An optimization framework for network annotation

Sushant Patkar, Roded Sharan

Research output: Contribution to journalArticlepeer-review


Motivation: A chief goal of systems biology is the reconstruction of large-scale executable models of cellular processes of interest. While accurate continuousmodels are still beyond reach, a powerful alternative is to learn a logical model of the processes under study, which predicts the logical state of any node of the model as a Boolean function of its incoming nodes. Key to learning such models is the functional annotation of the underlying physical interactions with activation/repression (sign) effects. Such annotations are pretty common for a few well-studied biological pathways. Results: Here we present a novel optimization framework for large-scale sign annotation that employs different plausible models of signaling and combines them in a rigorous manner. We apply our framework to two large-scale knockout datasets in yeast and evaluate its different components as well as the combined model to predict signs of different subsets of physical interactions. Overall, we obtain an accurate predictor that outperforms previous work by a considerable margin.

Original languageEnglish
Pages (from-to)i502-i508
Issue number13
StatePublished - 1 Jul 2018

All Science Journal Classification (ASJC) codes

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics


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