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Dec 16

SAFEFLOW: A Principled Protocol for Trustworthy and Transactional Autonomous Agent Systems

Recent advances in large language models (LLMs) and vision-language models (VLMs) have enabled powerful autonomous agents capable of complex reasoning and multi-modal tool use. Despite their growing capabilities, today's agent frameworks remain fragile, lacking principled mechanisms for secure information flow, reliability, and multi-agent coordination. In this work, we introduce SAFEFLOW, a new protocol-level framework for building trustworthy LLM/VLM-based agents. SAFEFLOW enforces fine-grained information flow control (IFC), precisely tracking provenance, integrity, and confidentiality of all the data exchanged between agents, tools, users, and environments. By constraining LLM reasoning to respect these security labels, SAFEFLOW prevents untrusted or adversarial inputs from contaminating high-integrity decisions. To ensure robustness in concurrent multi-agent settings, SAFEFLOW introduces transactional execution, conflict resolution, and secure scheduling over shared state, preserving global consistency across agents. We further introduce mechanisms, including write-ahead logging, rollback, and secure caches, that further enhance resilience against runtime errors and policy violations. To validate the performances, we built SAFEFLOWBENCH, a comprehensive benchmark suite designed to evaluate agent reliability under adversarial, noisy, and concurrent operational conditions. Extensive experiments demonstrate that agents built with SAFEFLOW maintain impressive task performance and security guarantees even in hostile environments, substantially outperforming state-of-the-art. Together, SAFEFLOW and SAFEFLOWBENCH lay the groundwork for principled, robust, and secure agent ecosystems, advancing the frontier of reliable autonomy.

Empirical Research on Utilizing LLM-based Agents for Automated Bug Fixing via LangGraph

This paper presents a novel framework for automated code generation and debugging, designed to improve accuracy, efficiency, and scalability in software development. The proposed system integrates three core components LangGraph, GLM4 Flash, and ChromaDB within a four step iterative workflow to deliver robust performance and seamless functionality. LangGraph serves as a graph-based library for orchestrating tasks, providing precise control and execution while maintaining a unified state object for dynamic updates and consistency. It supports multi-agent, hierarchical, and sequential processes, making it highly adaptable to complex software engineering workflows. GLM4 Flash, a large language model, leverages its advanced capabilities in natural language understanding, contextual reasoning, and multilingual support to generate accurate code snippets based on user prompts. ChromaDB acts as a vector database for semantic search and contextual memory storage, enabling the identification of patterns and the generation of context-aware bug fixes based on historical data. The system operates through a structured four-step process: (1) Code Generation, which translates natural language descriptions into executable code; (2) Code Execution, which validates the code by identifying runtime errors and inconsistencies; (3) Code Repair, which iteratively refines buggy code using ChromaDB's memory capabilities and LangGraph's state tracking; and (4) Code Update, which ensures the code meets functional and performance requirements through iterative modifications.

  • 2 authors
·
Jan 29

Failure Prediction at Runtime for Generative Robot Policies

Imitation learning (IL) with generative models, such as diffusion and flow matching, has enabled robots to perform complex, long-horizon tasks. However, distribution shifts from unseen environments or compounding action errors can still cause unpredictable and unsafe behavior, leading to task failure. Early failure prediction during runtime is therefore essential for deploying robots in human-centered and safety-critical environments. We propose FIPER, a general framework for Failure Prediction at Runtime for generative IL policies that does not require failure data. FIPER identifies two key indicators of impending failure: (i) out-of-distribution (OOD) observations detected via random network distillation in the policy's embedding space, and (ii) high uncertainty in generated actions measured by a novel action-chunk entropy score. Both failure prediction scores are calibrated using a small set of successful rollouts via conformal prediction. A failure alarm is triggered when both indicators, aggregated over short time windows, exceed their thresholds. We evaluate FIPER across five simulation and real-world environments involving diverse failure modes. Our results demonstrate that FIPER better distinguishes actual failures from benign OOD situations and predicts failures more accurately and earlier than existing methods. We thus consider this work an important step towards more interpretable and safer generative robot policies. Code, data and videos are available at https://tum-lsy.github.io/fiper_website.

  • 4 authors
·
Oct 10

Generating High-Precision Feedback for Programming Syntax Errors using Large Language Models

Large language models (LLMs), such as Codex, hold great promise in enhancing programming education by automatically generating feedback for students. We investigate using LLMs to generate feedback for fixing syntax errors in Python programs, a key scenario in introductory programming. More concretely, given a student's buggy program, our goal is to generate feedback comprising a fixed program along with a natural language explanation describing the errors/fixes, inspired by how a human tutor would give feedback. While using LLMs is promising, the critical challenge is to ensure high precision in the generated feedback, which is imperative before deploying such technology in classrooms. The main research question we study is: Can we develop LLMs-based feedback generation techniques with a tunable precision parameter, giving educators quality control over the feedback that students receive? To this end, we introduce PyFiXV, our technique to generate high-precision feedback powered by Codex. The key idea behind PyFiXV is to use a novel run-time validation mechanism to decide whether the generated feedback is suitable for sharing with the student; notably, this validation mechanism also provides a precision knob to educators. We perform an extensive evaluation using two real-world datasets of Python programs with syntax errors and show the efficacy of PyFiXV in generating high-precision feedback.

  • 7 authors
·
Jan 24, 2023

LDB: A Large Language Model Debugger via Verifying Runtime Execution Step-by-step

Large language models (LLMs) are leading significant progress in code generation. Beyond one-pass code generation, recent works further integrate unit tests and program verifiers into LLMs to iteratively refine the generated programs. However, these works consider the generated programs as an indivisible entity, which falls short for LLMs in debugging the programs, especially when the programs contain complex logic flows and data operations. In contrast, when human developers debug programs, they typically set breakpoints and selectively examine runtime execution information. The execution flow and the intermediate variables play a crucial role in the debugging process, yet they are underutilized in the existing literature on code generation. In this study, we introduce Large Language Model Debugger (LDB), a novel debugging framework that enables LLMs to refine their generated programs with the runtime execution information. Specifically, LDB segments the programs into basic blocks and tracks the values of intermediate variables after each block throughout the runtime execution. This allows LLMs to concentrate on simpler code units within the overall execution flow, verify their correctness against the task description block by block, and efficiently pinpoint any potential errors. Experiments demonstrate that LDB consistently enhances the baseline performance by up to 9.8% across the HumanEval, MBPP, and TransCoder benchmarks, archiving new state-of-the-art performance in code debugging for various LLM selections.

  • 3 authors
·
Feb 24, 2024

Tools and Benchmarks for Automated Log Parsing

Logs are imperative in the development and maintenance process of many software systems. They record detailed runtime information that allows developers and support engineers to monitor their systems and dissect anomalous behaviors and errors. The increasing scale and complexity of modern software systems, however, make the volume of logs explodes. In many cases, the traditional way of manual log inspection becomes impractical. Many recent studies, as well as industrial tools, resort to powerful text search and machine learning-based analytics solutions. Due to the unstructured nature of logs, a first crucial step is to parse log messages into structured data for subsequent analysis. In recent years, automated log parsing has been widely studied in both academia and industry, producing a series of log parsers by different techniques. To better understand the characteristics of these log parsers, in this paper, we present a comprehensive evaluation study on automated log parsing and further release the tools and benchmarks for easy reuse. More specifically, we evaluate 13 log parsers on a total of 16 log datasets spanning distributed systems, supercomputers, operating systems, mobile systems, server applications, and standalone software. We report the benchmarking results in terms of accuracy, robustness, and efficiency, which are of practical importance when deploying automated log parsing in production. We also share the success stories and lessons learned in an industrial application at Huawei. We believe that our work could serve as the basis and provide valuable guidance to future research and deployment of automated log parsing.

  • 7 authors
·
Nov 8, 2018 1

Feedback-Based Self-Learning in Large-Scale Conversational AI Agents

Today, most large-scale conversational AI agents (e.g. Alexa, Siri, or Google Assistant) are built using manually annotated data to train the different components of the system. Typically, the accuracy of the ML models in these components are improved by manually transcribing and annotating data. As the scope of these systems increase to cover more scenarios and domains, manual annotation to improve the accuracy of these components becomes prohibitively costly and time consuming. In this paper, we propose a system that leverages user-system interaction feedback signals to automate learning without any manual annotation. Users here tend to modify a previous query in hopes of fixing an error in the previous turn to get the right results. These reformulations, which are often preceded by defective experiences caused by errors in ASR, NLU, ER or the application. In some cases, users may not properly formulate their requests (e.g. providing partial title of a song), but gleaning across a wider pool of users and sessions reveals the underlying recurrent patterns. Our proposed self-learning system automatically detects the errors, generate reformulations and deploys fixes to the runtime system to correct different types of errors occurring in different components of the system. In particular, we propose leveraging an absorbing Markov Chain model as a collaborative filtering mechanism in a novel attempt to mine these patterns. We show that our approach is highly scalable, and able to learn reformulations that reduce Alexa-user errors by pooling anonymized data across millions of customers. The proposed self-learning system achieves a win/loss ratio of 11.8 and effectively reduces the defect rate by more than 30% on utterance level reformulations in our production A/B tests. To the best of our knowledge, this is the first self-learning large-scale conversational AI system in production.

  • 4 authors
·
Nov 6, 2019

Can ChatGPT replace StackOverflow? A Study on Robustness and Reliability of Large Language Model Code Generation

Recently, the large language models (LLMs) have shown extraordinary ability in understanding natural language and generating programming code. It has been a common practice of software engineers to consult LLMs when encountering coding questions. Although efforts have been made to avoid syntax errors and align the code with the intended semantics, the reliability and robustness of the code generationfrom LLMs have not yet been thoroughly studied. The executable code is not equivalent to the reliable and robust code, especially in the context of real-world software development. The misuse of APIs in the generated code could lead to severe problem, such as resource leaks, program crashes. To make things worse, the users of LLM code generation services are actually the developers that are most vulnerable to these code that seems right -- They are always novice developers that are not familiar with the APIs that LLMs generate code for them. Therefore, they could hardly tell the misuse in the code generated by LLMs, which further facilitates the incorrect code applied in real-world software. Existing code evaluation benchmark and datasets focus on crafting small tasks such as programming questions in coding interviews, which however deviates from the problem that developers would ask LLM for real-world coding help. To fill the missing piece, in this work, we propose a dataset RobustAPI for evaluating the reliability and robustness of code generated by LLMs. We collect 1208 coding questions from StackOverflow on 24 representative Java APIs. We summarize thecommon misuse patterns of these APIs and evaluate them oncurrent popular LLMs. The evaluation results show that evenfor GPT-4, 62% of the generated code contains API misuses,which would cause unexpected consequences if the code isintroduced into real-world software.

  • 2 authors
·
Aug 20, 2023

MRG-Bench: Evaluating and Exploring the Requirements of Context for Repository-Level Code Generation

Large Language Models (LLMs) have demonstrated impressive capabilities in code generation. However, current evaluation datasets suffer from issues such as the lack of runnable test cases, deviation from the distribution of real-world code, and the ability to evaluate only the Python language. These limitations undermine the credibility of the evaluation results. To address these limitations, we introduce MRG-Bench (Multi-language Repository-level Code Generation Benchmark), a novel dataset that provides a more accurate evaluation of LLMs in practical repository-level code generation tasks. MRG-Bench has three main features: (1) practical data sourced from real-world code repositories that align to the practical distribution, (2) multiple programming languages support, including Python, Java, and Go, and (3) project-level runnable test cases to assess the quality of the generated code. Based on MRG-Bench, we conducted extensive experiments including large language models, long-context models, and RAG-related methods. These evaluation results demonstrate that current repository-level code generation techniques suffer from significant performance deficiencies. To further investigate why models fail, we designed novel experiments to annotate the underlying causes of generation errors. The results explicitly show that the majority of methods suffer from "difficulty in understanding user requirements," failing to comprehend their assigned tasks accurately. Moreover, the impact of different repository-level contexts on this issue exhibits significant disparities across different programming languages, suggesting that, in practice, specialized contextual information needs to be designed for different languages.

  • 1 authors
·
Aug 4

What's Wrong with Your Code Generated by Large Language Models? An Extensive Study

The increasing development of large language models (LLMs) in code generation has drawn significant attention among researchers. To enhance LLM-based code generation ability, current efforts are predominantly directed towards collecting high-quality datasets and leveraging diverse training technologies. However, there is a notable lack of comprehensive studies examining the limitations and boundaries of these existing methods. To bridge this gap, we conducted an extensive empirical study evaluating the performance of three leading closed-source LLMs and four popular open-source LLMs on three commonly used benchmarks. Our investigation, which evaluated the length, cyclomatic complexity and API number of the generated code, revealed that these LLMs face challenges in generating successful code for more complex problems, and tend to produce code that is shorter yet more complicated as compared to canonical solutions. Additionally, we developed a taxonomy of bugs for incorrect codes that includes three categories and 12 sub-categories, and analyze the root cause for common bug types. Furthermore, to better understand the performance of LLMs in real-world projects, we manually created a real-world benchmark comprising 140 code generation tasks. Our analysis highlights distinct differences in bug distributions between actual scenarios and existing benchmarks. Finally, we propose a novel training-free iterative method that introduces self-critique, enabling LLMs to critique and correct their generated code based on bug types and compiler feedback. Experimental results demonstrate that our approach can significantly mitigate bugs and increase the passing rate by 29.2% after two iterations, indicating substantial potential for LLMs to handle more complex problems.

  • 24 authors
·
Jul 8, 2024

Evaluating LLMs at Detecting Errors in LLM Responses

With Large Language Models (LLMs) being widely used across various tasks, detecting errors in their responses is increasingly crucial. However, little research has been conducted on error detection of LLM responses. Collecting error annotations on LLM responses is challenging due to the subjective nature of many NLP tasks, and thus previous research focuses on tasks of little practical value (e.g., word sorting) or limited error types (e.g., faithfulness in summarization). This work introduces ReaLMistake, the first error detection benchmark consisting of objective, realistic, and diverse errors made by LLMs. ReaLMistake contains three challenging and meaningful tasks that introduce objectively assessable errors in four categories (reasoning correctness, instruction-following, context-faithfulness, and parameterized knowledge), eliciting naturally observed and diverse errors in responses of GPT-4 and Llama 2 70B annotated by experts. We use ReaLMistake to evaluate error detectors based on 12 LLMs. Our findings show: 1) Top LLMs like GPT-4 and Claude 3 detect errors made by LLMs at very low recall, and all LLM-based error detectors perform much worse than humans. 2) Explanations by LLM-based error detectors lack reliability. 3) LLMs-based error detection is sensitive to small changes in prompts but remains challenging to improve. 4) Popular approaches to improving LLMs, including self-consistency and majority vote, do not improve the error detection performance. Our benchmark and code are provided at https://github.com/psunlpgroup/ReaLMistake.

  • 15 authors
·
Apr 4, 2024

Program Synthesis with Large Language Models

This paper explores the limits of the current generation of large language models for program synthesis in general purpose programming languages. We evaluate a collection of such models (with between 244M and 137B parameters) on two new benchmarks, MBPP and MathQA-Python, in both the few-shot and fine-tuning regimes. Our benchmarks are designed to measure the ability of these models to synthesize short Python programs from natural language descriptions. The Mostly Basic Programming Problems (MBPP) dataset contains 974 programming tasks, designed to be solvable by entry-level programmers. The MathQA-Python dataset, a Python version of the MathQA benchmark, contains 23914 problems that evaluate the ability of the models to synthesize code from more complex text. On both datasets, we find that synthesis performance scales log-linearly with model size. Our largest models, even without finetuning on a code dataset, can synthesize solutions to 59.6 percent of the problems from MBPP using few-shot learning with a well-designed prompt. Fine-tuning on a held-out portion of the dataset improves performance by about 10 percentage points across most model sizes. On the MathQA-Python dataset, the largest fine-tuned model achieves 83.8 percent accuracy. Going further, we study the model's ability to engage in dialog about code, incorporating human feedback to improve its solutions. We find that natural language feedback from a human halves the error rate compared to the model's initial prediction. Additionally, we conduct an error analysis to shed light on where these models fall short and what types of programs are most difficult to generate. Finally, we explore the semantic grounding of these models by fine-tuning them to predict the results of program execution. We find that even our best models are generally unable to predict the output of a program given a specific input.

  • 11 authors
·
Aug 15, 2021

An Empirical Study of Flaky Tests in Python

Tests that cause spurious failures without any code changes, i.e., flaky tests, hamper regression testing, increase maintenance costs, may shadow real bugs, and decrease trust in tests. While the prevalence and importance of flakiness is well established, prior research focused on Java projects, thus raising the question of how the findings generalize. In order to provide a better understanding of the role of flakiness in software development beyond Java, we empirically study the prevalence, causes, and degree of flakiness within software written in Python, one of the currently most popular programming languages. For this, we sampled 22352 open source projects from the popular PyPI package index, and analyzed their 876186 test cases for flakiness. Our investigation suggests that flakiness is equally prevalent in Python as it is in Java. The reasons, however, are different: Order dependency is a much more dominant problem in Python, causing 59% of the 7571 flaky tests in our dataset. Another 28% were caused by test infrastructure problems, which represent a previously undocumented cause of flakiness. The remaining 13% can mostly be attributed to the use of network and randomness APIs by the projects, which is indicative of the type of software commonly written in Python. Our data also suggests that finding flaky tests requires more runs than are often done in the literature: A 95% confidence that a passing test case is not flaky on average would require 170 reruns.

  • 4 authors
·
Jan 22, 2021

LLM Interactive Optimization of Open Source Python Libraries -- Case Studies and Generalization

With the advent of large language models (LLMs) like GPT-3, a natural question is the extent to which these models can be utilized for source code optimization. This paper presents methodologically stringent case studies applied to well-known open source python libraries pillow and numpy. We find that contemporary LLM ChatGPT-4 (state September and October 2023) is surprisingly adept at optimizing energy and compute efficiency. However, this is only the case in interactive use, with a human expert in the loop. Aware of experimenter bias, we document our qualitative approach in detail, and provide transcript and source code. We start by providing a detailed description of our approach in conversing with the LLM to optimize the _getextrema function in the pillow library, and a quantitative evaluation of the performance improvement. To demonstrate qualitative replicability, we report further attempts on another locus in the pillow library, and one code locus in the numpy library, to demonstrate generalization within and beyond a library. In all attempts, the performance improvement is significant (factor up to 38). We have also not omitted reporting of failed attempts (there were none). We conclude that LLMs are a promising tool for code optimization in open source libraries, but that the human expert in the loop is essential for success. Nonetheless, we were surprised by how few iterations were required to achieve substantial performance improvements that were not obvious to the expert in the loop. We would like bring attention to the qualitative nature of this study, more robust quantitative studies would need to introduce a layer of selecting experts in a representative sample -- we invite the community to collaborate.

  • 1 authors
·
Dec 8, 2023

Lost in Translation: A Study of Bugs Introduced by Large Language Models while Translating Code

Code translation aims to convert source code from one programming language (PL) to another. Given the promising abilities of large language models (LLMs) in code synthesis, researchers are exploring their potential to automate code translation. The prerequisite for advancing the state of LLM-based code translation is to understand their promises and limitations over existing techniques. To that end, we present a large-scale empirical study to investigate the ability of general LLMs and code LLMs for code translation across pairs of different languages, including C, C++, Go, Java, and Python. Our study, which involves the translation of 1,700 code samples from three benchmarks and two real-world projects, reveals that LLMs are yet to be reliably used to automate code translation -- with correct translations ranging from 2.1% to 47.3% for the studied LLMs. Further manual investigation of unsuccessful translations identifies 15 categories of translation bugs. We also compare LLM-based code translation with traditional non-LLM-based approaches. Our analysis shows that these two classes of techniques have their own strengths and weaknesses. Finally, insights from our study suggest that providing more context to LLMs during translation can help them produce better results. To that end, we propose a prompt-crafting approach based on the symptoms of erroneous translations; this improves the performance of LLM-based code translation by 5.5% on average. Our study is the first of its kind, in terms of scale and breadth, that provides insights into the current limitations of LLMs in code translation and opportunities for improving them. Our dataset -- consisting of 1,700 code samples in five PLs with 10K+ tests, 43K+ translated code, 1,725 manually labeled bugs, and 1,365 bug-fix pairs -- can help drive research in this area.

  • 10 authors
·
Aug 6, 2023

The Fault in our Stars: Quality Assessment of Code Generation Benchmarks

Large Language Models (LLMs) are gaining popularity among software engineers. A crucial aspect of developing effective code generation LLMs is to evaluate these models using a robust benchmark. Evaluation benchmarks with quality issues can provide a false sense of performance. In this work, we conduct the first-of-its-kind study of the quality of prompts within benchmarks used to compare the performance of different code generation models. To conduct this study, we analyzed 3,566 prompts from 9 code generation benchmarks to identify quality issues in them. We also investigated whether fixing the identified quality issues in the benchmarks' prompts affects a model's performance. We also studied memorization issues of the evaluation dataset, which can put into question a benchmark's trustworthiness. We found that code generation evaluation benchmarks mainly focused on Python and coding exercises and had very limited contextual dependencies to challenge the model. These datasets and the developers' prompts suffer from quality issues like spelling and grammatical errors, unclear sentences to express developers' intent, and not using proper documentation style. Fixing all these issues in the benchmarks can lead to a better performance for Python code generation, but not a significant improvement was observed for Java code generation. We also found evidence that GPT-3.5-Turbo and CodeGen-2.5 models may have data contamination issues.

  • 4 authors
·
Apr 15, 2024

Developer-LLM Conversations: An Empirical Study of Interactions and Generated Code Quality

Large Language Models (LLMs) are becoming integral to modern software development workflows, assisting developers with code generation, API explanation, and iterative problem-solving through natural language conversations. Despite widespread adoption, there is limited understanding of how developers interact with LLMs in practice and how these conversational dynamics influence task outcomes, code quality, and software engineering workflows. To address this, we leverage CodeChat, a large dataset comprising 82,845 real-world developer-LLM conversations, containing 368,506 code snippets generated across over 20 programming languages, derived from the WildChat dataset. We find that LLM responses are substantially longer than developer prompts, with a median token-length ratio of 14:1. Multi-turn conversations account for 68% of the dataset and often evolve due to shifting requirements, incomplete prompts, or clarification requests. Topic analysis identifies web design (9.6% of conversations) and neural network training (8.7% of conversations) as the most frequent LLM-assisted tasks. Evaluation across five languages (i.e., Python, JavaScript, C++, Java, and C#) reveals prevalent and language-specific issues in LLM-generated code: generated Python and JavaScript code often include undefined variables (83.4% and 75.3% of code snippets, respectively); Java code lacks required comments (75.9%); C++ code frequently omits headers (41.1%) and C# code shows unresolved namespaces (49.2%). During a conversation, syntax and import errors persist across turns; however, documentation quality in Java improves by up to 14.7%, and import handling in Python improves by 3.7% over 5 turns. Prompts that point out mistakes in code generated in prior turns and explicitly request a fix are most effective for resolving errors.

  • 3 authors
·
Sep 12 2

CORRECT: COndensed eRror RECognition via knowledge Transfer in multi-agent systems

Multi-agent systems (MAS) are increasingly capable of tackling complex real-world tasks, yet their reliance on inter-agent coordination, tool use, and long-horizon reasoning makes error recognition particularly challenging. Minor errors can propagate across agents, escalating into task failures while producing long, intertwined execution trajectories that impose significant costs for both human developers and automated systems to debug and analyze. Our key insight is that, despite surface differences in failure trajectories (e.g., logs), MAS errors often recur with similar structural patterns. This paper presents CORRECT, the first lightweight, training-free framework that leverages an online cache of distilled error schemata to recognize and transfer knowledge of failure structures across new requests. This cache-based reuse allows LLMs to perform targeted error localization at inference time, avoiding the need for expensive retraining while adapting to dynamic MAS deployments in subseconds. To support rigorous study in this domain, we also introduce CORRECT-Error, a large-scale dataset of over 2,000 annotated trajectories collected through a novel error-injection pipeline guided by real-world distributions, and further validated through human evaluation to ensure alignment with natural failure patterns. Experiments across seven diverse MAS applications show that CORRECT improves step-level error localization up to 19.8% over existing advances while at near-zero overhead, substantially narrowing the gap between automated and human-level error recognition.

  • 7 authors
·
Sep 28 2

TestBench: Evaluating Class-Level Test Case Generation Capability of Large Language Models

Software testing is a crucial phase in the software life cycle, helping identify potential risks and reduce maintenance costs. With the advancement of Large Language Models (LLMs), researchers have proposed an increasing number of LLM-based software testing techniques, particularly in the area of test case generation. Despite the growing interest, limited efforts have been made to thoroughly evaluate the actual capabilities of LLMs in this task. In this paper, we introduce TestBench, a benchmark for class-level LLM-based test case generation. We construct a dataset of 108 Java programs from 9 real-world, large-scale projects on GitHub, each representing a different thematic domain. We then design three distinct types of prompts based on context descriptions, including self-contained context, full context, and simple context. Besides, we propose a fine-grained evaluation framework that considers five aspects of test cases: syntactic correctness, compilation correctness, test correctness, code coverage rate, and defect detection rate. Furthermore, we propose a heuristic algorithm to repair erroneous test cases generated by LLMs. We evaluate CodeLlama-13b, GPT-3.5, and GPT-4 on the TestBench, and our experimental results indicate that larger models demonstrate a greater ability to effectively utilize contextual information, thus generating higher-quality test cases. Smaller models may struggle with the noise introduced by the extensive information contained within the full context. However, when using the simplified version, namely the simple context, which is derived from the full context via abstract syntax tree analysis, the performance of these models improves significantly. Our analysis highlights the current progress and pinpoints future directions to further enhance the effectiveness of models by handling contextual information for test case generation.

  • 6 authors
·
Sep 26, 2024

RustMap: Towards Project-Scale C-to-Rust Migration via Program Analysis and LLM

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

  • 9 authors
·
Mar 22

Bugs in Large Language Models Generated Code: An Empirical Study

Large Language Models (LLMs) for code have gained significant attention recently. They can generate code in different programming languages based on provided prompts, fulfilling a long-lasting dream in Software Engineering (SE), i.e., automatic code generation. Similar to human-written code, LLM-generated code is prone to bugs, and these bugs have not yet been thoroughly examined by the community. Given the increasing adoption of LLM-based code generation tools (e.g., GitHub Copilot) in SE activities, it is critical to understand the characteristics of bugs contained in code generated by LLMs. This paper examines a sample of 333 bugs collected from code generated using three leading LLMs (i.e., CodeGen, PanGu-Coder, and Codex) and identifies the following 10 distinctive bug patterns: Misinterpretations, Syntax Error, Silly Mistake, Prompt-biased code, Missing Corner Case, Wrong Input Type, Hallucinated Object, Wrong Attribute, Incomplete Generation, and Non-Prompted Consideration. The bug patterns are presented in the form of a taxonomy. The identified bug patterns are validated using an online survey with 34 LLM practitioners and researchers. The surveyed participants generally asserted the significance and prevalence of the bug patterns. Researchers and practitioners can leverage these findings to develop effective quality assurance techniques for LLM-generated code. This study sheds light on the distinctive characteristics of LLM-generated code.

  • 6 authors
·
Mar 13, 2024

A Novel Approach for Automatic Program Repair using Round-Trip Translation with Large Language Models

Research shows that grammatical mistakes in a sentence can be corrected by translating it to another language and back using neural machine translation with language models. We investigate whether this correction capability of Large Language Models (LLMs) extends to Automatic Program Repair (APR). Current generative models for APR are pre-trained on source code and fine-tuned for repair. This paper proposes bypassing the fine-tuning step and using Round-Trip Translation (RTT): translation of code from one programming language to another programming or natural language, and back. We hypothesize that RTT with LLMs restores the most commonly seen patterns in code during pre-training, i.e., performs a regression toward the mean, which removes bugs as they are a form of noise w.r.t. the more frequent, natural, bug-free code in the training data. To test this hypothesis, we employ eight recent LLMs pre-trained on code, including the latest GPT versions, and four common program repair benchmarks in Java. We find that RTT with English as an intermediate language repaired 101 of 164 bugs with GPT-4 on the HumanEval-Java dataset. Moreover, 46 of these are unique bugs that are not repaired by other LLMs fine-tuned for APR. Our findings highlight the viability of round-trip translation with LLMs as a technique for automated program repair and its potential for research in software engineering. Keywords: automated program repair, large language model, machine translation

  • 4 authors
·
Jan 15, 2024

MultiMend: Multilingual Program Repair with Context Augmentation and Multi-Hunk Patch Generation

Context: Bugs in code are inevitable and can lead to severe consequences, ranging from security vulnerabilities to operational failures. Debugging software remains challenging despite advances in testing and verification, often requiring extensive manual effort. Learning-based automated program repair (APR) has shown promise in reducing the time, effort, and cost of manually fixing bugs. However, existing techniques face several challenges, including language-dependent strategies, limited bug context utilization, and difficulties in handling bugs that span multiple locations in the code. Objective: This paper introduces MultiMend, a learning-based APR approach designed to improve repair performance on multiple programming languages with language-independent context augmentation and multi-hunk patch generation. Method: MultiMend fine-tunes a pre-trained encoder-decoder transformer model (CodeT5) to generate bug-fixing patches. It embeds source code lines and applies retrieval-augmented generation to augment the buggy context with relevant lines during patch generation. The approach systematically constructs patches for multi-hunk bugs to reduce the needed patch validations. We evaluate MultiMend on four benchmarks with four programming languages and compare it with state-of-the-art methods. Results: Experimental results show that MultiMend achieves competitive effectiveness and efficiency against compared tools. Across all benchmarks, MultiMend fixes 2,077 bugs, of which 1,455 are identical to the developer's patch, and 106 are for multi-hunk bugs. Both context augmentation and multi-hunk patch generation positively contribute to the results. Conclusion: MultiMend shows promising performance across benchmarks. The findings highlight its applicability to real-world software maintenance and its potential to reduce manual debugging efforts.

  • 3 authors
·
Jan 27

SelfPiCo: Self-Guided Partial Code Execution with LLMs

Code executability plays a vital role in software debugging and testing (e.g., detecting runtime exceptions or assertion violations). However, code execution, especially partial or arbitrary code execution, is a non-trivial task due to missing definitions and complex third-party dependencies. To make partial code (such as code snippets posted on the web or code fragments deep inside complex software projects) executable, the existing study has proposed a machine learning model to predict the undefined element types and inject the pre-defined dummy values into execution. However, the performance of their tool is limited due to its simply designed dummy values and the inability to continue learning. In this paper, we design and implement a novel framework, named SelfPiCo (Self Guided Partial Code Executor), to dynamically guide partial code execution by incorporating the open-source LLM (i.e., Code Llama) within an interactive loop. Particularly, SelfPiCo leverages few-shot in-context learning and chain-of-thought reasoning to elicit human knowledge and logical reasoning based on fine-tuning the Code Llama model. SelfPiCo continuously learns from code execution results and refines its predictions step after step. Our evaluations demonstrate that SelfPiCo can execute 72.7% and 83.3% of all lines in the open-source code and Stack Overflow snippets, outperforming the most recent state-of-the-art Lexecutor by 37.9% and 33.5%, respectively. Moreover, SelfPiCo successfully detected 18 and 33 runtime type error issues by executing the partial code from eight GitHub software projects and 43 Stack Overflow posts, demonstrating the practical usage and potential application of our framework in practice.

  • 6 authors
·
Jul 23, 2024

Is Your Code Generated by ChatGPT Really Correct? Rigorous Evaluation of Large Language Models for Code Generation

Program synthesis has been long studied with recent approaches focused on directly using the power of Large Language Models (LLMs) to generate code. Programming benchmarks, with curated synthesis problems and test-cases, are used to measure the performance of various LLMs on code synthesis. However, these test-cases can be limited in both quantity and quality for fully assessing the functional correctness of the generated code. Such limitation in the existing benchmarks begs the following question: In the era of LLMs, is the code generated really correct? To answer this, we propose EvalPlus -- a code synthesis evaluation framework to rigorously benchmark the functional correctness of LLM-synthesized code. EvalPlus augments a given evaluation dataset with large amounts of test-cases newly produced by an automatic test input generator, powered by both LLM- and mutation-based strategies. While EvalPlus is general, we extend the test-cases of the popular HumanEval benchmark by 80x to build HumanEval+. Our extensive evaluation across 26 popular LLMs (e.g., GPT-4 and ChatGPT) demonstrates that HumanEval+ is able to catch significant amounts of previously undetected wrong code synthesized by LLMs, reducing the pass@k by up-to 19.3-28.9%. We also surprisingly found that test insufficiency can lead to mis-ranking. For example, both WizardCoder-CodeLlama and Phind-CodeLlama now outperform ChatGPT on HumanEval+, while none of them could on HumanEval. Our work not only indicates that prior popular code synthesis evaluation results do not accurately reflect the true performance of LLMs for code synthesis, but also opens up a new direction to improve such programming benchmarks through automated testing. We have open-sourced our tools, enhanced datasets as well as all LLM-generated code at https://github.com/evalplus/evalplus to facilitate and accelerate future LLM-for-code research.

  • 4 authors
·
May 2, 2023

Dissecting the Runtime Performance of the Training, Fine-tuning, and Inference of Large Language Models

Large Language Models (LLMs) have seen great advance in both academia and industry, and their popularity results in numerous open-source frameworks and techniques in accelerating LLM pre-training, fine-tuning, and inference. Training and deploying LLMs are expensive as it requires considerable computing resources and memory, hence many efficient approaches have been developed for improving system pipelines as well as operators. However, the runtime performance can vary significantly across hardware and software stacks, which makes it difficult to choose the best configuration. In this work, we aim to benchmark the performance from both macro and micro perspectives. First, we benchmark the end-to-end performance of pre-training, fine-tuning, and serving LLMs in different sizes , i.e., 7, 13, and 70 billion parameters (7B, 13B, and 70B) on three 8-GPU platforms with and without individual optimization techniques, including ZeRO, quantization, recomputation, FlashAttention. Then, we dive deeper to provide a detailed runtime analysis of the sub-modules, including computing and communication operators in LLMs. For end users, our benchmark and findings help better understand different optimization techniques, training and inference frameworks, together with hardware platforms in choosing configurations for deploying LLMs. For researchers, our in-depth module-wise analyses discover potential opportunities for future work to further optimize the runtime performance of LLMs.

  • 11 authors
·
Nov 6, 2023

ViTAD: Timing Violation-Aware Debugging of RTL Code using Large Language Models

In modern Very Large Scale Integrated (VLSI) circuit design flow, the Register-Transfer Level (RTL) stage presents a critical opportunity for timing optimization. Addressing timing violations at this early stage is essential, as modern systems demand higher speeds, where even minor timing violations can lead to functional failures or system crashes. However, traditional timing optimization heavily relies on manual expertise, requiring engineers to iteratively analyze timing reports and debug. To automate this process, this paper proposes ViTAD, a method that efficiently analyzes the root causes of timing violations and dynamically generates targeted repair strategies. Specifically, we first parse Verilog code and timing reports to construct a Signal Timing Dependency Graph (STDG). Based on the STDG, we perform violation path analysis and use large language models (LLMs) to infer the root causes of violations. Finally, by analyzing the causes of violations, we selectively retrieve relevant debugging knowledge from a domain-specific knowledge base to generate customized repair solutions. To evaluate the effectiveness of our method, we construct a timing violation dataset based on real-world open-source projects. This dataset contains 54 cases of violations. Experimental results show that our method achieves a 73.68% success rate in repairing timing violations, while the baseline using only LLM is 54.38%. Our method improves the success rate by 19.30%.

  • 4 authors
·
Aug 18

Helping LLMs Improve Code Generation Using Feedback from Testing and Static Analysis

Large Language Models (LLMs) are one of the most promising developments in the field of artificial intelligence, and the software engineering community has readily noticed their potential role in the software development life-cycle. Developers routinely ask LLMs to generate code snippets, increasing productivity but also potentially introducing ownership, privacy, correctness, and security issues. Previous work highlighted how code generated by mainstream commercial LLMs is often not safe, containing vulnerabilities, bugs, and code smells. In this paper, we present a framework that leverages testing and static analysis to assess the quality, and guide the self-improvement, of code generated by general-purpose, open-source LLMs. First, we ask LLMs to generate C code to solve a number of programming tasks. Then we employ ground-truth tests to assess the (in)correctness of the generated code, and a static analysis tool to detect potential safety vulnerabilities. Next, we assess the models ability to evaluate the generated code, by asking them to detect errors and vulnerabilities. Finally, we test the models ability to fix the generated code, providing the reports produced during the static analysis and incorrectness evaluation phases as feedback. Our results show that models often produce incorrect code, and that the generated code can include safety issues. Moreover, they perform very poorly at detecting either issue. On the positive side, we observe a substantial ability to fix flawed code when provided with information about failed tests or potential vulnerabilities, indicating a promising avenue for improving the safety of LLM-based code generation tools.

  • 6 authors
·
Dec 19, 2024

Towards Understanding Bugs in Distributed Training and Inference Frameworks for Large Language Models

With the rapid development of large language models (LLMs), distributed training and inference frameworks like DeepSpeed have become essential for scaling model training and inference across multiple GPUs or nodes. However, the increasing complexity of these frameworks brings non-trivial software bugs, which may degrade training performance, cause unexpected failures, and result in significant resource waste. Understanding framework bugs' characteristics is fundamental for quality assurance, allowing the design of more effective debugging and repair methods. Thus, our paper conducts the first large-scale empirical analysis of 308 fixed bugs across three popular distributed training/inference frameworks: DeepSpeed, Megatron-LM, and Colossal-AI. We examine bug symptoms, root causes, bug identification and fixing efforts, and common low-effort fixing strategies. Additionally, the distributed nature of these frameworks introduces unique bug root causes, such as allocation strategy error and distributed communication error. Diagnosing and fixing complex bugs remains challenging due to factors like the disconnect between symptoms and root causes, high bug reproduction costs, and low-level or cross-component interactions. Interestingly, we observe that 48% of bug fixes require minimal code changes (<=10 LOC) and follow simple strategies such as conditional logic optimization, parameter handling enhancement, or version compatibility handling, indicating potential for automation. Based on these insights, we offer several implications for improving the reliability of both distributed training and inference frameworks and their dependent LLM projects, while also identifying opportunities to leverage LLM-based tools for automated debugging and repair.

  • 6 authors
·
Jun 12 1

The Foundation Cracks: A Comprehensive Study on Bugs and Testing Practices in LLM Libraries

Large Language Model (LLM) libraries have emerged as the foundational infrastructure powering today's AI revolution, serving as the backbone for LLM deployment, inference optimization, fine-tuning, and production serving across diverse applications. Despite their critical role in the LLM ecosystem, these libraries face frequent quality issues and bugs that threaten the reliability of AI systems built upon them. To address this knowledge gap, we present the first comprehensive empirical investigation into bug characteristics and testing practices in modern LLM libraries. We examine 313 bug-fixing commits extracted across two widely-adopted LLM libraries: HuggingFace Transformers and vLLM.Through rigorous manual analysis, we establish comprehensive taxonomies categorizing bug symptoms into 5 types and root causes into 14 distinct categories.Our primary discovery shows that API misuse has emerged as the predominant root cause (32.17%-48.19%), representing a notable transition from algorithm-focused defects in conventional deep learning frameworks toward interface-oriented problems. Additionally, we examine 7,748 test functions to identify 7 distinct test oracle categories employed in current testing approaches, with predefined expected outputs (such as specific tensors and text strings) being the most common strategy. Our assessment of existing testing effectiveness demonstrates that the majority of bugs escape detection due to inadequate test cases (41.73%), lack of test drivers (32.37%), and weak test oracles (25.90%). Drawing from these findings, we offer some recommendations for enhancing LLM library quality assurance.

  • 7 authors
·
Jun 13

ClassEval: A Manually-Crafted Benchmark for Evaluating LLMs on Class-level Code Generation

In this work, we make the first attempt to evaluate LLMs in a more challenging code generation scenario, i.e. class-level code generation. We first manually construct the first class-level code generation benchmark ClassEval of 100 class-level Python code generation tasks with approximately 500 person-hours. Based on it, we then perform the first study of 11 state-of-the-art LLMs on class-level code generation. Based on our results, we have the following main findings. First, we find that all existing LLMs show much worse performance on class-level code generation compared to on standalone method-level code generation benchmarks like HumanEval; and the method-level coding ability cannot equivalently reflect the class-level coding ability among LLMs. Second, we find that GPT-4 and GPT-3.5 still exhibit dominate superior than other LLMs on class-level code generation, and the second-tier models includes Instruct-Starcoder, Instruct-Codegen, and Wizardcoder with very similar performance. Third, we find that generating the entire class all at once (i.e. holistic generation strategy) is the best generation strategy only for GPT-4 and GPT-3.5, while method-by-method generation (i.e. incremental and compositional) is better strategies for the other models with limited ability of understanding long instructions and utilizing the middle information. Lastly, we find the limited model ability of generating method-dependent code and discuss the frequent error types in generated classes. Our benchmark is available at https://github.com/FudanSELab/ClassEval.

  • 10 authors
·
Aug 3, 2023

CoderUJB: An Executable and Unified Java Benchmark for Practical Programming Scenarios

In the evolving landscape of large language models (LLMs) tailored for software engineering, the need for benchmarks that accurately reflect real-world development scenarios is paramount. Current benchmarks are either too simplistic or fail to capture the multi-tasking nature of software development. To address this, we introduce CoderUJB, a new benchmark designed to evaluate LLMs across diverse Java programming tasks that are executable and reflective of actual development scenarios, acknowledging Java's prevalence in real-world software production. CoderUJB comprises 2,239 programming questions derived from 17 real open-source Java projects and spans five practical programming tasks. Our empirical study on this benchmark investigates the coding abilities of various open-source and closed-source LLMs, examining the effects of continued pre-training in specific programming languages code and instruction fine-tuning on their performance. The findings indicate that while LLMs exhibit strong potential, challenges remain, particularly in non-functional code generation (e.g., test generation and defect detection). Importantly, our results advise caution in the specific programming languages continued pre-training and instruction fine-tuning, as these techniques could hinder model performance on certain tasks, suggesting the need for more nuanced strategies. CoderUJB thus marks a significant step towards more realistic evaluations of programming capabilities in LLMs, and our study provides valuable insights for the future development of these models in software engineering.

  • 5 authors
·
Mar 28, 2024

Can LLM Generate Regression Tests for Software Commits?

Large Language Models (LLMs) have shown tremendous promise in automated software engineering. In this paper, we investigate the opportunities of LLMs for automatic regression test generation for programs that take highly structured, human-readable inputs, such as XML parsers or JavaScript interpreters. Concretely, we explore the following regression test generation scenarios for such programs that have so far been difficult to test automatically in the absence of corresponding input grammars: bullet Bug finding. Given a code change (e.g., a commit or pull request), our LLM-based approach generates a test case with the objective of revealing any bugs that might be introduced if that change is applied. bullet Patch testing. Given a patch, our LLM-based approach generates a test case that fails before but passes after the patch. This test can be added to the regression test suite to catch similar bugs in the future. We implement Cleverest, a feedback-directed, zero-shot LLM-based regression test generation technique, and evaluate its effectiveness on 22 commits to three subject programs: Mujs, Libxml2, and Poppler. For programs using more human-readable file formats, like XML or JavaScript, we found Cleverest performed very well. It generated easy-to-understand bug-revealing or bug-reproduction test cases for the majority of commits in just under three minutes -- even when only the code diff or commit message (unless it was too vague) was given. For programs with more compact file formats, like PDF, as expected, it struggled to generate effective test cases. However, the LLM-supplied test cases are not very far from becoming effective (e.g., when used as a seed by a greybox fuzzer or as a starting point by the developer).

  • 4 authors
·
Jan 19

ReCatcher: Towards LLMs Regression Testing for Code Generation

Large Language Models (LLMs) for code generation evolve rapidly through fine-tuning, merging, or new model releases. However, such updates can introduce regressions, not only in correctness but also in code quality and performance. To address this, we present ReCatcher, a regression testing framework for Python code generation. ReCatcher systematically compares two LLMs, typically a current model and a candidate update, across three dimensions: logical correctness, static code quality, and execution performance. We apply ReCatcher to assess regressions across three update scenarios, fine-tuning, merging, and model release, using CodeLlama, DeepSeek-Coder, and GPT-4o. Our evaluation shows that fine-tuning with cross-language datasets increases syntax errors by up to 12%. Merging with general-purpose models like Llama2 leads to regressions in correctness by up to 18%. GPT-4o introduces regressions of up to 50% in handling missing imports compared to GPT-3.5-turbo, while GPT-4o-mini suffers up to 80% performance degradation in execution time versus GPT-4o. Overall, logical correctness, performance, and error handling (e.g., syntax errors and missing imports) are the most regression-prone areas. Comparing ReCatcher with baseline solutions, it presents better and consistent accuracy across logical and performance aspects. ReCatcher highlights the importance of systematic regression evaluation before adopting new models, while assisting researchers and practitioners in making more informed update decisions.

  • 4 authors
·
Jul 25

Error Classification of Large Language Models on Math Word Problems: A Dynamically Adaptive Framework

Large Language Models (LLMs) have demonstrated remarkable capabilities across various domains. Math Word Problems (MWPs) serve as a crucial benchmark for evaluating LLMs' reasoning abilities. While most research primarily focuses on improving accuracy, it often neglects understanding and addressing the underlying patterns of errors. Current error classification methods rely on static and predefined categories, which limit their ability to capture the full spectrum of error patterns in mathematical reasoning. To enable systematic error analysis, we collect error samples from 15 different LLMs of varying sizes across four distinct MWP datasets using multiple sampling strategies. Based on this extensive collection, we introduce MWPES-300K, a comprehensive dataset containing 304,865 error samples that cover diverse error patterns and reasoning paths. To reduce human bias and enable fine-grained analysis of error patterns, we propose a novel framework for automated dynamic error classification in mathematical reasoning. Experimental results demonstrate that dataset characteristics significantly shape error patterns, which evolve from basic to complex manifestations as model capabilities increase. With deeper insights into error patterns, we propose error-aware prompting that incorporates common error patterns as explicit guidance, leading to significant improvements in mathematical reasoning performance.

  • 5 authors
·
Jan 26

From Code to Correctness: Closing the Last Mile of Code Generation with Hierarchical Debugging

While large language models have made significant strides in code generation, the pass rate of the generated code is bottlenecked on subtle errors, often requiring human intervention to pass tests, especially for complex problems. Existing LLM-based debugging systems treat generated programs as monolithic units, failing to address bugs at multiple levels of granularity, from low-level syntax errors to high-level algorithmic flaws. In this paper, we introduce Multi-Granularity Debugger (MGDebugger), a hierarchical code debugger by isolating, identifying, and resolving bugs at various levels of granularity. MGDebugger decomposes problematic code into a hierarchical tree structure of subfunctions, with each level representing a particular granularity of error. During debugging, it analyzes each subfunction and iteratively resolves bugs in a bottom-up manner. To effectively test each subfunction, we propose an LLM-simulated Python executor, which traces code execution and tracks important variable states to pinpoint errors accurately. Extensive experiments demonstrate that MGDebugger outperforms existing debugging systems, achieving an 18.9% improvement in accuracy over seed generations in HumanEval and a 97.6% repair success rate in HumanEvalFix. Furthermore, MGDebugger effectively fixes bugs across different categories and difficulty levels, demonstrating its robustness and effectiveness.

  • 4 authors
·
Oct 1, 2024 9

PPTC Benchmark: Evaluating Large Language Models for PowerPoint Task Completion

Recent evaluations of Large Language Models (LLMs) have centered around testing their zero-shot/few-shot capabilities for basic natural language tasks and their ability to translate instructions into tool APIs. However, the evaluation of LLMs utilizing complex tools to finish multi-turn, multi-modal instructions in a complex multi-modal environment has not been investigated. To address this gap, we introduce the PowerPoint Task Completion (PPTC) benchmark to assess LLMs' ability to create and edit PPT files based on user instructions. It contains 279 multi-turn sessions covering diverse topics and hundreds of instructions involving multi-modal operations. We also propose the PPTX-Match Evaluation System that evaluates if LLMs finish the instruction based on the prediction file rather than the label API sequence, thus it supports various LLM-generated API sequences. We measure 3 closed LLMs and 6 open-source LLMs. The results show that GPT-4 outperforms other LLMs with 75.1\% accuracy in single-turn dialogue testing but faces challenges in completing entire sessions, achieving just 6\% session accuracy. We find three main error causes in our benchmark: error accumulation in the multi-turn session, long PPT template processing, and multi-modality perception. These pose great challenges for future LLM and agent systems. We release the data, code, and evaluation system of PPTC at https://github.com/gydpku/PPTC.

  • 5 authors
·
Nov 3, 2023 2

CYCLE: Learning to Self-Refine the Code Generation

Pre-trained code language models have achieved promising performance in code generation and improved the programming efficiency of human developers. However, their self-refinement capability is typically overlooked by the existing evaluations of code LMs, which focus only on the accuracy of the one-time prediction. For the cases when code LMs fail to implement the correct program, developers actually find it hard to debug and fix the faulty prediction since it is not written by the developers themselves. Unfortunately, our study reveals that code LMs cannot efficiently self-refine their faulty generations as well. In this paper, we propose CYCLE framework, learning to self-refine the faulty generation according to the available feedback, such as the execution results reported by the test suites. We evaluate CYCLE on three popular code generation benchmarks, HumanEval, MBPP, and APPS. The results reveal that CYCLE successfully maintains, sometimes improves, the quality of one-time code generation, while significantly improving the self-refinement capability of code LMs. We implement four variants of CYCLE with varied numbers of parameters across 350M, 1B, 2B, and 3B, and the experiments show that CYCLE consistently boosts the code generation performance, by up to 63.5%, across benchmarks and varied model sizes. We also notice that CYCLE outperforms code LMs that have 3times more parameters in self-refinement.

  • 4 authors
·
Mar 27, 2024

LEMMA: Learning from Errors for MatheMatical Advancement in LLMs

Large language models (LLMs) have demonstrated remarkable reasoning capability in solving mathematical problems. However, existing approaches primarily focus on improving the quality of correct training data, e.g., distilling high-quality correct solutions from advanced models, neglecting the value contained in error data, potentially hindering the model's reflective ability. Though some studies attempt to leverage error data, they often involve complex mechanisms, such as Monte Carlo Tree Search (MCTS) to explore error nodes. In this work, we propose to enhance LLMs' reasoning ability by Learning from Errors for Mathematical Advancement (LEMMA). LEMMA constructs data consisting of an incorrect solution with an erroneous step and a reflection connection to a correct solution for fine-tuning. Specifically, we systematically analyze the model-generated error types and introduce an error-type grounded mistake augmentation method to collect diverse and representative errors. Correct solutions are either from fixing the errors or generating a fresh start. Through a model-aware smooth reflection connection, the erroneous solution is transferred to the correct one. By fine-tuning on the constructed dataset, the model is able to self-correct errors autonomously within the generation process without relying on external critique models. Experimental results demonstrate that LEMMA achieves significant performance improvements over other strong baselines.

  • 10 authors
·
Mar 21 2

Frustrated with Code Quality Issues? LLMs can Help!

As software projects progress, quality of code assumes paramount importance as it affects reliability, maintainability and security of software. For this reason, static analysis tools are used in developer workflows to flag code quality issues. However, developers need to spend extra efforts to revise their code to improve code quality based on the tool findings. In this work, we investigate the use of (instruction-following) large language models (LLMs) to assist developers in revising code to resolve code quality issues. We present a tool, CORE (short for COde REvisions), architected using a pair of LLMs organized as a duo comprised of a proposer and a ranker. Providers of static analysis tools recommend ways to mitigate the tool warnings and developers follow them to revise their code. The proposer LLM of CORE takes the same set of recommendations and applies them to generate candidate code revisions. The candidates which pass the static quality checks are retained. However, the LLM may introduce subtle, unintended functionality changes which may go un-detected by the static analysis. The ranker LLM evaluates the changes made by the proposer using a rubric that closely follows the acceptance criteria that a developer would enforce. CORE uses the scores assigned by the ranker LLM to rank the candidate revisions before presenting them to the developer. CORE could revise 59.2% Python files (across 52 quality checks) so that they pass scrutiny by both a tool and a human reviewer. The ranker LLM is able to reduce false positives by 25.8% in these cases. CORE produced revisions that passed the static analysis tool in 76.8% Java files (across 10 quality checks) comparable to 78.3% of a specialized program repair tool, with significantly much less engineering efforts.

  • 8 authors
·
Sep 22, 2023

JavaBench: A Benchmark of Object-Oriented Code Generation for Evaluating Large Language Models

Code generation benchmarks such as HumanEval are widely adopted to evaluate LLMs' capabilities. However, after consolidating the latest 24 benchmarks, we noticed three significant imbalances. First, imbalanced programming language. 95.8% of benchmarks involve Python, while only 5 benchmarks involve Java. Second, imbalanced code granularity. Function-/statement-level benchmarks account for over 83.3% of benchmarks. Only a mere handful extends to class-/project-levels, and all are limited to Python. Third, lacking advanced features. Existing benchmarks primarily assess basic coding skills, while overlooking advanced Object-Oriented Programming (OOP) features (i.e., encapsulation, inheritance, and polymorphism). To fill these gaps, we propose JavaBench, a project-level Java benchmark that exercises OOP features. It comprises four Java projects with 389 methods in 106 Java classes. The test coverage is up to 92%, and JavaBench is attested by 282 undergraduate students, reaching a 90.93/100 average score (i.e., pass rate against the test suite), ensuring the quality of documentation, code skeleton, and tests. To better evaluate LLM's capability against JavaBench, we introduce a systematic evaluation design covering three context settings and five synthesis strategies at two granularities using three hierarchical metrics. Our extensive experiment yields several interesting findings. First, we noticed that regarding project-level Java programming, LLMs are far behind undergraduate students (no project can be correctly completed by any studied LLMs, and at most 41.17% Pass@5 in a more relaxed evaluation). Second, using method signature as prompt context may strike an ideal balance for project-level code generation. JavaBench is publicly available at https://github.com/java-bench/JavaBench.

  • 5 authors
·
Jun 10, 2024

COFFE: A Code Efficiency Benchmark for Code Generation

Code generation has largely improved development efficiency in the era of large language models (LLMs). With the ability to follow instructions, current LLMs can be prompted to generate code solutions given detailed descriptions in natural language. Many research efforts are being devoted to improving the correctness of LLM-generated code, and many benchmarks are proposed to evaluate the correctness comprehensively. Despite the focus on correctness, the time efficiency of LLM-generated code solutions is under-explored. Current correctness benchmarks are not suitable for time efficiency evaluation since their test cases cannot well distinguish the time efficiency of different code solutions. Besides, the current execution time measurement is not stable and comprehensive, threatening the validity of the time efficiency evaluation. To address the challenges in the time efficiency evaluation of code generation, we propose COFFE, a code generation benchmark for evaluating the time efficiency of LLM-generated code solutions. COFFE contains 398 and 358 problems for function-level and file-level code generation, respectively. To improve the distinguishability, we design a novel stressful test case generation approach with contracts and two new formats of test cases to improve the accuracy of generation. For the time evaluation metric, we propose efficienct@k based on CPU instruction count to ensure a stable and solid comparison between different solutions. We evaluate 14 popular LLMs on COFFE and identify four findings. Based on the findings, we draw some implications for LLM researchers and software practitioners to facilitate future research and usage of LLMs in code generation.

  • 4 authors
·
Feb 4

Knowledge Transfer from High-Resource to Low-Resource Programming Languages for Code LLMs

Over the past few years, Large Language Models of Code (Code LLMs) have started to have a significant impact on programming practice. Code LLMs are also emerging as a building block for research in programming languages and software engineering. However, the quality of code produced by a Code LLM varies significantly by programming languages. Code LLMs produce impressive results on programming languages that are well represented in their training data (e.g., Java, Python, or JavaScript), but struggle with low-resource languages, like OCaml and Racket. This paper presents an effective approach for boosting the performance of Code LLMs on low-resource languages using semi-synthetic data. Our approach generates high-quality datasets for low-resource languages, which can then be used to fine-tune any pretrained Code LLM. Our approach, called MultiPL-T, translates training data from high-resource languages into training data for low-resource languages. We apply our approach to generate tens of thousands of new, validated training items for Racket, OCaml, and Lua from Python. Moreover, we use an open dataset (The Stack) and model (StarCoderBase), which allow us to decontaminate benchmarks and train models on this data without violating the model license. With MultiPL-T generated data, we present fine-tuned versions of StarCoderBase that achieve state-of-the-art performance for Racket, OCaml, and Lua on benchmark problems. For Lua, our fine-tuned model achieves the same performance as StarCoderBase as Python -- a very high-resource language -- on the MultiPL-E benchmarks. For Racket and OCaml, we double their performance on MultiPL-E, bringing their performance close to higher-resource languages such as Ruby and C#.

  • 8 authors
·
Aug 18, 2023

UTFix: Change Aware Unit Test Repairing using LLM

Software updates, including bug repair and feature additions, are frequent in modern applications but they often leave test suites outdated, resulting in undetected bugs and increased chances of system failures. A recent study by Meta revealed that 14%-22% of software failures stem from outdated tests that fail to reflect changes in the codebase. This highlights the need to keep tests in sync with code changes to ensure software reliability. In this paper, we present UTFix, a novel approach for repairing unit tests when their corresponding focal methods undergo changes. UTFix addresses two critical issues: assertion failure and reduced code coverage caused by changes in the focal method. Our approach leverages language models to repair unit tests by providing contextual information such as static code slices, dynamic code slices, and failure messages. We evaluate UTFix on our generated synthetic benchmarks (Tool-Bench), and real-world benchmarks. Tool- Bench includes diverse changes from popular open-source Python GitHub projects, where UTFix successfully repaired 89.2% of assertion failures and achieved 100% code coverage for 96 tests out of 369 tests. On the real-world benchmarks, UTFix repairs 60% of assertion failures while achieving 100% code coverage for 19 out of 30 unit tests. To the best of our knowledge, this is the first comprehensive study focused on unit test in evolving Python projects. Our contributions include the development of UTFix, the creation of Tool-Bench and real-world benchmarks, and the demonstration of the effectiveness of LLM-based methods in addressing unit test failures due to software evolution.

  • 8 authors
·
Mar 19

ConAIR:Consistency-Augmented Iterative Interaction Framework to Enhance the Reliability of Code Generation

Code generation techniques generate code snippets automatically based on the problem requirements in natural language. Recently, large language models (LLMs) achieve the SOTA performance on code generation. However, LLMs still struggle at times to generate accurate code, which diminishes their promised efficiency as developers must spend significant effort evaluating and debugging the generated code. To improve the reliability and quality of the generated codes, researchers propose to leverage Consistency to obtain a better code based on generating and ranking multiple candidates. The existing approach is problematic as Consistency thinks a code is better when (1) the code pass more tests (inter-consistency) (2) more codes share the same behavior (intra-consistency). However, because the tests are also generated by LLMs, they could be wrong as well. As a result, majority voting based on testing results is unreliable. Relying solely on consistency is insufficient to address this issue; integrating user feedback is essential for effectively guiding consistency. We show that with minimal human effort, performance can be significantly enhanced. We propose Consistency-Augmented Iterative Interaction Framework to Enhance the Reliability of Code Generation, ConAIR, which is an approach that aims to improve the performance of a code generator through two distinctive ingredients, i.e., (1) lightweight user effort for validating the correctness of selected tests; and (2) a dynamic strategy for ranking, localizing and correcting multiple tests and codes. Overall, we propose a lightweight interaction framework that incorporates user feedback to correct identified tests and guide the iterative process. The iteration rounds are only 4 in average with the help of consistency. With only lightweight human efforts, we can achieve an improvement of 33% towards the base model.

  • 5 authors
·
Nov 23, 2024

Leveraging Reinforcement Learning and Large Language Models for Code Optimization

Code optimization is a daunting task that requires a significant level of expertise from experienced programmers. This level of expertise is not sufficient when compared to the rapid development of new hardware architectures. Towards advancing the whole code optimization process, recent approaches rely on machine learning and artificial intelligence techniques. This paper introduces a new framework to decrease the complexity of code optimization. The proposed framework builds on large language models (LLMs) and reinforcement learning (RL) and enables LLMs to receive feedback from their environment (i.e., unit tests) during the fine-tuning process. We compare our framework with existing state-of-the-art models and show that it is more efficient with respect to speed and computational usage, as a result of the decrement in training steps and its applicability to models with fewer parameters. Additionally, our framework reduces the possibility of logical and syntactical errors. Toward evaluating our approach, we run several experiments on the PIE dataset using a CodeT5 language model and RRHF, a new reinforcement learning algorithm. We adopt a variety of evaluation metrics with regards to optimization quality, and speedup. The evaluation results demonstrate that the proposed framework has similar results in comparison with existing models using shorter training times and smaller pre-trained models. In particular, we accomplish an increase of 5.6% and 2.2 over the baseline models concerning the %OP T and SP metrics.

  • 11 authors
·
Dec 9, 2023

Cracks in The Stack: Hidden Vulnerabilities and Licensing Risks in LLM Pre-Training Datasets

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

  • 2 authors
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Jan 5

Assessing the Quality and Security of AI-Generated Code: A Quantitative Analysis

This study presents a quantitative evaluation of the code quality and security of five prominent Large Language Models (LLMs): Claude Sonnet 4, Claude 3.7 Sonnet, GPT-4o, Llama 3.2 90B, and OpenCoder 8B. While prior research has assessed the functional performance of LLM-generated code, this research tested LLM output from 4,442 Java coding assignments through comprehensive static analysis using SonarQube. The findings suggest that although LLMs can generate functional code, they also introduce a range of software defects, including bugs, security vulnerabilities, and code smells. These defects do not appear to be isolated; rather, they may represent shared weaknesses stemming from systemic limitations within current LLM code generation methods. In particular, critically severe issues, such as hard-coded passwords and path traversal vulnerabilities, were observed across multiple models. These results indicate that LLM-generated code requires verification in order to be considered production-ready. This study found no direct correlation between a model's functional performance (measured by Pass@1 rate of unit tests) and the overall quality and security of its generated code, measured by the number of SonarQube issues in benchmark solutions that passed the functional tests. This suggests that functional benchmark performance score is not a good indicator of overall code quality and security. The goal of this study is not to rank LLM performance but to highlight that all evaluated models appear to share certain weaknesses. Consequently, these findings support the view that static analysis can be a valuable instrument for detecting latent defects and an important safeguard for organizations that deploy AI in software development.

  • 3 authors
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Aug 20

Sifting through the Chaff: On Utilizing Execution Feedback for Ranking the Generated Code Candidates

Large Language Models (LLMs), such as GPT-4, StarCoder, and CodeLlama, are transforming the way developers approach programming by automatically generating code based on given natural language descriptions. Despite advancements, generating syntactically and semantically correct code remains challenging, especially for complex programming tasks. Existing approaches typically generate multiple candidate solutions using LLMs to increase the likelihood of producing correct code. However, selecting the correct code from these candidates-a process known as code ranking-remains a major challenge. Current research on code ranking can be categorized into execution-based and non-execution-based methods. Execution-based methods, although effective, encounter notable limitations, such as scarcity of quality unit tests and security risks. Non-execution-based methods like CodeRanker, which rely solely on classification labels to train a code ranker, struggle to capture subtle errors and provide detailed error insights. Recognizing the strengths and limitations of both approaches, we propose a new method. The key insight of our work is that an effective code ranker is expected to truly comprehend the underlying causes of erroneous code, as relying solely on classification labels is insufficient. Inspired by this, this paper puts forward RankEF, an innovative approach for code ranking that leverages execution feedback. RankEF employs multi-task learning to integrate code classification with execution feedback generation. This approach enables the model to understand the reasons behind incorrect code, distinguishing between correct and incorrect solutions without the need to execute the code during the ranking phase. Experiments on three code generation benchmarks demonstrate that RankEF significantly outperforms the state-of-the-art CodeRanker.

  • 7 authors
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Aug 25, 2024

GitChameleon: Unmasking the Version-Switching Capabilities of Code Generation Models

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

  • 7 authors
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Nov 5, 2024 2

A Lightweight Framework for High-Quality Code Generation

In recent years, the use of automated source code generation utilizing transformer-based generative models has expanded, and these models can generate functional code according to the requirements of the developers. However, recent research revealed that these automatically generated source codes can contain vulnerabilities and other quality issues. Despite researchers' and practitioners' attempts to enhance code generation models, retraining and fine-tuning large language models is time-consuming and resource-intensive. Thus, we describe FRANC, a lightweight framework for recommending more secure and high-quality source code derived from transformer-based code generation models. FRANC includes a static filter to make the generated code compilable with heuristics and a quality-aware ranker to sort the code snippets based on a quality score. Moreover, the framework uses prompt engineering to fix persistent quality issues. We evaluated the framework with five Python and Java code generation models and six prompt datasets, including a newly created one in this work (SOEval). The static filter improves 9% to 46% Java suggestions and 10% to 43% Python suggestions regarding compilability. The average improvement over the NDCG@10 score for the ranking system is 0.0763, and the repairing techniques repair the highest 80% of prompts. FRANC takes, on average, 1.98 seconds for Java; for Python, it takes 0.08 seconds.

  • 3 authors
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Jul 16, 2023

On the Anatomy of Real-World R Code for Static Analysis

CONTEXT The R programming language has a huge and active community, especially in the area of statistical computing. Its interpreted nature allows for several interesting constructs, like the manipulation of functions at run-time, that hinder the static analysis of R programs. At the same time, there is a lack of existing research regarding how these features, or even the R language as a whole are used in practice. OBJECTIVE In this paper, we conduct a large-scale, static analysis of more than 50 million lines of real-world R programs and packages to identify their characteristics and the features that are actually used. Moreover, we compare the similarities and differences between the scripts of R users and the implementations of package authors. We provide insights for static analysis tools like the lintr package as well as potential interpreter optimizations and uncover areas for future research. METHOD We analyze 4230 R scripts submitted alongside publications and the sources of 19450 CRAN packages for over 350000 R files, collecting and summarizing quantitative information for features of interest. RESULTS We find a high frequency of name-based indexing operations, assignments, and loops, but a low frequency for most of R's reflective functions. Furthermore, we find neither testing functions nor many calls to R's foreign function interface (FFI) in the publication submissions. CONCLUSION R scripts and package sources differ, for example, in their size, the way they include other packages, and their usage of R's reflective capabilities. We provide features that are used frequently and should be prioritized by static analysis tools, like operator assignments, function calls, and certain reflective functions like load.

  • 6 authors
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Jan 29, 2024

GrammarGPT: Exploring Open-Source LLMs for Native Chinese Grammatical Error Correction with Supervised Fine-Tuning

Grammatical error correction aims to correct ungrammatical sentences automatically. Recently, some work has demonstrated the excellent capabilities of closed-source Large Language Models (LLMs, e.g., ChatGPT) in grammatical error correction. However, the potential of open-source LLMs remains unexplored. In this paper, we introduced GrammarGPT, an open-source LLM, to preliminary explore its potential for native Chinese grammatical error correction. The core recipe of GrammarGPT is to leverage the hybrid dataset of ChatGPT-generated and human-annotated. For grammatical errors with clues, we proposed a heuristic method to guide ChatGPT to generate ungrammatical sentences by providing those clues. For grammatical errors without clues, we collected ungrammatical sentences from publicly available websites and manually corrected them. In addition, we employed an error-invariant augmentation method to enhance the ability of the model to correct native Chinese grammatical errors. We ultimately constructed about 1k parallel data and utilized these data to fine-tune open-source LLMs (e.g., Phoenix, released by The Chinese University of Hong Kong, Shenzhen) with instruction tuning. The experimental results show that GrammarGPT outperforms the existing SOTA system significantly. Although model parameters are 20x larger than the SOTA baseline, the required amount of data for instruction tuning is 1200x smaller, illustrating the potential of open-source LLMs on native CGEC. Our GrammarGPT ranks 3^{rd} on NLPCC2023 SharedTask1, demonstrating our approach's effectiveness. The code and data are available at https://github.com/FreedomIntelligence/GrammarGPT.

  • 4 authors
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Jul 25, 2023 1

Reasoning Runtime Behavior of a Program with LLM: How Far Are We?

Large language models for code (i.e., code LLMs) have shown strong code understanding and generation capabilities. To evaluate the capabilities of code LLMs in various aspects, many benchmarks have been proposed (e.g., HumanEval and ClassEval). Code reasoning is one of the most essential abilities of code LLMs, but existing benchmarks for code reasoning are not sufficient. Typically, they focus on predicting the input and output of a program, ignoring the evaluation of the intermediate behavior during program execution, as well as the logical consistency (e.g., the model should not give the correct output if the prediction of execution path is wrong) when performing the reasoning. To address these problems, in this paper, we propose a framework, namely REval, for evaluating code reasoning abilities and consistency of code LLMs with program execution. We utilize existing code benchmarks and adapt them to new benchmarks within our framework. A large-scale empirical study is conducted and most LLMs show unsatisfactory performance on both Runtime Behavior Reasoning (i.e., an average accuracy of 44.4%) and Incremental Consistency Evaluation (i.e., an average IC score of 10.3). Evaluation results of current code LLMs reflect the urgent need for the community to strengthen the code reasoning capability of code LLMs. Our code, data, and \newname leaderboard are available at https://r-eval.github.io.

  • 6 authors
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Mar 25, 2024

Computational reproducibility of Jupyter notebooks from biomedical publications

Jupyter notebooks facilitate the bundling of executable code with its documentation and output in one interactive environment, and they represent a popular mechanism to document and share computational workflows. The reproducibility of computational aspects of research is a key component of scientific reproducibility but has not yet been assessed at scale for Jupyter notebooks associated with biomedical publications. We address computational reproducibility at two levels: First, using fully automated workflows, we analyzed the computational reproducibility of Jupyter notebooks related to publications indexed in PubMed Central. We identified such notebooks by mining the articles full text, locating them on GitHub and re-running them in an environment as close to the original as possible. We documented reproduction success and exceptions and explored relationships between notebook reproducibility and variables related to the notebooks or publications. Second, this study represents a reproducibility attempt in and of itself, using essentially the same methodology twice on PubMed Central over two years. Out of 27271 notebooks from 2660 GitHub repositories associated with 3467 articles, 22578 notebooks were written in Python, including 15817 that had their dependencies declared in standard requirement files and that we attempted to re-run automatically. For 10388 of these, all declared dependencies could be installed successfully, and we re-ran them to assess reproducibility. Of these, 1203 notebooks ran through without any errors, including 879 that produced results identical to those reported in the original notebook and 324 for which our results differed from the originally reported ones. Running the other notebooks resulted in exceptions. We zoom in on common problems, highlight trends and discuss potential improvements to Jupyter-related workflows associated with biomedical publications.

  • 2 authors
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Aug 10, 2023