With a view towards molecular communication systems and molecular multi-agent systems, we propose the Chemical Baum-Welch Algorithm, a novel reaction network scheme that learns parameters for Hidden Markov Models (HMMs). Each reaction in our scheme changes only one molecule of one species to one molecule of another. The reverse change is also accessible but via a different set of enzymes, in a design reminiscent of futile cycles in biochemical pathways. We show that every fixed point of the Baum-Welch algorithm for HMMs is a fixed point of our reaction network scheme, and every positive fixed point of our scheme is a fixed point of the Baum-Welch algorithm. We prove that the “Expectation” step and the “Maximization” step of our reaction network separately converge exponentially fast. We simulate mass-action kinetics for our network on an example sequence, and show that it learns the same parameters for the HMM as the Baum-Welch algorithm.
@cite_4 have described Chemical Boltzmann Machines, which are reaction network schemes whose dynamics reconstructs inference in Boltzmann Machines. This inference can be viewed as a version of E projection. No scheme for learning is presented. The exact schemes presented there are exponentially large. The more realistically sized schemes are presented there without proof. In comparison, our schemes are polynomially sized, provably correct if the equilibrium is positive, and perform both inference and learning for HMMs.
@cite_4
2963699962 189596042 2097006534 2243462087
How smart can a micron-sized bag of chemicals be? How can an artificial or real cell make inferences about its environment? From which kinds of probability distributions can chemical reaction networks sample? We begin tackling these questions by showing three ways in which a stochastic chemical reaction network can implement a Boltzmann machine, a stochastic neural network model that can generate a wide range of probability distributions and compute conditional probabilities. The resulting models, and the associated theorems, provide a road map for constructing chemical reaction networks that exploit their native stochasticity as a computational resource. Finally, to show the potential of our models, we simulate a chemical Boltzmann machine to classify and generate MNIST digits in-silico. We present a new learning algorithm for Boltzmann machines that contain many layers of hidden variables. Data-dependent expectations are estimated using a variational approximation that tends to focus on a single mode, and dataindependent expectations are approximated using persistent Markov chains. The use of two quite different techniques for estimating the two types of expectation that enter into the gradient of the log-likelihood makes it practical to learn Boltzmann machines with multiple hidden layers and millions of parameters. The learning can be made more efficient by using a layer-by-layer “pre-training” phase that allows variational inference to be initialized with a single bottomup pass. We present results on the MNIST and NORB datasets showing that deep Boltzmann machines learn good generative models and perform well on handwritten digit and visual object recognition tasks. We present a type of Temporal Restricted Boltzmann Machine that defines a probability distribution over an output sequence conditional on an input sequence. It shares the desirable properties of RBMs: efficient exact inference, an exponentially more expressive latent state than HMMs, and the ability to model nonlinear structure and dynamics. We apply our model to a challenging real-world graphics problem: facial expression transfer. Our results demonstrate improved performance over several baselines modeling high-dimensional 2D and 3D data. We develop a novel modeling framework for Boltzmann machines, augmenting each hidden unit with a latent transformation assignment variable which describes the selection of the transformed view of the canonical connection weights associated with the unit. This enables the inferences of the model to transform in response to transformed input data in a stable and predictable way, and avoids learning multiple features differing only with respect to the set of transformations. Extending prior work on translation equivariant (convolutional) models, we develop translation and rotation equivariant restricted Boltzmann machines (RBMs) and deep belief nets (DBNs), and demonstrate their effectiveness in learning frequently occurring statistical structure from artificial and natural images.