Daily Papers

We introduce AInsteinBench, a large-scale benchmark for evaluating whether large language model (LLM) agents can operate as scientific computing development agents within real research software ecosystems. Unlike existing scientific reasoning benchmarks which focus on conceptual knowledge, or software engineering benchmarks that emphasize generic feature implementation and issue resolving, AInsteinBench evaluates models in end-to-end scientific development settings grounded in production-grade scientific repositories. The benchmark consists of tasks derived from maintainer-authored pull requests across six widely used scientific codebases, spanning quantum chemistry, quantum computing, molecular dynamics, numerical relativity, fluid dynamics, and cheminformatics. All benchmark tasks are carefully curated through multi-stage filtering and expert review to ensure scientific challenge, adequate test coverage, and well-calibrated difficulty. By leveraging evaluation in executable environments, scientifically meaningful failure modes, and test-driven verification, AInsteinBench measures a model's ability to move beyond surface-level code generation toward the core competencies required for computational scientific research.

We present a multi-agent system for automation of scientific research tasks, cmbagent (https://github.com/CMBAgents/cmbagent). The system is formed by about 30 Large Language Model (LLM) agents and implements a Planning & Control strategy to orchestrate the agentic workflow, with no human-in-the-loop at any point. Each agent specializes in a different task (performing retrieval on scientific papers and codebases, writing code, interpreting results, critiquing the output of other agents) and the system is able to execute code locally. We successfully apply cmbagent to carry out a PhD level cosmology task (the measurement of cosmological parameters using supernova data) and evaluate its performance on two benchmark sets, finding superior performance over state-of-the-art LLMs. The source code is available on GitHub, demonstration videos are also available, and the system is deployed on HuggingFace and will be available on the cloud.

Optimizing scientific software is a difficult task because codebases are often large and complex, and performance can depend upon several factors including the algorithm, its implementation, and hardware among others. Causes of poor performance can originate from disparate sources and be difficult to diagnose. Recent years have seen a multitude of work that use large language models (LLMs) to assist in software development tasks. However, these tools are trained to model the distribution of code as text, and are not specifically designed to understand performance aspects of code. In this work, we introduce a reinforcement learning based methodology to align the outputs of code LLMs with performance. This allows us to build upon the current code modeling capabilities of LLMs and extend them to generate better performing code. We demonstrate that our fine-tuned model improves the expected speedup of generated code over base models for a set of benchmark tasks from 0.9 to 1.6 for serial code and 1.9 to 4.5 for OpenMP code.

Camera-based physiological measurement is a fast growing field of computer vision. Remote photoplethysmography (rPPG) utilizes imaging devices (e.g., cameras) to measure the peripheral blood volume pulse (BVP) via photoplethysmography, and enables cardiac measurement via webcams and smartphones. However, the task is non-trivial with important pre-processing, modeling, and post-processing steps required to obtain state-of-the-art results. Replication of results and benchmarking of new models is critical for scientific progress; however, as with many other applications of deep learning, reliable codebases are not easy to find or use. We present a comprehensive toolbox, rPPG-Toolbox, that contains unsupervised and supervised rPPG models with support for public benchmark datasets, data augmentation, and systematic evaluation: https://github.com/ubicomplab/rPPG-Toolbox

Scalable oversight studies methods of training and evaluating AI systems in domains where human judgment is unreliable or expensive, such as scientific research and software engineering in complex codebases. Most work in this area has focused on methods of improving the quality of labels. Recent work by Burns et al. (2023) considers the complementary problem of training models with low-quality labels, finding that large pretrained models often have an inductive bias towards producing correct answers. In practice, however, neither label quantity nor quality is fixed: practitioners face a quantity-quality tradeoff. In this paper, we explore the microeconomics of the quantity-quality tradeoff on binary NLP classification tasks used in Burns et al. (2023). While sample-efficient learning has been studied extensively, little public research has focused on scalable elicitation: eliciting capabilities from pretrained models subject to labeling cost constraints. We find that this setting has novel dynamics caused by the tradeoff between label quantity and quality, as well as the model's existing latent capabilities. We observe three regimes of eliciting classification knowledge from pretrained models using supervised finetuning: quantity-dominant, quality-dominant, and a mixed regime involving the use of low- and high-quality data together to attain higher accuracy at a lower cost than using either alone. We explore sample-efficient elicitation methods that make use of two datasets of differing qualities, and establish a Pareto frontier of scalable elicitation methods that optimally trade off labeling cost and classifier performance. We find that the accuracy of supervised fine-tuning can be improved by up to 5 percentage points at a fixed labeling budget by adding a few-shot prompt to make use of the model's existing knowledge of the task.

Code large language models mark a pivotal breakthrough in artificial intelligence. They are specifically crafted to understand and generate programming languages, significantly boosting the efficiency of coding development workflows. In this technical report, we present CodeShell-Base, a seven billion-parameter foundation model with 8K context length, showcasing exceptional proficiency in code comprehension. By incorporating Grouped-Query Attention and Rotary Positional Embedding into GPT-2, CodeShell-Base integrates the structural merits of StarCoder and CodeLlama and forms its unique architectural design. We then carefully built a comprehensive data pre-processing process, including similar data deduplication, perplexity-based data filtering, and model-based data filtering. Through this process, We have curated 100 billion high-quality pre-training data from GitHub. Benefiting from the high-quality data, CodeShell-Base outperforms CodeLlama in Humaneval after training on just 500 billion tokens (5 epochs). We have conducted extensive experiments across multiple language datasets, including Python, Java, and C++, and the results indicate that our model possesses robust foundational capabilities in code comprehension and generation.

Since language models (LMs) now outperform average humans on many challenging tasks, it has become increasingly difficult to develop challenging, high-quality, and realistic evaluations. We address this issue by examining LMs' capabilities to generate code for solving real scientific research problems. Incorporating input from scientists and AI researchers in 16 diverse natural science sub-fields, including mathematics, physics, chemistry, biology, and materials science, we created a scientist-curated coding benchmark, SciCode. The problems in SciCode naturally factorize into multiple subproblems, each involving knowledge recall, reasoning, and code synthesis. In total, SciCode contains 338 subproblems decomposed from 80 challenging main problems. It offers optional descriptions specifying useful scientific background information and scientist-annotated gold-standard solutions and test cases for evaluation. Claude3.5-Sonnet, the best-performing model among those tested, can solve only 4.6% of the problems in the most realistic setting. We believe that SciCode demonstrates both contemporary LMs' progress towards becoming helpful scientific assistants and sheds light on the development and evaluation of scientific AI in the future.

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.

Recent advances in large language models (LLMs) have given rise to powerful coding agents, making it possible for code assistants to evolve into code engineers. However, existing methods still face significant challenges in achieving high-fidelity document-to-codebase synthesis--such as scientific papers to code--primarily due to a fundamental conflict between information overload and the context bottlenecks of LLMs. In this work, we introduce DeepCode, a fully autonomous framework that fundamentally addresses this challenge through principled information-flow management. By treating repository synthesis as a channel optimization problem, DeepCode seamlessly orchestrates four information operations to maximize task-relevant signals under finite context budgets: source compression via blueprint distillation, structured indexing using stateful code memory, conditional knowledge injection via retrieval-augmented generation, and closed-loop error correction. Extensive evaluations on the PaperBench benchmark demonstrate that DeepCode achieves state-of-the-art performance, decisively outperforming leading commercial agents such as Cursor and Claude Code, and crucially, surpassing PhD-level human experts from top institutes on key reproduction metrics. By systematically transforming paper specifications into production-grade implementations comparable to human expert quality, this work establishes new foundations for autonomous scientific reproduction that can accelerate research evaluation and discovery.

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

Understanding and navigating large-scale codebases remains a significant challenge in software engineering. Existing methods often treat code as flat text or focus primarily on local structural relationships, limiting their ability to provide holistic, context-aware information retrieval. We present Hierarchical Code Graph Summarization (HCGS), a novel approach that constructs a multi-layered representation of a codebase by generating structured summaries in a bottom-up fashion from a code graph. HCGS leverages the Language Server Protocol for language-agnostic code analysis and employs a parallel level-based algorithm for efficient summary generation. Through extensive evaluation on five diverse codebases totaling 7,531 functions, HCGS demonstrates significant improvements in code retrieval accuracy, achieving up to 82 percentage relative improvement in top-1 retrieval precision for large codebases like libsignal (27.15 percentage points), and perfect Pass@3 scores for smaller repositories. The system's hierarchical approach consistently outperforms traditional code-only retrieval across all metrics, with particularly substantial gains in larger, more complex codebases where understanding function relationships is crucial.

Semantic code search, retrieving code that matches a given natural language query, is an important task to improve productivity in software engineering. Existing code search datasets are problematic: either using unrealistic queries, or with mismatched codes, and typically using one-to-one query-code pairing, which fails to reflect the reality that a query might have multiple valid code matches. This paper introduces CoSQA+, pairing high-quality queries (reused from CoSQA) with multiple suitable codes. We collect code candidates from diverse sources and form candidate pairs by pairing queries with these codes. Utilizing the power of large language models (LLMs), we automate pair annotation, filtering, and code generation for queries without suitable matches. Through extensive experiments, CoSQA+ has demonstrated superior quality over CoSQA. Models trained on CoSQA+ exhibit improved performance. Furthermore, we propose a new metric Mean Multi-choice Reciprocal Rank (MMRR), to assess one-to-N code search performance. We provide the code and data at https://github.com/DeepSoftwareAnalytics/CoSQA_Plus.

MimicKit is an open-source framework for training motion controllers using motion imitation and reinforcement learning. The codebase provides implementations of commonly-used motion-imitation techniques and RL algorithms. This framework is intended to support research and applications in computer graphics and robotics by providing a unified training framework, along with standardized environment, agent, and data structures. The codebase is designed to be modular and easily configurable, enabling convenient modification and extension to new characters and tasks. The open-source codebase is available at: https://github.com/xbpeng/MimicKit.

Code search is crucial for code reuse, enabling developers to efficiently locate relevant snippets. Current methods rely on encoder-based models, which suffer from limitations such as poor generalization and restricted input lengths. Decoder-only large language models (LLMs), with their extensive pre-training, larger size, and longer input capabilities, offer potential solutions to these issues, yet their effectiveness in code search remains underexplored. To fill this gap, our study presents the first systematic exploration of decoder-only LLMs for code search. We evaluate nine state-of-the-art decoder-only models using two fine-tuning methods, two datasets (CSN and CoSQA^+), and three model sizes. Our findings reveal that fine-tuned CodeGemma significantly outperforms encoder-only models like UniXcoder, achieving a 5.57% improvement in MRR on CSN and a 49.6% increase in MAP on CoSQA^+ compared to zero-shot UniXcoder. These results highlight the superior performance and adaptability of decoder-only models. Additionally, we provide valuable insights into optimizing these models for code search, covering aspects such as model selection, fine-tuning methods, training data, and model size, and discussing their strengths and limitations.

Large language models (LLMs) have fundamentally transformed automated software development by enabling direct translation of natural language descriptions into functional code, driving commercial adoption through tools like Github Copilot (Microsoft), Cursor (Anysphere), Trae (ByteDance), and Claude Code (Anthropic). While the field has evolved dramatically from rule-based systems to Transformer-based architectures, achieving performance improvements from single-digit to over 95\% success rates on benchmarks like HumanEval. In this work, we provide a comprehensive synthesis and practical guide (a series of analytic and probing experiments) about code LLMs, systematically examining the complete model life cycle from data curation to post-training through advanced prompting paradigms, code pre-training, supervised fine-tuning, reinforcement learning, and autonomous coding agents. We analyze the code capability of the general LLMs (GPT-4, Claude, LLaMA) and code-specialized LLMs (StarCoder, Code LLaMA, DeepSeek-Coder, and QwenCoder), critically examining the techniques, design decisions, and trade-offs. Further, we articulate the research-practice gap between academic research (e.g., benchmarks and tasks) and real-world deployment (e.g., software-related code tasks), including code correctness, security, contextual awareness of large codebases, and integration with development workflows, and map promising research directions to practical needs. Last, we conduct a series of experiments to provide a comprehensive analysis of code pre-training, supervised fine-tuning, and reinforcement learning, covering scaling law, framework selection, hyperparameter sensitivity, model architectures, and dataset comparisons.

Code Large Language Models (CodeLLMs) are increasingly used in code generation tasks across a wide range of applications. However, their performance is often inconsistent across different programming languages (PLs), with low-resource PLs suffering the most due to limited training data. In this paper, we present CodeChemist, a novel and efficient framework for test-time scaling that enables functional knowledge transfer from high-resource to low-resource PLs using generated test cases. CodeChemist first generates and executes code in high-resource PLs to create test cases that encapsulate functional knowledge. It then uses multi-temperature hedged sampling to generate code snippets in the low-resource PL and selects the best one based on the pass rate of the test cases. Our extensive experiments show that CodeChemist outperforms existing test-time scaling approaches, boosting the performance of code generation for low-resource PLs without requiring any model retraining.

Code search is a task to find programming codes that semantically match the given natural language queries. Even though some of the existing datasets for this task are multilingual on the programming language side, their query data are only in English. In this research, we create a multilingual code search dataset in four natural and four programming languages using a neural machine translation model. Using our dataset, we pre-train and fine-tune the Transformer-based models and then evaluate them on multiple code search test sets. Our results show that the model pre-trained with all natural and programming language data has performed best in most cases. By applying back-translation data filtering to our dataset, we demonstrate that the translation quality affects the model's performance to a certain extent, but the data size matters more.

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.

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

Semantic code search is the task of retrieving relevant code given a natural language query. While related to other information retrieval tasks, it requires bridging the gap between the language used in code (often abbreviated and highly technical) and natural language more suitable to describe vague concepts and ideas. To enable evaluation of progress on code search, we are releasing the CodeSearchNet Corpus and are presenting the CodeSearchNet Challenge, which consists of 99 natural language queries with about 4k expert relevance annotations of likely results from CodeSearchNet Corpus. The corpus contains about 6 million functions from open-source code spanning six programming languages (Go, Java, JavaScript, PHP, Python, and Ruby). The CodeSearchNet Corpus also contains automatically generated query-like natural language for 2 million functions, obtained from mechanically scraping and preprocessing associated function documentation. In this article, we describe the methodology used to obtain the corpus and expert labels, as well as a number of simple baseline solutions for the task. We hope that CodeSearchNet Challenge encourages researchers and practitioners to study this interesting task further and will host a competition and leaderboard to track the progress on the challenge. We are also keen on extending CodeSearchNet Challenge to more queries and programming languages in the future.

Code embedding models attract increasing attention due to the widespread popularity of retrieval-augmented generation (RAG) in software development. These models are expected to capture the rich semantic relationships inherent to code, which differ significantly from those found in text. However, existing models remain severely limited due to the scarcity of high-quality training data. In this work, we introduce CodeR (Code Retrieval), a state-of-the-art embedding model for general-purpose code retrieval. The superior performance of CodeR is built upon CodeR-Pile, a large-scale synthetic dataset constructed under the DRU (Diversity, Reliability, Usability) principle via a novel data synthesis pipeline. To optimize training effectiveness, we propose Annealing, a curriculum learning strategy that enables effective knowledge transfer across heterogeneous sources of data. We evaluate CodeR based on 16 diverse code retrieval tasks, where it significantly outperforms existing baselines and exhibits strong out-of-domain generalization performance. We have publicly released our code and the well-trained model to facilitate further research in this critical area. https://github.com/FlagOpen/FlagEmbedding/tree/master/research/BGE_Coder.

Code search is an important task that has seen many developments in recent years. However, previous attempts have mostly considered the problem of searching for code by a text query. We argue that using a code snippet (and possibly an associated traceback) as a query and looking for answers with bugfixing instructions and code samples is a natural use case that is not covered by existing approaches. Moreover, existing datasets use comments extracted from code rather than full-text descriptions as text, making them unsuitable for this use case. We present a new SearchBySnippet dataset implementing the search-by-code use case based on StackOverflow data; it turns out that in this setting, existing architectures fall short of the simplest BM25 baseline even after fine-tuning. We present a new single encoder model SnippeR that outperforms several strong baselines on the SearchBySnippet dataset with a result of 0.451 Recall@10; we propose the SearchBySnippet dataset and SnippeR as a new important benchmark for code search evaluation.

Detecting code clones is relevant to software maintenance and code refactoring. This challenge still presents unresolved cases, mainly when structural similarity does not reflect functional equivalence, though recent code models show promise. Therefore, this research aims to systematically measure the performance of several newly introduced small code models in classifying code pairs as clones or non-clones. The evaluation is based on five datasets: BigCloneBench, CodeJam, Karnalim, POJ104, and PoolC, as well as six code models: CodeBERT, GraphCodeBERT, Salesforce T5, UniXCoder, PLBART, and Polycoder. Most models performed well across standard metrics, including accuracy, precision, recall, and F1-score. However, a marginal fraction of clones remains challenging to detect, especially when the code looks similar but performs different operations. The source code that illustrates our approach is available at: https://github.com/jorge-martinez-gil/small-code-models

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

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

Large language models (LLMs) have shown promise in transforming machine learning research, yet their capability to faithfully implement novel ideas from recent research papers-ideas unseen during pretraining-remains unclear. We introduce ResearchCodeBench, a benchmark of 212 coding challenges that evaluates LLMs' ability to translate cutting-edge ML contributions from top 2024-2025 research papers into executable code. We assessed 30+ proprietary and open-source LLMs, finding that even the best models correctly implement less than 40% of the code. We find Gemini-2.5-Pro-Preview to perform best at 37.3% success rate, with O3 (High) and O4-mini (High) following behind at 32.3% and 30.8% respectively. We present empirical findings on performance comparison, contamination, and error patterns. By providing a rigorous and community-driven evaluation platform, ResearchCodeBench enables continuous understanding and advancement of LLM-driven innovation in research code generation.

Programming assistants powered by large language models have transformed software development, yet most benchmarks focus narrowly on code generation tasks. Recent efforts like InfiBench and StackEval attempt to address this gap using Stack Overflow data but remain limited to single-turn interactions in isolated contexts, require significant manual curation, and fail to represent complete project environments. We introduce CodeAssistBench (CAB), the first benchmark framework for evaluating multi-turn programming assistance in realistic settings that address real-world questions about actual codebases. Unlike existing programming Q&A benchmarks, CAB automatically generates scalable datasets from question-related GitHub issues using configurable parameters (e.g., repository creation date, star count, programming languages), and includes automatic containerization of codebases for evaluation. It then evaluates models through simulated users in these containerized environments with full codebase access. Using this framework, we constructed a test set of 3,286 real-world programming questions across 231 repositories, spanning seven programming languages and diverse problem domains. Our evaluation of leading LLMs reveals a substantial capability gap: while models perform well on Stack Overflow questions with success rates of 70-83%, they resolve only up to 16.49% of CAB's recent issues. This discrepancy highlights the challenges of providing assistance in complex, project-specific contexts versus answering standalone questions.

The capability of accurately determining code similarity is crucial in many tasks related to software development. For example, it might be essential to identify code duplicates for performing software maintenance. This research introduces a novel ensemble learning approach for code similarity assessment, combining the strengths of multiple unsupervised similarity measures. The key idea is that the strengths of a diverse set of similarity measures can complement each other and mitigate individual weaknesses, leading to improved performance. Preliminary results show that while Transformers-based CodeBERT and its variant GraphCodeBERT are undoubtedly the best option in the presence of abundant training data, in the case of specific small datasets (up to 500 samples), our ensemble achieves similar results, without prejudice to the interpretability of the resulting solution, and with a much lower associated carbon footprint due to training. The source code of this novel approach can be downloaded from https://github.com/jorge-martinez-gil/ensemble-codesim.

Despite the substantial success of Information Retrieval (IR) in various NLP tasks, most IR systems predominantly handle queries and corpora in natural language, neglecting the domain of code retrieval. Code retrieval is critically important yet remains under-explored, with existing methods and benchmarks inadequately representing the diversity of code in various domains and tasks. Addressing this gap, we present \name (Code Information Retrieval Benchmark), a robust and comprehensive benchmark specifically designed to assess code retrieval capabilities. \name comprises ten meticulously curated code datasets, spanning eight distinctive retrieval tasks across seven diverse domains. We first discuss the construction of \name and its diverse dataset composition. Further, we evaluate nine widely used retrieval models using \name, uncovering significant difficulties in performing code retrieval tasks even with state-of-the-art systems. To facilitate easy adoption and integration within existing research workflows, \name has been developed as a user-friendly Python framework, readily installable via pip. It shares same data schema as other popular benchmarks like MTEB and BEIR, enabling seamless cross-benchmark evaluations. Through \name, we aim to invigorate research in the code retrieval domain, providing a versatile benchmarking tool that encourages further development and exploration of code retrieval systems\url{ https://github.com/CoIR-team/coir}.

With the rapid increase in the amount of public code repositories, developers maintain a great desire to retrieve precise code snippets by using natural language. Despite existing deep learning based approaches(e.g., DeepCS and MMAN) have provided the end-to-end solutions (i.e., accepts natural language as queries and shows related code fragments retrieved directly from code corpus), the accuracy of code search in the large-scale repositories is still limited by the code representation (e.g., AST) and modeling (e.g., directly fusing the features in the attention stage). In this paper, we propose a novel learnable deep Graph for Code Search (calleddeGraphCS), to transfer source code into variable-based flow graphs based on the intermediate representation technique, which can model code semantics more precisely compared to process the code as text directly or use the syntactic tree representation. Furthermore, we propose a well-designed graph optimization mechanism to refine the code representation, and apply an improved gated graph neural network to model variable-based flow graphs. To evaluate the effectiveness of deGraphCS, we collect a large-scale dataset from GitHub containing 41,152 code snippets written in C language, and reproduce several typical deep code search methods for comparison. Besides, we design a qualitative user study to verify the practical value of our approach. The experimental results have shown that deGraphCS can achieve state-of-the-art performances, and accurately retrieve code snippets satisfying the needs of the users.

Over the last several decades, software has been woven into the fabric of every aspect of our society. As software development surges and code infrastructure of enterprise applications ages, it is now more critical than ever to increase software development productivity and modernize legacy applications. Advances in deep learning and machine learning algorithms have enabled numerous breakthroughs, motivating researchers to leverage AI techniques to improve software development efficiency. Thus, the fast-emerging research area of AI for Code has garnered new interest and gathered momentum. In this paper, we present a large-scale dataset CodeNet, consisting of over 14 million code samples and about 500 million lines of code in 55 different programming languages, which is aimed at teaching AI to code. In addition to its large scale, CodeNet has a rich set of high-quality annotations to benchmark and help accelerate research in AI techniques for a variety of critical coding tasks, including code similarity and classification, code translation between a large variety of programming languages, and code performance (runtime and memory) improvement techniques. Additionally, CodeNet provides sample input and output test sets for 98.5% of the code samples, which can be used as an oracle for determining code correctness and potentially guide reinforcement learning for code quality improvements. As a usability feature, we provide several pre-processing tools in CodeNet to transform source code into representations that can be readily used as inputs into machine learning models. Results of code classification and code similarity experiments using the CodeNet dataset are provided as a reference. We hope that the scale, diversity and rich, high-quality annotations of CodeNet will offer unprecedented research opportunities at the intersection of AI and Software Engineering.

As coding agents are increasingly deployed in large codebases, the need to automatically design challenging, codebase-level evaluation is central. We propose Gistify, a task where a coding LLM must create a single, minimal, self-contained file that can reproduce a specific functionality of a codebase. The coding LLM is given full access to a codebase along with a specific entrypoint (e.g., a python command), and the generated file must replicate the output of the same command ran under the full codebase, while containing only the essential components necessary to execute the provided command. Success on Gistify requires both structural understanding of the codebase, accurate modeling of its execution flow as well as the ability to produce potentially large code patches. Our findings show that current state-of-the-art models struggle to reliably solve Gistify tasks, especially ones with long executions traces.

Code generation aims to automatically generate code snippets of specific programming language according to natural language descriptions. The continuous advancements in deep learning, particularly pre-trained models, have empowered the code generation task to achieve remarkable performance. One main challenge of pre-trained models for code generation is the semantic gap between natural language requirements and source code. To address the issue, prior studies typically adopt a retrieval-augmented framework for the task, where the similar code snippets collected by a retrieval process can be leveraged to help understand the requirements and provide guidance for the generation process. However, there is a lack of systematic study on the application of this framework for code generation, including the impact of the final generated results and the specific usage of the framework. In this paper, we choose three popular pre-trained code models, namely CodeGen, UniXcoder, and CodeT5, to assess the impact of the quality and utilization of retrieved code on the retrieval-augmented framework. Our analysis shows that the retrieval-augmented framework is beneficial for improving the performance of the existing pre-trained models. We also provide suggestions on the utilization of the retrieval-augmented code generation framework: BM25 and Sequential Integration Fusion are recommended due to their convenience and superior performance. Sketch Filling Fusion, which extracts a sketch of relevant code, could help the model improve its performance further. Additionally, we conduct experiments to investigate the influence of the retrieval-augmented framework on large language models for code generation, showing the effectiveness of the framework, and we discuss the trade-off between performance improvement and computational costs in each phase within the framework.

Despite the success of text retrieval in many NLP tasks, code retrieval remains a largely underexplored area. Most text retrieval systems are tailored for natural language queries, often neglecting the specific challenges of retrieving code. This gap leaves existing models unable to effectively capture the diversity of programming languages and tasks across different domains, highlighting the need for more focused research in code retrieval. To address this, we introduce CodeXEmbed, a family of large-scale code embedding models ranging from 400M to 7B parameters. Our novel training pipeline unifies multiple programming languages and transforms various code-related tasks into a common retrieval framework, enhancing model generalizability and retrieval performance. Our 7B model sets a new state-of-the-art (SOTA) in code retrieval, outperforming the previous leading model, Voyage-Code, by over 20% on CoIR benchmark. In addition to excelling in code retrieval, our models demonstrate competitive performance on the widely adopted BeIR text retrieval benchmark, offering versatility across domains. Experimental results demonstrate that improving retrieval performance significantly enhances end-to-end Retrieval-Augmented Generation (RAG) performance for code-related tasks.

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.

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

Code search aims to retrieve semantically relevant code snippets for a given natural language query. Recently, many approaches employing contrastive learning have shown promising results on code representation learning and greatly improved the performance of code search. However, there is still a lot of room for improvement in using contrastive learning for code search. In this paper, we propose CoCoSoDa to effectively utilize contrastive learning for code search via two key factors in contrastive learning: data augmentation and negative samples. Specifically, soft data augmentation is to dynamically masking or replacing some tokens with their types for input sequences to generate positive samples. Momentum mechanism is used to generate large and consistent representations of negative samples in a mini-batch through maintaining a queue and a momentum encoder. In addition, multimodal contrastive learning is used to pull together representations of code-query pairs and push apart the unpaired code snippets and queries. We conduct extensive experiments to evaluate the effectiveness of our approach on a large-scale dataset with six programming languages. Experimental results show that: (1) CoCoSoDa outperforms 14 baselines and especially exceeds CodeBERT, GraphCodeBERT, and UniXcoder by 13.3%, 10.5%, and 5.9% on average MRR scores, respectively. (2) The ablation studies show the effectiveness of each component of our approach. (3) We adapt our techniques to several different pre-trained models such as RoBERTa, CodeBERT, and GraphCodeBERT and observe a significant boost in their performance in code search. (4) Our model performs robustly under different hyper-parameters. Furthermore, we perform qualitative and quantitative analyses to explore reasons behind the good performance of our model.

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.

Large language models (LLMs) have manifested strong ability to generate codes for productive activities. However, current benchmarks for code synthesis, such as HumanEval, MBPP, and DS-1000, are predominantly oriented towards introductory tasks on algorithm and data science, insufficiently satisfying challenging requirements prevalent in real-world coding. To fill this gap, we propose NaturalCodeBench (NCB), a challenging code benchmark designed to mirror the complexity and variety of scenarios in real coding tasks. NCB comprises 402 high-quality problems in Python and Java, meticulously selected from natural user queries from online coding services, covering 6 different domains. Noting the extraordinary difficulty in creating testing cases for real-world queries, we also introduce a semi-automated pipeline to enhance the efficiency of test case construction. Comparing with manual solutions, it achieves an efficiency increase of more than 4 times. Our systematic experiments on 39 LLMs find that performance gaps on NCB between models with close HumanEval scores could still be significant, indicating a lack of focus on practical code synthesis scenarios or over-specified optimization on HumanEval. On the other hand, even the best-performing GPT-4 is still far from satisfying on NCB. The evaluation toolkit and development set are available at https://github.com/THUDM/NaturalCodeBench.

Language models can serve as a valuable tool for software developers to increase productivity. Large generative models can be used for code generation and code completion, while smaller encoder-only models are capable of performing code search tasks using natural language queries.These capabilities are heavily influenced by the quality and diversity of the available training data. Source code datasets used for training usually focus on the most popular languages and testing is mostly conducted on the same distributions, often overlooking low-resource programming languages. Motivated by the NLP generalization taxonomy proposed by Hupkes et.\,al., we propose a new benchmark dataset called GenCodeSearchNet (GeCS) which builds upon existing natural language code search datasets to systemically evaluate the programming language understanding generalization capabilities of language models. As part of the full dataset, we introduce a new, manually curated subset StatCodeSearch that focuses on R, a popular but so far underrepresented programming language that is often used by researchers outside the field of computer science. For evaluation and comparison, we collect several baseline results using fine-tuned BERT-style models and GPT-style large language models in a zero-shot setting.

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

Recent code translation techniques exploit neural machine translation models to translate source code from one programming language to another to satisfy production compatibility or to improve efficiency of codebase maintenance. Most existing code translation datasets only focus on a single pair of popular programming languages. To advance research on code translation and meet diverse requirements of real-world applications, we construct CodeTransOcean, a large-scale comprehensive benchmark that supports the largest variety of programming languages for code translation. CodeTransOcean consists of three novel multilingual datasets, namely, MultilingualTrans supporting translations between multiple popular programming languages, NicheTrans for translating between niche programming languages and popular ones, and LLMTrans for evaluating executability of translated code by large language models (LLMs). CodeTransOcean also includes a novel cross-framework dataset, DLTrans, for translating deep learning code across different frameworks. We develop multilingual modeling approaches for code translation and demonstrate their great potential in improving the translation quality of both low-resource and high-resource language pairs and boosting the training efficiency. We also propose a novel evaluation metric Debugging Success Rate@K for program-level code translation. Last but not least, we evaluate LLM ChatGPT on our datasets and investigate its potential for fuzzy execution predictions. We build baselines for CodeTransOcean and analyze challenges of code translation for guiding future research. The CodeTransOcean datasets and code are publicly available at https://github.com/WeixiangYAN/CodeTransOcean.

Pre-trained language models like ChatGPT have significantly improved code generation. As these models scale up, there is an increasing need for the output to handle more intricate tasks. Moreover, in bioinformatics, generating functional programs poses additional notable challenges due to the amount of domain knowledge, the need for complicated data operations, and intricate functional dependencies between the operations. Here, we present BioCoder, a benchmark developed to evaluate existing pre-trained models in generating bioinformatics code. In relation to function-code generation, BioCoder covers potential package dependencies, class declarations, and global variables. It incorporates 1026 functions and 1243 methods in Python and Java from GitHub and 253 examples from the Rosalind Project. BioCoder incorporates a fuzz-testing framework for evaluation, and we have applied it to evaluate many models including InCoder, CodeGen, CodeGen2, SantaCoder, StarCoder, StarCoder+, InstructCodeT5+, and ChatGPT. Our detailed analysis of these models emphasizes the importance of domain knowledge, pragmatic code generation, and contextual understanding. Our dataset, benchmark, Docker images, and scripts required for testing are all available at https://github.com/gersteinlab/biocoder.

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

Code retrieval is a crucial component in modern software development, particularly in large-scale projects. However, existing approaches relying on sequence-based models often fail to fully exploit the structural dependencies inherent in code, leading to suboptimal retrieval performance, particularly with structurally complex code fragments. In this paper, we introduce GNN-Coder, a novel framework based on Graph Neural Network (GNN) to utilize Abstract Syntax Tree (AST). We make the first attempt to study how GNN-integrated Transformer can promote the development of semantic retrieval tasks by capturing the structural and semantic features of code. We further propose an innovative graph pooling method tailored for AST, utilizing the number of child nodes as a key feature to highlight the intrinsic topological relationships within the AST. This design effectively integrates both sequential and hierarchical representations, enhancing the model's ability to capture code structure and semantics. Additionally, we introduce the Mean Angular Margin (MAM), a novel metric for quantifying the uniformity of code embedding distributions, providing a standardized measure of feature separability. The proposed method achieves a lower MAM, indicating a more discriminative feature representation. This underscores GNN-Coder's superior ability to distinguish between code snippets, thereby enhancing retrieval accuracy. Experimental results show that GNN-Coder significantly boosts retrieval performance, with a 1\%-10\% improvement in MRR on the CSN dataset, and a notable 20\% gain in zero-shot performance on the CosQA dataset.

Language models have shown promising performance on the task of translating natural language questions into SQL queries (Text-to-SQL). However, most of the state-of-the-art (SOTA) approaches rely on powerful yet closed-source large language models (LLMs), such as ChatGPT and GPT-4, which may have the limitations of unclear model architectures, data privacy risks, and expensive inference overheads. To address the limitations, we introduce CodeS, a series of pre-trained language models with parameters ranging from 1B to 15B, specifically designed for the text-to-SQL task. CodeS is a fully open-source language model, which achieves superior accuracy with much smaller parameter sizes. This paper studies the research challenges in building CodeS. To enhance the SQL generation abilities of CodeS, we adopt an incremental pre-training approach using a specifically curated SQL-centric corpus. Based on this, we address the challenges of schema linking and rapid domain adaptation through strategic prompt construction and a bi-directional data augmentation technique. We conduct comprehensive evaluations on multiple datasets, including the widely used Spider benchmark, the newly released BIRD benchmark, robustness-diagnostic benchmarks such as Spider-DK, Spider-Syn, Spider-Realistic, and Dr.Spider, as well as two real-world datasets created for financial and academic applications. The experimental results show that our CodeS achieves new SOTA accuracy and robustness on nearly all challenging text-to-SQL benchmarks.

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

This paper presents NT-Java-1.1B, an open-source specialized code language model built on StarCoderBase-1.1B, designed for coding tasks in Java programming. NT-Java-1.1B achieves state-of-the-art performance, surpassing its base model and majority of other models of similar size on MultiPL-E Java code benchmark. While there have been studies on extending large, generic pre-trained models to improve proficiency in specific programming languages like Python, similar investigations on small code models for other programming languages are lacking. Large code models require specialized hardware like GPUs for inference, highlighting the need for research into building small code models that can be deployed on developer desktops. This paper addresses this research gap by focusing on the development of a small Java code model, NT-Java-1.1B, and its quantized versions, which performs comparably to open models around 1.1B on MultiPL-E Java code benchmarks, making them ideal for desktop deployment. This paper establishes the foundation for specialized models across languages and sizes for a family of NT Models.

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

Finding codes given natural language query isb eneficial to the productivity of software developers. Future progress towards better semantic matching between query and code requires richer supervised training resources. To remedy this, we introduce the CoSQA dataset.It includes 20,604 labels for pairs of natural language queries and codes, each annotated by at least 3 human annotators. We further introduce a contrastive learning method dubbed CoCLR to enhance query-code matching, which works as a data augmenter to bring more artificially generated training instances. We show that evaluated on CodeXGLUE with the same CodeBERT model, training on CoSQA improves the accuracy of code question answering by 5.1%, and incorporating CoCLR brings a further improvement of 10.5%.

Training machine learning approaches for vulnerability identification and producing reliable tools to assist developers in implementing quality software -- free of vulnerabilities -- is challenging due to the lack of large datasets and real data. Researchers have been looking at these issues and building datasets. However, these datasets usually miss natural language artifacts and programming language diversity. We scraped the entire CVE details database for GitHub references and augmented the data with 3 security-related datasets. We used the data to create a ground-truth dataset of natural language artifacts (such as commit messages, commits comments, and summaries), meta-data and code changes. Our dataset integrates a total of 8057 security-relevant commits -- the equivalent to 5942 security patches -- from 1339 different projects spanning 146 different types of vulnerabilities and 20 languages. A dataset of 110k non-security-related commits is also provided. Data and scripts are all available on GitHub. Data is stored in a .CSV file. Codebases can be downloaded using our scripts. Our dataset is a valuable asset to answer research questions on different topics such as the identification of security-relevant information using NLP models; software engineering and security best practices; and, vulnerability detection and patching; and, security program analysis.

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.

Using Large Language Models (LLMs) has gained popularity among software developers for generating source code. However, the use of LLM-generated code can introduce risks of adding suboptimal, defective, and vulnerable code. This makes it necessary to devise methods for the accurate detection of LLM-generated code. Toward this goal, we perform a case study of Claude 3 Haiku (or Claude 3 for brevity) on CodeSearchNet dataset. We divide our analyses into two parts: function-level and class-level. We extract 22 software metric features, such as Code Lines and Cyclomatic Complexity, for each level of granularity. We then analyze code snippets generated by Claude 3 and their human-authored counterparts using the extracted features to understand how unique the code generated by Claude 3 is. In the following step, we use the unique characteristics of Claude 3-generated code to build Machine Learning (ML) models and identify which features of the code snippets make them more detectable by ML models. Our results indicate that Claude 3 tends to generate longer functions, but shorter classes than humans, and this characteristic can be used to detect Claude 3-generated code with ML models with 82% and 66% accuracies for function-level and class-level snippets, respectively.

The performance of automatic code documentation generation models depends critically on the quality of the training data used for supervision. However, most existing code documentation datasets are constructed through large scale scraping of public repositories with limited quality control. As a result, they often contain noisy documentation, extensive duplication, and increasing contamination from AI generated content. These issues weaken the supervision signal available to learning-based models and complicate evaluation. We introduce Code2Doc, a quality-first curated dataset for function-level code documentation generation. Code2Doc consists of 13,358 high-quality function-documentation pairs extracted from widely used open-source repositories spanning five programming languages: Python, Java, TypeScript, JavaScript, and C++. The dataset is constructed using a four-stage curation pipeline that enforces documentation completeness and clarity, filters functions based on structural and complexity criteria, removes exact and near-duplicate code, and identifies documentation likely to be AI generated. Starting from 52,069 extracted candidates, only 25.6% satisfy all quality constraints. We provide a detailed analysis of the resulting dataset, which achieves a mean documentation quality score of 6.93 out of 10. Overall, 86.9% of samples contain explicit type annotations, and only 2.9% are flagged as potentially AI generated. Baseline experiments show that fine-tuning a large language model on Code2Doc yields relative improvements of 29.47% in BLEU and 24.04% in ROUGE-L over zero shot performance, despite the modest dataset size. We release both the dataset and the full curation pipeline to support reproducible research on automatic code documentation generation.

There has been an increase of interest in code search using natural language. Assessing the performance of such code search models can be difficult without a readily available evaluation suite. In this paper, we present an evaluation dataset consisting of natural language query and code snippet pairs, with the hope that future work in this area can use this dataset as a common benchmark. We also provide the results of two code search models ([1] and [6]) from recent work. The evaluation dataset is available at https://github.com/facebookresearch/Neural-Code-Search-Evaluation-Dataset

In code search, the Generation-Augmented Retrieval (GAR) framework, which generates exemplar code snippets to augment queries, has emerged as a promising strategy to address the principal challenge of modality misalignment between code snippets and natural language queries, particularly with the demonstrated code generation capabilities of Large Language Models (LLMs). Nevertheless, our preliminary investigations indicate that the improvements conferred by such an LLM-augmented framework are somewhat constrained. This limitation could potentially be ascribed to the fact that the generated codes, albeit functionally accurate, frequently display a pronounced stylistic deviation from the ground truth code in the codebase. In this paper, we extend the foundational GAR framework and propose a simple yet effective method that additionally Rewrites the Code (ReCo) within the codebase for style normalization. Experimental results demonstrate that ReCo significantly boosts retrieval accuracy across sparse (up to 35.7%), zero-shot dense (up to 27.6%), and fine-tuned dense (up to 23.6%) retrieval settings in diverse search scenarios. To further elucidate the advantages of ReCo and stimulate research in code style normalization, we introduce Code Style Similarity, the first metric tailored to quantify stylistic similarities in code. Notably, our empirical findings reveal the inadequacy of existing metrics in capturing stylistic nuances.

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

Large language models (LMs) of code have recently shown tremendous promise in completing code and synthesizing code from natural language descriptions. However, the current state-of-the-art code LMs (e.g., Codex (Chen et al., 2021)) are not publicly available, leaving many questions about their model and data design decisions. We aim to fill in some of these blanks through a systematic evaluation of the largest existing models: Codex, GPT-J, GPT-Neo, GPT-NeoX-20B, and CodeParrot, across various programming languages. Although Codex itself is not open-source, we find that existing open-source models do achieve close results in some programming languages, although targeted mainly for natural language modeling. We further identify an important missing piece in the form of a large open-source model trained exclusively on a multi-lingual corpus of code. We release a new model, PolyCoder, with 2.7B parameters based on the GPT-2 architecture, which was trained on 249GB of code across 12 programming languages on a single machine. In the C programming language, PolyCoder outperforms all models including Codex. Our trained models are open-source and publicly available at https://github.com/VHellendoorn/Code-LMs, which enables future research and application in this area.

Code search with natural language plays a crucial role in reusing existing code snippets and accelerating software development. Thanks to the Transformer-based pretraining models, the performance of code search has been improved significantly compared to traditional information retrieval (IR) based models. However, due to the quadratic complexity of multi-head self-attention, there is a limit on the input token length. For efficient training on standard GPUs like V100, existing pretrained code models, including GraphCodeBERT, CodeBERT, RoBERTa (code), take the first 256 tokens by default, which makes them unable to represent the complete information of long code that is greater than 256 tokens. Unlike long text paragraph that can be regarded as a whole with complete semantics, the semantics of long code is discontinuous as a piece of long code may contain different code modules. Therefore, it is unreasonable to directly apply the long text processing methods to long code. To tackle the long code problem, we propose SEA (Split, Encode and Aggregate for Long Code Search), which splits long code into code blocks, encodes these blocks into embeddings, and aggregates them to obtain a comprehensive long code representation. With SEA, we could directly use Transformer-based pretraining models to model long code without changing their internal structure and repretraining. Leveraging abstract syntax tree (AST) based splitting and attention-based aggregation methods, SEA achieves significant improvements in long code search performance. We also compare SEA with two sparse Trasnformer methods. With GraphCodeBERT as the encoder, SEA achieves an overall mean reciprocal ranking score of 0.785, which is 10.1% higher than GraphCodeBERT on the CodeSearchNet benchmark.

Despite long-standing efforts in accelerating scientific discovery with AI, building AI co-scientists remains challenging due to limited high-quality data for training and evaluation. To tackle this data scarcity issue, we present AutoSDT, an automatic pipeline that collects high-quality coding tasks in real-world data-driven discovery workflows. AutoSDT leverages the coding capabilities and parametric knowledge of LLMs to search for diverse sources, select ecologically valid tasks, and synthesize accurate task instructions and code solutions. Using our pipeline, we construct AutoSDT-5K, a dataset of 5,404 coding tasks for data-driven discovery that covers four scientific disciplines and 756 unique Python packages. To the best of our knowledge, AutoSDT-5K is the only automatically collected and the largest open dataset for data-driven scientific discovery. Expert feedback on a subset of 256 tasks shows the effectiveness of AutoSDT: 93% of the collected tasks are ecologically valid, and 92.2% of the synthesized programs are functionally correct. Trained on AutoSDT-5K, the Qwen2.5-Coder-Instruct LLM series, dubbed AutoSDT-Coder, show substantial improvement on two challenging data-driven discovery benchmarks, ScienceAgentBench and DiscoveryBench. Most notably, AutoSDT-Coder-32B reaches the same level of performance as GPT-4o on ScienceAgentBench with a success rate of 7.8%, doubling the performance of its base model. On DiscoveryBench, it lifts the hypothesis matching score to 8.1, bringing a 17.4% relative improvement and closing the gap between open-weight models and GPT-4o.

The ability to generate natural language sequences from source code snippets has a variety of applications such as code summarization, documentation, and retrieval. Sequence-to-sequence (seq2seq) models, adopted from neural machine translation (NMT), have achieved state-of-the-art performance on these tasks by treating source code as a sequence of tokens. We present {scriptsize CODE2SEQ}: an alternative approach that leverages the syntactic structure of programming languages to better encode source code. Our model represents a code snippet as the set of compositional paths in its abstract syntax tree (AST) and uses attention to select the relevant paths while decoding. We demonstrate the effectiveness of our approach for two tasks, two programming languages, and four datasets of up to 16M examples. Our model significantly outperforms previous models that were specifically designed for programming languages, as well as state-of-the-art NMT models. An interactive online demo of our model is available at http://code2seq.org. Our code, data and trained models are available at http://github.com/tech-srl/code2seq.

Code-LLMs, LLMs pre-trained on large code corpora, have shown great progress in learning rich representations of the structure and syntax of code, successfully using it to generate or classify code fragments. At the same time, understanding if they are able to do so because they capture code semantics, and how well, is still an open question. In this paper, we tackle this problem by introducing SeqCoBench, a benchmark for systematically assessing how Code-LLMs can capture code functional equivalence. SeqCoBench contains over 20 code transformations that either preserve or alter the semantics of Python programs. We conduct extensive evaluations in different settings, including zero-shot and parameter-efficient finetuning methods on state-of-the-art (Code)-LLMs to see if they can discern semantically equivalent or different pairs of programs in SeqCoBench. We find that the performance gap between these LLMs and classical match-based retrieval scores is minimal, with both approaches showing a concerning lack of depth in understanding code semantics.

We introduce KodCode, a synthetic dataset that addresses the persistent challenge of acquiring high-quality, verifiable training data across diverse difficulties and domains for training Large Language Models for coding. Existing code-focused resources typically fail to ensure either the breadth of coverage (e.g., spanning simple coding tasks to advanced algorithmic problems) or verifiable correctness (e.g., unit tests). In contrast, KodCode comprises question-solution-test triplets that are systematically validated via a self-verification procedure. Our pipeline begins by synthesizing a broad range of coding questions, then generates solutions and test cases with additional attempts allocated to challenging problems. Finally, post-training data synthesis is done by rewriting questions into diverse formats and generating responses under a test-based reject sampling procedure from a reasoning model (DeepSeek R1). This pipeline yields a large-scale, robust and diverse coding dataset. KodCode is suitable for supervised fine-tuning and the paired unit tests also provide great potential for RL tuning. Fine-tuning experiments on coding benchmarks (HumanEval(+), MBPP(+), BigCodeBench, and LiveCodeBench) demonstrate that KodCode-tuned models achieve state-of-the-art performance, surpassing models like Qwen2.5-Coder-32B-Instruct and DeepSeek-R1-Distill-Llama-70B.

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

Scientific knowledge is growing rapidly, making it challenging to track progress and high-level conceptual links across broad disciplines. While existing tools like citation networks and search engines make it easy to access a few related papers, they fundamentally lack the flexible abstraction needed to represent the density of activity in various scientific subfields. We motivate SCIENCE HIERARCHOGRAPHY, the goal of organizing scientific literature into a high-quality hierarchical structure that allows for the categorization of scientific work across varying levels of abstraction, from very broad fields to very specific studies. Such a representation can provide insights into which fields are well-explored and which are under-explored. To achieve the goals of SCIENCE HIERARCHOGRAPHY, we develop a range of algorithms. Our primary approach combines fast embedding-based clustering with LLM-based prompting to balance the computational efficiency of embedding methods with the semantic precision offered by LLM prompting. We demonstrate that this approach offers the best trade-off between quality and speed compared to methods that heavily rely on LLM prompting, such as iterative tree construction with LLMs. To better reflect the interdisciplinary and multifaceted nature of research papers, our hierarchy captures multiple dimensions of categorization beyond simple topic labels. We evaluate the utility of our framework by assessing how effectively an LLM-based agent can locate target papers using the hierarchy. Results show that this structured approach enhances interpretability, supports trend discovery, and offers an alternative pathway for exploring scientific literature beyond traditional search methods. Code, data and demo: https://github.com/JHU-CLSP/science-hierarchography{https://github.com/JHU-CLSP/science-hierarchography}

Large Language Models (LLMs) have exhibited exceptional performance in software engineering yet face challenges in adapting to continually evolving code knowledge, particularly regarding the frequent updates of third-party library APIs. This limitation, stemming from static pre-training datasets, often results in non-executable code or implementations with suboptimal safety and efficiency. To this end, this paper introduces CODESYNC, a data engine for identifying outdated code patterns and collecting real-time code knowledge updates from Python third-party libraries. Building upon CODESYNC, we develop CODESYNCBENCH, a comprehensive benchmark for assessing LLMs' ability to stay synchronized with code evolution, which covers real-world updates for 220 APIs from six Python libraries. Our benchmark offers 3,300 test cases across three evaluation tasks and an update-aware instruction tuning dataset consisting of 2,200 training samples. Extensive experiments on 14 state-of-the-art LLMs reveal that they struggle with dynamic code evolution, even with the support of advanced knowledge updating methods (e.g., DPO, ORPO, and SimPO). We believe that our benchmark can offer a strong foundation for the development of more effective methods for real-time code knowledge updating in the future. The experimental code and dataset are publicly available at: https://github.com/Lucky-voyage/Code-Sync.

Current benchmarks for coding evaluate language models (LMs) on concrete, well-specified tasks such as fixing specific bugs or writing targeted tests. However, human programmers do not spend all day incessantly addressing isolated tasks. Instead, real-world software development is grounded in the pursuit of high-level goals, like improving user retention or reducing costs. Evaluating whether LMs can also iteratively develop code to better accomplish open-ended objectives without any explicit guidance remains an open challenge. To address this, we introduce CodeClash, a benchmark where LMs compete in multi-round tournaments to build the best codebase for achieving a competitive objective. Each round proceeds in two phases: agents edit their code, then their codebases compete head-to-head in a code arena that determines winners based on objectives like score maximization, resource acquisition, or survival. Whether it's writing notes, scrutinizing documentation, analyzing competition logs, or creating test suites, models must decide for themselves how to improve their codebases both absolutely and against their opponents. We run 1680 tournaments (25,200 rounds total) to evaluate 8 LMs across 6 arenas. Our results reveal that while models exhibit diverse development styles, they share fundamental limitations in strategic reasoning. Models also struggle with long-term codebase maintenance, as repositories become progressively messy and redundant. These limitations are stark: top models lose every round against expert human programmers. We open-source CodeClash to advance the study of autonomous, goal-oriented code development.

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.

Large Language Models (LLMs) trained on code are revolutionizing the software development process. Increasingly, code LLMs are being integrated into software development environments to improve the productivity of human programmers, and LLM-based agents are beginning to show promise for handling complex tasks autonomously. Realizing the full potential of code LLMs requires a wide range of capabilities, including code generation, fixing bugs, explaining and documenting code, maintaining repositories, and more. In this work, we introduce the Granite series of decoder-only code models for code generative tasks, trained with code written in 116 programming languages. The Granite Code models family consists of models ranging in size from 3 to 34 billion parameters, suitable for applications ranging from complex application modernization tasks to on-device memory-constrained use cases. Evaluation on a comprehensive set of tasks demonstrates that Granite Code models consistently reaches state-of-the-art performance among available open-source code LLMs. The Granite Code model family was optimized for enterprise software development workflows and performs well across a range of coding tasks (e.g. code generation, fixing and explanation), making it a versatile all around code model. We release all our Granite Code models under an Apache 2.0 license for both research and commercial use.

Code intelligence plays a key role in transforming modern software engineering. Recently, deep learning-based models, especially Transformer-based large language models (LLMs), have demonstrated remarkable potential in tackling these tasks by leveraging massive open-source code data and programming language features. However, the development and deployment of such models often require expertise in both machine learning and software engineering, creating a barrier for the model adoption. In this paper, we present CodeTF, an open-source Transformer-based library for state-of-the-art Code LLMs and code intelligence. Following the principles of modular design and extensible framework, we design CodeTF with a unified interface to enable rapid access and development across different types of models, datasets and tasks. Our library supports a collection of pretrained Code LLM models and popular code benchmarks, including a standardized interface to train and serve code LLMs efficiently, and data features such as language-specific parsers and utility functions for extracting code attributes. In this paper, we describe the design principles, the architecture, key modules and components, and compare with other related library tools. Finally, we hope CodeTF is able to bridge the gap between machine learning/generative AI and software engineering, providing a comprehensive open-source solution for developers, researchers, and practitioners.

Understanding biodiversity is a global challenge, in which DNA barcodes - short snippets of DNA that cluster by species - play a pivotal role. In particular, invertebrates, a highly diverse and under-explored group, pose unique taxonomic complexities. We explore machine learning approaches, comparing supervised CNNs, fine-tuned foundation models, and a DNA barcode-specific masking strategy across datasets of varying complexity. While simpler datasets and tasks favor supervised CNNs or fine-tuned transformers, challenging species-level identification demands a paradigm shift towards self-supervised pretraining. We propose BarcodeBERT, the first self-supervised method for general biodiversity analysis, leveraging a 1.5 M invertebrate DNA barcode reference library. This work highlights how dataset specifics and coverage impact model selection, and underscores the role of self-supervised pretraining in achieving high-accuracy DNA barcode-based identification at the species and genus level. Indeed, without the fine-tuning step, BarcodeBERT pretrained on a large DNA barcode dataset outperforms DNABERT and DNABERT-2 on multiple downstream classification tasks. The code repository is available at https://github.com/Kari-Genomics-Lab/BarcodeBERT

To extend the scope of coding queries to more realistic settings, we propose ODEX, the first Open-Domain EXecution-based natural language (NL) to Python code generation dataset. ODEX has 945 NL-Code pairs spanning 79 diverse libraries, along with 1,707 human-written test cases for execution. Our NL-Code pairs are harvested from StackOverflow forums to encourage natural and practical coding queries. Moreover, ODEX supports four natural languages as intents, in English, Spanish, Japanese, and Russian. ODEX unveils intriguing behavioral differences among top-performing code language models (LM). While CODEX achieves better overall results, CODEGEN improves effectively via scaling -- CODEGEN 6.1B performs comparably with CODEX 12B. Both models show substantial gaps between open and closed domains, but CODEGEN gaps tend to decrease with model size while CODEX gaps increase. We release ODEX to facilitate research into open-domain problems for the code generation community.

The task of generating code solutions for a given programming problem can benefit from the use of pre-trained language models such as Codex, which can produce multiple diverse samples. However, a major challenge for this task is to select the most appropriate solution from the multiple samples generated by the pre-trained language models. A natural way to evaluate the quality and correctness of a code solution is to run it against a set of test cases, but the manual creation of such test cases is often costly and time-consuming. In this paper, we propose a novel method, CodeT, that leverages the same pre-trained language models to automatically generate test cases for the code samples, thus reducing the human effort and increasing the coverage of the test scenarios. CodeT then executes the code samples using the generated test cases, and performs a dual execution agreement, which considers both the consistency of the outputs against the generated test cases and the agreement of the outputs with other code samples. We conduct comprehensive experiments on four benchmarks, HumanEval, MBPP, APPS and CodeContests, using five different pre-trained language models with varying sizes and capabilities. Our results show that CodeT can significantly improve the performance of code solution selection over previous methods, achieving remarkable and consistent gains across different models and benchmarks. For instance, CodeT improves the pass@1 metric on HumanEval to 65.8%, which represents an absolute improvement of 18.8% over the code-davinci-002 model, and an absolute improvement of more than 20% over the previous state-of-the-art results.

The article explores an encoding and structural information processing approach using sparse bit vectors and fixed-length linear vectors. The following are presented: a discrete method of speculative stochastic dimensionality reduction of multidimensional code and linear spaces with linear asymptotic complexity; a geometric method for obtaining discrete embeddings of an organised code space that reflect the internal structure of a given modality. The structure and properties of a code space are investigated using three modalities as examples: morphology of Russian and English languages, and immunohistochemical markers. Parallels are drawn between the resulting map of the code space layout and so-called pinwheels appearing on the mammalian neocortex. A cautious assumption is made about similarities between neocortex organisation and processes happening in our models.

Context: Automated code generation using Foundation Models (FMs) offers promising solutions for enhancing software development efficiency. However, challenges remain in ensuring domain specificity, cost-effectiveness, and security - especially when relying on third-party APIs. This paper introduces CodeLSI, a framework that combines low-rank optimization and domain-specific instruction tuning to address these challenges. Objectives: The aim of this study is to develop and evaluate CodeLSI, a novel approach for generating high-quality code tailored to specific domains, using FMs fine-tuned on company infrastructure without dependence on external APIs. Methods: CodeLSI applies low-rank adaptation techniques to reduce the computational cost of model pre-training and fine-tuning. Domain-specific instruction tuning is employed to align code generation with organizational needs. We implemented and tested the framework on real-world JavaScript coding tasks using datasets drawn from internal software projects. Results: Experimental evaluations show that CodeLSI produces high-quality, context aware code. It outperforms baseline models in terms of relevance, accuracy, and domain fit. The use of low-rank optimization significantly reduced resource requirements, enabling scalable training on company-owned infrastructure. Conclusion: CodeLSI demonstrates that combining low-rank optimization with domain specific tuning can enhance the practicality and performance of FMs for automated code generation. This approach provides a secure, cost-efficient alternative to commercial API based solutions and supports faster, more targeted innovation in software development.

Recent breakthroughs in pre-trained code models, such as CodeBERT and Codex, have shown their superior performance in various downstream tasks. The correctness and unambiguity of API usage among these code models are crucial for achieving desirable program functionalities, requiring them to learn various API fully qualified names structurally and semantically. Recent studies reveal that even state-of-the-art pre-trained code models struggle with suggesting the correct APIs during code generation. However, the reasons for such poor API usage performance are barely investigated. To address this challenge, we propose using knowledge probing as a means of interpreting code models, which uses cloze-style tests to measure the knowledge stored in models. Our comprehensive study examines a code model's capability of understanding API fully qualified names from two different perspectives: API call and API import. Specifically, we reveal that current code models struggle with understanding API names, with pre-training strategies significantly affecting the quality of API name learning. We demonstrate that natural language context can assist code models in locating Python API names and generalize Python API name knowledge to unseen data. Our findings provide insights into the limitations and capabilities of current pre-trained code models, and suggest that incorporating API structure into the pre-training process can improve automated API usage and code representations. This work provides significance for advancing code intelligence practices and direction for future studies. All experiment results, data and source code used in this work are available at https://doi.org/10.5281/zenodo.7902072.

Machine Learning (ML) research is spread through academic papers featuring rich multimodal content, including text, diagrams, and tabular results. However, translating these multimodal elements into executable code remains a challenging and time-consuming process that requires substantial ML expertise. We introduce ``Paper-to-Code'' (P2C), a novel task that transforms the multimodal content of scientific publications into fully executable code repositories, which extends beyond the existing formulation of code generation that merely converts textual descriptions into isolated code snippets. To automate the P2C process, we propose AutoP2C, a multi-agent framework based on large language models that processes both textual and visual content from research papers to generate complete code repositories. Specifically, AutoP2C contains four stages: (1) repository blueprint extraction from established codebases, (2) multimodal content parsing that integrates information from text, equations, and figures, (3) hierarchical task decomposition for structured code generation, and (4) iterative feedback-driven debugging to ensure functionality and performance. Evaluation on a benchmark of eight research papers demonstrates the effectiveness of AutoP2C, which can successfully generate executable code repositories for all eight papers, while OpenAI-o1 or DeepSeek-R1 can only produce runnable code for one paper. The code is available at https://github.com/shoushouyu/Automated-Paper-to-Code.

This study aims to explore the implementation of Natural Language Processing (NLP) and machine learning (ML) techniques to automate the coding of medical letters with visualised explainability and light-weighted local computer settings. Currently in clinical settings, coding is a manual process that involves assigning codes to each condition, procedure, and medication in a patient's paperwork (e.g., 56265001 heart disease using SNOMED CT code). There are preliminary research on automatic coding in this field using state-of-the-art ML models; however, due to the complexity and size of the models, the real-world deployment is not achieved. To further facilitate the possibility of automatic coding practice, we explore some solutions in a local computer setting; in addition, we explore the function of explainability for transparency of AI models. We used the publicly available MIMIC-III database and the HAN/HLAN network models for ICD code prediction purposes. We also experimented with the mapping between ICD and SNOMED CT knowledge bases. In our experiments, the models provided useful information for 97.98\% of codes. The result of this investigation can shed some light on implementing automatic clinical coding in practice, such as in hospital settings, on the local computers used by clinicians , project page https://github.com/Glenj01/Medical-Coding.

With the increasing code reasoning capabilities of existing large language models (LLMs) and breakthroughs in reasoning models like OpenAI o1 and o3, there is a growing need to develop more challenging and comprehensive benchmarks that effectively test their sophisticated competition-level coding abilities. Existing benchmarks, like LiveCodeBench and USACO, fall short due to the unavailability of private test cases, lack of support for special judges, and misaligned execution environments. To bridge this gap, we introduce CodeElo, a standardized competition-level code generation benchmark that effectively addresses all these challenges for the first time. CodeElo benchmark is mainly based on the official CodeForces platform and tries to align with the platform as much as possible. We compile the recent six months of contest problems on CodeForces with detailed information such as contest divisions, problem difficulty ratings, and problem algorithm tags. We introduce a unique judging method in which problems are submitted directly to the platform and develop a reliable Elo rating calculation system that aligns with the platform and is comparable with human participants but has lower variance. By testing on our CodeElo, we provide the Elo ratings of 30 existing popular open-source and 3 proprietary LLMs for the first time. The results show that o1-mini and QwQ-32B-Preview stand out significantly, achieving Elo ratings of 1578 and 1261, respectively, while other models struggle even with the easiest problems, placing in the lowest 20 percent among all human participants. Detailed analysis experiments are also conducted to provide insights into performance across algorithms and comparisons between using C++ and Python, which can suggest directions for future studies.

Semantic code search is the task of retrieving a code snippet given a textual description of its functionality. Recent work has been focused on using similarity metrics between neural embeddings of text and code. However, current language models are known to struggle with longer, compositional text, and multi-step reasoning. To overcome this limitation, we propose supplementing the query sentence with a layout of its semantic structure. The semantic layout is used to break down the final reasoning decision into a series of lower-level decisions. We use a Neural Module Network architecture to implement this idea. We compare our model - NS3 (Neuro-Symbolic Semantic Search) - to a number of baselines, including state-of-the-art semantic code retrieval methods, and evaluate on two datasets - CodeSearchNet and Code Search and Question Answering. We demonstrate that our approach results in more precise code retrieval, and we study the effectiveness of our modular design when handling compositional queries.

Recent developments show that Large Language Models (LLMs) produce state-of-the-art performance on natural language (NL) to code generation for resource-rich general-purpose languages like C++, Java, and Python. However, their practical usage for structured domain-specific languages (DSLs) such as YAML, JSON is limited due to domain-specific schema, grammar, and customizations generally unseen by LLMs during pre-training. Efforts have been made to mitigate this challenge via in-context learning through relevant examples or by fine-tuning. However, it suffers from problems, such as limited DSL samples and prompt sensitivity but enterprises maintain good documentation of the DSLs. Therefore, we propose DocCGen, a framework that can leverage such rich knowledge by breaking the NL-to-Code generation task for structured code languages into a two-step process. First, it detects the correct libraries using the library documentation that best matches the NL query. Then, it utilizes schema rules extracted from the documentation of these libraries to constrain the decoding. We evaluate our framework for two complex structured languages, Ansible YAML and Bash command, consisting of two settings: Out-of-domain (OOD) and In-domain (ID). Our extensive experiments show that DocCGen consistently improves different-sized language models across all six evaluation metrics, reducing syntactic and semantic errors in structured code. We plan to open-source the datasets and code to motivate research in constrained code generation.

Reasoning is a fundamental capability of Large Language Models. While prior research predominantly focuses on enhancing narrow skills like math or code generation, improving performance on many other reasoning tasks remains challenging due to sparse and fragmented training data. To address this issue, we propose CodeI/O, a novel approach that systematically condenses diverse reasoning patterns inherently embedded in contextually-grounded codes, through transforming the original code into a code input-output prediction format. By training models to predict inputs/outputs given code and test cases entirely in natural language as Chain-of-Thought (CoT) rationales, we expose them to universal reasoning primitives -- like logic flow planning, state-space searching, decision tree traversal, and modular decomposition -- while decoupling structured reasoning from code-specific syntax and preserving procedural rigor. Experimental results demonstrate CodeI/O leads to consistent improvements across symbolic, scientific, logic, math & numerical, and commonsense reasoning tasks. By matching the existing ground-truth outputs or re-executing the code with predicted inputs, we can verify each prediction and further enhance the CoTs through multi-turn revision, resulting in CodeI/O++ and achieving higher performance. Our data and models are available at https://github.com/hkust-nlp/CodeIO.

Pre-trained models for programming languages have recently demonstrated great success on code intelligence. To support both code-related understanding and generation tasks, recent works attempt to pre-train unified encoder-decoder models. However, such encoder-decoder framework is sub-optimal for auto-regressive tasks, especially code completion that requires a decoder-only manner for efficient inference. In this paper, we present UniXcoder, a unified cross-modal pre-trained model for programming language. The model utilizes mask attention matrices with prefix adapters to control the behavior of the model and leverages cross-modal contents like AST and code comment to enhance code representation. To encode AST that is represented as a tree in parallel, we propose a one-to-one mapping method to transform AST in a sequence structure that retains all structural information from the tree. Furthermore, we propose to utilize multi-modal contents to learn representation of code fragment with contrastive learning, and then align representations among programming languages using a cross-modal generation task. We evaluate UniXcoder on five code-related tasks over nine datasets. To further evaluate the performance of code fragment representation, we also construct a dataset for a new task, called zero-shot code-to-code search. Results show that our model achieves state-of-the-art performance on most tasks and analysis reveals that comment and AST can both enhance UniXcoder.

Large-scale code generation models such as Codex and CodeT5 have achieved impressive performance. However, libraries are upgraded or deprecated very frequently and re-training large-scale language models is computationally expensive. Therefore, Continual Learning (CL) is an important aspect that remains underexplored in the code domain. In this paper, we introduce a benchmark called CodeTask-CL that covers a wide range of tasks, including code generation, translation, summarization, and refinement, with different input and output programming languages. Next, on our CodeTask-CL benchmark, we compare popular CL techniques from NLP and Vision domains. We find that effective methods like Prompt Pooling (PP) suffer from catastrophic forgetting due to the unstable training of the prompt selection mechanism caused by stark distribution shifts in coding tasks. We address this issue with our proposed method, Prompt Pooling with Teacher Forcing (PP-TF), that stabilizes training by enforcing constraints on the prompt selection mechanism and leads to a 21.54% improvement over Prompt Pooling. Along with the benchmark, we establish a training pipeline that can be used for CL on code models, which we believe can motivate further development of CL methods for code models. Our code is available at https://github.com/amazon-science/codetaskcl-pptf

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

Recently, deep learning techniques have shown great success in automatic code generation. Inspired by the code reuse, some researchers propose copy-based approaches that can copy the content from similar code snippets to obtain better performance. Practically, human developers recognize the content in the similar code that is relevant to their needs, which can be viewed as a code sketch. The sketch is further edited to the desired code. However, existing copy-based approaches ignore the code sketches and tend to repeat the similar code without necessary modifications, which leads to generating wrong results. In this paper, we propose a sketch-based code generation approach named SkCoder to mimic developers' code reuse behavior. Given a natural language requirement, SkCoder retrieves a similar code snippet, extracts relevant parts as a code sketch, and edits the sketch into the desired code. Our motivations are that the extracted sketch provides a well-formed pattern for telling models "how to write". The post-editing further adds requirement-specific details to the sketch and outputs the complete code. We conduct experiments on two public datasets and a new dataset collected by this work. We compare our approach to 20 baselines using 5 widely used metrics. Experimental results show that (1) SkCoder can generate more correct programs, and outperforms the state-of-the-art - CodeT5-base by 30.30%, 35.39%, and 29.62% on three datasets. (2) Our approach is effective to multiple code generation models and improves them by up to 120.1% in Pass@1. (3) We investigate three plausible code sketches and discuss the importance of sketches. (4) We manually evaluate the generated code and prove the superiority of our SkCoder in three aspects.

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

Understanding neural networks is challenging in part because of the dense, continuous nature of their hidden states. We explore whether we can train neural networks to have hidden states that are sparse, discrete, and more interpretable by quantizing their continuous features into what we call codebook features. Codebook features are produced by finetuning neural networks with vector quantization bottlenecks at each layer, producing a network whose hidden features are the sum of a small number of discrete vector codes chosen from a larger codebook. Surprisingly, we find that neural networks can operate under this extreme bottleneck with only modest degradation in performance. This sparse, discrete bottleneck also provides an intuitive way of controlling neural network behavior: first, find codes that activate when the desired behavior is present, then activate those same codes during generation to elicit that behavior. We validate our approach by training codebook Transformers on several different datasets. First, we explore a finite state machine dataset with far more hidden states than neurons. In this setting, our approach overcomes the superposition problem by assigning states to distinct codes, and we find that we can make the neural network behave as if it is in a different state by activating the code for that state. Second, we train Transformer language models with up to 410M parameters on two natural language datasets. We identify codes in these models representing diverse, disentangled concepts (ranging from negative emotions to months of the year) and find that we can guide the model to generate different topics by activating the appropriate codes during inference. Overall, codebook features appear to be a promising unit of analysis and control for neural networks and interpretability. Our codebase and models are open-sourced at https://github.com/taufeeque9/codebook-features.

How to evaluate Large Language Models (LLMs) in code generation is an open question. Existing benchmarks demonstrate poor alignment with real-world code repositories and are insufficient to evaluate the coding abilities of LLMs. This paper proposes a new benchmark - EvoCodeBench to address the preceding problems, which has three primary advances. (1) EvoCodeBench aligns with real-world repositories in multiple dimensions, e.g., code distributions and dependency distributions. (2) EvoCodeBench offers comprehensive annotations (e.g., requirements, reference code, and reference dependencies), and robust evaluation metrics (e.g., Pass@k and Recall@k). (3) EvoCodeBench is an evolving benchmark to avoid data leakage. We build an automatic pipeline to update EvoCodeBench from the latest repositories. We release the first version - EvoCodeBench-2403, containing 275 samples from 25 real-world repositories. Based on EvoCodeBench, we propose repository-level code generation and evaluate 10 popular LLMs (e.g., gpt-4, gpt-3.5, DeepSeek Coder, StarCoder 2, CodeLLaMa, Gemma, and Qwen 1.5). Our experiments reveal the coding abilities of these LLMs in real-world repositories. For example, the highest Pass@1 of gpt-4 only is 20.73% in our experiments. We also analyze failed cases and summarize the shortcomings of existing LLMs in EvoCodeBench. We release EvoCodeBench, all prompts, and LLMs' completions for further community analysis.

Deploying language models often requires handling model size vs. performance trade-offs to satisfy downstream latency constraints while preserving the model's usefulness. Model distillation is commonly employed to reduce model size while maintaining acceptable performance. However, distillation can be inefficient since it involves multiple training steps. In this work, we introduce MODULARSTARENCODER, a modular multi-exit encoder with 1B parameters, useful for multiple tasks within the scope of code retrieval. MODULARSTARENCODER is trained with a novel self-distillation mechanism that significantly improves lower-layer representations-allowing different portions of the model to be used while still maintaining a good trade-off in terms of performance. Our architecture focuses on enhancing text-to-code and code-to-code search by systematically capturing syntactic and semantic structures across multiple levels of representation. Specific encoder layers are targeted as exit heads, allowing higher layers to guide earlier layers during training. This self-distillation effect improves intermediate representations, increasing retrieval recall at no extra training cost. In addition to the multi-exit scheme, our approach integrates a repository-level contextual loss that maximally utilizes the training context window, further enhancing the learned representations. We also release a new dataset constructed via code translation, seamlessly expanding traditional text-to-code benchmarks with code-to-code pairs across diverse programming languages. Experimental results highlight the benefits of self-distillation through multi-exit supervision.

Competition-level code generation tasks pose significant challenges for current state-of-the-art large language models (LLMs). For example, on the LiveCodeBench-Hard dataset, models such as O1-Mini and O1-Preview achieve pass@1 rates of only 0.366 and 0.143, respectively. While tree search techniques have proven effective in domains like mathematics and general coding, their potential in competition-level code generation remains under-explored. In this work, we propose a novel token-level tree search method specifically designed for code generation. Leveraging Qwen2.5-Coder-32B-Instruct, our approach achieves a pass rate of 0.305 on LiveCodeBench-Hard, surpassing the pass@100 performance of GPT4o-0513 (0.245). Furthermore, by integrating Chain-of-Thought (CoT) prompting, we improve our method's performance to 0.351, approaching O1-Mini's pass@1 rate. To ensure reproducibility, we report the average number of generations required per problem by our tree search method on the test set. Our findings underscore the potential of tree search to significantly enhance performance on competition-level code generation tasks. This opens up new possibilities for large-scale synthesis of challenging code problems supervised fine-tuning (SFT) data, advancing competition-level code generation tasks.

Code completion models have made significant progress in recent years. Recently, repository-level code completion has drawn more attention in modern software development, and several baseline methods and benchmarks have been proposed. However, existing repository-level code completion methods often fall short of fully using the extensive context of a project repository, such as the intricacies of relevant files and class hierarchies. Besides, the existing benchmarks usually focus on limited code completion scenarios, which cannot reflect the repository-level code completion abilities well of existing methods. To address these limitations, we propose the R2C2-Coder to enhance and benchmark the real-world repository-level code completion abilities of code Large Language Models, where the R2C2-Coder includes a code prompt construction method R2C2-Enhance and a well-designed benchmark R2C2-Bench. Specifically, first, in R2C2-Enhance, we first construct the candidate retrieval pool and then assemble the completion prompt by retrieving from the retrieval pool for each completion cursor position. Second, based on R2C2 -Enhance, we can construct a more challenging and diverse R2C2-Bench with training, validation and test splits, where a context perturbation strategy is proposed to simulate the real-world repository-level code completion well. Extensive results on multiple benchmarks demonstrate the effectiveness of our R2C2-Coder.

Prediction sets have recently been shown to be a promising strategy for quantifying the uncertainty of deep neural networks in a way that provides theoretical guarantees. However, existing techniques have largely targeted settings where the space of labels is simple, so prediction sets can be arbitrary subsets of labels. For structured prediction problems where the space of labels is exponential in size, even prediction sets containing a small fraction of all labels can be exponentially large. In the context of code generation, we propose a solution that considers a restricted set of prediction sets that can compactly be represented as partial programs, which are programs with portions replaced with holes. Given a trained code generation model, our algorithm leverages a programming language's abstract syntax tree to generate a set of programs such that the correct program is in the set with high-confidence. Valuable applications of our algorithm include a Codex-style code generator with holes in uncertain parts of the generated code, which provides a partial program with theoretical guarantees. We evaluate our approach on PICARD (a T5 model for SQL semantic parsing) and Codex (a GPT model for over a dozen programming languages, including Python), demonstrating that our approach generates compact PAC prediction sets. This is the first research contribution that generates PAC prediction sets for generative code models.

The scientific research paradigm is undergoing a profound transformation owing to the development of Artificial Intelligence (AI). Recent works demonstrate that various AI-assisted research methods can largely improve research efficiency by improving data analysis, accelerating computation, and fostering novel idea generation. To further move towards the ultimate goal (i.e., automatic scientific research), in this paper, we propose Dolphin, the first closed-loop open-ended auto-research framework to further build the entire process of human scientific research. Dolphin can generate research ideas, perform experiments, and get feedback from experimental results to generate higher-quality ideas. More specifically, Dolphin first generates novel ideas based on relevant papers which are ranked by the topic and task attributes. Then, the codes are automatically generated and debugged with the exception-traceback-guided local code structure. Finally, Dolphin automatically analyzes the results of each idea and feeds the results back to the next round of idea generation. Experiments are conducted on the benchmark datasets of different topics and results show that Dolphin can generate novel ideas continuously and complete the experiment in a loop. We highlight that Dolphin can automatically propose methods that are comparable to the state-of-the-art in some tasks such as 2D image classification and 3D point classification.

Large Language Models (LLMs) have demonstrated remarkable capabilities in various tasks, yet code generation remains a major challenge. Current approaches for obtaining high-quality code data primarily focus on (i) collecting large-scale pre-training data and (ii) synthesizing instruction data through prompt engineering with powerful models. While pre-training data faces quality consistency issues, instruction-based synthesis suffers from limited instruction diversity and inherent biases of LLMs. To address this gap, we introduce UnitCoder, a systematic pipeline leveraging model-generated unit tests to both guide and validate the code generation process. Combined with large-scale package-based retrieval from pre-training corpus, we generate a dataset of 500K+ verifiable programs containing diverse API calls. Evaluations on multiple Python benchmarks (BigCodeBench, HumanEval, MBPP) demonstrate that models fine-tuned on our synthetic data exhibit consistent performance improvements. Notably, Llama3.1-8B and InternLM2.5-7B improve from 31\% and 28\% to 40\% and 39\% success rates on BigCodeBench, respectively. Our work presents a scalable approach that leverages model-generated unit tests to guide the synthesis of high-quality code data from pre-training corpora, demonstrating the potential for producing diverse and high-quality post-training data at scale. All code and data will be released (https://github.com).

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

We consider the task of mapping pseudocode to long programs that are functionally correct. Given test cases as a mechanism to validate programs, we search over the space of possible translations of the pseudocode to find a program that passes the validation. However, without proper credit assignment to localize the sources of program failures, it is difficult to guide search toward more promising programs. We propose to perform credit assignment based on signals from compilation errors, which constitute 88.7% of program failures. Concretely, we treat the translation of each pseudocode line as a discrete portion of the program, and whenever a synthesized program fails to compile, an error localization method tries to identify the portion of the program responsible for the failure. We then focus search over alternative translations of the pseudocode for those portions. For evaluation, we collected the SPoC dataset (Search-based Pseudocode to Code) containing 18,356 programs with human-authored pseudocode and test cases. Under a budget of 100 program compilations, performing search improves the synthesis success rate over using the top-one translation of the pseudocode from 25.6% to 44.7%.

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

In this study, we present a novel dataset for training machine learning models translating between OpenMP Fortran and C++ code. To ensure reliability and applicability, the dataset is created from a range of representative open-source OpenMP benchmarks. It is also refined using a meticulous code similarity test. The effectiveness of our dataset is assessed using both quantitative (CodeBLEU) and qualitative (human evaluation) methods. We showcase how this dataset significantly elevates the translation competencies of large language models (LLMs). Specifically, models without prior coding knowledge experienced a boost of times~5.1 in their CodeBLEU scores, while models with some coding familiarity saw an impressive times~9.9-fold increase. The best fine-tuned model using our dataset outperforms GPT-4. It is also reaching human-level accuracy. This work underscores the immense potential of our dataset in propelling advancements in the domain of code translation for high-performance computing. The dataset is accessible at https://github.com/bin123apple/Fortran-CPP-HPC-code-translation-dataset{OpenMP-Fortran-CPP-Translation}.

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

Jupyter notebook allows data scientists to write machine learning code together with its documentation in cells. In this paper, we propose a new task of code documentation generation (CDG) for computational notebooks. In contrast to the previous CDG tasks which focus on generating documentation for single code snippets, in a computational notebook, one documentation in a markdown cell often corresponds to multiple code cells, and these code cells have an inherent structure. We proposed a new model (HAConvGNN) that uses a hierarchical attention mechanism to consider the relevant code cells and the relevant code tokens information when generating the documentation. Tested on a new corpus constructed from well-documented Kaggle notebooks, we show that our model outperforms other baseline models.

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

Source code is rarely written in isolation. It depends significantly on the programmatic context, such as the class that the code would reside in. To study this phenomenon, we introduce the task of generating class member functions given English documentation and the programmatic context provided by the rest of the class. This task is challenging because the desired code can vary greatly depending on the functionality the class provides (e.g., a sort function may or may not be available when we are asked to "return the smallest element" in a particular member variable list). We introduce CONCODE, a new large dataset with over 100,000 examples consisting of Java classes from online code repositories, and develop a new encoder-decoder architecture that models the interaction between the method documentation and the class environment. We also present a detailed error analysis suggesting that there is significant room for future work on this task.

We introduce API Pack, a multilingual dataset featuring over one million instruction-API call pairs aimed at advancing large language models' API call generation capabilities. Through experiments, we demonstrate API Pack's efficacy in enhancing models for this specialized task while maintaining their overall proficiency at general coding. Fine-tuning CodeLlama-13B on just 20,000 Python instances yields over 10% and 5% higher accuracy than GPT-3.5 and GPT-4 respectively in generating unseen API calls. Scaling to 100k examples improves generalization to new APIs not seen during training. In addition, cross-lingual API call generation is achieved without needing extensive data per language. The dataset, fine-tuned models, and overall code base are publicly available at https://github.com/zguo0525/API-Pack.

With the emergence of Large Language Models (LLMs), there has been a significant improvement in the programming capabilities of models, attracting growing attention from researchers. We propose CodeApex, a bilingual benchmark dataset focusing on the programming comprehension and code generation abilities of LLMs. CodeApex comprises three types of multiple-choice questions: conceptual understanding, commonsense reasoning, and multi-hop reasoning, designed to evaluate LLMs on programming comprehension tasks. Additionally, CodeApex utilizes algorithmic questions and corresponding test cases to assess the code quality generated by LLMs. We evaluate 14 state-of-the-art LLMs, including both general-purpose and specialized models. GPT exhibits the best programming capabilities, achieving approximate accuracies of 50% and 56% on the two tasks, respectively. There is still significant room for improvement in programming tasks. We hope that CodeApex can serve as a reference for evaluating the coding capabilities of LLMs, further promoting their development and growth. Datasets are released at https://github.com/APEXLAB/CodeApex.git. CodeApex submission website is https://apex.sjtu.edu.cn/codeapex/.

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.

The advent of pre-trained code language models (CodeLMs) has lead to significant progress in language-to-code generation. State-of-the-art approaches in this area combine CodeLM decoding with sample pruning and reranking using test cases or heuristics based on the execution results. However, it is challenging to obtain test cases for many real-world language-to-code applications, and heuristics cannot well capture the semantic features of the execution results, such as data type and value range, which often indicates the correctness of the program. In this work, we propose LEVER, a simple approach to improve language-to-code generation by learning to verify the generated programs with their execution results. Specifically, we train verifiers to determine whether a program sampled from the CodeLM is correct or not based on the natural language input, the program itself and its execution results. The sampled programs are reranked by combining the verification score with the CodeLM generation probability, and marginalizing over programs with the same execution results. On four datasets across the domains of table QA, math QA and basic Python programming, LEVER consistently improves over the base CodeLMs (4.6% to 10.9% with code-davinci-002) and achieves new state-of-the-art results on all of them.

Images are increasingly becoming the currency for documenting biodiversity on the planet, providing novel opportunities for accelerating scientific discoveries in the field of organismal biology, especially with the advent of large vision-language models (VLMs). We ask if pre-trained VLMs can aid scientists in answering a range of biologically relevant questions without any additional fine-tuning. In this paper, we evaluate the effectiveness of 12 state-of-the-art (SOTA) VLMs in the field of organismal biology using a novel dataset, VLM4Bio, consisting of 469K question-answer pairs involving 30K images from three groups of organisms: fishes, birds, and butterflies, covering five biologically relevant tasks. We also explore the effects of applying prompting techniques and tests for reasoning hallucination on the performance of VLMs, shedding new light on the capabilities of current SOTA VLMs in answering biologically relevant questions using images. The code and datasets for running all the analyses reported in this paper can be found at https://github.com/sammarfy/VLM4Bio.

Despite the huge success of Large Language Models (LLMs) in coding assistants like GitHub Copilot, these models struggle to understand the context present in the repository (e.g., imports, parent classes, files with similar names, etc.), thereby producing inaccurate code completions. This effect is more pronounced when using these assistants for repositories that the model has not seen during training, such as proprietary software or work-in-progress code projects. Recent work has shown the promise of using context from the repository during inference. In this work, we extend this idea and propose RepoFusion, a framework to train models to incorporate relevant repository context. Experiments on single-line code completion show that our models trained with repository context significantly outperform much larger code models as CodeGen-16B-multi (sim73times larger) and closely match the performance of the sim 70times larger StarCoderBase model that was trained with the Fill-in-the-Middle objective. We find these results to be a novel and compelling demonstration of the gains that training with repository context can bring. We carry out extensive ablation studies to investigate the impact of design choices such as context type, number of contexts, context length, and initialization within our framework. Lastly, we release Stack-Repo, a dataset of 200 Java repositories with permissive licenses and near-deduplicated files that are augmented with three types of repository contexts. Additionally, we are making available the code and trained checkpoints for our work. Our released resources can be found at https://huggingface.co/RepoFusion.

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 .

Recently, pre-trained foundation models have enabled significant advancements in multiple fields. In molecular machine learning, however, where datasets are often hand-curated, and hence typically small, the lack of datasets with labeled features, and codebases to manage those datasets, has hindered the development of foundation models. In this work, we present seven novel datasets categorized by size into three distinct categories: ToyMix, LargeMix and UltraLarge. These datasets push the boundaries in both the scale and the diversity of supervised labels for molecular learning. They cover nearly 100 million molecules and over 3000 sparsely defined tasks, totaling more than 13 billion individual labels of both quantum and biological nature. In comparison, our datasets contain 300 times more data points than the widely used OGB-LSC PCQM4Mv2 dataset, and 13 times more than the quantum-only QM1B dataset. In addition, to support the development of foundational models based on our proposed datasets, we present the Graphium graph machine learning library which simplifies the process of building and training molecular machine learning models for multi-task and multi-level molecular datasets. Finally, we present a range of baseline results as a starting point of multi-task and multi-level training on these datasets. Empirically, we observe that performance on low-resource biological datasets show improvement by also training on large amounts of quantum data. This indicates that there may be potential in multi-task and multi-level training of a foundation model and fine-tuning it to resource-constrained downstream tasks.

Scientific reasoning is critical for developing AI scientists and supporting human researchers in advancing the frontiers of natural science discovery. However, the open-source community has primarily focused on mathematics and coding while neglecting the scientific domain, largely due to the absence of open, large-scale, high-quality, verifiable scientific reasoning datasets. To bridge this gap, we first present TextbookReasoning, an open dataset featuring truthful reference answers extracted from 12k university-level scientific textbooks, comprising 650k reasoning questions spanning 7 scientific disciplines. We further introduce MegaScience, a large-scale mixture of high-quality open-source datasets totaling 1.25 million instances, developed through systematic ablation studies that evaluate various data selection methodologies to identify the optimal subset for each publicly available scientific dataset. Meanwhile, we build a comprehensive evaluation system covering diverse subjects and question types across 15 benchmarks, incorporating comprehensive answer extraction strategies to ensure accurate evaluation metrics. Our experiments demonstrate that our datasets achieve superior performance and training efficiency with more concise response lengths compared to existing open-source scientific datasets. Furthermore, we train Llama3.1, Qwen2.5, and Qwen3 series base models on MegaScience, which significantly outperform the corresponding official instruct models in average performance. In addition, MegaScience exhibits greater effectiveness for larger and stronger models, suggesting a scaling benefit for scientific tuning. We release our data curation pipeline, evaluation system, datasets, and seven trained models to the community to advance scientific reasoning research.

Imagine a developer who can only change their last line of code, how often would they have to start writing a function from scratch before it is correct? Auto-regressive models for code generation from natural language have a similar limitation: they do not easily allow reconsidering earlier tokens generated. We introduce CodeFusion, a pre-trained diffusion code generation model that addresses this limitation by iteratively denoising a complete program conditioned on the encoded natural language. We evaluate CodeFusion on the task of natural language to code generation for Bash, Python, and Microsoft Excel conditional formatting (CF) rules. Experiments show that CodeFusion (75M parameters) performs on par with state-of-the-art auto-regressive systems (350M-175B parameters) in top-1 accuracy and outperforms them in top-3 and top-5 accuracy due to its better balance in diversity versus quality.

Scaling test-time compute is a promising axis for improving LLM capabilities. However, test-time compute can be scaled in a variety of ways, and effectively combining different approaches remains an active area of research. Here, we explore this problem in the context of solving real-world GitHub issues from the SWE-bench dataset. Our system, named CodeMonkeys, allows models to iteratively edit a codebase by jointly generating and running a testing script alongside their draft edit. We sample many of these multi-turn trajectories for every issue to generate a collection of candidate edits. This approach lets us scale "serial" test-time compute by increasing the number of iterations per trajectory and "parallel" test-time compute by increasing the number of trajectories per problem. With parallel scaling, we can amortize up-front costs across multiple downstream samples, allowing us to identify relevant codebase context using the simple method of letting an LLM read every file. In order to select between candidate edits, we combine voting using model-generated tests with a final multi-turn trajectory dedicated to selection. Overall, CodeMonkeys resolves 57.4% of issues from SWE-bench Verified using a budget of approximately 2300 USD. Our selection method can also be used to combine candidates from different sources. Selecting over an ensemble of edits from existing top SWE-bench Verified submissions obtains a score of 66.2% and outperforms the best member of the ensemble on its own. We fully release our code and data at https://scalingintelligence.stanford.edu/pubs/codemonkeys.

Large Language Models (LLMs) have demonstrated remarkable performance on coding related tasks, particularly on assisting humans in programming and facilitating programming automation. However, existing benchmarks for evaluating the code understanding and generation capacities of LLMs suffer from severe limitations. First, most benchmarks are deficient as they focus on a narrow range of popular programming languages and specific tasks, whereas the real-world software development scenarios show dire need to implement systems with multilingual programming environments to satisfy diverse requirements. Practical programming practices also strongly expect multi-task settings for testing coding capabilities of LLMs comprehensively and robustly. Second, most benchmarks also fail to consider the actual executability and the consistency of execution results of the generated code. To bridge these gaps between existing benchmarks and expectations from practical applications, we introduce CodeScope, an execution-based, multilingual, multi-task, multi-dimensional evaluation benchmark for comprehensively gauging LLM capabilities on coding tasks. CodeScope covers 43 programming languages and 8 coding tasks. It evaluates the coding performance of LLMs from three dimensions (perspectives): difficulty, efficiency, and length. To facilitate execution-based evaluations of code generation, we develop MultiCodeEngine, an automated code execution engine that supports 14 programming languages. Finally, we systematically evaluate and analyze 8 mainstream LLMs on CodeScope tasks and demonstrate the superior breadth and challenges of CodeScope for evaluating LLMs on code understanding and generation tasks compared to other benchmarks. The CodeScope benchmark and datasets are publicly available at https://github.com/WeixiangYAN/CodeScope.

Medical coding is the task of assigning medical codes to clinical free-text documentation. Healthcare professionals manually assign such codes to track patient diagnoses and treatments. Automated medical coding can considerably alleviate this administrative burden. In this paper, we reproduce, compare, and analyze state-of-the-art automated medical coding machine learning models. We show that several models underperform due to weak configurations, poorly sampled train-test splits, and insufficient evaluation. In previous work, the macro F1 score has been calculated sub-optimally, and our correction doubles it. We contribute a revised model comparison using stratified sampling and identical experimental setups, including hyperparameters and decision boundary tuning. We analyze prediction errors to validate and falsify assumptions of previous works. The analysis confirms that all models struggle with rare codes, while long documents only have a negligible impact. Finally, we present the first comprehensive results on the newly released MIMIC-IV dataset using the reproduced models. We release our code, model parameters, and new MIMIC-III and MIMIC-IV training and evaluation pipelines to accommodate fair future comparisons.

In deep learning, performance is strongly affected by the choice of architecture and hyperparameters. While there has been extensive work on automatic hyperparameter optimization for simple spaces, complex spaces such as the space of deep architectures remain largely unexplored. As a result, the choice of architecture is done manually by the human expert through a slow trial and error process guided mainly by intuition. In this paper we describe a framework for automatically designing and training deep models. We propose an extensible and modular language that allows the human expert to compactly represent complex search spaces over architectures and their hyperparameters. The resulting search spaces are tree-structured and therefore easy to traverse. Models can be automatically compiled to computational graphs once values for all hyperparameters have been chosen. We can leverage the structure of the search space to introduce different model search algorithms, such as random search, Monte Carlo tree search (MCTS), and sequential model-based optimization (SMBO). We present experiments comparing the different algorithms on CIFAR-10 and show that MCTS and SMBO outperform random search. In addition, these experiments show that our framework can be used effectively for model discovery, as it is possible to describe expressive search spaces and discover competitive models without much effort from the human expert. Code for our framework and experiments has been made publicly available.

Code Large Language Models (CodeLLMs) have ushered in a new era of code generation advancements. However, selecting the best solutions from among all possible CodeLLM solutions remains a challenge. Previous methods frequently overlooked the intricate functional similarities and interactions between clusters, resulting in suboptimal results. In this work, we introduce SRank, a novel reranking strategy for selecting the best solution from code generation that focuses on modeling inter-cluster relationship. By quantifying the functional overlap between clusters, our approach provides a better ranking strategy of code solutions. Empirical results show that our method achieves a remarkable results on pass@1 score. For instance, on the Human-Eval benchmark, we achieve 69.66\% in pass@1 with Codex002, 75.31\% for WizardCoder, 53.99\% for StarCoder and 60.55\% for CodeGen, which surpass the state-of-the-arts solution ranking methods, such as CodeT and Coder-Reviewer on the same CodeLLM with significant margin (approx 6.1% improvement on average). Comparing to the random sampling method, we can achieve an average improvement of approx 23.07% on Human-Eval and 17.64\% on MBPP. Even in scenarios with limited test inputs, our approach demonstrates robustness and superiority, marking a new state-of-the-arts in code generation reranking.

jina-code-embeddings is a novel code embedding model suite designed to retrieve code from natural language queries, perform technical question-answering, and identify semantically similar code snippets across programming languages. It makes innovative use of an autoregressive backbone pre-trained on both text and code, generating embeddings via last-token pooling. We outline the training recipe and demonstrate state-of-the-art performance despite the relatively small size of the models, validating this approach to code embedding model construction.

The rapid development of large language models has revolutionized code intelligence in software development. However, the predominance of closed-source models has restricted extensive research and development. To address this, we introduce the DeepSeek-Coder series, a range of open-source code models with sizes from 1.3B to 33B, trained from scratch on 2 trillion tokens. These models are pre-trained on a high-quality project-level code corpus and employ a fill-in-the-blank task with a 16K window to enhance code generation and infilling. Our extensive evaluations demonstrate that DeepSeek-Coder not only achieves state-of-the-art performance among open-source code models across multiple benchmarks but also surpasses existing closed-source models like Codex and GPT-3.5. Furthermore, DeepSeek-Coder models are under a permissive license that allows for both research and unrestricted commercial use.