Do Papers Tell the Whole Story? A Benchmark and Framework for Uncovering Hidden Implementation Gaps in Bioinformatics

Abstract

Ensuring consistency between research papers and their corresponding software code implementations is a fundamental prerequisite for guaranteeing the reproducibility of scientific findings and the reliability of software systems. However, this issue has received limited attention to date, particularly in the field of bioinformatics, where inconsistencies between methodological descriptions in papers and their actual code implementations are prevalent. To address this gap, we introduce a novel research task, namely paper-code consistency detection, which aims to characterize the cross-modal semantic alignment between methodological descriptions in papers and their corresponding code implementations. At the data level, we construct the first benchmark dataset for this task in the bioinformatics domain, termed BioCon, comprising 48 bioinformatics software projects and their associated publications. BioCon is built by fine-grained alignment between sentence-level methodological descriptions in papers and function-level code snippets, combined with expert annotation and hard negative sampling strategies, resulting in a high-quality sentence-code paired dataset. At the methodological level, we propose a unified cross-modal consistency detection framework that leverages pre-trained models to jointly encode paper sentences and code functions. We conduct a systematic analysis from three perspectives: sentence-level classification, cross-modal retrieval, and project-level consistency assessment. Experimental results demonstrate that the proposed approach achieves strong performance in both consistency discrimination and semantic alignment. Overall, this work establishes the first systematic benchmark and framework for paper-code consistency analysis, opening a new research direction and providing a foundation for improving reproducibility and reliability in bioinformatics software.