dream3 network inference using dynamic context likelihood of relatedness and the inferelatordream3网络推理使用动态上下文亲缘和inferelator的可能性.pdfVIP

DREAM3: Network Inference Using Dynamic Context Likelihood of Relatedness and the Inferelator 1 2 2,3 1,2,4 Aviv Madar , Alex Greenfield , Eric Vanden-Eijnden , Richard Bonneau * 1 Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America, 2 Computational Biology Program, New York University School of Medicine, New York, New York, United States of America, 3 Department of Mathematics, Courant Institute of Mathematical Sciences, New York University, New York, New York, United States of America, 4 Department of Computer Science, Courant Institute of Mathematical Sciences, New York University, New York, New York, United States of America Abstract Background: Many current works aiming to learn regulatory networks from systems biology data must balance model complexity with respect to data availability and quality. Methods that learn regulatory associations based on unit-less metrics, such as Mutual Information, are attractive in that they scale well and reduce the number of free parameters (model complexity) per interaction to a minimum. In contrast, methods for learning regulatory networks based on explicit dynamical models are more complex and scale less gracefully, but are attractive as they may allow direct prediction of transcriptional dynamics and resolve the directionality of many regulatory interactions. Methodology: We aim to investigate whether scalable information based methods (like the Context Likelihood of Relatedness method) and more explicit dynamical models (like Inferelator 1.0) prove synergistic when combined. We test a pipeline wh