Yangruibo Ding

Yangruibo Ding, Zijian Wang, Wasi Uddin Ahmad et al. · stanford

While pre-trained language models (LM) for code have achieved great success in code completion, they generate code conditioned only on the contents within the file, i.e., in-file context, but ignore the rich semantics in other files within the same project, i.e., cross-file context, a critical source of information that is especially useful in modern modular software development. Such overlooking constrains code language models' capacity in code completion, leading to unexpected behaviors such as generating hallucinated class member functions or function calls with unexpected arguments. In this work, we develop a cross-file context finder tool, CCFINDER, that effectively locates and retrieves the most relevant cross-file context. We propose CoCoMIC, a framework that incorporates cross-file context to learn the in-file and cross-file context jointly on top of pretrained code LMs. CoCoMIC successfully improves the existing code LM with a 33.94% relative increase in exact match and a 28.69% relative increase in identifier matching for code completion when the cross-file context is provided.

Yangruibo Ding, Zijian Wang, Wasi Uddin Ahmad et al.

Code completion models have made significant progress in recent years, yet current popular evaluation datasets, such as HumanEval and MBPP, predominantly focus on code completion tasks within a single file. This over-simplified setting falls short of representing the real-world software development scenario where repositories span multiple files with numerous cross-file dependencies, and accessing and understanding cross-file context is often required to complete the code correctly. To fill in this gap, we propose CrossCodeEval, a diverse and multilingual code completion benchmark that necessitates an in-depth cross-file contextual understanding to complete the code accurately. CrossCodeEval is built on a diverse set of real-world, open-sourced, permissively-licensed repositories in four popular programming languages: Python, Java, TypeScript, and C#. To create examples that strictly require cross-file context for accurate completion, we propose a straightforward yet efficient static-analysis-based approach to pinpoint the use of cross-file context within the current file. Extensive experiments on state-of-the-art code language models like CodeGen and StarCoder demonstrate that CrossCodeEval is extremely challenging when the relevant cross-file context is absent, and we see clear improvements when adding these context into the prompt. However, despite such improvements, the pinnacle of performance remains notably unattained even with the highest-performing model, indicating that CrossCodeEval is also capable of assessing model's capability in leveraging extensive context to make better code completion. Finally, we benchmarked various methods in retrieving cross-file context, and show that CrossCodeEval can also be used to measure the capability of code retrievers.

Saikat Chakraborty, Toufique Ahmed, Yangruibo Ding et al.

Pre-trained Generative Language models (e.g. PLBART, CodeT5, SPT-Code) for source code yielded strong results on several tasks in the past few years, including code generation and translation. These models have adopted varying pre-training objectives to learn statistics of code construction from very large-scale corpora in a self-supervised fashion; the success of pre-trained models largely hinges on these pre-training objectives. This paper proposes a new pre-training objective, "Naturalizing" of source code, exploiting code's bimodal, dual-channel (formal & natural channels) nature. Unlike natural language, code's bimodal, dual-channel nature allows us to generate semantically equivalent code at scale. We introduce six classes of semantic preserving transformations to introduce un-natural forms of code, and then force our model to produce more natural original programs written by developers. Learning to generate equivalent, but more natural code, at scale, over large corpora of open-source code, without explicit manual supervision, helps the model learn to both ingest & generate code. We fine-tune our model in three generative Software Engineering tasks: code generation, code translation, and code refinement with limited human-curated labeled data and achieve state-of-the-art performance rivaling CodeT5. We show that our pre-trained model is especially competitive at zero-shot and few-shot learning, and better at learning code properties (e.g., syntax, data flow).

Marcus J. Min, Yangruibo Ding, Luca Buratti et al. · ibm-research

Code Large Language Models (Code LLMs) are being increasingly employed in real-life applications, so evaluating them is critical. While the conventional accuracy evaluates the performance of Code LLMs on a set of individual tasks, their self-consistency across different tasks is overlooked. Intuitively, a trustworthy model should be self-consistent when generating natural language specifications for its own code and generating code for its own specifications. Failure to preserve self-consistency reveals a lack of understanding of the shared semantics underlying natural language and programming language, and therefore undermines the trustworthiness of a model. In this paper, we first formally define the self-consistency of Code LLMs and then design a framework, IdentityChain, which effectively and efficiently evaluates the self-consistency and conventional accuracy of a model at the same time. We study eleven Code LLMs and show that they fail to preserve self-consistency, which is indeed a distinct aspect from conventional accuracy. Furthermore, we show that IdentityChain can be used as a model debugging tool to expose weaknesses of Code LLMs by demonstrating three major weaknesses that we identify in current models using IdentityChain. Our code is available at https://github.com/marcusm117/IdentityChain.

Jinjun Peng, Magnus Saebo, Tianjun Zhong et al.

The deployment of coding agents in privacy-sensitive and resource-constrained environments drives the demand for capable open-weight Small Language Models (SLMs). However, they suffer from a fundamental capability gap: unlike frontier large models, they lack the inference-time strong generalization to work with complicated, unfamiliar codebases. We identify that the prevailing Task-Centric Learning (TCL) paradigm, which scales exposure across disparate repositories, fails to address this limitation. In response, we propose Repository-Centric Learning (RCL), a paradigm shift that prioritizes vertical repository depth over horizontal task breadth, suggesting SLMs must internalize the "physics" of a target software environment through parametric knowledge acquisition, rather than attempting to recover it via costly inference-time search. Following this new paradigm, we design a four-unit Repository-Centric Experience, transforming static codebases into interactive learning signals, to train SWE-Spot-4B, a family of highly compact models built as repo-specialized experts that breaks established scaling trends, outperforming open-weight models up to larger (e.g., CWM by Meta, Qwen3-Coder-30B) and surpassing/matching efficiency-focused commercial models (e.g., GPT-4.1-mini, GPT-5-nano) across multiple SWE tasks. Further analysis reveals that RCL yields higher training sample efficiency and lower inference costs, emphasizing that for building efficient intelligence, repository mastery is a distinct and necessary dimension that complements general coding capability.

Hongwei Li, Zhun Wang, Qinrun Dai et al.

Agent development kits (ADKs) provide effective platforms and tooling for constructing agents, and their designs are critical to the constructed agents' performance, especially the functionality for agent topology, tools, and memory. However, current ADKs either lack sufficient functional support or rely on humans to manually design these components, limiting agents' generalizability and overall performance. We propose OpenSage, the first ADK that enables LLMs to automatically create agents with self-generated topology and toolsets while providing comprehensive and structured memory support. OpenSage offers effective functionality for agents to create and manage their own sub-agents and toolkits. It also features a hierarchical, graph-based memory system for efficient management and a specialized toolkit tailored to software engineering tasks. Extensive experiments across three state-of-the-art benchmarks with various backbone models demonstrate the advantages of OpenSage over existing ADKs. We also conduct rigorous ablation studies to demonstrate the effectiveness of our design for each component. We believe OpenSage can pave the way for the next generation of agent development, shifting the focus from human-centered to AI-centered paradigms.

Yangruibo Ding, Yanjun Fu, Omniyyah Ibrahim et al.

In the context of the rising interest in code language models (code LMs) and vulnerability detection, we study the effectiveness of code LMs for detecting vulnerabilities. Our analysis reveals significant shortcomings in existing vulnerability datasets, including poor data quality, low label accuracy, and high duplication rates, leading to unreliable model performance in realistic vulnerability detection scenarios. Additionally, the evaluation methods used with these datasets are not representative of real-world vulnerability detection. To address these challenges, we introduce PrimeVul, a new dataset for training and evaluating code LMs for vulnerability detection. PrimeVul incorporates a novel set of data labeling techniques that achieve comparable label accuracy to human-verified benchmarks while significantly expanding the dataset. It also implements a rigorous data de-duplication and chronological data splitting strategy to mitigate data leakage issues, alongside introducing more realistic evaluation metrics and settings. This comprehensive approach aims to provide a more accurate assessment of code LMs' performance in real-world conditions. Evaluating code LMs on PrimeVul reveals that existing benchmarks significantly overestimate the performance of these models. For instance, a state-of-the-art 7B model scored 68.26% F1 on BigVul but only 3.09% F1 on PrimeVul. Attempts to improve performance through advanced training techniques and larger models like GPT-3.5 and GPT-4 were unsuccessful, with results akin to random guessing in the most stringent settings. These findings underscore the considerable gap between current capabilities and the practical requirements for deploying code LMs in security roles, highlighting the need for more innovative research in this domain.

Yangruibo Ding, Jinjun Peng, Marcus J. Min et al.

Code Large Language Models (Code LLMs) have excelled at tasks like code completion but often miss deeper semantics such as execution effects and dynamic states. This paper aims to bridge the gap between Code LLMs' reliance on static text data and the need for semantic understanding for complex tasks like debugging and program repair. We introduce a novel strategy, monologue reasoning, to train Code LLMs to reason comprehensive semantics, encompassing high-level functional descriptions, local execution effects of individual statements, and overall input/output behavior, thereby linking static code text with dynamic execution states. We begin by collecting PyX, a clean Python corpus of fully executable code samples with functional descriptions and test cases. We propose training Code LLMs not only to write code but also to understand code semantics by reasoning about key properties, constraints, and execution behaviors using natural language, mimicking human verbal debugging, i.e., rubber-duck debugging. This approach led to the development of SemCoder, a Code LLM with only 6.7B parameters, which shows competitive performance with GPT-3.5-turbo on code generation and execution reasoning tasks. SemCoder achieves 79.3% on HumanEval (GPT-3.5-turbo: 76.8%), 63.6% on CRUXEval-I (GPT-3.5-turbo: 50.3%), and 63.9% on CRUXEval-O (GPT-3.5-turbo: 59.0%). We also study the effectiveness of SemCoder's monologue-style execution reasoning compared to concrete scratchpad reasoning, showing that our approach integrates semantics from multiple dimensions more smoothly. Finally, we demonstrate the potential of applying learned semantics to improve Code LLMs' debugging and self-refining capabilities. Our data, code, and models are available at: https://github.com/ARiSE-Lab/SemCoder.

Yangruibo Ding, Baishakhi Ray, Premkumar Devanbu et al.

Machine Learning models from other fields, like Computational Linguistics, have been transplanted to Software Engineering tasks, often quite successfully. Yet a transplanted model's initial success at a given task does not necessarily mean it is well-suited for the task. In this work, we examine a common example of this phenomenon: the conceit that "software patching is like language translation". We demonstrate empirically that there are subtle, but critical distinctions between sequence-to-sequence models and translation model: while program repair benefits greatly from the former, general modeling architecture, it actually suffers from design decisions built into the latter, both in terms of translation accuracy and diversity. Given these findings, we demonstrate how a more principled approach to model design, based on our empirical findings and general knowledge of software development, can lead to better solutions. Our findings also lend strong support to the recent trend towards synthesizing edits of code conditional on the buggy context, to repair bugs. We implement such models ourselves as "proof-of-concept" tools and empirically confirm that they behave in a fundamentally different, more effective way than the studied translation-based architectures. Overall, our results demonstrate the merit of studying the intricacies of machine learned models in software engineering: not only can this help elucidate potential issues that may be overshadowed by increases in accuracy; it can also help innovate on these models to raise the state-of-the-art further. We will publicly release our replication data and materials at https://github.com/ARiSE-Lab/Patch-as-translation.

Saikat Chakraborty, Yangruibo Ding, Miltiadis Allamanis et al.

The way developers edit day-to-day code tends to be repetitive, often using existing code elements. Many researchers have tried to automate repetitive code changes by learning from specific change templates which are applied to limited scope. The advancement of deep neural networks and the availability of vast open-source evolutionary data opens up the possibility of automatically learning those templates from the wild. However, deep neural network based modeling for code changes and code in general introduces some specific problems that needs specific attention from research community. For instance, compared to natural language, source code vocabulary can be significantly larger. Further, good changes in code do not break its syntactic structure. Thus, deploying state-of-the-art neural network models without adapting the methods to the source code domain yields sub-optimal results. To this end, we propose a novel tree-based neural network system to model source code changes and learn code change patterns from the wild. Specifically, we propose a tree-based neural machine translation model to learn the probability distribution of changes in code. We realize our model with a change suggestion engine, CODIT, and train the model with more than 24k real-world changes and evaluate it on 5k patches. Our evaluation shows the effectiveness of CODITin learning and suggesting patches. CODIT can also learn specific bug fix pattern from bug fixing patches and can fix 25 bugs out of 80 bugs in Defects4J.

Yangruibo Ding, Marcus J. Min, Gail Kaiser et al.

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 3$\times$ more parameters in self-refinement.

Yuheng Tang, Hongwei Li, Kaijie Zhu et al.

Motivated by the success of general-purpose large language models (LLMs) in software patching, recent works started to train specialized patching models. Most works trained one model to handle the end-to-end patching pipeline (including issue localization, patch generation, and patch validation). However, it is hard for a small model to handle all tasks, as different sub-tasks have different workflows and require different expertise. As such, by using a 70 billion model, SOTA methods can only reach up to 41% resolved rate on SWE-bench-Verified. Motivated by the collaborative nature, we propose Co-PatcheR, the first collaborative patching system with small and specialized reasoning models for individual components. Our key technique novelties are the specific task designs and training recipes. First, we train a model for localization and patch generation. Our localization pinpoints the suspicious lines through a two-step procedure, and our generation combines patch generation and critique. We then propose a hybrid patch validation that includes two models for crafting issue-reproducing test cases with and without assertions and judging patch correctness, followed by a majority vote-based patch selection. Through extensive evaluation, we show that Co-PatcheR achieves 46% resolved rate on SWE-bench-Verified with only 3 x 14B models. This makes Co-PatcheR the best patcher with specialized models, requiring the least training resources and the smallest models. We conduct a comprehensive ablation study to validate our recipes, as well as our choice of training data number, model size, and testing-phase scaling strategy.

Yangruibo Ding, Sahil Suneja, Yunhui Zheng et al.

Automatically locating vulnerable statements in source code is crucial to assure software security and alleviate developers' debugging efforts. This becomes even more important in today's software ecosystem, where vulnerable code can flow easily and unwittingly within and across software repositories like GitHub. Across such millions of lines of code, traditional static and dynamic approaches struggle to scale. Although existing machine-learning-based approaches look promising in such a setting, most work detects vulnerable code at a higher granularity -- at the method or file level. Thus, developers still need to inspect a significant amount of code to locate the vulnerable statement(s) that need to be fixed. This paper presents VELVET, a novel ensemble learning approach to locate vulnerable statements. Our model combines graph-based and sequence-based neural networks to successfully capture the local and global context of a program graph and effectively understand code semantics and vulnerable patterns. To study VELVET's effectiveness, we use an off-the-shelf synthetic dataset and a recently published real-world dataset. In the static analysis setting, where vulnerable functions are not detected in advance, VELVET achieves 4.5x better performance than the baseline static analyzers on the real-world data. For the isolated vulnerability localization task, where we assume the vulnerability of a function is known while the specific vulnerable statement is unknown, we compare VELVET with several neural networks that also attend to local and global context of code. VELVET achieves 99.6% and 43.6% top-1 accuracy over synthetic data and real-world data, respectively, outperforming the baseline deep-learning models by 5.3-29.0%.

Yangruibo Ding, Luca Buratti, Saurabh Pujar et al.

Understanding the functional (dis)-similarity of source code is significant for code modeling tasks such as software vulnerability and code clone detection. We present DISCO(DIS-similarity of COde), a novel self-supervised model focusing on identifying (dis)similar functionalities of source code. Different from existing works, our approach does not require a huge amount of randomly collected datasets. Rather, we design structure-guided code transformation algorithms to generate synthetic code clones and inject real-world security bugs, augmenting the collected datasets in a targeted way. We propose to pre-train the Transformer model with such automatically generated program contrasts to better identify similar code in the wild and differentiate vulnerable programs from benign ones. To better capture the structural features of source code, we propose a new cloze objective to encode the local tree-based context (e.g., parents or sibling nodes). We pre-train our model with a much smaller dataset, the size of which is only 5% of the state-of-the-art models' training datasets, to illustrate the effectiveness of our data augmentation and the pre-training approach. The evaluation shows that, even with much less data, DISCO can still outperform the state-of-the-art models in vulnerability and code clone detection tasks.

Saikat Chakraborty, Rahul Krishna, Yangruibo Ding et al.

Automated detection of software vulnerabilities is a fundamental problem in software security. Existing program analysis techniques either suffer from high false positives or false negatives. Recent progress in Deep Learning (DL) has resulted in a surge of interest in applying DL for automated vulnerability detection. Several recent studies have demonstrated promising results achieving an accuracy of up to 95% at detecting vulnerabilities. In this paper, we ask, "how well do the state-of-the-art DL-based techniques perform in a real-world vulnerability prediction scenario?". To our surprise, we find that their performance drops by more than 50%. A systematic investigation of what causes such precipitous performance drop reveals that existing DL-based vulnerability prediction approaches suffer from challenges with the training data (e.g., data duplication, unrealistic distribution of vulnerable classes, etc.) and with the model choices (e.g., simple token-based models). As a result, these approaches often do not learn features related to the actual cause of the vulnerabilities. Instead, they learn unrelated artifacts from the dataset (e.g., specific variable/function names, etc.). Leveraging these empirical findings, we demonstrate how a more principled approach to data collection and model design, based on realistic settings of vulnerability prediction, can lead to better solutions. The resulting tools perform significantly better than the studied baseline: up to 33.57% boost in precision and 128.38% boost in recall compared to the best performing model in the literature. Overall, this paper elucidates existing DL-based vulnerability prediction systems' potential issues and draws a roadmap for future DL-based vulnerability prediction research. In that spirit, we make available all the artifacts supporting our results: https://git.io/Jf6IA.