[Solomonov Seminar] 256. Solomonov seminar

[Mateja Zver]

V četrtek, 6. junija bo ob 13h v Veliki predavalnici IJS
(prvo nadstropje glavne stavbe) 256. Solomonov seminar.
Posnetki preteklih seminarjev so na http://videolectures.net/solomon/

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Speaker: Pierre Geurts
http://www.montefiore.ulg.ac.be/~geurts/

Title: Gene regulatory network inference using tree-based ensemble methods

Abstract:
One of the pressing open problems of computational systems biology is 
the elucidation of the topology of genetic regulatory networks. In this 
talk, we first present a method, called GENIE3, for the unsupervised 
inference of gene regulatory networks from expression data. This method 
decomposes the prediction of a regulatory network between p genes into p 
different feature selection (regression) problems and solves each of 
these problems using feature importance scores obtained from tree-based 
ensemble methods such as Random Forests. After a presentation of the 
method, we discuss its performance in the context of the Dialogue for 
Reverse Engineering Assessments and Methods (DREAM) challenges, which is 
an annual international competition aiming at the evaluation of GRN 
inference algorithms on benchmarks of simulated and real data. GENIE3 
was best performer on the DREAM4 In Silico Multifactorial challenge and 
on the DREAM5 Network Inference challenge. We then present two 
adaptations of the method for handling time series expression and 
systems genetics data. In the latter case, the good performance of the 
method is illustrated on the data from the DREAM5 systems genetics 
challenge and the more recent StatSeq benchmark.