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}

1http://www.db.cs.cmu.edu:8080/cdem/demo.html

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.

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The Graph Representation

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Images

Genes

Keywords

• Image-layer edges: nearest neighbors in feature space

embryonic hindgut

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)

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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

• Computing the Steady-State Probability

Proximity Measure

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)

Multi-Modal Query Results

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2D Expression Images

GenesAnnotation Terms

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

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Related Work• Berkeley Drosophila Genome Project (www.fruitfly.org)

• FlyExpress (www.flyexpress.net)

• Berkeley Drosophila Transcription Network Project(bdtnp.lbl.gov)

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System Architecture

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Browser-based UI

Tomcat Web ServerJSP Application

Computing Engine

Queries Result Pages

ResultsRemote Function

Calls

HTTP

RMI