PSB 2019 Text Mining and Machine Learning for Precision Medicine Workshop

Call for Participation
Pacific Symposium on Biocomputing
January 3-7, 2019 – Big Island of Hawaii


*** The workshop program is now available here ***

This 3-hour workshop features an invited panel of experts and individual presentations of published and ongoing efforts by informatics researchers, bench scientists and clinicians that are actively collaborating for the deployment of integrative approaches in precision medicine that incorporate text mining and/or machine learning.

The workshop is a forum to present recent work in this area recently published at other venues, or advances on funded research for dissemination, and an opportunity to discuss challenges and opportunities with other PSB attendees. Invited talks will be competitively selected from submitted abstracts.

Topics of interest include novel natural language processing (NLP) and/or machine learning approaches at the intersection of lifestyle, environment, and genetics that enable further understanding of disease processes and effective treatment for individuals and cohorts that share specific characteristics. Examples of topics that could be of interest:

  • Predictive systems from EHR data.
  • Text mining and/or machine learning for disease diagnosis and prognosis
  • Genotype-phenotype association methods.
  • Extraction, validation, or discovery of disease-gene or gene-drug associations
  • Text mining for pharmacogenomics
  • Exploiting integrated datasets for hypothesis generation
  • Decision support in precision medicine thru text mining or machine learning.
  • Social media mining for linking lifestyle and environmental factors
  • Social media and clinical data integration efforts
  • Pathway generation or validation
  • Automatic extraction and integration of literature data for demographic-specific systematic reviews of drug adverse effects or effectiveness studies
  • Drug effectiveness prediction at the general, population, or individual level
  • Human computer interaction / visualization of extracted data

We invite abstracts for relevant research that is in progress (unpublished) or has been published after January 8, 2017 for consideration for oral and/or poster presentation.

Your abstract should convey a scientific result and should not be an advertisement for any commercial software package.

Abstracts: Submission Guidelines

The presenter should be identified during the submission process. Presenters of accepted abstracts are required to make the presentation themselves, and must register and pay to attend the PSB conference by September 30, 2018. If you submit an abstract by the August 15, 2018 deadline, you will be notified whether or not your abstract has been accepted by September 1, 2018.

Submitters may choose to have their submission reviewed for: talk only; talk and poster; or poster only. If you select talk and poster and are unsuccessful for a talk your poster will automatically be reviewed for a poster presentation.

  • Authors are required to submit a brief abstract (maximum 200 words) by the abstract deadline: August 15, 2018 (You have until 11:59 p.m. GST–6).
  • The abstract should be a brief and concise summary of the background/motivation for the study, method and result(s), as well as conclusion/statement of significance. If the abstract represents published work, the full reference should be included and does not count towards the 200 word limit.
  • For authors requesting a talk, a one (1) page long PDF abstract should be uploaded during the submission process that provides detail on the topic. The one page limit includes references, tables, and graphics. *Do not submit more than one page*
  • Selected Abstract talks will be presented during the workshop. The length of a talk is 15 minutes, PSB style (10 minutes of slides plus 5 minutes for questions).
  • All submissions must be sent directly to Davy Weissenbacher, email:

Abstracts: Review Criteria

All submissions will be evaluated by a program committee. Submitters may choose to have their submission reviewed for talk only; talk and poster; or poster only. If you select talk and poster and are unsuccessful for a talk, your submission will automatically be considered for a poster.

Key Dates

Abstract submissions due: August 15, 2018 11:59PM PT.
Notification of acceptance: September 1, 2018 PT.
Oral presentation slides submission deadline: December 8, 2018 11:59PM PT.
Meeting: January 3-7, 2019.


Graciela Gonzalez-Hernandez, Ph.D., is an Associate Professor of Informatics in the Department of Biostatistics and Epidemiology and Director of the Health Language Processing Lab at the Perelman School of Medicine, University of Pennsylvania (gragon AT pennmedicine DOT upenn DOT edu)
Hongfang Liu, Ph.D., is a professor of biomedical informatics in the Mayo Clinic College of Medicine, consultant in the Department of Health Sciences Research at Mayo Clinic, and leads Mayo Clinic’s clinical natural language processing (Liu.Hongfang AT mayo DOT edu)
Zhiyong Lu, Ph.D., Deputy Director for Literature Search at the National Center for Biotechnology Information (NCBI) (Zhiyong.Lu AT nih DOT gov)
Leaman Robert, Ph.D., is a research fellow at the National Center for Biotechnology Information (NCBI), focuses on natural language processing and machine learning to support biocuration and biomedical knowledge discovery (Robert.Leaman AT nih DOT edu)