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Natural Language Processing of Medical Texts

This project focuses on the application of natural language processing techniques on medical texts. We pay special emphasis on finding methods to help the practice of evidence based medicine.

Resources

• Corpus for EBM Query-based Summarisation
• Clinical Evidence Detector

Members

• Diego Mollá (project director and chief investigator)
• Cécile Paris (partner investigator, CSIRO ICT Centre)
• Abeed Sarker (PhD student)
• Sara Faisal Shash (Masters student)

Past Members

The following people had done significant work for the project, leading to publication.

• Maria Elena Santiago-Martinez (research programmer)
• Andreea Tutos (Masters student)
• Patrick Davis-Desmond (Masters student)

Join this Project

There are several ways you can join this project:

• As a PhD student: If you have an interesting topic of research that has to do with question answering and/or summarisation, send us an email and we will get in touch with you.
• As a Masters/Honours student: If you are a Masters or an Honours student in Macquarie University and you are searching for a project, consult the list of Honours projects. Many of these projects can be adapted to Masters projects.
• As an undergraduate student: If you are a student enrolled in Macquarie University you can also work for AnswerFinder and get paid for it. Consult the list of summer projects.

Related Links

• Related Honours Projects
• Related PhD Scholarships
• Other projects at the Centre for Language Technology

Publications

1. A. Sarker, D. Mollá and C. Paris. An Approach for Automatic Multi-label Classification of Medical Sentences (2013). Proceedings of the Fourth International Workshop on Health Document Text Mining and Information Analysis (LOUHI 2013), Sydney, Australia.
2. D. Mollá. Experiments with Clustering-based Features for Sentence Classification in Medical Publications: Macquarie Test's participation in the ALTA 2012 shared task. . Proceedings of the 2012 Australasian Language Technology Workshop (ALTA 2012), Dunedin, New Zealand.
3. I. Amini, D. Martinez and D. Mollá. Overview of the ALTA 2012 Shared Task (2012). Proceedings of the 2012 Australasian Language Technology Workshop (ALTA 2012), Dunedin, New Zealand.
4. A. Sarker, D. Mollá and C. Paris. Towards Two-step Multi-document Summarisation for Evidence Based Medicine: A Quantitative Analysis (2012). Proceedings of the 2012 Australasian Language Technology Workshop (ALTA 2012), Dunedin, New Zealand.
5. D. Martinez, A. MacKinlay, D. Mollá, L. Cavedon and K. Verspoor. Simple similarity-based question answering strategies for biomedical text (2012). QA4MRE Workshop at Conference and Labs of the Evaluation Forum, CLEF 2012. September 17-20, 2012.
6. D. Mollá and M.E. Santiago-Martínez. Creation of a Corpus for Evidence Based Medicine Summarisation (2012). Australasian Medical Journal, 5(9).
7. A. Sarker, D. Mollá and C. Paris. Extractive Summarisation of Medical Documents using Domain Knowledge and Corpus Statistics (2012). Australasian Medical Journal.
8. A. Sarker, D. Mollá and C. Paris. Extractive Evidence Based Medicine Summarisation Based on Sentence-Specific Statistics (2012). Proceedings of the 25th IEEE International Symposium on Computer-based Medical Systems (CBMS2012), Rome, Italy. [slides]
9. P. Davis-Desmond and Diego Mollá. Detection of Evidence in Clinical Research Papers (2012). Australasian Workshop On Health Informatics and Knowledge Management (HIKM 2012), Melbourne, Australia. [slides]
10. D. Mollá and María Elena Santiago-Martínez. Creation of a Corpus for Evidence Medicine Summarisation (2011). Proceedings of the First Australian Workshop on Artificial Intelligence in Health (AIH 2011), Perth, Australia. [poster]
11. A. Sarker, D. Mollá and Cécile Paris. Extractive Summarisation of Medical Documents using Domain Knowledge and Corpus Statistics (2011). Proceedings of the First Australian Workshop on Artificial Intelligence in Health (AIH 2011), Perth, Australia.
12. D. Mollá and A. Sarker. Automatic Grading of Evidence: The 2011 ALTA Shared Task (2011). Proceedings of the 2011 Australasian Language Technology Workshop (ALTA 2011), Canberra, Australia.
13. A. Sarker, D. Mollá and Cécile Paris. Outcome Polarity Identification of Medical Papers (2011). Proceedings of the 2011 Australasian Language Technology Workshop (ALTA 2011), Canberra, Australia.
14. D. Mollá and María Elena Santiago-Martínez. Development of a Corpus for Evidence Medicine Summarisation (2011). Proceedings of the 2011 Australasian Language Technology Workshop (ALTA 2011), Canberra, Australia. [slides]
15. A. Sarker, D. Mollá and Cécile Paris. Towards Automatic Grading of Evidence (2011). Proceedings of the Third International Workshop on Health Document Text Mining and Information Analysis (LOUHI 2011), pp51-58. Bled, Slovenia.
16. A. Sarker and D. Mollá. A Rule-based Approach for Automatic Identification of Publication Types of Medical Papers (2010). Proceedings ADCS 2010, 5 pages. Melbourne.
17. D. Mollá. A Corpus for Evidence Based Medicine Summarisation (2010). Proceedings ALTA 2010, pp.76-80. Melbourne. [slides]
18. A. Tutos and D. Mollá. A Study on the Use of Search Engines for Question Answering in Biomedicine (2010). Australasian Workshop On Health Informatics and Knowledge Management (HIKM), 8 pages. Brisbane. [slides]

Other Presentations

1. Text Summarisation for Evidence Based Medicine, presentation at the Indo-Australia Workshop on Optimization Techniques for Human Language Technology, India Institute of Technology Patna, December 16 2012.
2. Automated Summarisation for Evidence Based Medicine, HAIL seminar 22 March 2012.

Funding

This research is partly funded by a Macquarie University Research Development Grant and by CSIRO.

Parts of this work are licensed under a GNU General Public License GPLv3.
Parts of this work are licensed under an Apache License, Version 2.0.