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Goal: Reconstruct Cellular Networks

Conditions. Genes. Biocarta. http://www.biocarta.com/. Goal: Reconstruct Cellular Networks. Causal Reconstruction for Gene Expression. Gene A. Gene B. Use language of Bayesian networks to reconstruct causal connections. Gene C. Gene D. Gene E. Friedman et al, JCB 2000.

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Goal: Reconstruct Cellular Networks

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  1. Conditions Genes Biocarta. http://www.biocarta.com/ Goal: Reconstruct Cellular Networks

  2. Causal Reconstruction for Gene Expression Gene A Gene B • Use language of Bayesian networks to reconstruct causal connections Gene C Gene D Gene E Friedman et al, JCB 2000

  3. Qualitative part: Directed acyclic graph (DAG) Nodes - random variables Edges - direct influence Family of Alarm E B P(A | E,B) e b 0.9 0.1 e b 0.2 0.8 e b 0.9 0.1 0.01 0.99 e b Bayesian Networks Compact representation of probability distributions via conditional independence Burglary Earthquake Radio Alarm Call Together: Define a unique distribution in a factored form Quantitative part: Set of conditional probability distributions

  4. E B P(A | E,B) B E .9 .1 e b e b .7 .3 .8 .2 e b R A .99 .01 e b C Learning Bayesian networks Data + Prior Information Learner

  5. E B P(A | E,B) .9 .1 e b e b .7 .3 .8 .2 e b .99 .01 e b E B P(A | E,B) B B E E ? ? e b A A e b ? ? ? ? e b ? ? e b Known Structure, Complete Data E, B, A <Y,N,N> <Y,N,Y> <N,N,Y> <N,Y,Y> . . <N,Y,Y> • Network structure is specified • Inducer needs to estimate parameters • Data does not contain missing values Learner

  6. E B P(A | E,B) .9 .1 e b e b .7 .3 .8 .2 e b B E .99 .01 e b A E B P(A | E,B) B E ? ? e b A e b ? ? ? ? e b ? ? e b Unknown Structure, Complete Data E, B, A <Y,N,N> <Y,N,Y> <N,N,Y> <N,Y,Y> . . <N,Y,Y> • Network structure is not specified • Inducer needs to select arcs & estimate parameters • Data does not contain missing values Learner

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