David N. Palacio

David N. Palacio, Alejandro Velasco, Nathan Cooper et al.

Neural Language Models of Code, or Neural Code Models (NCMs), are rapidly progressing from research prototypes to commercial developer tools. As such, understanding the capabilities and limitations of such models is becoming critical. However, the abilities of these models are typically measured using automated metrics that often only reveal a portion of their real-world performance. While, in general, the performance of NCMs appears promising, currently much is unknown about how such models arrive at decisions. To this end, this paper introduces $do_{code}$, a post hoc interpretability method specific to NCMs that is capable of explaining model predictions. $do_{code}$ is based upon causal inference to enable programming language-oriented explanations. While the theoretical underpinnings of $do_{code}$ are extensible to exploring different model properties, we provide a concrete instantiation that aims to mitigate the impact of spurious correlations by grounding explanations of model behavior in properties of programming languages. To demonstrate the practical benefit of $do_{code}$, we illustrate the insights that our framework can provide by performing a case study on two popular deep learning architectures and ten NCMs. The results of this case study illustrate that our studied NCMs are sensitive to changes in code syntax. All our NCMs, except for the BERT-like model, statistically learn to predict tokens related to blocks of code (\eg brackets, parenthesis, semicolon) with less confounding bias as compared to other programming language constructs. These insights demonstrate the potential of $do_{code}$ as a useful method to detect and facilitate the elimination of confounding bias in NCMs.

Daniel Rodriguez-Cardenas, David N. Palacio, Dipin Khati et al.

One of the most common solutions adopted by software researchers to address code generation is by training Large Language Models (LLMs) on massive amounts of source code. Although a number of studies have shown that LLMs have been effectively evaluated on popular accuracy metrics (e.g., BLEU, CodeBleu), previous research has largely overlooked the role of Causal Inference as a fundamental component of the interpretability of LLMs' performance. Existing benchmarks and datasets are meant to highlight the difference between the expected and the generated outcome, but do not take into account confounding variables (e.g., lines of code, prompt size) that equally influence the accuracy metrics. The fact remains that, when dealing with generative software tasks by LLMs, no benchmark is available to tell researchers how to quantify neither the causal effect of SE-based treatments nor the correlation of confounders to the model's performance. In an effort to bring statistical rigor to the evaluation of LLMs, this paper introduces a benchmarking strategy named Galeras comprised of curated testbeds for three SE tasks (i.e., code completion, code summarization, and commit generation) to help aid the interpretation of LLMs' performance. We illustrate the insights of our benchmarking strategy by conducting a case study on the performance of ChatGPT under distinct prompt engineering methods. The results of the case study demonstrate the positive causal influence of prompt semantics on ChatGPT's generative performance by an average treatment effect of $\approx 3\%$. Moreover, it was found that confounders such as prompt size are highly correlated with accuracy metrics ($\approx 0.412\%$). The end result of our case study is to showcase causal inference evaluations, in practice, to reduce confounding bias. By reducing the bias, we offer an interpretable solution for the accuracy metric under analysis.

David N Palacio, Alejandro Velasco, Daniel Rodriguez-Cardenas et al.

Large Language Models (LLMs) for code are a family of high-parameter, transformer-based neural networks pre-trained on massive datasets of both natural and programming languages. These models are rapidly being employed in commercial AI-based developer tools, such as GitHub CoPilot. However, measuring and explaining their effectiveness on programming tasks is a challenging proposition, given their size and complexity. The methods for evaluating and explaining LLMs for code are inextricably linked. That is, in order to explain a model's predictions, they must be reliably mapped to fine-grained, understandable concepts. Once this mapping is achieved, new methods for detailed model evaluations are possible. However, most current explainability techniques and evaluation benchmarks focus on model robustness or individual task performance, as opposed to interpreting model predictions. To this end, this paper introduces ASTxplainer, an explainability method specific to LLMs for code that enables both new methods for LLM evaluation and visualizations of LLM predictions that aid end-users in understanding model predictions. At its core, ASTxplainer provides an automated method for aligning token predictions with AST nodes, by extracting and aggregating normalized model logits within AST structures. To demonstrate the practical benefit of ASTxplainer, we illustrate the insights that our framework can provide by performing an empirical evaluation on 12 popular LLMs for code using a curated dataset of the most popular GitHub projects. Additionally, we perform a user study examining the usefulness of an ASTxplainer-derived visualization of model predictions aimed at enabling model users to explain predictions. The results of these studies illustrate the potential for ASTxplainer to provide insights into LLM effectiveness, and aid end-users in understanding predictions.

David N. Palacio, Daniel Rodriguez-Cardenas, Alejandro Velasco et al.

Trustworthiness and interpretability are inextricably linked concepts for LLMs. The more interpretable an LLM is, the more trustworthy it becomes. However, current techniques for interpreting LLMs when applied to code-related tasks largely focus on accuracy measurements, measures of how models react to change, or individual task performance instead of the fine-grained explanations needed at prediction time for greater interpretability, and hence trust. To improve upon this status quo, this paper introduces ASTrust, an interpretability method for LLMs of code that generates explanations grounded in the relationship between model confidence and syntactic structures of programming languages. ASTrust explains generated code in the context of syntax categories based on Abstract Syntax Trees and aids practitioners in understanding model predictions at both local (individual code snippets) and global (larger datasets of code) levels. By distributing and assigning model confidence scores to well-known syntactic structures that exist within ASTs, our approach moves beyond prior techniques that perform token-level confidence mapping by offering a view of model confidence that directly aligns with programming language concepts with which developers are familiar. To put ASTrust into practice, we developed an automated visualization that illustrates the aggregated model confidence scores superimposed on sequence, heat-map, and graph-based visuals of syntactic structures from ASTs. We examine both the practical benefit that ASTrust can provide through a data science study on 12 popular LLMs on a curated set of GitHub repos and the usefulness of ASTrust through a human study.

David N. Palacio, Daniel McCrystal, Kevin Moran et al.

Software security is becoming a high priority for both large companies and start-ups alike due to the increasing potential for harm that vulnerabilities and breaches carry with them. However, attaining robust security assurance while delivering features requires a precarious balancing act in the context of agile development practices. One path forward to help aid development teams in securing their software products is through the design and development of security-focused automation. Ergo, we present a novel approach, called SecureReqNet, for automatically identifying whether issues in software issue tracking systems describe security-related content. Our approach consists of a two-phase neural net architecture that operates purely on the natural language descriptions of issues. The first phase of our approach learns high dimensional word embeddings from hundreds of thousands of vulnerability descriptions listed in the CVE database and issue descriptions extracted from open source projects. The second phase then utilizes the semantic ontology represented by these embeddings to train a convolutional neural network capable of predicting whether a given issue is security-related. We evaluated SecureReqNet by applying it to identify security-related issues from a dataset of thousands of issues mined from popular projects on GitLab and GitHub. In addition, we also applied our approach to identify security-related requirements from a commercial software project developed by a major telecommunication company. Our preliminary results are encouraging, with SecureReqNet achieving an accuracy of 96% on open source issues and 71.6% on industrial requirements.

David N. Palacio, Dipin Khati, Daniel Rodriguez-Cardenas et al.

In recent years, Language Models for Code (LLM4Code) have significantly changed the landscape of software engineering (SE) on downstream tasks, such as code generation, by making software development more efficient. Therefore, a growing interest has emerged in further evaluating these Language Models to homogenize the quality assessment of generated code. As the current evaluation process can significantly overreact on accuracy-based metrics, practitioners often seek methods to interpret LLM4Code outputs beyond canonical benchmarks. While the majority of research reports on code generation effectiveness in terms of expected ground truth, scant attention has been paid to LLMs' explanations. In essence, the decision-making process to generate code is hard to interpret. To bridge this evaluation gap, we introduce code rationales (Code$Q$), a technique with rigorous mathematical underpinning, to identify subsets of tokens that can explain individual code predictions. We conducted a thorough Exploratory Analysis to demonstrate the method's applicability and a User Study to understand the usability of code-based explanations. Our evaluation demonstrates that Code$Q$ is a powerful interpretability method to explain how (less) meaningful input concepts (i.e., natural language particle `at') highly impact output generation. Moreover, participants of this study highlighted Code$Q$'s ability to show a causal relationship between the input and output of the model with readable and informative explanations on code completion and test generation tasks. Additionally, Code$Q$ also helps to uncover model rationale, facilitating comparison with a human rationale to promote a fair level of trust and distrust in the model.

Alejandro Velasco, Daniel Rodriguez-Cardenas, Luftar Rahman Alif et al.

Large Language Models (LLMs) have shown significant potential in automating software engineering tasks, particularly in code generation. However, current evaluation benchmarks, which primarily focus on accuracy, fall short in assessing the quality of the code generated by these models, specifically their tendency to produce code smells. To address this limitation, we introduce CodeSmellEval, a benchmark designed to evaluate the propensity of LLMs for generating code smells. Our benchmark includes a novel metric: Propensity Smelly Score (PSC), and a curated dataset of method-level code smells: CodeSmellData. To demonstrate the use of CodeSmellEval, we conducted a case study with two state-of-the-art LLMs, CodeLlama and Mistral. The results reveal that both models tend to generate code smells, such as simplifiable-condition and consider-merging-isinstance. These findings highlight the effectiveness of our benchmark in evaluating LLMs, providing valuable insights into their reliability and their propensity to introduce code smells in code generation tasks.

David N. Palacio

This dissertation addresses achieving causal interpretability in Deep Learning for Software Engineering (DL4SE). While Neural Code Models (NCMs) show strong performance in automating software tasks, their lack of transparency in causal relationships between inputs and outputs limits full understanding of their capabilities. To build trust in NCMs, researchers and practitioners must explain code predictions. Associational interpretability, which identifies correlations, is often insufficient for tasks requiring intervention and change analysis. To address this, the dissertation introduces DoCode, a novel post hoc interpretability method for NCMs. DoCode uses causal inference to provide programming language-oriented explanations of model predictions. It follows a four-step pipeline: modeling causal problems using Structural Causal Models (SCMs), identifying the causal estimand, estimating effects with metrics like Average Treatment Effect (ATE), and refuting effect estimates. Its framework is extensible, with an example that reduces spurious correlations by grounding explanations in programming language properties. A case study on deep code generation across interpretability scenarios and various deep learning architectures demonstrates DoCode's benefits. Results show NCMs' sensitivity to code syntax changes and their ability to learn certain programming concepts while minimizing confounding bias. The dissertation also examines associational interpretability as a foundation, analyzing software information's causal nature using tools like COMET and TraceXplainer for traceability. It highlights the need to identify code confounders and offers practical guidelines for applying causal interpretability to NCMs, contributing to more trustworthy AI in software engineering.

Alejandro Velasco, Aya Garryyeva, David N. Palacio et al.

Recent advancements in Large Language Models (LLMs) have paved the way for Large Code Models (LCMs), enabling automation in complex software engineering tasks, such as code generation, software testing, and program comprehension, among others. Tools like GitHub Copilot and ChatGPT have shown substantial benefits in supporting developers across various practices. However, the ambition to scale these models to trillion-parameter sizes, exemplified by GPT-4, poses significant challenges that limit the usage of Artificial Intelligence (AI)-based systems powered by large Deep Learning (DL) models. These include rising computational demands for training and deployment and issues related to trustworthiness, bias, and interpretability. Such factors can make managing these models impractical for many organizations, while their "black-box'' nature undermines key aspects, including transparency and accountability. In this paper, we question the prevailing assumption that increasing model parameters is always the optimal path forward, provided there is sufficient new data to learn additional patterns. In particular, we advocate for a Neurosymbolic research direction that combines the strengths of existing DL techniques (e.g., LLMs) with traditional symbolic methods--renowned for their reliability, speed, and determinism. To this end, we outline the core features and present preliminary results for our envisioned approach, aimed at establishing the first Neurosymbolic Program Comprehension (NsPC) framework to aid in identifying defective code components.

David N. Palacio, Daniel Rodriguez-Cardenas, Denys Poshyvanyk et al.

Traceability is a cornerstone of modern software development, ensuring system reliability and facilitating software maintenance. While unsupervised techniques leveraging Information Retrieval (IR) and Machine Learning (ML) methods have been widely used for predicting trace links, their effectiveness remains underexplored. In particular, these techniques often assume traceability patterns are present within textual data - a premise that may not hold universally. Moreover, standard evaluation metrics such as precision, recall, accuracy, or F1 measure can misrepresent the model performance when underlying data distributions are not properly analyzed. Given that automated traceability techniques tend to struggle to establish links, we need further insight into the information limits related to traceability artifacts. In this paper, we propose an approach, TraceXplainer, for using information theory metrics to evaluate and better understand the performance (limits) of unsupervised traceability techniques. Specifically, we introduce self-information, cross-entropy, and mutual information (MI) as metrics to measure the informativeness and reliability of traceability links. Through a comprehensive replication and analysis of well-studied datasets and techniques, we investigate the effectiveness of unsupervised techniques that predict traceability links using IR/ML. This application of TraceXplainer illustrates an imbalance in typical traceability datasets where the source code has on average 1.48 more information bits (i.e., entropy) than the linked documentation. Additionally, we demonstrate that an average MI of 4.81 bits, loss of 1.75, and noise of 0.28 bits signify that there are information-theoretic limits on the effectiveness of unsupervised traceability techniques. We hope these findings spur additional research on understanding the limits and progress of traceability research.

Anamaria Mojica-Hanke, David Nader Palacio, Denys Poshyvanyk et al.

Context: Machine Learning (ML) significantly impacts Software Engineering (SE), but studies mainly focus on practitioners, neglecting researchers. This overlooks practices and challenges in teaching, researching, or reviewing ML applications in SE. Objective: This study aims to contribute to the knowledge, about the synergy between ML and SE from the perspective of SE researchers, by providing insights into the practices followed when researching, teaching, and reviewing SE studies that apply ML. Method: We analyzed SE researchers familiar with ML or who authored SE articles using ML, along with the articles themselves. We examined practices, SE tasks addressed with ML, challenges faced, and reviewers' and educators' perspectives using grounded theory coding and qualitative analysis. Results: We found diverse practices focusing on data collection, model training, and evaluation. Some recommended practices (e.g., hyperparameter tuning) appeared in less than 20\% of literature. Common challenges involve data handling, model evaluation (incl. non-functional properties), and involving human expertise in evaluation. Hands-on activities are common in education, though traditional methods persist. Conclusion: Despite accepted practices in applying ML to SE, significant gaps remain. By enhancing guidelines, adopting diverse teaching methods, and emphasizing underrepresented practices, the SE community can bridge these gaps and advance the field.

Antonio Mastropaolo, Simone Scalabrino, Nathan Cooper et al.

Deep learning (DL) techniques are gaining more and more attention in the software engineering community. They have been used to support several code-related tasks, such as automatic bug fixing and code comments generation. Recent studies in the Natural Language Processing (NLP) field have shown that the Text-To-Text Transfer Transformer (T5) architecture can achieve state-of-the-art performance for a variety of NLP tasks. The basic idea behind T5 is to first pre-train a model on a large and generic dataset using a self-supervised task ( e.g: filling masked words in sentences). Once the model is pre-trained, it is fine-tuned on smaller and specialized datasets, each one related to a specific task ( e.g: language translation, sentence classification). In this paper, we empirically investigate how the T5 model performs when pre-trained and fine-tuned to support code-related tasks. We pre-train a T5 model on a dataset composed of natural language English text and source code. Then, we fine-tune such a model by reusing datasets used in four previous works that used DL techniques to: (i) fix bugs, (ii) inject code mutants, (iii) generate assert statements, and (iv) generate code comments. We compared the performance of this single model with the results reported in the four original papers proposing DL-based solutions for those four tasks. We show that our T5 model, exploiting additional data for the self-supervised pre-training phase, can achieve performance improvements over the four baselines.

Cody Watson, Nathan Cooper, David Nader Palacio et al.

An increasingly popular set of techniques adopted by software engineering (SE) researchers to automate development tasks are those rooted in the concept of Deep Learning (DL). The popularity of such techniques largely stems from their automated feature engineering capabilities, which aid in modeling software artifacts. However, due to the rapid pace at which DL techniques have been adopted, it is difficult to distill the current successes, failures, and opportunities of the current research landscape. In an effort to bring clarity to this crosscutting area of work, from its modern inception to the present, this paper presents a systematic literature review of research at the intersection of SE & DL. The review canvases work appearing in the most prominent SE and DL conferences and journals and spans 128 papers across 23 unique SE tasks. We center our analysis around the components of learning, a set of principles that govern the application of machine learning techniques (ML) to a given problem domain, discussing several aspects of the surveyed work at a granular level. The end result of our analysis is a research roadmap that both delineates the foundations of DL techniques applied to SE research, and highlights likely areas of fertile exploration for the future.

Kevin Moran, David N. Palacio, Carlos Bernal-Cárdenas et al.

Traceability is a fundamental component of the modern software development process that helps to ensure properly functioning, secure programs. Due to the high cost of manually establishing trace links, researchers have developed automated approaches that draw relationships between pairs of textual software artifacts using similarity measures. However, the effectiveness of such techniques are often limited as they only utilize a single measure of artifact similarity and cannot simultaneously model (implicit and explicit) relationships across groups of diverse development artifacts. In this paper, we illustrate how these limitations can be overcome through the use of a tailored probabilistic model. To this end, we design and implement a HierarchiCal PrObabilistic Model for SoftwarE Traceability (Comet) that is able to infer candidate trace links. Comet is capable of modeling relationships between artifacts by combining the complementary observational prowess of multiple measures of textual similarity. Additionally, our model can holistically incorporate information from a diverse set of sources, including developer feedback and transitive (often implicit) relationships among groups of software artifacts, to improve inference accuracy. We conduct a comprehensive empirical evaluation of Comet that illustrates an improvement over a set of optimally configured baselines of $\approx$14% in the best case and $\approx$5% across all subjects in terms of average precision. The comparative effectiveness of Comet in practice, where optimal configuration is typically not possible, is likely to be higher. Finally, we illustrate Comets potential for practical applicability in a survey with developers from Cisco Systems who used a prototype Comet Jenkins plugin.