PSB-2018 Session on Text Mining and Visualization for Precision Medicine

Motivation

According to the National Institutes of Health (NIH), precision medicine is “an emerging approach for disease treatment and prevention that takes into account individual variability in genes, environment, and lifestyle for each person.” Announced in 2015 by President Obama, the Precision Medicine Initiative (PMI) seeks to promote research at the intersection of lifestyle, environment, and genetics to produce new knowledge for more effective ways to prolong health and treat disease.
This session focuses on efforts where informatics researchers are actively collaborating with bench scientists and clinicians for the deployment of integrative approaches in precision medicine that could impact scientific discovery.

Topics

Topics of interest to this session include novel natural language processing (NLP) and visual analytics 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:

  • Text mining and visual analytics for genotype-phenotype association
  • Decision support systems that utilize unstructured portions of EHRs
  • Extraction, validation, or discovery of disease-drug or disease-gene interations
  • Text mining methods for personalized interventions
  • Text mining for pharmacogenomics
  • Visualization of integrated datasets for hypothesis generation or decision support
  • Social media mining for linking lifestyle and environmental factors to disease conditions
  • Longitudinal modeling from EHR text
  • Cohort selection from unstructured text
  • Integrating Social media and clinical data for precision medicine
  • Text mining for pathway generation or validation
  • Text mining for disease detection and prognosis
  • Generating patient-centric measures of quality of care
  • Behavioral profiling and intervention
  • Normalization systems for concept mapping

Submissions should clearly state the translational value of their contribution and explicitly link the described advance to its impact on precision medicine.

KEY DATES

Paper submissions due: August 1, 2017 11:59PM PT.
Notification of paper acceptance: September 15, 2017.
Final paper deadline: October 2, 2017 11:59PM PT.
Abstract deadline: November 13, 2017 11:59PM PT.
Conference: January 3-7, 2018.

Paper Format

Please see the official PSB website for more details on manuscript submission: http://psb.stanford.edu/psb-online/psb-submit

Each paper must be accompanied by a cover letter. The cover letter must state the following:

  • The email address of the corresponding author.
  • The specific PSB session that should review the paper or abstract.
  • The submitted paper contains original, unpublished results, and is not currently under consideration elsewhere.
  • All co-authors concur with the contents of the paper.

Submitted papers are limited to twelve (12) pages in our publication format. If figures cannot be easily resized and placed precisely in the text, then it should be clear that with appropriate modifications, the total manuscript length would be within the page limit.

Organizers

Graciela Gonzalez, Ph.D., Univ. of Pennsylvania (gragon AT upenn DOT edu)
Casey Greene, Ph.D., Univ. of Pennsylvania (csgreene AT upenn DOT edu)
Hongfang Liu, Ph.D., Mayo Clinic (Liu.Hongfang AT mayo DOT edu)
Abeed Sarker, Ph.D., Univ. of Pennsylvania (abeed AT upenn DOT edu)