Text Summarisation for Evidence Based Medicine Diego Moll a Centre - PowerPoint PPT Presentation

Text Summarisation for Evidence Based Medicine Diego Moll´ a Centre for Language Technology, Macquarie University IIT Patna, 16 December 2012

Evidence Based Medicine Text Summarisation Proposals for Text Summarisation Contents Evidence Based Medicine What is Evidence Based Medicine? EBM and NLP A Corpus for Summarisation Text Summarisation Sentence Extraction Cohesion Check Balance and Coverage Proposals for Text Summarisation Single-document Summarisation Optimisation and Summarisation EBM Summarisation Diego Moll´ a 2/79

Evidence Based Medicine Text Summarisation Proposals for Text Summarisation About us: Macquarie University EBM Summarisation Diego Moll´ a 3/79

Evidence Based Medicine Text Summarisation Proposals for Text Summarisation About us: Centre for Language Technology http://www.clt.mq.edu.au Core Staff (* involved in the AISRF project) ◮ Prof. Robert Dale * Prof. Mark Johnson * A. Prof. Mark Dras ◮ A. Prof. Steve Cassidy * Dr. Diego Molla-Aliod ◮ Dr. Rolf Schwitter EBM Summarisation Diego Moll´ a 4/79

Evidence Based Medicine Text Summarisation Proposals for Text Summarisation About Us: Research Group on Natural Language Processing of Medical Texts http://web.science.mq.edu.au/~diego/medicalnlp/ Active Members Diego Moll´ a Senior lecturer at Macquarie University. Abeed Sarker PhD student at Macquarie University. Sara Faisal Shash Masters student. Past Members Mar´ ıa Elena Santiago-Mart´ ınez Research programmer. Patrick Davis-Desmond Masters student. Andreea Tutos Masters student. EBM Summarisation Diego Moll´ a 5/79

Evidence Based Medicine Text Summarisation Proposals for Text Summarisation About Me: Diego Moll´ a-Aliod Some Highlights ◮ MSc (1992), PhD (1996) University of Edinburgh. ◮ ExtrAns and WebExtrAns projects at University of Zurich. ◮ AnswerFinder project and Medical NLP research at Macquarie University. Research interests ◮ Question Answering. ◮ Summarisation. ◮ Information Extraction. EBM Summarisation Diego Moll´ a 6/79

Evidence Based Medicine Text Summarisation Proposals for Text Summarisation Contents Evidence Based Medicine What is Evidence Based Medicine? EBM and NLP A Corpus for Summarisation Text Summarisation Sentence Extraction Cohesion Check Balance and Coverage Proposals for Text Summarisation Single-document Summarisation Optimisation and Summarisation EBM Summarisation Diego Moll´ a 7/79

Evidence Based Medicine Text Summarisation Proposals for Text Summarisation Contents Evidence Based Medicine What is Evidence Based Medicine? EBM and NLP A Corpus for Summarisation Text Summarisation Sentence Extraction Cohesion Check Balance and Coverage Proposals for Text Summarisation Single-document Summarisation Optimisation and Summarisation EBM Summarisation Diego Moll´ a 8/79

Evidence Based Medicine Text Summarisation Proposals for Text Summarisation Evidence Based Medicine http://laikaspoetnik.wordpress.com/2009/04/04/evidence-based-medicine-the-facebook-of-medicine/ EBM Summarisation Diego Moll´ a 9/79

Evidence Based Medicine Text Summarisation Proposals for Text Summarisation Suggested Steps in EBM http://hlwiki.slais.ubc.ca/index.php?title=Five_steps_of_EBM EBM Summarisation Diego Moll´ a 10/79

Evidence Based Medicine Text Summarisation Proposals for Text Summarisation PICO for Asking the Right Question EBM Summarisation Diego Moll´ a 11/79

Evidence Based Medicine Text Summarisation Proposals for Text Summarisation Where to search for external evidence? 1. Evidence-based Summaries (Systematic Reviews): ◮ The Cochrane Library (http://www.thecochranelibrary.com/). ◮ EBM Online (http://ebm.bmj.com). ◮ UptoDate (http://www.uptodate.com). ◮ . . . EBM Summarisation Diego Moll´ a 12/79

Evidence Based Medicine Text Summarisation Proposals for Text Summarisation Where to search for external evidence? 1. Evidence-based Summaries (Systematic Reviews): ◮ The Cochrane Library (http://www.thecochranelibrary.com/). ◮ EBM Online (http://ebm.bmj.com). ◮ UptoDate (http://www.uptodate.com). ◮ . . . 2. Search the Medical Literature: ◮ E.g. PubMed (http://www.ncbi.nlm.nih.gov/pubmed/). EBM Summarisation Diego Moll´ a 12/79

Evidence Based Medicine Text Summarisation Proposals for Text Summarisation Searching Cochrane EBM Summarisation Diego Moll´ a 13/79

Evidence Based Medicine Text Summarisation Proposals for Text Summarisation Searching PubMed EBM Summarisation Diego Moll´ a 14/79

Evidence Based Medicine Text Summarisation Proposals for Text Summarisation Searching the Trip Database EBM Summarisation Diego Moll´ a 15/79

Evidence Based Medicine Text Summarisation Proposals for Text Summarisation Appraising the Evidence The SORT Taxonomy Level A Consistent and good-quality patient-oriented evidence. Level B Inconsistent or limited-quality patient-oriented evidence. Level C Consensus, usual practise, opinion, disease-oriented evidence, or case series for studies of diagnosis, treatment, prevention, or screening. EBM Summarisation Diego Moll´ a 16/79

Evidence Based Medicine Text Summarisation Proposals for Text Summarisation Contents Evidence Based Medicine What is Evidence Based Medicine? EBM and NLP A Corpus for Summarisation Text Summarisation Sentence Extraction Cohesion Check Balance and Coverage Proposals for Text Summarisation Single-document Summarisation Optimisation and Summarisation EBM Summarisation Diego Moll´ a 17/79

Evidence Based Medicine Text Summarisation Proposals for Text Summarisation Where can NLP Help? ◮ Questions: ◮ Help formulate answerable questions. ◮ From natural question to PICO frames? ◮ Question analysis and classification. EBM Summarisation Diego Moll´ a 18/79

Evidence Based Medicine Text Summarisation Proposals for Text Summarisation Where can NLP Help? ◮ Questions: ◮ Help formulate answerable questions. ◮ From natural question to PICO frames? ◮ Question analysis and classification. ◮ Search: ◮ Retrieve and rank relevant literature. ◮ Extract the evidence-based information. ◮ Summarise the results. EBM Summarisation Diego Moll´ a 18/79

Evidence Based Medicine Text Summarisation Proposals for Text Summarisation Where can NLP Help? (II) ◮ Appraisal: Classify the evidence. EBM Summarisation Diego Moll´ a 19/79

Evidence Based Medicine Text Summarisation Proposals for Text Summarisation Contents Evidence Based Medicine What is Evidence Based Medicine? EBM and NLP A Corpus for Summarisation Text Summarisation Sentence Extraction Cohesion Check Balance and Coverage Proposals for Text Summarisation Single-document Summarisation Optimisation and Summarisation EBM Summarisation Diego Moll´ a 20/79

Evidence Based Medicine Text Summarisation Proposals for Text Summarisation Where’s the Corpus for Summarisation? Summarisation Systems ◮ CENTRIFUSER/PERSIVAL: Developed and tested using user feedback (iterative design). ◮ SemRep: Evaluation based on human judgement. ◮ Demner-Fushman & Lin: ROUGE on original paper abstracts. ◮ Fiszman: Factoid-based evaluation. EBM Summarisation Diego Moll´ a 21/79

Evidence Based Medicine Text Summarisation Proposals for Text Summarisation Where’s the Corpus for Summarisation? Summarisation Systems ◮ CENTRIFUSER/PERSIVAL: Developed and tested using user feedback (iterative design). ◮ SemRep: Evaluation based on human judgement. ◮ Demner-Fushman & Lin: ROUGE on original paper abstracts. ◮ Fiszman: Factoid-based evaluation. Corpora ◮ Several corpora of questions/answers available. ◮ Answers lack explicit pointers to primary literature. ◮ Medical doctors want to know the primary sources. EBM Summarisation Diego Moll´ a 21/79

Evidence Based Medicine Text Summarisation Proposals for Text Summarisation Journal of Family Practice’s “Clinical Inquiries” EBM Summarisation Diego Moll´ a 22/79