A detailed algorithmic explanation is required for how a network of chemical reactions can generate the sophisticated behavior displayed by living cells. Though several previous works have shown that reaction networks are computationally universal and can in principle implement any algorithm, there is scope for constructions that map well onto biological reality, make efficient use of the computational potential of the native dynamics of reaction networks, and make contact with statistical mechanics. We describe a new reaction network scheme for solving a large class of statistical problems. Specifically we show how reaction networks can implement information projection, and consequently a generalized Expectation-Maximization algorithm, to solve maximum likelihood estimation problems in partially-observed exponential families on categorical data. Our scheme can be thought of as an algorithmic interpretation of E. T. Jaynes’s vision of statistical mechanics as statistical inference.
The belief propagation scheme of Napp and Adams @cite_15 shows how reaction networks can implement sum-product algorithms from probabilistic graphical models to compute marginals of joint distributions. There is some formal similarity between the reaction networks of Napp and Adams, and our EM reaction network. In particular, their scheme also has two sets of species, sum'' and product'' species, and two subnetworks. In each subnetwork, one set of species changes in number, and the other set appears catalytically. We speculate that this may be because message passing algorithms are themselves a special case of the EM algorithm @cite_22 @cite_38 , in which case possibly the Napp-Adams scheme may be related in some as-yet-undiscovered way to our EM scheme.
@cite_38 @cite_15 @cite_22
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Since the proposal of turbo codes in 1993, many studies have appeared on this simple and new type of codes which give a powerful and practical performance of error correction. Although experimental results strongly support the efficacy of turbo codes, further theoretical analysis is necessary, which is not straightforward. It is pointed out that the iterative decoding algorithm of turbo codes shares essentially similar ideas with low-density parity-check (LDPC) codes, with Pearl's belief propagation algorithm applied to a cyclic belief diagram, and with the Bethe approximation in statistical physics. Therefore, the analysis of the turbo decoding algorithm will reveal the mystery of those similar iterative methods. In this paper, we recapture and extend the geometrical framework initiated by Richardson to the information geometrical framework of dual affine connections, focusing on both of the turbo and LDPC decoding algorithms. The framework helps our intuitive understanding of the algorithms and opens a new prospect of further analysis. We reveal some properties of these codes in the proposed framework, including the stability and error analysis. Based on the error analysis, we finally propose a correction term for improving the approximation. Recent work on molecular programming has explored new possibilities for computational abstractions with biomolecules, including logic gates, neural networks, and linear systems. In the future such abstractions might enable nanoscale devices that can sense and control the world at a molecular scale. Just as in macroscale robotics, it is critical that such devices can learn about their environment and reason under uncertainty. At this small scale, systems are typically modeled as chemical reaction networks. In this work, we develop a procedure that can take arbitrary probabilistic graphical models, represented as factor graphs over discrete random variables, and compile them into chemical reaction networks that implement inference. In particular, we show that marginalization based on sum-product message passing can be implemented in terms of reactions between chemical species whose concentrations represent probabilities. We show algebraically that the steady state concentration of these species correspond to the marginal distributions of the random variables in the graph and validate the results in simulations. As with standard sum-product inference, this procedure yields exact results for tree-structured graphs, and approximate solutions for loopy graphs. Belief propagation (BP) is a universal method of stochastic reasoning. It gives exact inference for stochastic models with tree interactions and works surprisingly well even if the models have loopy interactions. Its performance has been analyzed separately in many fields, such as AI, statistical physics, information theory, and information geometry. This article gives a unified framework for understanding BP and related methods and summarizes the results obtained in many fields. In particular, BP and its variants, including tree reparameterization and concave-convex procedure, are reformulated with information-geometrical terms, and their relations to the free energy function are elucidated from an information-geometrical viewpoint. We then propose a family of new algorithms. The stabilities of the algorithms are analyzed, and methods to accelerate them are investigated.