arXiv subjects

David N. Palacio

Publications and source records attributed to David N. Palacio.

15 recordsLinked to original sources

arXiv2026

A Causal Perspective on Measuring, Explaining and Mitigating Smells in LLM-Generated Code

Recent advances in large language models (LLMs) have accelerated their adoption in software engineering contexts. However, concerns persist about the structural quality of the code they produce. In particular, LLMs often replicate poor coding practices, introducing code smells (i.e., patterns that hinder readability, maintainability, or design integrity). Although prior research has examined the detection or repair of smells, we still lack a clear understanding of how and when these issues emerge in generated code. This paper addresses this gap by systematically measuring, explaining and mitigating smell propensity in LLM-generated code. We build on the Propensity Smelly Score (PSC), a probabilistic metric that estimates the likelihood of generating particular smell types, and establish its robustness as a signal of structural quality. Using PSC as an instrument for causal analysis, we identify how generation strategy, model size, model architecture and prompt formulation shape the structural properties of generated code. Our findings show that prompt design and architectural choices play a decisive role in smell propensity and motivate practical mitigation strategies that reduce its occurrence. A user study further demonstrates that PSC helps developers interpret model behavior and assess code quality, providing evidence that smell propensity signals can support human judgement. Taken together, our work lays the groundwork for integrating quality-aware assessments into the evaluation and deployment of LLMs for code.

cs.SE↗

arXiv2026

ECLAIR: A Causally-Grounded AI Framework for Scientific Discovery in Empirical Software Engineering

The scientific method has long guided empirical research in Software Engineering (SE), but the complexity of modern software systems often hinders its systematic application. This paper introduces ECLAIR, a causally grounded AI framework that integrates Large Language Models (LLMs) into every stage of the scientific process, from hypothesis generation to analysis and interpretation. ECLAIR treats LLMs as active scientific agents operating under the principles of causal inference, within a human-in-the-loop design that safeguards against the risks of unsound automated reasoning. We demonstrate the framework through a case study examining how prompt design influences code generation accuracy in two LLMs. Results show that, for both models, instruction-style, longer few-shot, and signature-augmented prompts yield small negative causal effects on accuracy, illustrating how causal reasoning provides a principled foundation for explaining why software phenomena occur. This study presents the first causally grounded structured methodology for embedding LLMs within the scientific method in SE, designed around the epistemological demands of empirical SE research, establishing a basis for rigorous AI-assisted research.

cs.SE↗

arXiv2026

Lost in Transmission: An Information-Theoretic Account of Unsupervised Software Traceability

Traceability remains a critical capability to ensure system reliability, maintainability, and compliance in modern software development. Although unsupervised Information Retrieval (IR) and Machine Learning (ML) techniques are widely adopted for automated trace link recovery, their effectiveness is often limited by the quality and structure of the underlying artifacts. In practice, these approaches assume that meaningful traceability signals are embedded in textual data, an assumption that rarely holds in industrial settings with sparse, inconsistent, or unbalanced documentation. Furthermore, conventional evaluation metrics (e.g., precision, recall, F1) can misrepresent performance when data characteristics are not explicitly considered. We introduce TraceXplainer, an information-theoretic framework for evaluating the reliability and limits of unsupervised traceability. Our approach leverages self-information and mutual information (MI) to quantify the informativeness and alignment of source and target artifacts. Through a comprehensive empirical analysis of industry datasets, we show that typical traceability corpora exhibit significant information imbalances, where the source code contains on average more information than the corresponding documentation. In addition, the observed levels of mutual information, loss, and noise reveal inherent constraints on the ability of unsupervised techniques to recover accurate trace links. These findings suggest that improving traceability in practice requires a shift to data-centric engineering, focusing on artifact quality, consistency, and information alignment; rather than solely advancing model sophistication (or complexity). Our results provide insights for practitioners to better assess traceability readiness and guide improvements in documentation and development workflows.

cs.SE↗

arXiv2026

Enabling Global, Human-Centered Explanations for LLMs:From Tokens to Interpretable Code and Test Generation

As Large Language Models for Code (LM4Code) become integral to software engineering, establishing trust in their output becomes critical. However, standard accuracy metrics obscure the underlying reasoning of generative models, offering little insight into how decisions are made. Although post-hoc interpretability methods attempt to fill this gap, they often restrict explanations to local, token-level insights, which fail to provide a developer-understandable global analysis. Our work highlights the urgent need for \textbf{global, code-based} explanations that reveal how models reason across code. To support this vision, we introduce \textit{code rationales} (CodeQ), a framework that enables global interpretability by mapping token-level rationales to high-level programming categories. Aggregating thousands of these token-level explanations allows us to perform statistical analyses that expose systemic reasoning behaviors. We validate this aggregation by showing it distills a clear signal from noisy token data, reducing explanation uncertainty (Shannon entropy) by over 50%. Additionally, we find that a code generation model (\textit{codeparrot-small}) consistently favors shallow syntactic cues (e.g., \textbf{indentation}) over deeper semantic logic. Furthermore, in a user study with 37 participants, we find its reasoning is significantly misaligned with that of human developers. These findings, hidden from traditional metrics, demonstrate the importance of global interpretability techniques to foster trust in LM4Code.

cs.SE↗

arXiv2025

Mapping the Trust Terrain: LLMs in Software Engineering -- Insights and Perspectives

Applications of Large Language Models (LLMs) are rapidly growing in industry and academia for various software engineering (SE) tasks. As these models become more integral to critical processes, ensuring their reliability and trustworthiness becomes essential. Consequently, the concept of trust in these systems is becoming increasingly critical. Well-calibrated trust is important, as excessive trust can lead to security vulnerabilities, and risks, while insufficient trust can hinder innovation. However, the landscape of trust-related concepts in LLMs in SE is relatively unclear, with concepts such as trust, distrust, and trustworthiness lacking clear conceptualizations in the SE community. To bring clarity to the current research status and identify opportunities for future work, we conducted a comprehensive review of $88$ papers: a systematic literature review of $18$ papers focused on LLMs in SE, complemented by an analysis of 70 papers from broader trust literature. Additionally, we conducted a survey study with 25 domain experts to gain insights into practitioners' understanding of trust and identify gaps between existing literature and developers' perceptions. The result of our analysis serves as a roadmap that covers trust-related concepts in LLMs in SE and highlights areas for future exploration.

cs.SE↗

arXiv2025

Towards a Science of Causal Interpretability in Deep Learning for Software Engineering

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.

cs.SE↗

arXiv2025

Toward Neurosymbolic Program Comprehension

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.

cs.SE↗

arXiv2025

How Propense Are Large Language Models at Producing Code Smells? A Benchmarking Study

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.

cs.SE↗

arXiv2024

Measuring Emergent Capabilities of LLMs for Software Engineering: How Far Are We?

The adoption of Large Language Models (LLMs) across multiple contexts has sparked interest in understanding how scaling model size might lead to behavioral changes, as LLMs can exhibit behaviors not observed in their smaller counterparts. Understanding these emergent capabilities is essential for advancing LLM development and improving their interpretability across diverse tasks. However, whether LLMs exhibit true emergence in the context of Software Engineering remains an unexplored topic, as most research has focused on NLP tasks. In this paper, we investigate the emergence of capabilities in the context of SE. We propose a model-agnostic pipeline for evaluating this phenomenon across three SE tasks: bug fixing, code translation, and commit message generation. More precisely, for each task, we present a case study instantiating our pipeline to analyze the emergence of capabilities in CodeGen1-multi across four scales ranging from 350M to 16.1B parameters. Our findings do not not provide evidence to support the idea of emergent capabilities resulting from scaling the model size in the selected set of tasks. We hope our results can pave the way to a more nuanced understanding of emergent capabilities of LLMs within the SE domain, guiding future research to focus on task-specific evaluations and the identification of alternative factors contributing to this phenomenon. Our work underscores the importance of task diversity in examining model behaviors and highlights potential limitations in transferring prior understandings of and approaches to emergence from NLP to Software Engineering.

cs.SE↗

arXiv2024

Towards More Trustworthy and Interpretable LLMs for Code through Syntax-Grounded Explanations

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.

cs.SE↗

arXiv2024

Toward a Theory of Causation for Interpreting Neural Code Models

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.

cs.SE↗

arXiv2024

Which Syntactic Capabilities Are Statistically Learned by Masked Language Models for Code?

This paper discusses the limitations of evaluating Masked Language Models (MLMs) in code completion tasks. We highlight that relying on accuracy-based measurements may lead to an overestimation of models' capabilities by neglecting the syntax rules of programming languages. To address these issues, we introduce a technique called SyntaxEval in which Syntactic Capabilities are used to enhance the evaluation of MLMs. SyntaxEval automates the process of masking elements in the model input based on their Abstract Syntax Trees (ASTs). We conducted a case study on two popular MLMs using data from GitHub repositories. Our results showed negative causal effects between the node types and MLMs' accuracy. We conclude that MLMs under study fail to predict some syntactic capabilities.

cs.SE↗

arXiv2023

Benchmarking Causal Study to Interpret Large Language Models for Source Code

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.

cs.SE↗

arXiv2022

Improving the Effectiveness of Traceability Link Recovery using Hierarchical Bayesian Networks

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.

cs.SE↗

arXiv2019

Learning to Identify Security-Related Issues Using Convolutional Neural Networks

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.

cs.SE↗