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The importance of better models in stochastic optimization.

ABSTRACT: Standard stochastic optimization methods are brittle, sensitive to stepsize choice and other algorithmic parameters, and they exhibit instability outside of well-behaved families of objectives. To address these challenges, we investigate models for stochastic optimization and learning problems that exhibit better robustness to problem families and algorithmic parameters. With appropriately accurate models-which we call the aprox family-stochastic methods can be made stable, provably convergent, and asymptotically optimal; even modeling that the objective is nonnegative is sufficient for this stability. We extend these results beyond convexity to weakly convex objectives, which include compositions of convex losses with smooth functions common in modern machine learning. We highlight the importance of robustness and accurate modeling with experimental evaluation of convergence time and algorithm sensitivity.

SUBMITTER: Asi H

PROVIDER: S-EPMC6859306 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

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The importance of better models in stochastic optimization.

Asi Hilal H Duchi John C JC

Proceedings of the National Academy of Sciences of the United States of America 20191030 46

Standard stochastic optimization methods are brittle, sensitive to stepsize choice and other algorithmic parameters, and they exhibit instability outside of well-behaved families of objectives. To address these challenges, we investigate models for stochastic optimization and learning problems that exhibit better robustness to problem families and algorithmic parameters. With appropriately accurate models-which we call the aprox family-stochastic methods can be made stable, provably convergent, ...[more]

PMID: 31666325

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Project description:BackgroundStochastic effects can be important for the behavior of processes involving small population numbers, so the study of stochastic models has become an important topic in the burgeoning field of computational systems biology. However analysis techniques for stochastic models have tended to lag behind their deterministic cousins due to the heavier computational demands of the statistical approaches for fitting the models to experimental data. There is a continuing need for more effective and efficient algorithms. In this article we focus on the parameter inference problem for stochastic kinetic models of biochemical reactions given discrete time-course observations of either some or all of the molecular species.ResultsWe propose an algorithm for inference of kinetic rate parameters based upon maximum likelihood using stochastic gradient descent (SGD). We derive a general formula for the gradient of the likelihood function given discrete time-course observations. The formula applies to any explicit functional form of the kinetic rate laws such as mass-action, Michaelis-Menten, etc. Our algorithm estimates the gradient of the likelihood function by reversible jump Markov chain Monte Carlo sampling (RJMCMC), and then gradient descent method is employed to obtain the maximum likelihood estimation of parameter values. Furthermore, we utilize flux balance analysis and show how to automatically construct reversible jump samplers for arbitrary biochemical reaction models. We provide RJMCMC sampling algorithms for both fully observed and partially observed time-course observation data. Our methods are illustrated with two examples: a birth-death model and an auto-regulatory gene network. We find good agreement of the inferred parameters with the actual parameters in both models.ConclusionsThe SGD method proposed in the paper presents a general framework of inferring parameters for stochastic kinetic models. The method is computationally efficient and is effective for both partially and fully observed systems. Automatic construction of reversible jump samplers and general formulation of the likelihood gradient function makes our method applicable to a wide range of stochastic models. Furthermore our derivations can be useful for other purposes such as using the gradient information for parametric sensitivity analysis or using the reversible jump samplers for full Bayesian inference. The software implementing the algorithms is publicly available at http://cbcl.ics.uci.edu/sgd.

Dataset Information

The importance of better models in stochastic optimization.

Publications

The importance of better models in stochastic optimization.

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