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_34 have shown that Kalman filters can be implemented with reactions networks. Kalman filters can be thought of as a version of Hidden Markov Models with continuous hidden states @cite_40 . It would be instructive to compare their scheme with ours, and note similarities and differences. In passing from position @math to position @math along the sequence, our scheme repeats the same reaction network that updates @math using @math values. It is worth examining if this can be done in place'' so that the same species can be reused, and a reaction network can be described that is not tied to the length @math of the sequence to be observed.
@cite_40 @cite_34
2171077154 2102716594 1749494163 2792169732
We present a switching Kalman filter model for the real-time inference of hand kinematics from a population of motor cortical neurons. Firing rates are modeled as a Gaussian mixture where the mean of each Gaussian component is a linear function of hand kinematics. A "hidden state" models the probability of each mixture component and evolves over time in a Markov chain. The model generalizes previous encoding and decoding methods, addresses the non-Gaussian nature of firing rates, and can cope with crudely sorted neural data common in on-line prosthetic applications. We introduce a new statistical model for time series that iteratively segments data into regimes with approximately linear dynamics and learns the parameters of each of these linear regimes. This model combines and generalizes two of the most widely used stochastic time-series models— hidden Markov models and linear dynamical systems—and is closely related to models that are widely used in the control and econometrics literatures. It can also be derived by extending the mixture of experts neural network (Jacobs, Jordan, Nowlan, & Hinton, 1991) to its fully dynamical version, in which both expert and gating networks are recurrent. Inferring the posterior probabilities of the hidden states of this model is computationally intractable, and therefore the exact expectation maximization (EM) algorithm cannot be applied. However, we present a variational approximation that maximizes a lower bound on the log-likelihood and makes use of both the forward and backward recursions for hidden Markov models and the Kalman filter recursions for linear dynamical systems. We tested the algorithm on artificial data sets and a natural data set of respiration force from a patient with sleep apnea. The results suggest that variational approximations are a viable method for inference and learning in switching state-space models. This paper points out the flaws in using the extended Kalman filter (EKE) and introduces an improvement, the unscented Kalman filter (UKF), proposed by Julier and Uhlman (1997). A central and vital operation performed in the Kalman filter is the propagation of a Gaussian random variable (GRV) through the system dynamics. In the EKF the state distribution is approximated by a GRV, which is then propagated analytically through the first-order linearization of the nonlinear system. This can introduce large errors in the true posterior mean and covariance of the transformed GRV, which may lead to sub-optimal performance and sometimes divergence of the filter. The UKF addresses this problem by using a deterministic sampling approach. The state distribution is again approximated by a GRV, but is now represented using a minimal set of carefully chosen sample points. These sample points completely capture the true mean and covariance of the GRV, and when propagated through the true nonlinear system, captures the posterior mean and covariance accurately to the 3rd order (Taylor series expansion) for any nonlinearity. The EKF in contrast, only achieves first-order accuracy. Remarkably, the computational complexity of the UKF is the same order as that of the EKF. Julier and Uhlman demonstrated the substantial performance gains of the UKF in the context of state-estimation for nonlinear control. Machine learning problems were not considered. We extend the use of the UKF to a broader class of nonlinear estimation problems, including nonlinear system identification, training of neural networks, and dual estimation problems. In this paper, the algorithms are further developed and illustrated with a number of additional examples. In this paper, online detection of false data injection attacks and denial of service attacks in the smart grid is studied. The system is modeled as a discrete-time linear dynamic system and state estimation is performed using the Kalman filter. The generalized cumulative sum algorithm is employed for quickest detection of the cyber-attacks. Detectors are proposed in both centralized and distributed settings. The proposed detectors are robust to time-varying states, attacks, and set of attacked meters. Online estimates of the unknown attack variables are provided, that can be crucial for a quick system recovery. In the distributed setting, due to bandwidth constraints, local centers can only transmit quantized messages to the global center, and a novel event-based sampling scheme called level-crossing sampling with hysteresis is proposed that is shown to exhibit significant advantages compared with the conventional uniform-in-time sampling scheme. Moreover, a distributed dynamic state estimator is proposed based on information filters. Numerical examples illustrate the fast and accurate response of the proposed detectors in detecting both structured and random attacks and their advantages over existing methods.