Towards automatic generation of gene summary

Authors:
Feng Jin;Minlie Huang;Zhiyong Lu;Xiaoyan Zhu
Affiliations:
Tsinghua University, Beijing, China;Tsinghua University, Beijing, China;National Center for Biotechnology Information, Bethesda;Tsinghua University, Beijing, China
Venue:
BioNLP '09 Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing
Year:
2009

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Abstract

In this paper we present an extractive system that automatically generates gene summaries from the biomedical literature. The proposed text summarization system selects and ranks sentences from multiple MEDLINE abstracts by exploiting gene-specific information and similarity relationships between sentences. We evaluate our system on a large dataset of 7,294 human genes and 187,628 MEDLINE abstracts using Recall-Oriented Understudy for Gisting Evaluation (ROUGE), a widely used automatic evaluation metric in the text summarization community. Two baseline methods are used for comparison. Experimental results show that our system significantly outperforms the other two methods with regard to all ROUGE metrics. A demo website of our system is freely accessible at http://60.195.250.72/onbires/summary.jsp.