Zicheng Zhang1,2. 1. School of Information Management, Nanjing University, Nanjing, 210023, China. 18551701375@163.com. 2. Jiangsu Key Laboratory of Data Engineering and Knowledge Service, Nanjing, 210023, China. 18551701375@163.com.
Abstract
BACKGROUND: Retrieving gene and disease information from a vast collection of biomedical abstracts to provide doctors with clinical decision support is one of the important research directions of Precision Medicine. METHOD: We propose a novel article retrieval method based on expanded word and co-word analyses, also conducting Cuckoo Search to optimize parameters of the retrieval function. The main goal is to retrieve the abstracts of biomedical articles that refer to treatments. The methods mentioned in this manuscript adopt the BM25 algorithm to calculate the score of abstracts. We, however, propose an improved version of BM25 that computes the scores of expanded words and co-word leading to a composite retrieval function, which is then optimized using the Cuckoo Search. The proposed method aims to find both disease and gene information in the abstract of the same biomedical article. This is to achieve higher relevance and hence score of articles. Besides, we investigate the influence of different parameters on the retrieval algorithm and summarize how they meet various retrieval needs. RESULTS: The data used in this manuscript is sourced from medical articles presented in Text Retrieval Conference (TREC): Clinical Decision Support (CDS) Tracks of 2017, 2018, and 2019 in Precision Medicine. A total of 120 topics are tested. Three indicators are employed for the comparison of utilized methods, which are selected among the ones based only on the BM25 algorithm and its improved version to conduct comparable experiments. The results showed that the proposed algorithm achieves better results. CONCLUSION: The proposed method, an improved version of the BM25 algorithm, utilizes both co-word implementation and Cuckoo Search, which has been verified achieving better results on a large number of experimental sets. Besides, a relatively simple query expansion method is implemented in this manuscript. Future research will focus on ontology and semantic networks to expand the query vocabulary.
BACKGROUND: Retrieving gene and disease information from a vast collection of biomedical abstracts to provide doctors with clinical decision support is one of the important research directions of Precision Medicine. METHOD: We propose a novel article retrieval method based on expanded word and co-word analyses, also conducting Cuckoo Search to optimize parameters of the retrieval function. The main goal is to retrieve the abstracts of biomedical articles that refer to treatments. The methods mentioned in this manuscript adopt the BM25 algorithm to calculate the score of abstracts. We, however, propose an improved version of BM25 that computes the scores of expanded words and co-word leading to a composite retrieval function, which is then optimized using the Cuckoo Search. The proposed method aims to find both disease and gene information in the abstract of the same biomedical article. This is to achieve higher relevance and hence score of articles. Besides, we investigate the influence of different parameters on the retrieval algorithm and summarize how they meet various retrieval needs. RESULTS: The data used in this manuscript is sourced from medical articles presented in Text Retrieval Conference (TREC): Clinical Decision Support (CDS) Tracks of 2017, 2018, and 2019 in Precision Medicine. A total of 120 topics are tested. Three indicators are employed for the comparison of utilized methods, which are selected among the ones based only on the BM25 algorithm and its improved version to conduct comparable experiments. The results showed that the proposed algorithm achieves better results. CONCLUSION: The proposed method, an improved version of the BM25 algorithm, utilizes both co-word implementation and Cuckoo Search, which has been verified achieving better results on a large number of experimental sets. Besides, a relatively simple query expansion method is implemented in this manuscript. Future research will focus on ontology and semantic networks to expand the query vocabulary.
Entities:
Keywords:
Clinical decision support; Co-word analysis; Cuckoo Search; Improved BM25; Information retrieval; Precision Medicine
Authors: Monika Kastner; Nancy L Wilczynski; Cindy Walker-Dilks; Kathleen Ann McKibbon; Brian Haynes Journal: J Med Internet Res Date: 2006-10-25 Impact factor: 5.428