Generative AI for code generation has transformed software development, but it has also introduced a critical transparency problem: the origins of AI-generated code are opaque to the developers who use it, the organizations that deploy it, and the compliance professionals responsible for ensuring its legal and quality standards. Existing mitigations flag problematic outputs after the fact without explaining why a model produced them or how future generation could be improved. We present a research vision, grounded in a U.S. NSF-funded research grant, that argues that the next generation of CodeGenAI tools must be built on a foundation of explainable provenance: automated, post-hoc traceability that links generated code back to the prompt components, training data instances, global data features, and internal model components that caused its generation. We grounded this vision in empirical evidence from studies of software developers, model users, and compliance/legal professionals, which show that provenance information is a practical necessity that current tools do not provide. We characterize the problem across four traceability dimensions, outline a research program combining large-scale empirical studies with post-hoc causal and interpretability techniques, and identify the key open challenges that the community must address to realize this vision.
Alejandro Velasco, Nathan Wintersgill, Trevor Stalnaker et al.· 1 citation
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.
Alejandro Velasco, Daniel Rodríguez-Cárdenas, Dipin Khati et al.· 0 citations
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