arXiv subjects

Mohammed Latif Siddiq

Publications and source records attributed to Mohammed Latif Siddiq.

12 recordsLinked to original sources

arXiv2026

Security in the Age of AI Teammates: An Empirical Study of Agentic Pull Requests on GitHub

Autonomous coding agents are increasingly deployed as AI teammates in modern software engineering, independently authoring pull requests (PRs) that modify production code at scale. This study aims to systematically characterize how autonomous coding agents contribute to software security in practice, how these security-related contributions are reviewed and accepted, and which observable signals are associated with PR rejection. We conduct a large-scale empirical analysis of agent-authored PRs using the AIDev dataset, comprising of over 33,000 curated PRs from popular GitHub repositories. Security-relevant PRs are identified using a keyword filtering strategy, followed by manual validation, resulting in 1,293 confirmed security-related agentic-PRs. We then analyze prevalence, acceptance outcomes, and review latency across autonomous agents, programming ecosystems, and types of code changes. Moreover, we apply qualitative open coding to identify recurring security-related actions and underlying intents, and examine review metadata to identify early signals associated with PR rejection. Security-related Agentic-PRs constitute a meaningful share of agent activity (approximately 4\%). Rather than focusing solely on narrow vulnerability fixes, agents most frequently perform supportive security hardening activities, including testing, documentation, configuration, and improved error handling. Compared to non-security PRs, security-related Agentic-PRs exhibit lower merge rates and longer review latency, reflecting heightened human scrutiny, with variation across agents and programming ecosystems. PR rejection is more strongly associated with PR complexity and verbosity than with explicit security topics.

cs.CR↗

arXiv2026

An Empirical Study of Security Calibration in Large Language Models for Code

Large Language Models (LLMs) are rapidly transforming software development, yet their use in security-critical contexts raises a key question: do models know when their generated code is insecure? This property, known as calibration, measures whether a model's confidence aligns with the true correctness of its outputs. We present the first large-scale empirical study of security calibration in LLM-generated code. We evaluate GPT-4o-mini, Gemini-2.0-Flash, and Qwen3-Coder-Next across multiple temperature settings on two complementary benchmarks: self-contained security tasks and multi-language repository-level contexts. Our results suggest that overconfidence is prevalent across the evaluated LLMs. Functional calibration is consistently worse than security calibration, suggesting that models estimate security outcomes more reliably than functional correctness, potentially because functional correctness depends on complex execution behavior. We also examine whether calibration-guided automated repair can help remediate vulnerabilities in LLM-generated code, finding only limited improvements while frequently introducing functional regressions. Moreover, we study different mitigation strategies for reducing False Trust, where models assign high confidence to vulnerable code. The results show that although architectural gating improves calibration on controlled benchmarks, calibration deteriorates in realistic repository-level settings, increasing the risk of high-confidence vulnerable outputs.

cs.SE↗

arXiv2026

An Empirical Study on Remote Code Execution in Machine Learning Model Hosting Ecosystems

Model-sharing platforms, such as Hugging Face, ModelScope, and OpenCSG, have become central to modern machine learning development, enabling developers to share, load, and fine-tune pre-trained models with minimal effort. However, the flexibility of these ecosystems introduces a critical security concern: the execution of untrusted code during model loading (i.e., via trust_remote_code or trust_repo). In this work, we conduct the first large-scale empirical study of custom model loading practices across five major model-sharing platforms to assess their prevalence, associated risks, and developer perceptions. We first quantify the frequency with which models require custom code to function and identify those that execute arbitrary Python files during loading. We then apply three complementary static analysis tools: Bandit, CodeQL, and Semgrep, to detect security smells and potential vulnerabilities, categorizing our findings by CWE identifiers to provide a standardized risk taxonomy. We also use YARA to identify malicious patterns and payload signatures. In parallel, we systematically analyze the documentation, API design, and safety mechanisms of each platform to understand their mitigation strategies and enforcement levels. Finally, we conduct a qualitative analysis of over 600 developer discussions from GitHub, Hugging Face, and PyTorch Hub forums, as well as Stack Overflow, to capture community concerns and misconceptions regarding security and usability. Our findings reveal widespread reliance on unsafe defaults, uneven security enforcement across platforms, and persistent confusion among developers about the implications of executing remote code. We conclude with actionable recommendations for designing safer model-sharing infrastructures and striking a balance between usability and security in future AI ecosystems.

cs.SE↗

arXiv2025

Assessing the Software Security Comprehension of Large Language Models

Large language models (LLMs) are increasingly used in software development, but their level of software security expertise remains unclear. This work systematically evaluates the security comprehension of five leading LLMs: GPT-4o-Mini, GPT-5-Mini, Gemini-2.5-Flash, Llama-3.1, and Qwen-2.5, using Blooms Taxonomy as a framework. We assess six cognitive dimensions: remembering, understanding, applying, analyzing, evaluating, and creating. Our methodology integrates diverse datasets, including curated multiple-choice questions, vulnerable code snippets (SALLM), course assessments from an Introduction to Software Security course, real-world case studies (XBOW), and project-based creation tasks from a Secure Software Engineering course. Results show that while LLMs perform well on lower-level cognitive tasks such as recalling facts and identifying known vulnerabilities, their performance degrades significantly on higher-order tasks that require reasoning, architectural evaluation, and secure system creation. Beyond reporting aggregate accuracy, we introduce a software security knowledge boundary that identifies the highest cognitive level at which a model consistently maintains reliable performance. In addition, we identify 51 recurring misconception patterns exhibited by LLMs across Blooms levels.

cs.SE↗

arXiv2025

Large Language Models for Software Engineering: A Reproducibility Crisis

Reproducibility is a cornerstone of scientific progress, yet its state in large language model (LLM)-based software engineering (SE) research remains poorly understood. This paper presents the first large-scale, empirical study of reproducibility practices in LLM-for-SE research. We systematically mined and analyzed 640 papers published between 2017 and 2025 across premier software engineering, machine learning, and natural language processing venues, extracting structured metadata from publications, repositories, and documentation. Guided by four research questions, we examine (i) the prevalence of reproducibility smells, (ii) how reproducibility has evolved over time, (iii) whether artifact evaluation badges reliably reflect reproducibility quality, and (iv) how publication venues influence transparency practices. Using a taxonomy of seven smell categories: Code and Execution, Data, Documentation, Environment and Tooling, Versioning, Model, and Access and Legal, we manually annotated all papers and associated artifacts. Our analysis reveals persistent gaps in artifact availability, environment specification, versioning rigor, and documentation clarity, despite modest improvements in recent years and increased adoption of artifact evaluation processes at top SE venues. Notably, we find that badges often signal artifact presence but do not consistently guarantee execution fidelity or long-term reproducibility. Motivated by these findings, we provide actionable recommendations to mitigate reproducibility smells and introduce a Reproducibility Maturity Model (RMM) to move beyond binary artifact certification toward multi-dimensional, progressive evaluation of reproducibility rigor.

cs.SE↗

arXiv2024

Large Language Models in Computer Science Education: A Systematic Literature Review

Large language models (LLMs) are becoming increasingly better at a wide range of Natural Language Processing tasks (NLP), such as text generation and understanding. Recently, these models have extended their capabilities to coding tasks, bridging the gap between natural languages (NL) and programming languages (PL). Foundational models such as the Generative Pre-trained Transformer (GPT) and LLaMA series have set strong baseline performances in various NL and PL tasks. Additionally, several models have been fine-tuned specifically for code generation, showing significant improvements in code-related applications. Both foundational and fine-tuned models are increasingly used in education, helping students write, debug, and understand code. We present a comprehensive systematic literature review to examine the impact of LLMs in computer science and computer engineering education. We analyze their effectiveness in enhancing the learning experience, supporting personalized education, and aiding educators in curriculum development. We address five research questions to uncover insights into how LLMs contribute to educational outcomes, identify challenges, and suggest directions for future research.

cs.LG↗

arXiv2024

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.

cs.SE↗

arXiv2024

SALLM: Security Assessment of Generated Code

With the growing popularity of Large Language Models (LLMs) in software engineers' daily practices, it is important to ensure that the code generated by these tools is not only functionally correct but also free of vulnerabilities. Although LLMs can help developers to be more productive, prior empirical studies have shown that LLMs can generate insecure code. There are two contributing factors to the insecure code generation. First, existing datasets used to evaluate LLMs do not adequately represent genuine software engineering tasks sensitive to security. Instead, they are often based on competitive programming challenges or classroom-type coding tasks. In real-world applications, the code produced is integrated into larger codebases, introducing potential security risks. Second, existing evaluation metrics primarily focus on the functional correctness of the generated code while ignoring security considerations. Therefore, in this paper, we described SALLM, a framework to benchmark LLMs' abilities to generate secure code systematically. This framework has three major components: a novel dataset of security-centric Python prompts, configurable assessment techniques to evaluate the generated code, and novel metrics to evaluate the models' performance from the perspective of secure code generation.

cs.SE↗

arXiv2024

FRANC: 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.

cs.SE↗

arXiv2024

Using Large Language Models to Generate JUnit Tests: An Empirical Study

A code generation model generates code by taking a prompt from a code comment, existing code, or a combination of both. Although code generation models (e.g., GitHub Copilot) are increasingly being adopted in practice, it is unclear whether they can successfully be used for unit test generation without fine-tuning for a strongly typed language like Java. To fill this gap, we investigated how well three models (Codex, GPT-3.5-Turbo, and StarCoder) can generate unit tests. We used two benchmarks (HumanEval and Evosuite SF110) to investigate the effect of context generation on the unit test generation process. We evaluated the models based on compilation rates, test correctness, test coverage, and test smells. We found that the Codex model achieved above 80% coverage for the HumanEval dataset, but no model had more than 2% coverage for the EvoSuite SF110 benchmark. The generated tests also suffered from test smells, such as Duplicated Asserts and Empty Tests.

cs.SE↗

arXiv2023

Enhancing Automated Program Repair through Fine-tuning and Prompt Engineering

Sequence-to-sequence models have been used to transform erroneous programs into correct ones when trained with a large enough dataset. Some recent studies also demonstrated strong empirical evidence that code review could improve the program repair further. Large language models, trained with Natural Language (NL) and Programming Language (PL), can contain inherent knowledge of both. In this study, we investigate if this inherent knowledge of PL and NL can be utilized to improve automated program repair. We applied PLBART and CodeT5, two state-of-the-art language models that are pre-trained with both PL and NL, on two such natural language-based program repair datasets and found that the pre-trained language models fine-tuned with datasets containing both code review and subsequent code changes notably outperformed each of the previous models. With the advent of code generative models like Codex and GPT-3.5-Turbo, we also performed zero-shot and few-shots learning-based prompt engineering to assess their performance on these datasets. However, the practical application of using LLMs in the context of automated program repair is still a long way off based on our manual analysis of the generated repaired codes by the learning models.

cs.LG↗

arXiv2022

Shashthosheba: Dissecting Perception of Bangladeshi People towards Telemedicine Apps through the Lens of Features of the Apps

Bangladesh, a developing country with a large and dense population, has recently seen significant economic as well as technological developments. The growth of technology has resulted in a dramatic increase in the number of smartphone users in Bangladesh, and as such, mobile apps have become an increasingly important part of peoples' life, even encompassing healthcare services. However, the apps used in healthcare (telemedicine to be specific) in Bangladesh are yet to be studied from the perspective of their features as per the voices of the users as well as service providers. Therefore, in this study, we focus on the features of the telemedicine apps used in Bangladesh. First, we evaluated the present status of existing telemedicine apps in Bangladesh, as well as their benefits and drawbacks in the context of HCI. We analyzed publicly accessible reviews of several Bangladeshi telemedicine apps (N = 14) to evaluate the user impressions. Additionally, to ascertain the public opinion of these apps, we performed a survey in which the patients (N = 87) participated willingly. Our analysis of the collected opinions reveals what users experience, what they appreciate, and what they are concerned about when they use telemedicine apps. Additionally, our study demonstrates what users expect from telemedicine apps, independent of their past experience. Finally, we explore how to address the issues we discovered and how telemedicine may be used to effectively offer healthcare services throughout the country. To the best of our knowledge, this study is the first to analyze the perception of the people of Bangladesh towards telemedicine apps from the perspective of features of the apps.

cs.HC↗