Hidden Markov Models (HMMs) are fundamental for modeling sequential data, yet learning their parameters from observations remains challenging. Classical methods like the Baum-Welch (EM) algorithm are computationally intensive and prone to local optima, while modern spectral algorithms offer provable guarantees but may produce probability outputs outside valid ranges. This work introduces Belief Net, a novel framework that learns HMM parameters through gradient-based optimization by formulating the HMM's forward filter as a structured neural network. Unlike black-box Transformer models, Belief Net's learnable weights are explicitly the logits of the initial distribution, transition matrix, and emission matrix, ensuring full interpretability. The model processes observation sequences using a decoder-only architecture and is trained end-to-end with standard autoregressive next-observation prediction loss. On synthetic HMM data, Belief Net achieves superior convergence speed compared to Baum-Welch, successfully recovering parameters in both undercomplete and overcomplete settings where spectral methods fail. Comparisons with Transformer-based models are also presented on real-world language data.

We use coupled hidden Markov models to automatically annotate the 371 Bach chorales in the Riemenschneider edition, a corpus containing approximately 100,000 notes and 20,000 chords. We give three separate analyses that achieve progressively greater accuracy at the cost of making increasingly strong assumptions about musical syntax. Although our method makes almost no use of human input, we are able to identify both chords and keys with an accuracy of 85% or greater when compared to an expert human analysis, resulting in annotations accurate enough to be used for a range of music-theoretical purposes, while also being free of subjective human judgments. Our work bears on longstanding debates about the objective reality of the structures postulated by standard Western harmonic theory, as well as on specific questions about the nature of Western harmonic syntax.

Profile hidden Markov models (pHMMs) are widely employed in various bioinformatics applications to identify similarities between biological sequences, such as DNA or protein sequences. In pHMMs, sequences are represented as graph structures. These probabilities are subsequently used to compute the similarity score between a sequence and a pHMM graph. The Baum-Welch algorithm, a prevalent and highly accurate method, utilizes these probabilities to optimize and compute similarity scores. However, the Baum-Welch algorithm is computationally intensive, and existing solutions offer either software-only or hardware-only approaches with fixed pHMM designs. We identify an urgent need for a flexible, high-performance, and energy-efficient HW/SW co-design to address the major inefficiencies in the Baum-Welch algorithm for pHMMs. We introduce ApHMM, the first flexible acceleration framework designed to significantly reduce both computational and energy overheads associated with the Baum-Welch algorithm for pHMMs. ApHMM tackles the major inefficiencies in the Baum-Welch algorithm by 1) designing flexible hardware to accommodate various pHMM designs, 2) exploiting predictable data dependency patterns through on-chip memory with memoization techniques, 3) rapidly filtering out negligible computations using a hardware-based filter, and 4) minimizing redundant computations. ApHMM achieves substantial speedups of 15.55x - 260.03x, 1.83x - 5.34x, and 27.97x when compared to CPU, GPU, and FPGA implementations of the Baum-Welch algorithm, respectively. ApHMM outperforms state-of-the-art CPU implementations in three key bioinformatics applications: 1) error correction, 2) protein family search, and 3) multiple sequence alignment, by 1.29x - 59.94x, 1.03x - 1.75x, and 1.03x - 1.95x, respectively, while improving their energy efficiency by 64.24x - 115.46x, 1.75x, 1.96x.

Trajectory forecasting has become an interesting research area driven by advancements in wearable sensing technology. Sensors can be seamlessly integrated into clothing using cutting-edge electronic textiles technology, allowing long-term recording of human movements outside the laboratory. Motivated by the recent findings that clothing-attached sensors can achieve higher activity recognition accuracy than body-attached sensors, this work investigates motion prediction and trajectory forecasting using rigid-attached and clothing-attached sensors. The future trajectory is forecasted from the probabilistic trajectory model formulated by left-to-right hidden Markov model (LR-HMM) and motion prediction accuracy is computed by the classification rule. Surprisingly, the results show that clothing-attached sensors can forecast the future trajectory and have better performance than body-attached sensors in terms of motion prediction accuracy. In some cases, the clothing-attached sensor can enhance accuracy by 45% compared to the body-attached sensor and requires approximately 80% less duration of the historical trajectory to achieve the same level of accuracy as the body-attached sensor.

Herein, the Hidden Markov Model is expanded to allow for Markov chain observations. In particular, the observations are assumed to be a Markov chain whose one step transition probabilities depend upon the hidden Markov chain. An Expectation-Maximization analog to the Baum-Welch algorithm is developed for this more general model to estimate the transition probabilities for both the hidden state and for the observations as well as to estimate the probabilities for the initial joint hidden-state-observation distribution. A believe state or filter recursion to track the hidden state then arises from the calculations of this Expectation-Maximization algorithm. A dynamic programming analog to the Viterbi algorithm is also developed to estimate the most likely sequence of hidden states given the sequence of observations.

Psychiatric patients' passive activity monitoring is crucial to detect behavioural shifts in real-time, comprising a tool that helps clinicians supervise patients' evolution over time and enhance the associated treatments' outcomes. Frequently, sleep disturbances and mental health deterioration are closely related, as mental health condition worsening regularly entails shifts in the patients' circadian rhythms. Therefore, Sleep Activity Recognition constitutes a behavioural marker to portray patients' activity cycles and to detect behavioural changes among them. Moreover, mobile passively sensed data captured from smartphones, thanks to these devices' ubiquity, constitute an excellent alternative to profile patients' biorhythm. In this work, we aim to identify major sleep episodes based on passively sensed data. To do so, a Heterogeneous Hidden Markov Model is proposed to model a discrete latent variable process associated with the Sleep Activity Recognition task in a self-supervised way. We validate our results against sleep metrics reported by clinically tested wearables, proving the effectiveness of the proposed approach.

Hidden Markov models (HMMs) are commonly used for sequential data modeling when the true state of the system is not fully known. We formulate a special case of recurrent neural networks (RNNs), which we name hidden Markov recurrent neural networks (HMRNNs), and prove that each HMRNN has the same likelihood function as a corresponding discrete-observation HMM. We experimentally validate this theoretical result on synthetic datasets by showing that parameter estimates from HMRNNs are numerically close to those obtained from HMMs via the Baum-Welch algorithm. We demonstrate our method's utility in a case study on Alzheimer's disease progression, in which we augment HMRNNs with other predictive neural networks. The augmented HMRNN yields parameter estimates that offer a novel clinical interpretation and fit the patient data better than HMM parameter estimates from the Baum-Welch algorithm.

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.

A Semi-Hidden Markov Model (SHMM) for bursty error channels is defined by a state transition probability matrix $A$, a prior probability vector $\Pi$, and the state dependent output symbol error probability matrix $B$. Several processes are utilized for estimating $A$, $\Pi$ and $B$ from a given empirically obtained or simulated error sequence. However, despite placing some restrictions on the underlying Markov model structure, we still have a computationally intensive estimation procedure, especially given a large error sequence containing long burst of identical symbols. Thus, in this paper, we utilize under some moderate assumptions, a Markov model with random state transition matrix $A$ equivalent to a unique Block Diagonal Markov model with state transition matrix $\Lambda$ to model an indoor software-defined power line communication system. A computationally efficient modified Baum-Welch algorithm for estimation of $\Lambda$ given an experimentally obtained error sequence from the indoor PLC channel is utilized. Resulting Equivalent Block Diagonal Markov models assist designers to accelerate and facilitate the procedure of novel PLC systems design and evaluation.

Sequence modeling is a fundamental real-world problem with a wide range of applications. Recurrent neural networks (RNNs) are currently preferred in sequence prediction tasks due to their ability to model long-term and variable order dependencies. However, RNNs have disadvantages in several applications because of their inability to natively handle uncertainty, and because of the inscrutable internal representations. Probabilistic sequence models like Hidden Markov Models (HMM) have the advantage of more interpretable representations and the ability to handle uncertainty. Although overcomplete HMMs with many more hidden states compared to the observed states can, in theory, model long-term temporal dependencies [23], training HMMs is challenging due to credit diffusion [3]. For this reason, simpler and inflexible n-gram models are preferred to HMMs for tasks like language modeling. Tensor decomposition methods [1] have been suggested for the learning of HMMs in order to overcome the credit diffusion problem, but current methods are not applicable to the overcomplete setting where the full-rank requirements on the transition and emission matrices are not fulfilled. Recently there has been renewed interest in the topic of training overcomplete HMMs for higher-order dependencies with the expectation that sparsity structures could potentially alleviate the credit diffusion problem [23]. In this paper we demonstrate that a particular sparsity structure on the emission matrix can help HMMs learn higher-order temporal structure using the standard Expectation-Maximization algorithms [26] (Baum-Welch) and its online variants.