DeepAI AI Chat
Log In Sign Up

A Medical Literature Search System for Identifying Effective Treatments in Precision Medicine

by   Jiaming Qu, et al.
University of North Carolina at Chapel Hill

The Precision Medicine Initiative states that treatments for a patient should take into account not only the patient's disease, but his/her specific genetic variation as well. The vast biomedical literature holds the potential for physicians to identify effective treatment options for a cancer patient. However, the complexity and ambiguity of medical terms can result in vocabulary mismatch between the physician's query and the literature. The physician's search intent (finding treatments instead of other types of studies) is difficult to explicitly formulate in a query. Therefore, simple ad hot retrieval approach will suffer from low recall and precision. In this paper, we propose a new retrieval system that helps physicians identify effective treatments in precision medicine. Given a cancer patient with a specific disease, genetic variation, and demographic information, the system aims to identify biomedical publications that report effective treatments. We approach this goal from two directions. First, we expand the original disease and gene terms using biomedical knowledge bases to improve recall of the initial retrieval. We then improve precision by promoting treatment-related publications to the top using a machine learning reranker trained on 2017 Text Retrieval Conference Precision Medicine (PM) track corpus. Batch evaluation results on 2018 PM track corpus show that the proposed approach effectively improves both recall and precision, achieving performance comparable to the top entries on the leaderboard of 2018 PM track.


page 1

page 2

page 3

page 4


Building a Controlled Vocabulary for Standardizing Precision Medicine Terms

Rapid advances of technology and development of research in precision me...

Automatically extracting, ranking and visually summarizing the treatments for a disease

Clinicians are expected to have up-to-date and broad knowledge of diseas...

SUBIC: A Supervised Bi-Clustering Approach for Precision Medicine

Traditional medicine typically applies one-size-fits-all treatment for t...

An Ontology-driven Treatment Article Retrieval System for Precision Oncology

This paper presents an ontology-driven treatment article retrieval syste...

Bibliometric Data Fusion for Biomedical Information Retrieval

Digital libraries in the scientific domain provide users access to a wid...

What Makes a Top-Performing Precision Medicine Search Engine? Tracing Main System Features in a Systematic Way

From 2017 to 2019 the Text REtrieval Conference (TREC) held a challenge ...