BioSearch08: HCSNet Next-Generation Search Workshop on Search in Biomedical Information

Details Date: 30 November 2008
Location: Queensland University of Technology, Brisbane
Contact: Diego Molla, diego@ics.mq.edu.au; Robert Dale, Robert.Dale@mq.edu.au
Links
Workshop information

CALL FOR ABSTRACTS

There are many aspects of research and practice in medical environments that require searching for medical information in large information repositories of published research papers (such as PubMed), and large ontologies and other structured resources (such as UMLS). The availability of these resources and the need to find information in them has prompted intensive research on the treatment of medical text, images and videos for information extraction and retrieval.

All of these tasks require the development of techniques that go beyond the localisation of generic search and information extraction techniques, given the high level of complexity in terminology, and the need for achieving high performance.

The aim of HCSNet's Priority Research Area in Next Generation Search is to bring together researchers from a wide range of disciplines to address issues related to search and information extraction. This specialised workshop will focus on the medical and biological domains and will take place just before GIW 2008, in Brisbane.

AUDIENCE

We welcome anyone from academia and industry with an interest in any area related to search and information extraction from biomedical information, including but not limited to the following:

  • Text search
  • Text mining
  • Named entity recognition
  • Information extraction
  • Linguistic analysis
  • Parsing
  • Text pre-processing
  • Text summarisation
  • Video retrieval
  • Image retrieval
  • Question answering
  • Ontologies
  • Human-computer interaction

KEYNOTE PRESENTATIONS

There will be keynote presentations by Dr. Dina Demner-Fushman and Prof. Limsoon Wong:

Dina Demner-Fushman

Information retrieval and Natural Language Processing for Clinical Decision Support

Information retrieval and natural language processing methods are instrumental in enhancing healthcare by providing clinicians, patients and other involved individuals with knowledge and person-specific information presented at appropriate times. Some of the specific challenges of Clinical Decision Support (CDS) are: using free-text information to drive CDS, representing clinical knowledge and CDS interventions in standardized formats, and leveraging the data available in Electronic Health Records (EHRs), which often contain narrative healthcare data.

This talk will present research on several aspects of the CDS challenges: developing strategies for automatic question and query formulation using information extracted from clinical narratives; finding adequate evidence and extracting answers to clinical and translational research questions; and retrieving images to illustrate evidence.

Dr. Dina Demner-Fushman is a Staff Scientist for the Communications Engineering Branch at the National Library of Medicine. She conducts research in clinical decision support, clinical question answering, use of natural language processing in information retrieval, human computer interaction aspects of information retrieval, and information retrieval in biomedical domain. Her interest in biomedical language processing stems from years of clinical practice (M.D. obtained from Kazan State Medical Institute in 1980) and clinical research (Doctorate (Ph.D.) in Medical Science earned from Moscow Medical and Stomatological Institute in 1989.) She earned her MS and PhD in Computer Science from the University of Maryland, College Park in 2003 and 2006, respectively.

Limsoon Wong

Guilt by Association as a Search Principle

The exploitation of fundamental invariants is among the most elegant solutions to many computational problems in a wide variety of domains. One of the more powerful approaches to exploit invariants is the principle of "guilt by association". In particular, the principle of guilt by association is the foundation of remote homolog detection, protein function prediction, disease subtype diagnosis, treatment plan prognosis, and other challenges in computational biology. The principle suggests that two entities are in a specific relationship if they exhibit invariant properties underlying that relationship. For example, a protein is predicted to have a particular biological function if it exhibits the underlying invariant properties of that functional group---viz., guilty by association to other members of that functional group through the shared invariant properties.

In my talk, I plan to present several facets of guilt by association in the computational prediction of protein function and draw parallels of these facets in information retrieval. Specifically, I plan to touch on the following facets: (a) the issue of chance associations; (b) novel generalizable forms of association; (c) fusion of multiple heterogeneous sources of evidence; (d) the dichotomy of knowing to a high degree of reliability that two entities are in some relationship and yet not knowing what that relationship is. I hope this talk will be, for the informational retrieval community, a window to the opportunities in computational biology that may benefit from the depth and variety of solutions information retrieval has to offer.

Limsoon Wong is Professor and Head of Computer Science and Professor of Pathology at the National University of Singapore. He currently works mostly on knowledge discovery technologies and is especially interested in their application to biomedicine. He has written about 150 research papers, a few of which are among the best cited of their respective fields. He serves on the editorial boards of Journal of Bioinformatics and Computational Biology (ICP), Bioinformatics (OUP), and Drug Discovery Today (Elsevier). He is chairman of Molecular Connections and scientific advisor to CellSafe International. Limsoon received his BSc(Eng) from Imperial College London and his PhD from University of Pennsylvania.

WORKSHOP FORMAT

We aim to facilitate an environment that helps to further develop grounds for collaboration across the research and development communities. Accordingly, the workshop will consist of a number of presentations of different types with this focus in mind:

  • 10 minute speed presentations that describe a new project or specific idea to be shared with the community, with the aim of encouraging cross-disciplinary collaboration;

  • 10 minute student project presentations, with the aim of informing the community of new ideas being developed, and to get feedback from an interdisciplinary audience; and

  • 3 minute poster presentations for those presenting a poster only.

SUBMISSIONS

We want to involve as many as possible in discussion, so the effort required for attendance is deliberately small.

Those interested in making a speed presentation, student presentation or poster should submit a brief abstract of 100-150 words in length.

In addition, we ask all those interested in attending to submit a 100-150 word statement indicating their research interests pertinent to the workshop theme. These will be made available as part of the workshop materials.

Please send all submissions by using the submission form.

FUNDING

HCSNet will fund travel and accommodation to a maximum of $500 for a number of participating Australian-based HCSNet members from outside the Brisbane metropolitan area. The provision of a submission as described above is a prerequisite for funding. If not all participants can be covered, funding grants may be allocated based on the relevance of your abstract to the workshop theme; also, early career researchers (in HCSNet terms, those who have received their PhDs in the last fifteen years) will have priority.

In addition, 10 student travel awards will be available for Australian-based postgraduate student members of HCSNet outside the Brisbane metropolitan area. To apply for this funding stream, include a short CV in plain text in the submission form.

Note that, although attendance at the workshop is free, membership of HCSNet (join via the website) and prior registration for this workshop are required.

IMPORTANT DATES

  • Submission of Abstracts: 19 October 2008 23 October 2008
  • Notification of Awards: 24 October 2008 28 October 2008
  • Workshop: 30 November 2008

CONTACT

Diego Molla-Aliod diego@ics.mq.edu.au
Robert Dale Robert.Dale@mq.edu.au