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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} 1 http://www.db.cs.cmu.edu:8080/cdem/demo.html
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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. 2
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The Graph Representation 3 Images Genes Keywords Image-layer edges: nearest neighbors in feature space embryonic hindgut
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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) 4
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Random Walk with Restart – Starting from a node s – Randomly walk to a neighbor, with probability 1-c – Restart at s, with probability c Proximity Measure
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Computing the Steady-State Probability Proximity Measure Desired probability vector Adjacency matrixVector w/ non-zero entry for restart nodes Complexity: O(E), but faster methods exist (Tong et al., ICDM’06)
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Multi-Modal Query Results 7 2D Expression Images Genes Annotation Terms
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More Mining Tasks Image Auto-Caption Gene function identification 8
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Related Work Berkeley Drosophila Genome Project (www.fruitfly.org)www.fruitfly.org FlyExpress (www.flyexpress.net)www.flyexpress.net Berkeley Drosophila Transcription Network Project (bdtnp.lbl.gov)bdtnp.lbl.gov 9
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System Architecture 10 Browser-based UI Tomcat Web Server JSP Application Computing Engine QueriesResult Pages Results Remote Function Calls HTTP RMI
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