Fang-Yi Su, Gia-Han Ngo, Ben Phan, Jung-Hsien Chiang
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Although CAS is primarily designed for biomedical relation extraction, its versatile design extends its applicability to tasks with implicit constraints, such as code completion, mathematical reasoning, and information retrieval. Through extensive experiments across multiple domains, CAS demonstrates its ability to enhance model performance by maintaining structural fidelity and semantic accuracy in augmented data. These results highlight the potential of CAS not only in advancing biomedical NLP research but also in addressing data augmentation challenges in diverse constrained-task settings within natural language processing. Database URL: https://github.com/ngogiahan149/CAS.</p>","PeriodicalId":10923,"journal":{"name":"Database: The Journal of Biological Databases and Curation","volume":"2025 ","pages":""},"PeriodicalIF":3.4000,"publicationDate":"2025-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12224179/pdf/","citationCount":"0","resultStr":"{\"title\":\"CAS: enhancing implicit constrained data augmentation with semantic enrichment for biomedical relation extraction and beyond.\",\"authors\":\"Fang-Yi Su, Gia-Han Ngo, Ben Phan, Jung-Hsien Chiang\",\"doi\":\"10.1093/database/baaf025\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>Biomedical relation extraction often involves datasets with implicit constraints, where structural, syntactic, or semantic rules must be strictly preserved to maintain data integrity. Traditional data augmentation techniques struggle in these scenarios, as they risk violating domain-specific constraints. To address these challenges, we propose CAS (Constrained Augmentation and Semantic-Quality), a novel framework designed for constrained datasets. CAS employs large language models to generate diverse data variations while adhering to predefined rules, and it integrates the SemQ Filter. This self-evaluation mechanism ensures the quality and consistency of augmented data by filtering out noisy or semantically incongruent samples. Although CAS is primarily designed for biomedical relation extraction, its versatile design extends its applicability to tasks with implicit constraints, such as code completion, mathematical reasoning, and information retrieval. Through extensive experiments across multiple domains, CAS demonstrates its ability to enhance model performance by maintaining structural fidelity and semantic accuracy in augmented data. 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CAS: enhancing implicit constrained data augmentation with semantic enrichment for biomedical relation extraction and beyond.
Biomedical relation extraction often involves datasets with implicit constraints, where structural, syntactic, or semantic rules must be strictly preserved to maintain data integrity. Traditional data augmentation techniques struggle in these scenarios, as they risk violating domain-specific constraints. To address these challenges, we propose CAS (Constrained Augmentation and Semantic-Quality), a novel framework designed for constrained datasets. CAS employs large language models to generate diverse data variations while adhering to predefined rules, and it integrates the SemQ Filter. This self-evaluation mechanism ensures the quality and consistency of augmented data by filtering out noisy or semantically incongruent samples. Although CAS is primarily designed for biomedical relation extraction, its versatile design extends its applicability to tasks with implicit constraints, such as code completion, mathematical reasoning, and information retrieval. Through extensive experiments across multiple domains, CAS demonstrates its ability to enhance model performance by maintaining structural fidelity and semantic accuracy in augmented data. These results highlight the potential of CAS not only in advancing biomedical NLP research but also in addressing data augmentation challenges in diverse constrained-task settings within natural language processing. Database URL: https://github.com/ngogiahan149/CAS.
期刊介绍:
Huge volumes of primary data are archived in numerous open-access databases, and with new generation technologies becoming more common in laboratories, large datasets will become even more prevalent. The archiving, curation, analysis and interpretation of all of these data are a challenge. Database development and biocuration are at the forefront of the endeavor to make sense of this mounting deluge of data.
Database: The Journal of Biological Databases and Curation provides an open access platform for the presentation of novel ideas in database research and biocuration, and aims to help strengthen the bridge between database developers, curators, and users.