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The use of visual features in audio-visual speech recognition (AVSR) is justified by both the speech generation mechanism, which is essentially bimodal in audio and visual representation, and by the need for features that are invariant to acoustic noise perturbation. As a result, current AVSR systems demonstrate significant accuracy improvements in environments affected by acoustic noise. In this paper, we describe the use of two statistical models for audio-visual integration, the coupled HMM (CHMM) and the factorial HMM (FHMM), and compare the performance of these models with the existing models used in speaker dependent audio-visual isolated word recognition. The statistical properties of both the CHMM and FHMM allow to model the state asynchrony of the audio and visual observation sequences while preserving their natural correlation over time. In our experiments, the CHMM performs best overall, outperforming all the existing models and the FHMM.

Driven by recent advances in technology, tracking devices allow to collect high-frequency data on the position of players in (association) football matches and in many other sports. Although such data sets are available to every professional team, most teams still rely on time-consuming video analysis when analysing future opponents, for example with regard to how goals were scored or a team’s general style of play. In this contribution, we provide a data-driven approach for automated classification of tactics in football. For that purpose, we consider hidden Markov models (HMMs) to analyse high-frequency tracking data, where the underlying states serve for a team’s tactic. In particular, as space control in football has been considered a major driver of success, we focus on the effective playing space, which is the convex hull created by the players excluding the goalkeeper. This quantity relates to both playing style and team behavior. Using copula-based HMMs, we model jointly the effective playing space of both teams to account for the competitive nature of the game. Our model thus provides an estimate of a team’s playing style at each time point, which can be beneficial for team managers but also of huge interest to football fans.

Depression is closely associated with abnormalities in brain function. Traditional static functional connectivity analyses offer limited insight into the temporal variability of brain activity. Recent advances in dynamic analyses enable a deeper understanding of how depression relates to temporal fluctuations in brain activity. This study utilized a large resting-state functional magnetic resonance imaging dataset (  = 696) to examine the association between brain dynamics and depression. Two complementary approaches were employed. Hidden Markov modeling (HMM) was used to identify discrete brain states and quantify their temporal switching patterns; temporal variability was computed within and between large-scale functional networks to capture time-varying fluctuations in functional connectivity. Depression scores were positively associated with switching rate and negatively associated with maximum fractional occupancy. Furthermore, depression scores were significantly associated with greater temporal variability both within and between networks, with particularly strong effects observed in the default mode network, ventral attention network, and frontoparietal network. Together, these findings suggest that individuals with higher depression scores exhibit more unstable brain dynamics. Our findings reveal that individuals with higher depression levels exhibit greater instability in brain state transitions and increased temporal variability in functional connectivity across large-scale networks. This instability in brain dynamics may contribute to difficulties in emotion regulation and cognitive control. By capturing whole-brain temporal patterns, this study offers a novel perspective on the neural basis of depression.

Background Approximating the recent phylogeny of N phased haplotypes at a set of variants along the genome is a core problem in modern population genomics and central to performing genome-wide screens for association, selection, introgression, and other signals. The Li & Stephens (LS) model provides a simple yet powerful hidden Markov model for inferring the recent ancestry at a given variant, represented as an N × N distance matrix based on posterior decodings. Results We provide a high-performance engine to make these posterior decodings readily accessible with minimal pre-processing via an easy to use package kalis, in the statistical programming language R . kalis enables investigators to rapidly resolve the ancestry at loci of interest and developers to build a range of variant-specific ancestral inference pipelines on top. kalis exploits both multi-core parallelism and modern CPU vector instruction sets to enable scaling to hundreds of thousands of genomes. Conclusions The resulting distance matrices accessible via kalis enable local ancestry, selection, and association studies in modern large scale genomic datasets.

Brain-related disorders are characterized by observable behavioral symptoms, for example, social withdrawal. Smartphones can passively collect behavioral data reflecting digital activities such as communication app usage and calls. These data are collected objectively in real time, avoiding recall bias, and may, therefore, be a useful tool for measuring behaviors related to social functioning. Despite promising clinical utility, analyzing smartphone data is challenging as datasets often include a range of temporal features prone to missingness. Hidden Markov models (HMMs) provide interpretable, lower-dimensional temporal representations of data, allowing for missingness. This study aimed to investigate the HMM as a method for modeling smartphone time series data. We applied an HMM to an aggregate dataset of smartphone measures designed to assess phone-related social functioning in healthy controls (HCs) and participants with schizophrenia, Alzheimer disease (AD), and memory complaints. We trained the HMM on a subset of HCs (91/348, 26.1%) and selected a model with socially active and inactive states. Then, we generated hidden state sequences per participant and calculated their \"total dwell time,\" that is, the percentage of time spent in the socially active state. Linear regression models were used to compare the total dwell time to social and clinical measures in a subset of participants with available measures, and logistic regression was used to compare total dwell times between diagnostic groups and HCs. We primarily reported results from a 2-state HMM but also verified results in HMMs with more hidden states and trained on the whole participant dataset. We identified lower total dwell times in participants with AD (26/257, 10.1%) versus withheld HCs (156/257, 60.7%; odds ratio 0.95, 95% CI 0.92-0.97; false discovery rate [FDR]-corrected P<.001), as well as in participants with memory complaints (57/257, 22.2%; odds ratio 0.97, 95% CI 0.96-0.99; FDR-corrected P=.004). The result in the AD group was very robust across HMM variations, whereas the result in the memory complaints group was less robust. We also observed an interaction between the AD group and total dwell time when predicting social functioning (FDR-corrected P=.02). No significant relationships regarding total dwell time were identified for participants with schizophrenia (18/257, 7%; P>.99). We found the HMM to be a practical, interpretable method for digital phenotyping analysis, providing an objective phenotype that is a possible indicator of social functioning.

Fetal heart rate variability (FHRV) is a critical indicator of fetal well-being and autonomic nervous system development during labor. Traditional monitoring methods often provide limited insights, potentially leading to delayed interventions and suboptimal outcomes. This study proposes an advanced predictive analytics approach by integrating approximate entropy analysis with a hidden Markov model (HMM) within a digital twin framework to enhance real-time fetal monitoring. We utilized a dataset of 469 fetal electrocardiogram (ECG) recordings, each exceeding one hour in duration, to ensure sufficient temporal information for reliable modeling. The FHRV data were preprocessed and partitioned into parasympathetic and sympathetic components based on downward and non-downward beat detection. Approximate entropy was calculated to quantify the complexity of FHRV patterns, revealing significant correlations with umbilical cord blood gas parameters, particularly pH levels. The HMM was developed with four hidden states representing discrete pH levels and eight observed states derived from FHRV data. By employing the Baum–Welch and Viterbi algorithms for training and decoding, respectively, the model effectively captured temporal dependencies and provided early predictions of the fetal acid–base status. Experimental results demonstrated that the model achieved 85% training and 79% testing accuracy on the balanced dataset distribution, improving from 78% and 71% on the imbalanced dataset. The integration of this predictive model into a digital twin framework offers significant benefits for timely clinical interventions, potentially improving prenatal outcomes.

Background Pseudogenes are non-functional copies of protein coding genes that typically follow a different molecular evolutionary path as compared to functional genes. The inclusion of pseudogene sequences in DNA barcoding and metabarcoding analysis can lead to misleading results. None of the most widely used bioinformatic pipelines used to process marker gene (metabarcode) high throughput sequencing data specifically accounts for the presence of pseudogenes in protein-coding marker genes. The purpose of this study is to develop a method to screen for nuclear mitochondrial DNA segments (nuMTs) in large COI datasets. We do this by: (1) describing gene and nuMT characteristics from an artificial COI barcode dataset, (2) show the impact of two different pseudogene removal methods on perturbed community datasets with simulated nuMTs, and (3) incorporate a pseudogene filtering step in a bioinformatic pipeline that can be used to process Illumina paired-end COI metabarcode sequences. Open reading frame length and sequence bit scores from hidden Markov model (HMM) profile analysis were used to detect pseudogenes. Results Our simulations showed that it was more difficult to identify nuMTs from shorter amplicon sequences such as those typically used in metabarcoding compared with full length DNA barcodes that are used in the construction of barcode libraries. It was also more difficult to identify nuMTs in datasets where there is a high percentage of nuMTs. Existing bioinformatic pipelines used to process metabarcode sequences already remove some nuMTs, especially in the rare sequence removal step, but the addition of a pseudogene filtering step can remove up to 5% of sequences even when other filtering steps are in place. Conclusions Open reading frame length filtering alone or combined with hidden Markov model profile analysis can be used to effectively screen out apparent pseudogenes from large datasets. There is more to learn from COI nuMTs such as their frequency in DNA barcoding and metabarcoding studies, their taxonomic distribution, and evolution. Thus, we encourage the submission of verified COI nuMTs to public databases to facilitate future studies.

The study of functional brain networks has grown rapidly over the past decade. While most functional connectivity (FC) analyses estimate one static network structure for the entire length of the functional magnetic resonance imaging (fMRI) time series, recently there has been increased interest in studying time-varying changes in FC. Hidden Markov models (HMMs) have proven to be a useful modeling approach for discovering repeating graphs of interacting brain regions (brain states). However, a limitation lies in HMMs assuming that the sojourn time, the number of consecutive time points in a state, is geometrically distributed. This may encourage inaccurate estimation of the time spent in a state before switching to another state. We propose a hidden semi-Markov model (HSMM) approach for inferring time-varying brain networks from fMRI data, which explicitly models the sojourn distribution. Specifically, we propose using HSMMs to find each subject's most probable series of network states and the graphs associated with each state, while properly estimating and modeling the sojourn distribution for each state. We perform a simulation study, as well as an analysis on both task-based fMRI data from an anxiety-inducing experiment and resting-state fMRI data from the Human Connectome Project. Our results demonstrate the importance of model choice when estimating sojourn times and reveal their potential for understanding healthy and diseased brain mechanisms. •The HSMM and HMM perform similarly when estimating dynamic brain states.•The HSMM is more flexible than the HMM when estimating sojourn times.•The HMM and HSMM estimate different empirical sojourn distributions in rs-fMRI.•Multidimensional scaling reveals rs-fMRI states are reproducible.•Sojourn distributions are associated with sustained attention scores.

Background Hidden Markov models (HMM) are a powerful tool for analyzing biological sequences in a wide variety of applications, from profiling functional protein families to identifying functional domains. The standard method used for HMM training is either by maximum likelihood using counting when sequences are labelled or by expectation maximization, such as the Baum–Welch algorithm, when sequences are unlabelled. However, increasingly there are situations where sequences are just partially labelled. In this paper, we designed a new training method based on the Baum–Welch algorithm to train HMMs for situations in which only partial labeling is available for certain biological problems. Results Compared with a similar method previously reported that is designed for the purpose of active learning in text mining, our method achieves significant improvements in model training, as demonstrated by higher accuracy when the trained models are tested for decoding with both synthetic data and real data. Conclusions A novel training method is developed to improve the training of hidden Markov models by utilizing partial labelled data. The method will impact on detecting de novo motifs and signals in biological sequence data. In particular, the method will be deployed in active learning mode to the ongoing research in detecting plasmodesmata targeting signals and assess the performance with validations from wet-lab experiments.

Uncertainty-aware soft sensors in sign language recognition (SLR) integrate methods to quantify and manage the uncertainty in their predictions. This is particularly crucial in SLR due to the variability in sign language gestures and differences in individual signing styles. Managing uncertainty allows the system to handle variations in signing styles, lighting conditions, and occlusions more effectively. While current techniques for handling uncertainty in SLR systems offer significant benefits in terms of improved accuracy and robustness, they also come with notable disadvantages. High computational complexity, data dependency, scalability issues, sensor and environmental limitations, and real-time constraints all pose significant hurdles. The aim of the work is to develop and evaluate a Type-2 Neutrosophic Hidden Markov Model (HMM) for SLR that leverages the advanced uncertainty handling capabilities of Type-2 neutrosophic sets. In the suggested soft sensor model, the Foot of Uncertainty (FOU) allows Type-2 Neutrosophic HMMs to represent uncertainty as intervals, capturing the range of possible values for truth, falsity, and indeterminacy. This is especially useful in SLR, where gestures can be ambiguous or imprecise. This enhances the model’s ability to manage complex uncertainties in sign language gestures and mitigate issues related to model drift. The FOU provides a measure of confidence for each recognition result by indicating the range of uncertainty. By effectively addressing uncertainty and enhancing subject independence, the model can be integrated into real-life applications, improving interactions, learning, and accessibility for the hearing-impaired. Examples such as assistive devices, educational tools, and customer service automation highlight its transformative potential. The experimental evaluation demonstrates the superiority of the Type-2 Neutrosophic HMM over the Type-1 Neutrosophic HMM in terms of accuracy for SLR. Specifically, the Type-2 Neutrosophic HMM consistently outperforms its Type-1 counterpart across various test scenarios, achieving an average accuracy improvement of 10%.