# Gaussian Processes for Missing Species in Biochemical Systems

Neil D. Lawrence, University of Sheffield
Magnus Rattray, University of Manchester
Pei Gao, Peking University
Michalis K. Titsias, University of Athens

Chapter 9 in Learning and Inference in Computational Systems Biology

#### Abstract

Computational systems biology aims to develop algorithms that uncover the structure and parameterization of the underlying mechanistic model—in other words, to answer specific questions about the underlying mechanisms of a biological system—in a process that can be thought of as learning or inference. This volume offers state-of-the-art perspectives from computational biology, statistics, modeling, and machine learning on new methodologies for learning and inference in biological networks. The chapters offer practical approaches to biological inference problems ranging from genome-wide inference of genetic regulation to pathway-specific studies. Both deterministic models (based on ordinary differential equations) and stochastic models (which anticipate the increasing availability of data from small populations of cells) are considered. Several chapters emphasize Bayesian inference, so the editors have included an introduction to the philosophy of the Bayesian approach and an overview of current work on Bayesian inference. Taken together, the methods discussed by the experts in Learning and Inference in Computational Systems Biology provide a foundation upon which the next decade of research in systems biology can be built.

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 %T Gaussian Processes for Missing Species in Biochemical Systems %A Neil D. Lawrence and Magnus Rattray and Pei Gao and Michalis K. Titsias %B %C Learning and Inference in Computational Systems Biology %D %E Neil D. Lawrence and Mark Girolami and Magnus Rattray and Guido Sanguinetti %F lawrence-licsbgp10 %I MIT Press %P -- %R %U http://inverseprobability.com/publications/lawrence-licsbgp10.html %X Computational systems biology aims to develop algorithms that uncover the structure and parameterization of the underlying mechanistic model—in other words, to answer specific questions about the underlying mechanisms of a biological system—in a process that can be thought of as learning or inference. This volume offers state-of-the-art perspectives from computational biology, statistics, modeling, and machine learning on new methodologies for learning and inference in biological networks. The chapters offer practical approaches to biological inference problems ranging from genome-wide inference of genetic regulation to pathway-specific studies. Both deterministic models (based on ordinary differential equations) and stochastic models (which anticipate the increasing availability of data from small populations of cells) are considered. Several chapters emphasize Bayesian inference, so the editors have included an introduction to the philosophy of the Bayesian approach and an overview of current work on Bayesian inference. Taken together, the methods discussed by the experts in Learning and Inference in Computational Systems Biology provide a foundation upon which the next decade of research in systems biology can be built. 
 TY - CPAPER TI - Gaussian Processes for Missing Species in Biochemical Systems AU - Neil D. Lawrence AU - Magnus Rattray AU - Pei Gao AU - Michalis K. Titsias BT - Learning and Inference in Computational Systems Biology PY - 2010/01/01 DA - 2010/01/01 ED - Neil D. Lawrence ED - Mark Girolami ED - Magnus Rattray ED - Guido Sanguinetti ID - lawrence-licsbgp10 PB - MIT Press SP - EP - UR - http://inverseprobability.com/publications/lawrence-licsbgp10.html AB - Computational systems biology aims to develop algorithms that uncover the structure and parameterization of the underlying mechanistic model—in other words, to answer specific questions about the underlying mechanisms of a biological system—in a process that can be thought of as learning or inference. This volume offers state-of-the-art perspectives from computational biology, statistics, modeling, and machine learning on new methodologies for learning and inference in biological networks. The chapters offer practical approaches to biological inference problems ranging from genome-wide inference of genetic regulation to pathway-specific studies. Both deterministic models (based on ordinary differential equations) and stochastic models (which anticipate the increasing availability of data from small populations of cells) are considered. Several chapters emphasize Bayesian inference, so the editors have included an introduction to the philosophy of the Bayesian approach and an overview of current work on Bayesian inference. Taken together, the methods discussed by the experts in Learning and Inference in Computational Systems Biology provide a foundation upon which the next decade of research in systems biology can be built. ER - 
 Lawrence, N.D., Rattray, M., Gao, P. & Titsias, M.K.. (2010). Gaussian Processes for Missing Species in Biochemical Systems. Learning and Inference in Computational Systems Biology :-