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C-DEM: A Multi-Modal Query System for Drosophila Embryo Databases

C-DEM: A Multi-Modal Query System for Drosophila Embryo Databases. Fan Guo , Lei Li, Eric Xing, Christos Faloutsos Carnegie Mellon University {fanguo, leili, epxing, christos@cs.cmu.edu}. http://www.db.cs.cmu.edu:8080/cdem/demo.html. Background. Fruit-fly development in genetic study:

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C-DEM: A Multi-Modal Query System for Drosophila Embryo Databases

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  1. C-DEM: A Multi-Modal Query System for Drosophila Embryo Databases Fan Guo, Lei Li, Eric Xing, Christos FaloutsosCarnegie Mellon University{fanguo, leili, epxing, christos@cs.cmu.edu} http://www.db.cs.cmu.edu:8080/cdem/demo.html

  2. Background • Fruit-fly development in genetic study: • Genes controlling the body plan and patterning organs are similar to higher animals including human. • Objective: a framework for applying data mining techniques to assist biological research.

  3. The Graph Representation Images Genes Keywords embryonic hindgut • Image-layer edges: nearest neighbors in feature space

  4. Proximity Measure • Random Walk with Restart • Starting from a node s; • Randomly walk to a neighbor, with probability 1-c; • Restart at s, with probability c; • Compute the steady-state probability vector. • Complexity: O(E), but faster methods exist (Tong et al., ICDM’06)

  5. Proximity Measure • Random Walk with Restart • Starting from a node s • Randomly walk to a neighbor, with probability 1-c • Restart at s, with probability c

  6. Proximity Measure • Computing the Steady-State Probability Desired probability vector Adjacency matrix Vector w/ non-zero entry for restart nodes • Complexity: O(E), but faster methods exist (Tong et al., ICDM’06)

  7. Multi-Modal Query Results 2D Expression Images Annotation Terms Genes

  8. More Mining Tasks • Image Auto-Caption • Gene function identification

  9. Related Work • Berkeley Drosophila Genome Project (www.fruitfly.org) • FlyExpress (www.flyexpress.net) • Berkeley Drosophila Transcription Network Project(bdtnp.lbl.gov)

  10. System Architecture Browser-based UI HTTP Queries Result Pages Tomcat Web ServerJSP Application RMI Remote Function Calls Results Computing Engine

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