Upgrade to Pro — share decks privately, control downloads, hide ads and more …

Feature-Centric Visual Exploration of Genome Interaction Maps

Feature-Centric Visual Exploration of Genome Interaction Maps

Venue: ISMB 2018 in Chicago
Session: BioVis

Fritz Lekschas

July 09, 2018
Tweet

More Decks by Fritz Lekschas

Other Decks in Science

Transcript

  1. Feature-Centric Visual
    Exploration of Genome
    Interaction Maps
    Fritz Lekschas, PhD candidate

    Harvard University
    Benjamin Bach, Peter Kerpedjiev, Michael Behrisch, Nils Gehlenborg,
    and Hanspeter Pfister
    July 9th, 2018
    ISMB 2018

    View full-size slide

  2. Cell Nucleus Contact Sequencing Heatmap
    3D GENOME

    View full-size slide

  3. Gene regulation:
    Enhancer-promoter
    Structural variation:
    Break points
    Cell dynamics:
    Differentiation
    Cell cycle
    WHY CARE?

    View full-size slide

  4. 3 million × 3 million

    View full-size slide

  5. CHALLENGES
    • Size of the heatmap
    • Many called features
    • No ground truth
    GOALS
    • Quality control
    • Pattern discovery
    • Pattern correlation
    CHALLENGES

    View full-size slide

  6. Efficiency
    Show all insets

    Close to origin
    Minimize occlusion
    Show all insets

    View full-size slide

  7. Efficiency
    Show all insets

    Close to origin
    Minimize occlusion
    Close to origin

    View full-size slide

  8. Efficiency
    Show all insets

    Close to origin
    Minimize occlusion
    Minimize occlusion

    View full-size slide

  9. Performance comparison in pattern search on images and
    genome interaction maps
    User study: 18 participants and 6 domain experts
    Techniques:
    Results: faster pattern search

    more accurate pattern comparison

    easy-to-learn & easy-to-use
    EVALUATION

    View full-size slide

  10. CONCLUSION
    Explore local features in
    spatial context
    Faster pattern search
    Improved navigation

    View full-size slide

  11. Thank You!
    MORE INFORMATION
    scalable-insets.lekschas.de
    SOURCE CODE
    github.com/flekschas/higlass-scalable-insets
    CONTACT
    [email protected]
    @flekschas
    lekschas.de
    POSTER: B-765

    View full-size slide