[institut] Reminder - SCL Seminar: Vladimir Gligorijevic, Thursday, 8 March, 14:00
Marija Mitrovic Dankulov
mitrovic at ipb.ac.rs
Thu Mar 8 09:07:38 CET 2018
Dear colleagues,
You are cordially invited to the SCL seminar of the Center for the Study
of Complex Systems, which will be held on Thursday, 8 March 2018 at
14:00 in the library reading room “Dr. Dragan Popović" of the Institute
of Physics Belgrade. The talk entitled
Deep Multi-network Embedding for Protein Function Prediction
will be given by Vladimir Gligorijević (Flatiron Institute, New York,
USA). Abstract of the talk:
The prevalence of high-throughput experimental methods has resulted in
an abundance of large-scale molecular and functional interaction
networks. The connectivity of these networks provides a rich source of
information for inferring functional annotations for genes and proteins.
An important challenge has been to develop methods for combining these
heterogeneous networks to extract useful protein feature representations
for function prediction. Most of the existing approaches for network
integration use shallow models that cannot capture complex and
highly-nonlinear network structures. We introduce deepNF, our novel
deep-learning based network integration method for protein function
prediction. deepNF consists of two steps: 1) creating a low-dimensional
dense vector representation of proteins (i.e., embedding) using
Multimodal Deep Autoencoders and 2) training a classifier on the
resulting representation to predict protein functions.
We apply deepNF on 6 different networks obtained from the STRING db to
construct a compact low-dimensional representation containing high-level
protein features. We will present an extensive performance analysis
comparing our method with the state-of-the-art network integration
methods for protein function prediction. In addition to
cross-validation, the analysis also includes a temporal holdout
validation evaluation similar to the measures in Critical Assessment of
Functional Annotation (CAFA). Our results show that our method
outperforms previous methods for both human and yeast STRING networks.
Our method offers a great advantage of being able to capture non-linear
information conveyed by large-scale biological networks, leading to
improved network representations. Features learned by our method lead to
substantial improvements in protein function prediction accuracy, which
could enable novel protein function discoveries.
Best regards,
Marija Mitrovic Dankulov
--
Marija Mitrovic Dankulov
E-mail: mitrovic at ipb.ac.rs
Phone: +381 11 3713068
Fax: +381 11 3162190
Scientific Computing Laboratory
Institute of Physics Belgrade
Pregrevica 118, 11080 Belgrade, Serbia
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