closest to the ground truth across most benchmarks. Smaller and open-weight GPT-oss-120B and Llama3.1-8B models remain effective for simpler, localized changes but struggle with complex migration scenarios. We also observe non-negligible generalizability through the usage of meta-variables and through a high reuse score in the first quartile of many datasets. Finally, when compared to the anti-unification algorithm, LLMs outperform it in correctness, but underperform in rule applicability. Overall, our results show great potential for LLMs to generate sound, correct, generalizable, and reusable rules.

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

Large Language Models (LLMs) have demonstrated impressive capabilities as intelligent agents capable of solving complex problems. However, effective planning in scenarios involving dependencies between API or tool calls-particularly in multi-turn conversations-remains a significant challenge. To address this, we introduce T1, a tool-augmented, multi-domain, multi-turn conversational dataset specifically designed to capture and manage inter-tool dependencies across diverse domains. T1 enables rigorous evaluation of agents' ability to coordinate tool use across nine distinct domains (4 single domain and 5 multi-domain) with the help of an integrated caching mechanism for both short- and long-term memory, while supporting dynamic replanning-such as deciding whether to recompute or reuse cached results. Beyond facilitating research on tool use and planning, T1 also serves as a benchmark for evaluating the performance of open-source language models. We present results powered by T1-Agent, highlighting their ability to plan and reason in complex, tool-dependent scenarios.

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

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

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

One of the most reliable ways to create deployable models for specialized tasks is to obtain an adequate amount of high-quality task-specific data. However, for specialized tasks, often such datasets do not exist. Existing methods address this by creating such data from large language models (LLMs) and then distilling such knowledge into smaller models. However, these methods are limited by the quality of the LLMs output, and tend to generate repetitive or incorrect data. In this work, we present Retrieval Based Distillation (ReBase), a method that first retrieves data from rich online sources and then transforms them into domain-specific data. This method greatly enhances data diversity. Moreover, ReBase generates Chain-of-Thought reasoning and distills the reasoning capacity of LLMs. We test our method on 4 benchmarks and results show that our method significantly improves performance by up to 7.8% on SQuAD, 1.37% on MNLI, and 1.94% on BigBench-Hard.

Large Language Models (LLMs) increasingly act as agents whose procedural knowledge is stored in reusable skill packages and loaded at inference time. As skill libraries grow, a central challenge is to expose the smallest sufficient executable context under a limited context budget. Existing systems struggle to reuse routines below the whole-skill level, preserve procedural contracts during compression, keep compressed routines executable and expandable, and update the compressed library as skills evolve. These challenges reveal a unit mismatch: skills are retrieved as packages, compressed as text, and converted into execution graphs only after retrieval, whereas reliable reuse requires a contract-bearing procedural unit. We propose SkillZip, an execution-aware procedural abstraction framework that performs contract-preserving compression over section-level graphs. SkillZip rewrites recurring contract-valid motifs into reversible ported macros while preserving boundary signatures, dependency closure, verifier reachability, and source-level expansion. At inference time, it hydrates a compact, dependency-closed context and expands macros only when required. ReZip further integrates new skills and revises risky macros using execution evidence. Comprehensive experiments1 on technical and embodied agent benchmarks show SkillZip consistently outperforms the strongest baseline by up to 12.2 points, while achieving a 3.46x compression ratio with 99.2% dependency preservation and 98.7% verifier reachability. Scaling analyses further confirm robust retrieval across skill libraries ranging from 200 to 100K skills.

As autonomous coding agents become capable of handling increasingly long-horizon tasks, they have gradually demonstrated the potential to complete end-to-end software development. Although existing benchmarks have recently evolved from localized code editing to from-scratch project generation, they remain confined to structurally simplified, single-stack applications. Consequently, they fail to capture the heterogeneous environments, full-stack orchestration, and system-level complexity of real enterprise Software as a Service (SaaS) systems, leaving a critical gap in assessing agents under realistic engineering constraints. To fill this gap, we introduce SaaSBench, the first benchmark designed to explore the boundaries of AI agents in enterprise SaaS engineering. Spanning 30 complex tasks across 6 SaaS domains with 5,370 validation nodes, it incorporates 8 programming languages, 6 databases, and 13 frameworks to meticulously mirror real-world software heterogeneity. Furthermore, we design a dependency-aware hybrid evaluation paradigm tailored for complex systems with long horizons and multi-component coupling, enabling fine-grained, reproducible assessment. Crucially, our extensive experiments reveal a striking insight: the primary bottleneck for state-of-the-art agents is not generating isolated code logic, but successfully configuring and integrating a multi-component system. Over 95\% of task failures occur before agents even reach deep business logic, with models often falling victim to overconfidence and prematurely halting during foundational system setup, or getting trapped in ineffective debugging loops. We hope SaaSBench serves as a practical and challenging testbed to drive the evolution of reliable, system-level coding agents. The code is available at https://github.com/ShadeCloak/SaaSbench.

Retrieval-Augmented Generation (RAG) is often used with Large Language Models (LLMs) to infuse domain knowledge or user-specific information. In RAG, given a user query, a retriever extracts chunks of relevant text from a knowledge base. These chunks are sent to an LLM as part of the input prompt. Typically, any given chunk is repeatedly retrieved across user questions. However, currently, for every question, attention-layers in LLMs fully compute the key values (KVs) repeatedly for the input chunks, as state-of-the-art methods cannot reuse KV-caches when chunks appear at arbitrary locations with arbitrary contexts. Naive reuse leads to output quality degradation. This leads to potentially redundant computations on expensive GPUs and increases latency. In this work, we propose Cache-Craft, a system for managing and reusing precomputed KVs corresponding to the text chunks (we call chunk-caches) in RAG-based systems. We present how to identify chunk-caches that are reusable, how to efficiently perform a small fraction of recomputation to fix the cache to maintain output quality, and how to efficiently store and evict chunk-caches in the hardware for maximizing reuse while masking any overheads. With real production workloads as well as synthetic datasets, we show that Cache-Craft reduces redundant computation by 51% over SOTA prefix-caching and 75% over full recomputation. Additionally, with continuous batching on a real production workload, we get a 1.6X speed up in throughput and a 2X reduction in end-to-end response latency over prefix-caching while maintaining quality, for both the LLaMA-3-8B and LLaMA-3-70B models.

The growing number of parameter-efficient adaptations of a base large language model (LLM) calls for studying whether we can reuse such trained adapters to improve performance for new tasks. We study how to best build a library of adapters given multi-task data and devise techniques for both zero-shot and supervised task generalization through routing in such library. We benchmark existing approaches to build this library and introduce model-based clustering, MBC, a method that groups tasks based on the similarity of their adapter parameters, indirectly optimizing for transfer across the multi-task dataset. To re-use the library, we present a novel zero-shot routing mechanism, Arrow, which enables dynamic selection of the most relevant adapters for new inputs without the need for retraining. We experiment with several LLMs, such as Phi-2 and Mistral, on a wide array of held-out tasks, verifying that MBC-based adapters and Arrow routing lead to superior generalization to new tasks. We make steps towards creating modular, adaptable LLMs that can match or outperform traditional joint training.

Migrating existing C programs into Rust is increasingly desired, as Rust offers superior memory safety while maintaining C's high performance. However, vastly different features between C and Rust--e.g., distinct definitions and usages of pointers and references--pose significant challenges beyond mere syntactic translation. Existing automated translation tools, such as C2Rust, may rely too much on syntactic, template-based translation and generate unsafe Rust code that is hard for human developers to read, maintain, or even compile. More semantic-aware translation that produces safer, idiomatic, and runnable Rust code is much needed. This paper introduces a novel dependency-guided and large language model (LLM)-based C-to-Rust translation approach, RustMap, based on three key ideas: (1) Utilize LLM capabilities to produce idiomatic Rust code from given small pieces of C code, (2) Mitigate LLM limitations in handling large codebases by breaking project-scale C programs into smaller units for translation according to their usage dependencies and composing them into a runnable Rust program, and (3) Enhance the correctness of the translated Rust program by using test cases to check input/output equivalence, isolate faulty code when execution states deviate, and iteratively refine the translation using feedback from compilation and test errors. We empirically evaluate RustMap on 126 real-world programs, including 125 from Rosetta Code and a 7000+ line bzip2 implementation using GPT-4o as the LLM. RustMap shows promising results, guiding GPT-4o to produce idiomatic, readable, and functional Rust code with significantly less unsafe code than other tools, and revealing non-trivial translation patterns reusable for future research.

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.

Code evolution is inevitable in modern software development. Changes to third-party APIs frequently break existing code and complicate maintenance, posing practical challenges for developers. While large language models (LLMs) have shown promise in code generation, they struggle to reason without a structured representation of these evolving relationships, often leading them to produce outdated APIs or invalid outputs. In this work, we propose a knowledge graph-augmented framework that decomposes the migration task into two synergistic stages: evolution path retrieval and path-informed code generation. Our approach constructs static and dynamic API graphs to model intra-version structures and cross-version transitions, enabling structured reasoning over API evolution. Both modules are trained with synthetic supervision automatically derived from real-world API diffs, ensuring scalability and minimal human effort. Extensive experiments across single-package and multi-package benchmarks demonstrate that our framework significantly improves migration accuracy, controllability, and execution success over standard LLM baselines. The source code and datasets are available at: https://github.com/kangjz1203/KCoEvo.

Type inference for dynamically typed languages must reconcile four qualitatively different sources of information about a parameter: values assigned inside a definition, explicit declarations, contextual requirements, and structural operations. Existing systems often combine these sources into one constraint set, causing spurious conflicts and requiring redundant annotations. We present Generic Constraint Projection (GCP), a zero-annotation inference framework that stores the four sources in separate monotone slots on a stable definition-time template and checks each call in a fresh projection session. Ordinary calls verify concrete arguments and specialize returns without mutating the template, while partial calls produce residual projected functions. On the success fragment of a finite-height type preorder, we prove monotonicity, local and global convergence, conditional projection-obligation soundness, projection termination, multi-module convergence, and order-independence under fair iteration. For the pure recursion-free core Outline_0, we also prove evaluation definedness, type preservation, runtime receiver retention, and projection-evaluation coherence. GCP uses Outline Equational Matching as an extensible structural compatibility relation and future this to preserve concrete receiver shape across fluent method chains. We instantiate the framework in Outline for typed ontology worlds and in Python for recovery of PEP 484 annotations from unannotated source.

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.

Code efficiency is a fundamental aspect of software quality, yet how to harness large language models (LLMs) to optimize programs remains challenging. Prior approaches have sought for one-shot rewriting, retrieved exemplars, or prompt-based search, but they do not explicitly distill reusable optimization knowledge, which limits generalization beyond individual instances. In this paper, we present EffiSkill, a framework for code-efficiency optimization that builds a portable optimization toolbox for LLM-based agents. The key idea is to model recurring slow-to-fast transformations as reusable agent skills that capture both concrete transformation mechanisms and higher-level optimization strategies. EffiSkill adopts a two-stage design: Stage I mines Operator and Meta Skills from large-scale slow/fast program pairs to build a skill library; Stage II applies this library to unseen programs through execution-free diagnosis, skill retrieval, plan composition, and candidate generation, without runtime feedback. Results on EffiBench-X show that EffiSkill achieves higher optimization success rates, improving over the strongest baseline by 3.69 to 12.52 percentage points across model and language settings. These findings suggest that mechanism-level skill reuse provides a useful foundation for execution-free code optimization, and that the resulting skill library can serve as a reusable resource for broader agent workflows.

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

Harness self-evolution revises an agent's software scaffolding, including prompts, memory, workflows, and executable components, while keeping model weights fixed. We formalize a feedback-driven process in which accepted revisions persist across runs. The framework separates update targets from proposal and admission mechanisms. It distinguishes changes to interpreted state from revisions to tools and code, repository-level control logic, and plugin composition. We characterize search through evolutionary optimization and examine its reliability through continual PAC-learning. Under explicit assumptions, the analysis yields an expected generalization bound, a retention bound conditional on historical regression budgets, and a high-probability admission rule using fresh, independent validation data. We examine how persistent harness revisions affect knowledge sharing and organizational workflows, with implications for scientific reliability, physical safety, and institutional accountability. Cases from prior work illustrate model--harness co-design, distributed execution, and plugin reuse. Reliable deployment requires continual validation as task distributions and evaluators change, with independent safeguards for learning, runtime privileges, and consequential actions. We provide a comprehensive 66-page discussion of related work, theory, algorithms, evaluation, applications, and the broader impact of Harness RSI, together with continuously updated code and supplementary materials, at https://github.com/zgcagi/Harness-RSI.

Agent-evolution methods use execution feedback to improve prompts, skills, tools, and orchestration, but their implementations often rebuild the same experimental machinery. We present RSIHub, an open-source framework for building, comparing, and extending these methods on shared infrastructure. Recipes compose reusable operators and declare mutable resources; RSIHub supplies execution, evaluation, recovery, and lineage. Researchers can focus on evolution policy while evaluation stays outside the mutable surface and results remain tied to candidates and evaluation conditions. We instantiate AHE, Hyperagents, A-Evolve, and GEPA without modifying the framework core, keeping method-specific logic in recipes and operators. We evaluate them with MiniSWE and Codex on Terminal Bench 2 and τ^3 Banking under fixed model and evaluator configurations. The largest observed overall pass@1 gain is 13.5 percentage points, while method rankings vary across settings and optimization gains do not always transfer to held-out tasks. RSIHub provides a common protocol for comparing evolution policies, inspectable candidate histories, and reusable components for developing new methods.

Modern LLM agents increasingly rely on dynamic structured generation, such as tool calling and response protocols. Unlike traditional structured generation with static structures, these workloads vary both across requests and within a request, posing new challenges to existing engines. We present XGrammar-2, a structured generation engine for dynamic agentic workloads. Our design is based on two key ideas: first-class support for tag-triggered structure switching, and fine-grained reuse across requests with different output structures. Concretely, XGrammar-2 introduces TagDispatch for dynamic structural dispatching and Cross-Grammar Cache for substructure-level cache reuse across grammars. It further improves efficiency with an Earley-based adaptive token mask cache, just-in-time compilation, and repetition state compression. Experiments show that XGrammar-2 achieves over 6x faster compilation than prior structured generation engines, and incurs near-zero end-to-end overhead in modern LLM serving systems.

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

Large language models (LLMs) have advanced automatic program repair (APR) to the point where agentic systems routinely resolve real-world, repository-level issues. Yet the generated patch has received little scrutiny beyond whether it passes tests. In this paper, we identify patch verbosity as a major yet overlooked concern in LLM-based APR. Characterizing 28 state-of-the-art approaches on SWE-bench Verified, we find that even successful patches are consistently larger and more complex than developer patches, with the median approach producing 121.78% more total changes, 80.91% more net changes, and 43.99% higher cyclomatic complexity. We further show that this verbosity is rooted in capability-oriented design choices such as iterative refinement and broad context, and can hardly be reduced by surface-level controls such as output format or minimality prompts. Motivated by these findings, we formulate post-generation patch refinement and propose RECAP, a lightweight, plug-and-play adapter that attaches to existing repair frameworks after generation. RECAP's refiner is trained via supervised fine-tuning and direct preference optimization with distilled reasoning traces, on a dataset of patch pairs we construct from multiple sources. Across four host systems, prompting, commit-untangling, and minimality-aware baselines reduce patch size only by sacrificing 49 to 217 resolved instances. In contrast, RECAP achieves a substantially better size-correctness tradeoff, cutting average total changes from +242.14% to +4.24% and net changes from +348.24% to -39.75% relative to developer patches while preserving or improving resolution by up to 42 instances. Our results indicate that minimality cannot be simply reduced to syntactic compression, and that decoupling minimization from generation offers a practical path to more reviewable repairs.

Multimodal agents repeatedly re-examine the same video frames, UI screenshots, and rendered artifacts as their context window slides and reasoning iterates, yet every look-back re-encodes from scratch, because prefix caches serve reuse only at a fixed leading position. We show this recompute is avoidable, and identify exactly what naive KV reuse loses: the cross-chunk conditioning a chunk absorbs from its neighbours. This loss is asymmetric. The direct readout of a cached chunk is recovered exactly and for free by the standard state-merge. What remains is a diffuse, low-rank residue concentrated in deep layers, invisible to single-hop retrieval but precisely what multi-hop reasoning binds on. Blind reuse therefore leaves single-hop recall intact while halving multi-hop accuracy; this is the failure mode prior position-independent caches, designed for single-context or single-image reuse, do not address. We repair it with a small, training-free low-rank conditioning patch stored alongside each position-free chunk. Reuse reduces to one operator across MLA, GQA, and MHA: exact RoPE re-rotation to any target position, plus the patch that restores cross-chunk binding. This makes three window operations cheap: reorder (one patch serves every ordering of a cached set), sliding-window survival (surviving chunks relocate via rotation only, zero re-encode), and recall (an evicted chunk is rehydrated by its patch, never re-encoded). A rank-m patch recovers full task accuracy on cross-chunk-binding benchmarks, MM-NIAH across two attention families and two-page doc-QA, at a fraction of the KV footprint, and reconstructs re-prefill KV to within bf16 rounding in a production SGLang kernel across six backbones. The conditioning signal is strongest in redundant vision and video streams, making our solution most impactful where multimodal agents spend their recompute budget.

Engineering efficient implementations of compact and succinct structures is a time-consuming and challenging task, since there is no standard library of easy-to- use, highly optimized, and composable components. One consequence is that measuring the practical impact of new theoretical proposals is a difficult task, since older base- line implementations may not rely on the same basic components, and reimplementing from scratch can be very time-consuming. In this paper we present a framework for experimentation with succinct data structures, providing a large set of configurable components, together with tests, benchmarks, and tools to analyze resource requirements. We demonstrate the functionality of the framework by recomposing succinct solutions for document retrieval.

Modern code intelligence agents operate in contexts exceeding 1 million tokens--far beyond the scale where humans manually locate relevant files. Yet agents consistently fail to discover architecturally critical files when solving real-world coding tasks. We identify the Navigation Paradox: agents perform poorly not due to context limits, but because navigation and retrieval are fundamentally distinct problems. Through 258 automated trials across 30 benchmark tasks on a production FastAPI repository, we demonstrate that graph-based structural navigation via CodeCompass--a Model Context Protocol server exposing dependency graphs--achieves 99.4% task completion on hidden-dependency tasks, a 23.2 percentage-point improvement over vanilla agents (76.2%) and 21.2 points over BM25 retrieval (78.2%).However, we uncover a critical adoption gap: 58% of trials with graph access made zero tool calls, and agents required explicit prompt engineering to adopt the tool consistently. Our findings reveal that the bottleneck is not tool availability but behavioral alignment--agents must be explicitly guided to leverage structural context over lexical heuristics. We contribute: (1) a task taxonomy distinguishing semantic-search, structural, and hidden-dependency scenarios; (2) empirical evidence that graph navigation outperforms retrieval when dependencies lack lexical overlap; and (3) open-source infrastructure for reproducible evaluation of navigation tools.

Large language model (LLM)-powered coding agents have made rapid progress in automating software engineering tasks, yet repository-level issue resolution remains challenging. Beyond generating a plausible patch, an agent must localize relevant code across interdependent files and maintain repository context that is both sufficient and focused. Code graphs expose non-local relations, but linear text interfaces obscure their topology; rendering the full repository graph yields visual representations that are too dense to perceive reliably, whereas a one-shot local view becomes stale as exploration proceeds. We present RepoAtlas, a training-free module that maintains evolving multimodal repository views through a select--project--refresh loop over a repository code graph. RepoAtlas combines evidence from the issue with the agent's current exploration state to select a task-relevant region under a fixed budget, projects the selected structure into complementary visual and textual representations, and refreshes the view when changes in the exploration state render it outdated. We evaluate RepoAtlas on SWE-bench Verified, where it improves the resolve rate by 2.4 points while reducing input tokens and model calls by 5.8\% and 7.8\% on average, relative to the strongest multimodal graph baseline, with consistent gains across three models of different families and scales.

There is a growing need for Large Language Models (LLMs) to effectively use tools and external Application Programming Interfaces (APIs) to plan and complete tasks. As such, there is tremendous interest in methods that can acquire sufficient quantities of train and test data that involve calls to tools / APIs. Two lines of research have emerged as the predominant strategies for addressing this challenge. The first has focused on synthetic data generation techniques, while the second has involved curating task-adjacent datasets which can be transformed into API / Tool-based tasks. In this paper, we focus on the task of identifying, curating, and transforming existing datasets and, in turn, introduce API-BLEND, a large corpora for training and systematic testing of tool-augmented LLMs. The datasets mimic real-world scenarios involving API-tasks such as API / tool detection, slot filling, and sequencing of the detected APIs. We demonstrate the utility of the API-BLEND dataset for both training and benchmarking purposes.

Large language model agents have made substantial progress in code generation, yet most existing systems assume a predefined repository architecture. This assumption does not hold in zero-to-all code generation, where an agent must construct an entire software project directly from natural-language requirements while maintaining a modular repository architecture throughout development. We present Repo0, a continuous structural evolution framework for zero-to-all code generation. Repo0 maintains an explicit architectural state instantiated as a Dual-Directed-Acyclic-Graph (Dual-DAG), consisting of a requirement-level DAG, a component-level DAG, and their alignment relation. Starting from natural-language requirements, it iteratively evolves component boundaries through structural actions guided by modularity metrics until structural convergence, after which the converged architecture guides test-driven development code generation. We evaluate Repo0 on six real-world repositories from RepoCraft using GPT-5 mini and DeepSeek V3.2. Repo0 achieves the highest Functionality Coverage and Pass Rate across all settings. Compared with RPG, the strongest repository-planning baseline, Repo0 improves Functionality Coverage by up to 20.08 percentage points and Pass Rate by up to 29.74 percentage points. Ablation and structural-evolution analyses further demonstrate the importance of the Dual-DAG architectural state, modularity-guided structural evolution, and explicit structural convergence.

In modern data-driven science, reproducibility and reusability are key challenges. Scientists are well skilled in the process from data to publication. Although some publication channels require source code and data to be made accessible, rerunning and verifying experiments is usually hard due to a lack of standards. Therefore, reusing existing scientific data processing code from state-of-the-art research is hard as well. This is why we introduce CLAIMED, which has a proven track record in scientific research for addressing the repeatability and reusability issues in modern data-driven science. CLAIMED is a framework to build reusable operators and scalable scientific workflows by supporting the scientist to draw from previous work by re-composing workflows from existing libraries of coarse-grained scientific operators. Although various implementations exist, CLAIMED is programming language, scientific library, and execution environment agnostic.

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.

Retrieval-augmented generation (RAG) enhances large language models (LLMs) with retrieved context but often suffers from downgraded prefill performance as modern applications demand longer and more complex inputs. Existing caching techniques either preserve accuracy with low cache reuse or improve reuse at the cost of degraded reasoning quality. We present RAGBoost, an efficient RAG system that achieves high cache reuse without sacrificing accuracy through accuracy-preserving context reuse. RAGBoost detects overlapping retrieved items across concurrent sessions and multi-turn interactions, using efficient context indexing, ordering, and de-duplication to maximize reuse, while lightweight contextual hints maintain reasoning fidelity. It integrates seamlessly with existing LLM inference engines and improves their prefill performance by 1.5-3X over state-of-the-art methods, while preserving or even enhancing reasoning accuracy across diverse RAG and agentic AI workloads. Our code is released at: https://github.com/Edinburgh-AgenticAI/RAGBoost.

Recent developments in retrieval-augmented generation (RAG) for selecting relevant tools from a tool knowledge base enable LLM agents to scale their complex tool calling capabilities to hundreds or thousands of external tools, APIs, or agents-as-tools. However, traditional RAG-based tool retrieval fails to capture structured dependencies between tools, limiting the retrieval accuracy of a retrieved tool's dependencies. For example, among a vector database of tools, a "get stock price" API requires a "stock ticker" parameter from a "get stock ticker" API, and both depend on OS-level internet connectivity tools. In this paper, we address this limitation by introducing Graph RAG-Tool Fusion, a novel plug-and-play approach that combines the strengths of vector-based retrieval with efficient graph traversal to capture all relevant tools (nodes) along with any nested dependencies (edges) within the predefined tool knowledge graph. We also present ToolLinkOS, a new tool selection benchmark of 573 fictional tools, spanning over 15 industries, each with an average of 6.3 tool dependencies. We demonstrate that Graph RAG-Tool Fusion achieves absolute improvements of 71.7% and 22.1% over na\"ive RAG on ToolLinkOS and ToolSandbox benchmarks, respectively (mAP@10). ToolLinkOS dataset is available at https://github.com/EliasLumer/Graph-RAG-Tool-Fusion-ToolLinkOS

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

Collaborative conversations frequently contain references whose targets are indirect rather than named: resolving "this looks like the fix discussed yesterday" requires combining conversational context with evidence from the surrounding workspace which is accessible through APIs or user interfaces. We formalize this problem as Conversational Reference Grounding (CoRG): using a given set of tools to resolve a reference in conversation to the unique external item intended by the speaker. CoRG is challenging because it combines lexical, semantic, and temporal cues distributed across the conversation and the external workspace. Agents must translate these heterogeneous signals into effective tool use: formulating strategies, discovering plausible candidates, inspecting their metadata and content, and ruling out close alternatives. We study CoRG through RepoRef, a benchmark of 400 developer-chat segments grounded in GitHub issues, pull requests, and commits across 92 repositories. Unlike single-shot retrieval tasks, RepoRef often requires multi-step tool use. Our results show that CoRG remains challenging for current agents, even the best agent reaches only 67.0% success rate, leaving one third of references unresolved. These findings position CoRG as a concrete benchmark for studying how agents search, inspect, and verify information in realistic multi-tool environments.

Software engineering tools increasingly rely on LLM based agents to localize files to change to resolve a software issue. Most AI agents explore repositories linearly, that is, visiting one directory or file per step. We postulate that this is a structural mismatch for changes that span several subsystems. We compare linear sequential exploration against non-linear, domain-scoped parallel agentic exploration. Using SWE Bench Pro as initial benchmark, we focus on ansible as an exemplar. We construct an approach for persistent-session evaluation of GitHub issues anchored at a single base commit. We compare our non-linear domain-agent file traversal system against a base LLM without direct repository access, a single agent Recursive Language Model (RLM) baseline with a persistent Python REPL and an external CLI baseline using Codex 5.5 High. Domain scoped parallel agent spawning with a small Haiku-class model achieves the highest micro F1 among Haiku class models by a large margin. Domain-agents is the second highest behind only the much larger Codex 5.5 High on our own expanded benchmark including over more recent PRs from 2025 and 2026. On the original, curated, 2020 SWE-bench Pro benchmark, a larger Sonnet plain LLM baseline attains higher micro F1 by predicting few files, leading to higher precision, but at significantly lower all gold recall. We also present three additional findings. First, documentation evolution is a latent dependency unresolved by any approach. Second, naive file system access can degrade localization driven by test-file over prediction. Lastly, forced multi-agent consultation does not measurably help and raises token cost substantially.

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

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.

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

Language model (LM) agents have driven substantial progress in automated software engineering (SWE), yet building and testing software repositories at scale remains a largely manual and labor-intensive bottleneck. In this work, we introduce RepoLaunch, a novel agentic framework that automatically resolves dependencies, compiles source code, and extracts test results across diverse programming languages and operating systems. RepoLaunch achieves a 78% build success rate, outperforming the Python/Linux-only prior system by 18%. To demonstrate its application, we further present a fully automated pipeline for SWE dataset creation driven by RepoLaunch, which only requires human input at the task-design stage. RepoLaunch is open-sourced, and its automated task-generation pipeline has already been adopted by several recent works on agentic benchmarking and training.

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.

Document repositories evolve continuously. Guidelines and policies are revised, superseded, and re-uploaded, so the same content recurs in different wording and newer versions refine or contradict earlier ones. These inconsistencies belong to the growing collection rather than to any single document, yet existing work treats versioning, duplicate detection, and contradiction detection as isolated pairwise tasks and stops once a pair is labeled. We present GVD (Governed Versioning and Deduplication), a framework that unifies cross-document version linking with rule-level conflict resolution under an auditable update policy. Incoming documents are assigned to version families through bidirectional rule alignment, and their rules are compared against the family memory to identify duplicates, contradictions, asymmetric refinements, and new knowledge, with Counterfactual Span Probing (CSP) resolving related pairs that inference misclassifies as neutral. Relation-specific policies suppress duplicates and escalate only consequential changes for review, retaining version lineage as an audit trail. The pipeline runs fully locally, with no large language model. On 120 enterprise documents processed as 140 ingestions across 59 version families, GVD reaches an F1 of 0.97 for version-family construction and 0.94 for rule-level consistency, with CSP raising rule consistency from 0.90 to 0.94.

This study evaluates large language models (LLMs) in generating code from algorithm descriptions from recent NLP papers. The task requires two key competencies: (1) algorithm comprehension: synthesizing information from papers and academic literature to understand implementation logic, and (2) coding expertise: identifying dependencies and correctly implementing necessary APIs. To facilitate rigorous evaluation, we introduce SciReplicate-Bench, a benchmark of 100 tasks from 36 NLP papers published in 2024, featuring detailed annotations and comprehensive test cases. Building on SciReplicate-Bench, we propose Sci-Reproducer, a multi-agent framework consisting of a Paper Agent that interprets algorithmic concepts from literature and a Code Agent that retrieves dependencies from repositories and implement solutions. To assess algorithm understanding, we introduce reasoning graph accuracy, which quantifies similarity between generated and reference reasoning graphs derived from code comments and structure. For evaluating implementation quality, we employ execution accuracy, CodeBLEU, and repository dependency/API recall metrics. In our experiments, we evaluate various powerful Non-Reasoning LLMs and Reasoning LLMs as foundational models. The best-performing LLM using Sci-Reproducer achieves only 39% execution accuracy, highlighting the benchmark's difficulty.Our analysis identifies missing or inconsistent algorithm descriptions as key barriers to successful reproduction. We will open-source our benchmark, and code at https://github.com/xyzCS/SciReplicate-Bench.