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Fleming-Viot diffusions are widely used stochastic models for population dynamics that extend the celebrated Wright-Fisher diffusions. They describe the temporal evolution of the relative frequencies of the allelic types in an ideally infinite panmictic population, whose individuals undergo random genetic drift and at birth can mutate to a new allelic type drawn from a possibly infinite potential pool, independently of their parent. Recently, Bayesian nonparametric inference has been considered for this model when a finite sample of individuals is drawn from the population at several discrete time points. Previous works have fully described the relevant estimators for this problem, but current software is available only for the Wright-Fisher finite-dimensional case. Here, we provide software for the general case, overcoming some nontrivial computational challenges posed by this setting. The R package FVDDPpkg efficiently approximates the filtering and smoothing distribution for Fleming-Viot diffusions, given finite samples of individuals collected at different times. A suitable Monte Carlo approximation is also introduced in order to reduce the computational cost.

This study addresses the environmental problem of PET plastic through in silico bioprospecting for the identification and experimental validation of novel PET degrading eukaryotes through the in silico bioprospectingI of PETases, employing a methodology that combines Hidden Markov Models (HMMs), clustering techniques, molecular docking, and dynamic simulations. A total of 424 putative PETase sequences were identified from 219 eukaryotic organisms, highlighting six sequences with low affinity energies. The Aspergillus luchuensis sequence showed the lowest Gibbs free energy and exhibited stability at different temperatures in molecular dynamics assays. Experimental validation, through a plate clearance assay and HPLC, confirmed PETase activity in three wild-type fungal strains, with A. luchuensis showing the highest efficiency. The results obtained demonstrate the effectiveness of combining computational and experimental approaches as proof of concept to discover and validate eukaryotes with PET-degrading capabilities opening new perspectives for the sustainable management of this type of waste and contributing to its environmental mitigation., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier B.V.)

Background: Anthropogenic activities occurring throughout the Sonoran Desert are replacing and fragmenting habitat and reducing landscape connectivity for the Sonoran desert tortoise (Gopherus morafkai). Understanding how the structure of the landscape influences tortoise habitat use and movement can help develop strategies for mitigating the impacts of these landscape alterations, which are conservation actions needed to support the species' long-term persistence. However, how natural and anthropogenic features influence fine-scale habitat use and movement of Sonoran desert tortoises remains unclear., Methods: The goals of this study were to (1) understand how characteristics of the landscape shape tortoise habitat use and movement in order to (2) identify factors that may reduce habitat use or threaten landscape connectivity for the species by discouraging or restricting movement. We collected GPS telemetry data from 17 adult tortoises tracked for two summer monsoon seasons, when tortoises are most active, in a U.S. National Monument along the international border between Arizona, USA and Sonora, Mexico. We used Hidden Markov Models (HMMs) to assign GPS locations to an encamped or a moving state. We used the moving state data in integrated Step Selection Analyses (iSSA) to examine how range-resident Sonoran desert tortoises select habitat and respond to landscape features while moving., Results: Tortoises selected to move through areas of intermediate vegetation cover and terrain ruggedness and avoided areas far from desert washes and close to low-traffic roads. Tortoises increased their speed when approaching or crossing low-traffic roads but showed no detectable response to a highway., Conclusion: Bare earth or high vegetation cover, flat or extremely rugged terrain, areas far from desert washes, and low-traffic roads may discourage or restrict tortoise movement. Therefore, preventing the development of roads, activities that degrade washes, and activities that thin, remove, or greatly increase vegetation cover may encourage tortoise habitat use and movement within those habitats., (© 2024. The Author(s).)

Understanding and remembering the complex experiences of everyday life relies critically on prior schematic knowledge about how events in our world unfold over time. How does the brain construct event representations from a library of schematic scripts, and how does activating a specific script impact the way that events are segmented in time? We developed a novel set of 16 audio narratives, each of which combines one of four location-relevant event scripts (restaurant, airport, grocery store, and lecture hall) with one of four socially relevant event scripts (breakup, proposal, business deal, and meet cute), and presented them to participants in an fMRI study and a separate online study. Responses in the angular gyrus, parahippocampal gyrus, and subregions of the medial prefrontal cortex (mPFC) were driven by scripts related to both location and social information, showing that these regions can track schematic sequences from multiple domains. For some stories, participants were primed to attend to one of the two scripts by training them to listen for and remember specific script-relevant episodic details. Activating a location-related event script shifted the timing of subjective event boundaries to align with script-relevant changes in the narratives, and this behavioral shift was mirrored in the timing of neural responses, with mPFC event boundaries (identified using a hidden Markov model) aligning to location-relevant rather than socially relevant boundaries when participants were location primed. Our findings demonstrate that neural event dynamics are actively modulated by top-down goals and provide new insight into how narrative event representations are constructed through the activation of temporally structured prior knowledge., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Theta oscillations, ranging from 4-8 Hz, play a significant role in spatial learning and memory functions during navigation tasks. Frontal theta oscillations are thought to play an important role in spatial navigation and memory. Electroencephalography (EEG) datasets are very complex, making any changes in the neural signal related to behaviour difficult to interpret. However, multiple analytical methods are available to examine complex data structures, especially machine learning-based techniques. These methods have shown high classification performance, and their combination with feature engineering enhances their capability. This paper proposes using hidden Markov and linear mixed effects models to extract features from EEG data. Based on the engineered features obtained from frontal theta EEG data during a spatial navigation task in two key trials (first, last) and between two conditions (learner and non-learner), we analysed the performance of six machine learning methods on classifying learner and non-learner participants. We also analysed how different standardisation methods used to pre-process the EEG data contribute to classification performance. We compared the classification performance of each trial with data gathered from the same subjects, including solely coordinate-based features, such as idle time and average speed. We found that more machine learning methods perform better classification using coordinate-based data. However, only deep neural networks achieved an area under the ROC curve higher than 80% using the theta EEG data alone. Our findings suggest that standardising the theta EEG data and using deep neural networks enhances the classification of learner and non-learner subjects in a spatial learning task., (© 2024. The Author(s).)

Single-particle tracking is a powerful technique to investigate the motion of molecules or particles. Here, we review the methods for analyzing the reconstructed trajectories, a fundamental step for deciphering the underlying mechanisms driving the motion. First, we review the traditional analysis based on the mean squared displacement (MSD), highlighting the sometimes-neglected factors potentially affecting the accuracy of the results. We then report methods that exploit the distribution of parameters other than displacements, e.g., angles, velocities, and times and probabilities of reaching a target, discussing how they are more sensitive in characterizing heterogeneities and transient behaviors masked in the MSD analysis. Hidden Markov Models are also used for this purpose, and these allow for the identification of different states, their populations and the switching kinetics. Finally, we discuss a rapidly expanding field-trajectory analysis based on machine learning. Various approaches, from random forest to deep learning, are used to classify trajectory motions, which can be identified by motion models or by model-free sets of trajectory features, either previously defined or automatically identified by the algorithms. We also review free software available for some of the analysis methods. We emphasize that approaches based on a combination of the different methods, including classical statistics and machine learning, may be the way to obtain the most informative and accurate results.

This paper focuses on inferring a general class of hidden Markov models (HMMs) using data acquired from experts. Expert-acquired data contain decisions/actions made by humans/users for various objectives, such as navigation data reflecting drivers' behavior, cybersecurity data carrying defender decisions, and biological data containing the biologist's actions (e.g., interventions and experiments). Conventional inference methods rely on temporal changes in data without accounting for expert knowledge. This paper incorporates expert knowledge into the inference of HMMs by modeling expert behavior as an imperfect reinforcement learning agent. The proposed method optimally quantifies experts' perceptions about the system model, which, alongside the temporal changes in data, contributes to the inference process. The proposed inference method is derived through a combination of dynamic programming and optimal recursive Bayesian estimation. The applicability of this method is demonstrated to a wide range of inference criteria, such as maximum likelihood and maximum a posteriori. The performance of the proposed method is investigated through a comprehensive numerical experiment using a benchmark problem and biological networks.

Background: Movement plays a key role in allowing animal species to adapt to sudden environmental shifts. Anthropogenic climate and land use change have accelerated the frequency of some of these extreme disturbances, including megafire. These megafires dramatically alter ecosystems and challenge the capacity of several species to adjust to a rapidly changing landscape. Ungulates and their movement behaviors play a central role in the ecosystem functions of fire-prone ecosystems around the world. Previous work has shown behavioral plasticity is an important mechanism underlying whether large ungulates are able to adjust to recent changes in their environments effectively. Ungulates may respond to the immediate effects of megafire by adjusting their movement and behavior, but how these responses persist or change over time following disturbance is poorly understood., Methods: We examined how an ecologically dominant ungulate with strong site fidelity, Columbian black-tailed deer (Odocoileus hemionus columbianus), adjusted its movement and behavior in response to an altered landscape following a megafire. To do so, we collected GPS data from 21 individual female deer over the course of a year to compare changes in home range size over time and used resource selection functions (RSFs) and hidden Markov movement models (HMMs) to assess changes in behavior and habitat selection., Results: We found compelling evidence of adaptive capacity across individual deer in response to megafire. Deer avoided exposed and severely burned areas that lack forage and could be riskier for predation immediately following megafire, but they later altered these behaviors to select areas that burned at higher severities, potentially to take advantage of enhanced forage., Conclusions: These results suggest that despite their high site fidelity, deer can navigate altered landscapes to track rapid shifts in encounter risk with predators and resource availability. This successful adjustment of movement and behavior following extreme disturbance could help facilitate resilience at broader ecological scales., (© 2024. The Author(s).)

Determining movement parameters for pest insects such as tephritid fruit flies is critical to developing models which can be used to increase the effectiveness of surveillance and control strategies. In this study, harmonic radar was used to track wild-caught male Queensland fruit flies (Qflies), Bactrocera tryoni, in papaya fields. Experiment 1 continuously tracked single flies which were prodded to induce movement. Qfly movements from this experiment showed greater mean squared displacement than predicted by both a simple random walk (RW) or a correlated random walk (CRW) model, suggesting that movement parameters derived from the entire data set do not adequately describe the movement of individual Qfly at all spatial scales or for all behavioral states. This conclusion is supported by both fractal and hidden Markov model (HMM) analysis. Lower fractal dimensions (straighter movement paths) were observed at larger spatial scales (> 2.5 m) suggesting that Qflies have qualitatively distinct movement at different scales. Further, a two-state HMM fit the observed movement data better than the CRW or RW models. Experiment 2 identified individual landing locations, twice a day, for groups of released Qflies, demonstrating that flies could be tracked over longer periods of time., (© 2024. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.)

Player movement in rugby league is complex, being spatiotemporal and multifaceted. Modeling this complexity to provide robust measures of player activity and load has proved difficult, with important aspects of player movement yet to be considered. These include the influence of time-varying covariates on player activity and the combination of different dimensions of player movement. Few studies have simultaneously categorized player activity into different activity states and investigated factors influencing the transition between states, or compared player activity and load profiles between matches and training. This study applied hidden Markov models (HMMs)-a data-driven, multivariate approach-to rugby league training and match GPS data to i) demonstrate how HMMs can combine multiple variables in a data-driven way to effectively categorize player movement states, ii) investigate the influence of two time-varying covariates, score difference and elapsed match time on player activity states, and iii) compare player activity and load profiles within and between training and match modalities. HMMs were fitted to player GPS, accelerometer and heart rate data of one English Super League team across 60 training sessions and 35 matches. Distinct activity states were detected for both matches and training, with transitions between states in matches influenced by score difference and elapsed time and clear differences in activity and load profiles between training and matches. HMMs can model the complexity of player movement to effectively profile player activity and load in rugby league and have the potential to facilitate new research across several sports.

Improving the management of diabetic patients is receiving increasing attention in the health policy agenda due to increasing prevalence in the population and raising pressure on healthcare resources. This paper examines the determinants of healthcare services utilisation in patients with type-2 diabetes, investigating the potential substitution effect of general practice visits on the utilisation of emergency department visits. By using rich longitudinal data from Denmark and a bivariate econometric model, our analysis highlights primary care services that are more effective in preventing emergency department visits and socioeconomic groups of patients with a weak substitution response. Our results suggest that empowering primary care services, such as preventive assessment visits, may contribute to reducing emergency department visits significantly. Moreover, special attention should be devoted to vulnerable groups, such as patients from low socioeconomic background and older patients, who may find more difficult achieving a large substitution response., Competing Interests: Declaration of competing interest None., (Copyright © 2024 The Author(s). Published by Elsevier B.V. All rights reserved.)

A pervasive challenge in neuroscience is testing whether neuronal connectivity changes over time due to specific causes, such as stimuli, events, or clinical interventions. Recent hardware innovations and falling data storage costs enable longer, more naturalistic neuronal recordings. The implicit opportunity for understanding the self-organised brain calls for new analysis methods that link temporal scales: from the order of milliseconds over which neuronal dynamics evolve, to the order of minutes, days, or even years over which experimental observations unfold. This review article demonstrates how hierarchical generative models and Bayesian inference help to characterise neuronal activity across different time scales. Crucially, these methods go beyond describing statistical associations among observations and enable inference about underlying mechanisms. We offer an overview of fundamental concepts in state-space modeling and suggest a taxonomy for these methods. Additionally, we introduce key mathematical principles that underscore a separation of temporal scales, such as the slaving principle, and review Bayesian methods that are being used to test hypotheses about the brain with multiscale data. We hope that this review will serve as a useful primer for experimental and computational neuroscientists on the state of the art and current directions of travel in the complex systems modelling literature., Competing Interests: Competing Interests: The authors have declared that no competing interests exist., (© 2023 Massachusetts Institute of Technology.)

Response process data from computer-based problem-solving items describe respondents' problem-solving processes as sequences of actions. Such data provide a valuable source for understanding respondents' problem-solving behaviors. Recently, data-driven feature extraction methods have been developed to compress the information in unstructured process data into relatively low-dimensional features. Although the extracted features can be used as covariates in regression or other models to understand respondents' response behaviors, the results are often not easy to interpret since the relationship between the extracted features, and the original response process is often not explicitly defined. In this paper, we propose a statistical model for describing response processes and how they vary across respondents. The proposed model assumes a response process follows a hidden Markov model given the respondent's latent traits. The structure of hidden Markov models resembles problem-solving processes, with the hidden states interpreted as problem-solving subtasks or stages. Incorporating the latent traits in hidden Markov models enables us to characterize the heterogeneity of response processes across respondents in a parsimonious and interpretable way. We demonstrate the performance of the proposed model through simulation experiments and case studies of PISA process data., (© 2023. The Author(s), under exclusive licence to The Psychometric Society.)

Step-selection models are widely used to study animals' fine-scale habitat selection based on movement data. Resource preferences and movement patterns, however, often depend on the animal's unobserved behavioral states, such as resting or foraging. As this is ignored in standard (integrated) step-selection analyses (SSA, iSSA), different approaches have emerged to account for such states in the analysis. The performance of these approaches and the consequences of ignoring the states in step-selection analysis, however, have rarely been quantified. We evaluate the recent idea of combining iSSAs with hidden Markov models (HMMs), which allows for a joint estimation of the unobserved behavioral states and the associated state-dependent habitat selection. Besides theoretical considerations, we use an extensive simulation study and a case study on fine-scale interactions of simultaneously tracked bank voles ( Myodes glareolus ) to compare this HMM-iSSA empirically to both the standard and a widely used classification-based iSSA (i.e., a two-step approach based on a separate prior state classification). Moreover, to facilitate its use, we implemented the basic HMM-iSSA approach in the R package HMMiSSA available on GitHub., Competing Interests: The authors declare that there are no competing interests., (©2024 Pohle et al.)

There is some evidence for heterogeneity in attentional processes among individuals with social anxiety. However, there is limited work considering how attentional processes may differ as a mechanism in a naturalistic task-based context (e.g., public speaking). In this secondary analysis we tested attentional heterogeneity among individuals diagnosed with social anxiety disorder (N = 21) in the context of a virtual reality exposure treatment study. Participants completed a public speaking challenge in an immersive 360°-video virtual reality environment with eye tracking at pre-treatment, post-treatment, and at 1-week follow-up. Using a Hidden Markov Model (HMM) approach with clustering we tested whether there were distinct profiles of attention pre-treatment and whether there were changes following the intervention. As a secondary aim we tested whether the distinct attentional profiles at pre-treatment predicted differential treatment outcomes. We found two distinct attentional profiles pre-treatment that we characterized as audience-focused and audience-avoidant. However, by the 1-week follow-up the two profiles were no longer meaningfully different. We found a meaningful difference between HMM groups for fear of public speaking at post-treatment b = -8.54, 95% Highest Density Interval (HDI) [-16.00, -0.90], Bayes Factor (BF) = 8.31 but not at one-week follow-up b = -5.83, 95% HDI [-13.25, 1.81], BF = 2.28. These findings provide support for heterogeneity in attentional processes among socially anxious individuals, but our findings indicate that this may change following treatment. Moreover, our results offer preliminary mechanistic evidence that patterns of avoidance may be specifically related to poorer treatment outcomes for virtual reality exposure therapy., Competing Interests: Declaration of competing interest The authors have no conflicts of interest to report., (Copyright © 2023 Elsevier Ltd. All rights reserved.)

Advances in technology have enabled the use of sensors with varied modalities to monitor different parts of systems, each providing diverse levels of information about the underlying system. However, resource limitations and computational power restrict the number of sensors/data that can be processed in real-time in most complex systems. These challenges necessitate the need for selecting/scheduling a subset of sensors to obtain measurements that guarantee the best monitoring objectives. This paper focuses on sensor scheduling for systems modeled by hidden Markov models. Despite the development of several sensor selection and scheduling methods, existing methods tend to be greedy and do not take into account the long-term impact of selected sensors on monitoring objectives. This paper formulates optimal sensor scheduling as a reinforcement learning problem defined over the posterior distribution of system states. Further, the paper derives a deep reinforcement learning policy for offline learning of the sensor scheduling policy, which can then be executed in real-time as new information unfolds. The proposed method applies to any monitoring objective that can be expressed in terms of the posterior distribution of the states (e.g., state estimation, information gain, etc.). The performance of the proposed method in terms of accuracy and robustness is investigated for monitoring the security of networked systems and the health monitoring of gene regulatory networks., Competing Interests: Disclosure Statement The authors declare no conflict of interest.

The multilevel hidden Markov model (MHMM) is a promising method to investigate intense longitudinal data obtained within the social and behavioral sciences. The MHMM quantifies information on the latent dynamics of behavior over time. In addition, heterogeneity between individuals is accommodated with the inclusion of individual-specific random effects, facilitating the study of individual differences in dynamics. However, the performance of the MHMM has not been sufficiently explored. We performed an extensive simulation to assess the effect of the number of dependent variables (1-8), number of individuals (5-90), and number of observations per individual (100-1600) on the estimation performance of a Bayesian MHMM with categorical data including various levels of state distinctiveness and separation. We found that using multivariate data generally alleviates the sample size needed and improves the stability of the results. Moreover, including variables only consisting of random noise was generally not detrimental to model performance. Regarding the estimation of group-level parameters, the number of individuals and observations largely compensate for each other. However, only the former drives the estimation of between-individual variability. We conclude with guidelines on the sample size necessary based on the level of state distinctiveness and separation and study objectives of the researcher.

Data collected from wearable devices can shed light on an individual's pattern of behavioral and circadian routine. Phone use can be modeled as alternating processes, between the state of active use and the state of being idle. Markov chains and alternating recurrent event models are commonly used to model state transitions in cases such as these, and the incorporation of random effects can be used to introduce diurnal effects. While state labels can be derived prior to modeling dynamics, this approach omits informative regression covariates that can influence state memberships. We instead propose an alternating recurrent event proportional hazards (PH) regression to model the transitions between latent states. We propose an expectation-maximization algorithm for imputing latent state labels and estimating parameters. We show that our E-step simplifies to the hidden Markov model (HMM) forward-backward algorithm, allowing us to recover an HMM with logistic regression transition probabilities. In addition, we show that PH modeling of discrete-time transitions implicitly penalizes the logistic regression likelihood and results in shrinkage estimators for the relative risk. This new estimator favors an extended stay in a state and is useful for modeling diurnal rhythms. We derive asymptotic distributions for our parameter estimates and compare our approach against competing methods through simulation as well as in a digital phenotyping study that followed smartphone use in a cohort of adolescents with mood disorders., (© 2023 The International Biometric Society.)

Presence sensing systems are gaining importance and are utilized in various contexts such as smart homes, Ambient Assisted Living (AAL) and surveillance technology. Typically, these systems utilize motion sensors or cameras that have a limited field of view, leading to potential monitoring gaps within a room. However, humans release carbon dioxide (CO 2 ) through respiration which spreads within an enclosed space. Consequently, an observable rise in CO 2 concentration is noted when one or more individuals are present in a room. This study examines an approach to detect the presence or absence of individuals indoors by analyzing the ambient air's CO 2 concentration using simple Markov Chain Models. The proposed scheme achieved an accuracy of up to 97% in both experimental and real data demonstrating its efficacy in practical scenarios., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision., (Copyright © 2023 Karasoulas, Keroglou, Katsiri and Sirakoulis.)

An essential factor toward ensuring the security of individuals and critical infrastructures is the timely detection of potentially threatening situations. To this end, especially in the law enforcement context, the availability of effective and efficient threat assessment mechanisms for identifying and eventually preventing crime- and terrorism-related threatening situations is of utmost importance. Toward this direction, this work proposes a hidden Markov model-based threat assessment framework for effectively and efficiently assessing threats in specific situations, such as public events. Specifically, a probabilistic approach is adopted to estimate the threat level of a situation at each point in time. The proposed approach also permits the reflection of the dynamic evolution of a threat over time by considering that the estimation of the threat level at a given time is affected by past observations. This estimation of the dynamic evolution of the threat is very useful, since it can support the decisions by security personnel regarding the taking of precautionary measures in case the threat level seems to adopt an upward trajectory, even before it reaches the highest level. In addition, its probabilistic basis allows for taking into account noisy data. The applicability of the proposed framework is showcased in a use case that focuses on the identification of potential threats in public events on the basis of evidence obtained from the automatic visual analysis of the footage of surveillance cameras., (© 2023 Society for Risk Analysis.)

Conservation of migratory species exhibiting wide-ranging and multidimensional behaviors is challenged by management efforts that only utilize horizontal movements or produce static spatial-temporal products. For the deep-diving, critically endangered eastern Pacific leatherback turtle, tools that predict where turtles have high risks of fisheries interactions are urgently needed to prevent further population decline. We incorporated horizontal-vertical movement model results with spatial-temporal kernel density estimates and threat data (gear-specific fishing) to develop monthly maps of spatial risk. Specifically, we applied multistate hidden Markov models to a biotelemetry data set (n = 28 leatherback tracks, 2004-2007). Tracks with dive information were used to characterize turtle behavior as belonging to 1 of 3 states (transiting, residential with mixed diving, and residential with deep diving). Recent fishing effort data from Global Fishing Watch were integrated with predicted behaviors and monthly space-use estimates to create maps of relative risk of turtle-fisheries interactions. Drifting (pelagic) longline fishing gear had the highest average monthly fishing effort in the study region, and risk indices showed this gear to also have the greatest potential for high-risk interactions with turtles in a residential, deep-diving behavioral state. Monthly relative risk surfaces for all gears and behaviors were added to South Pacific TurtleWatch (SPTW) (https://www.upwell.org/sptw), a dynamic management tool for this leatherback population. These modifications will refine SPTW's capability to provide important predictions of potential high-risk bycatch areas for turtles undertaking specific behaviors. Our results demonstrate how multidimensional movement data, spatial-temporal density estimates, and threat data can be used to create a unique conservation tool. These methods serve as a framework for incorporating behavior into similar tools for other aquatic, aerial, and terrestrial taxa with multidimensional movement behaviors., (© 2023 The Authors. Conservation Biology published by Wiley Periodicals LLC on behalf of Society for Conservation Biology.)

Background and Objectives: Computerized Cardiotocography (cCTG) allows to analyze the Fetal Heart Rate (FHR) objectively and thoroughly, providing valuable insights on fetal condition. A challenging but crucial task in this context is the automatic identification of fetal activity and quiet periods within the tracings. Different neural mechanisms are involved in the regulation of the fetal heart, depending on the behavioral states. Thereby, their correct identification has the potential to increase the interpretability and diagnostic capabilities of FHR quantitative analysis. Moreover, the most common pathologies in pregnancy have been associated with variations in the alternation between quiet and activity states., Methods: We address the problem of fetal states clustering by means of an unsupervised approach, resorting to the use of a multivariate Hidden Markov Models (HMM) with discrete emissions. A fixed length sliding window is shifted on the CTG traces and a small set of features is extracted at each slide. After an encoding procedure, these features become the emissions of a multivariate HMM in which quiet and activity are the hidden states. After an unsupervised training procedure, the model is used to automatically segment signals., Results: The achieved results indicate that our developed model exhibits a high degree of reliability in identifying quiet and activity states within FHR signals. A set of 35 CTG signals belonging to different pregnancies were independently annotated by an expert gynecologist and segmented using the proposed HMM. To avoid any bias, the physician was blinded to the results provided by the algorithm. The overall agreement between the HMM's predictions and the clinician's interpretations was 90%., Conclusions: The proposed method reliably identified fetal behavioral states, the alternance of which is an important factor in the fetal development. One key strength of our approach lies in the ease of interpreting the obtained results. By utilizing a small set of parameters that are already used in cCTG and possess clear intrinsic meanings, our method provides a high level of explainability. Another significant advantage of our approach is its fully unsupervised learning process. The states identified by our model using the Baum-Welch algorithm are associated with the "Active" and "Quiet" states only after the clustering process, removing the reliance on expert annotations. By autonomously identifying the clusters based solely on the intrinsic characteristics of the signal, our method achieves a more objective evaluation that overcomes the limitations of subjective interpretations. Indeed, we believe it could be integrated in cCTG systems to obtain a more complete signal analysis., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Author(s). Published by Elsevier B.V. All rights reserved.)

Various computational approaches have been developed to annotate epigenomes on a per-position basis by modeling combinatorial and spatial patterns within epigenomic data. However, such annotations are less suitable for gene-based analyses. We present ChromGene, a method based on a mixture of learned hidden Markov models, to annotate genes based on multiple epigenomic maps across the gene body and flanks. We provide ChromGene assignments for over 100 cell and tissue types. We characterize the mixture components in terms of gene expression, constraint, and other gene annotations. The ChromGene method and annotations will provide a useful resource for gene-based epigenomic analyses., (© 2023. BioMed Central Ltd., part of Springer Nature.)

Behavioural plasticity can allow populations to adjust to environmental change when genetic evolution is too slow to keep pace. However, its constraints are not well understood. Personality is known to shape individual behaviour, but its relationship to behavioural plasticity is unclear. We studied the relationship between boldness and behavioural plasticity in response to wind conditions in wandering albatrosses (Diomedea exulans). We fitted multivariate hidden Markov models to an 11-year GPS dataset collected from 294 birds to examine whether the probability of transitioning between behavioural states (rest, prey search and travel) varied in response to wind, boldness and their interaction. We found that movement decisions varied with boldness, with bolder birds showing preferences for travel, and shyer birds showing preferences for search. For females, these effects depended on wind speed. In strong winds, which are optimal for movement, females increased time spent in travel, while in weaker winds, shyer individuals showed a slight preference for search, while bolder individuals maintained preference for travel. Our findings suggest that individual variation in behavioural plasticity may limit the capacity of bolder females to adjust to variable conditions and highlight the important role of behavioural plasticity in population responses to climate change., (© 2023 The Authors. Journal of Animal Ecology published by John Wiley & Sons Ltd on behalf of British Ecological Society.)

Exposure to air pollution is associated with increased morbidity and mortality. Recent technological advancements permit the collection of time-resolved personal exposure data. Such data are often incomplete with missing observations and exposures below the limit of detection, which limit their use in health effects studies. In this paper, we develop an infinite hidden Markov model for multiple asynchronous multivariate time series with missing data. Our model is designed to include covariates that can inform transitions among hidden states. We implement beam sampling, a combination of slice sampling and dynamic programming, to sample the hidden states, and a Bayesian multiple imputation algorithm to impute missing data. In simulation studies, our model excels in estimating hidden states and state-specific means and imputing observations that are missing at random or below the limit of detection. We validate our imputation approach on data from the Fort Collins Commuter Study. We show that the estimated hidden states improve imputations for data that are missing at random compared to existing approaches. In a case study of the Fort Collins Commuter Study, we describe the inferential gains obtained from our model including improved imputation of missing data and the ability to identify shared patterns in activity and exposure among repeated sampling days for individuals and among distinct individuals., (© 2022 The Authors. Biometrics published by Wiley Periodicals LLC on behalf of International Biometric Society.)

Background: Freshwater ecosystems are some of the most affected by biological invasions due, in part, to the introduction of invasive carp worldwide. Where carp have become established, management programs often seek to limit further range expansion into new areas by reducing their movement through interconnected rivers and waterways. Lock and dams are important locations for non-physical deterrents, such as carbon dioxide (CO 2 ), to reduce unwanted fish passage without disrupting human use. The purpose of this study was to evaluate the behavioral responses of common carp (Cyprinus carpio) to non-physical deterrents within a navigation structure on the Fox River, Wisconsin. Acoustic telemetry combined with hidden Markov models (HMMs) was used to analyze variation in carp responses to treatments. Outcomes may inform CO 2 effectiveness at preventing invasive carp movement through movement pinch-points., Methods: Carbon dioxide (CO 2 ) was recently registered as a pesticide in the United States for use as a deterrent to invasive carp movement. As a part of a multi-component study to test a large-scale CO 2 delivery system within a navigation lock, we characterized the influence of elevated CO 2 and forced water circulation in the lock chamber on carp movements and behavior. Through time-to-event analyses, we described the responses of acoustic-tagged carp to experimental treatments including (1) CO 2 injection in water with forced water circulation, (2) forced water circulation without CO 2 and (3) no forced water circulation or CO 2 . We then used hidden Markov models (HMMs) to define fine-scale carp movement and evaluate the relationships between carp behavioral states and CO 2 concentration, forced water circulation, and temperature., Results: Forced water circulation with and without CO 2 injection were effective at expelling carp from the lock chamber relative to null treatments where no stimulus was applied. A portion of carp exposed to forced water circulation with CO 2 transitioned from an exploratory to an encamped behavioral state with shorter step-lengths and a unimodal distribution in turning angles, resulting in some carp remaining in the lock chamber. Whereas carp exposed to forced water circulation only remained primarily in an exploratory behavioral state, resulting in all carp exiting the lock chamber., Conclusion: Our findings illustrate the potential of forced water circulation, alone, as a non-physical deterrent and the efficacy of CO 2 injection with forced water circulation in expelling carp from a navigation lock. Results demonstrate how acoustic telemetry and HMMs in an experimental context can describe fish behavior and inform management strategies., (© 2023. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.)

Human cytomegalovirus (CMV) has infected humans since the origin of our species and currently infects most of the world's population. Variability between CMV genomes is the highest of any human herpesvirus, yet large portions of the genome are conserved. Here, we show that the genome encodes 74 regions of relatively high variability each with 2 to 8 alleles. We then identified two patterns in the CMV genome. Conserved parts of the genome and a minority (32) of variable regions show geographic population structure with evidence for African or European clustering, although hybrid strains are present. We find no evidence that geographic segregation has been driven by host immune pressure affecting known antigenic sites. Forty-two variable regions show no geographical structure, with similar allele distributions across different continental populations. These "nongeographical" regions are significantly enriched for genes encoding immunomodulatory functions suggesting a core functional importance. We hypothesize that at least two CMV founder populations account for the geographical differences that are largely seen in the conserved portions of the genome, although the timing of separation and direction of spread between the two are not clear. In contrast, the similar allele frequencies among 42 variable regions of the genome, irrespective of geographical origin, are indicative of a second evolutionary process, namely balancing selection that may preserve properties critical to CMV biological function. Given that genetic differences between CMVs are postulated to alter immunogenicity and potentially function, understanding these two evolutionary processes could contribute important information for the development of globally effective vaccines and the identification of novel drug targets.

Background: There is strong incentive to model behaviour-dependent habitat selection, as this can help delineate critical habitats for important life processes and reduce bias in model parameters. For this purpose, a two-stage modelling approach is often taken: (i) classify behaviours with a hidden Markov model (HMM), and (ii) fit a step selection function (SSF) to each subset of data. However, this approach does not properly account for the uncertainty in behavioural classification, nor does it allow states to depend on habitat selection. An alternative approach is to estimate both state switching and habitat selection in a single, integrated model called an HMM-SSF., Methods: We build on this recent methodological work to make the HMM-SSF approach more efficient and general. We focus on writing the model as an HMM where the observation process is defined by an SSF, such that well-known inferential methods for HMMs can be used directly for parameter estimation and state classification. We extend the model to include covariates on the HMM transition probabilities, allowing for inferences into the temporal and individual-specific drivers of state switching. We demonstrate the method through an illustrative example of plains zebra (Equus quagga), including state estimation, and simulations to estimate a utilisation distribution., Results: In the zebra analysis, we identified two behavioural states, with clearly distinct patterns of movement and habitat selection ("encamped" and "exploratory"). In particular, although the zebra tended to prefer areas higher in grassland across both behavioural states, this selection was much stronger in the fast, directed exploratory state. We also found a clear diel cycle in behaviour, which indicated that zebras were more likely to be exploring in the morning and encamped in the evening., Conclusions: This method can be used to analyse behaviour-specific habitat selection in a wide range of species and systems. A large suite of statistical extensions and tools developed for HMMs and SSFs can be applied directly to this integrated model, making it a very versatile framework to jointly learn about animal behaviour, habitat selection, and space use., (© 2023. The Author(s).)

Background: Chicks of precocial birds hatch well-developed and can search actively for food but their homeothermy develops gradually during growth. This makes them dependent on heat provided by parents ("brooding"), which is then traded off against other activities, mainly foraging. Although brooding has been documented in many precocial birds, little is known about the differences in the amount and efficiency of brooding care, brooding diel rhythmicity, and impact on the chick's growth, particularly between species living in different climatic conditions., Results: We used multisensory dataloggers to evaluate brooding patterns in two congeneric species inhabiting contrasting climate zones: temperate Northern lapwing (Vanellus vanellus) and desert Red-wattled lapwing (Vanellus indicus). In accordance with our expectation, the adult desert lapwings brooded the chicks slightly less compared to the adult temperate lapwings. However, the desert lapwings brooded their chicks in higher ambient temperatures and less efficiently (i.e. they could not reach the same brooding temperature as the temperate lapwings), which are new and hitherto unknown brooding patterns in precocial birds. In both species, night brooding prevailed even during warm nights, suggesting a general brooding rule among birds. Although the high rates of brooding can reduce the time spent by foraging, we found no negative effect of the high brooding rate on the growth rate in either species., Conclusions: Our data suggest that the chicks of species breeding in colder climates may reduce their thermal demands, while their parents may increase the efficiency of parental brooding care. More research is however needed to confirm this as a rule across species., (© 2023. The Author(s).)

G-quadruplexes (G4s) are short secondary DNA structures located throughout genomic DNA and transcribed RNA. Although G4 structures have been shown to form in vivo, no current search tools that examine these structures based on previously identified G-quadruplexes and filter them based on similar sequence, structure, and thermodynamic properties are known to exist. We present a framework for clustering G-quadruplex sequences into families using the CD-HIT, MeShClust, and DNACLUST methods along with a combination of Starcode and BLAST. Utilizing this framework to filter and annotate clusters, 95 families of G-quadruplex sequences were identified within the human genome. Profiles for each family were created using hidden Markov models to allow for the identification of additional family members and generate homology probability scores. The thermodynamic folding energy properties, functional annotation of genes associated with the sequences, scores from different prediction algorithms, and transcription factor binding motifs within a family were used to annotate and compare the diversity within and across clusters. The resulting set of G-quadruplex families can be used to further understand how different regions of the genome are regulated by factors targeting specific structures common to members of a specific cluster.

A major issue in the clinical management of epilepsy is the unpredictability of seizures. Yet, traditional approaches to seizure forecasting and risk assessment in epilepsy rely heavily on raw seizure frequencies, which are a stochastic measurement of seizure risk. We consider a Bayesian non-homogeneous hidden Markov model for unsupervised clustering of zero-inflated seizure count data. The proposed model allows for a probabilistic estimate of the sequence of seizure risk states at the individual level. It also offers significant improvement over prior approaches by incorporating a variable selection prior for the identification of clinical covariates that drive seizure risk changes and accommodating highly granular data. For inference, we implement an efficient sampler that employs stochastic search and data augmentation techniques. We evaluate model performance on simulated seizure count data. We then demonstrate the clinical utility of the proposed model by analyzing daily seizure count data from 133 patients with Dravet syndrome collected through the Seizure Tracker ™ system, a patient-reported electronic seizure diary. We report on the dynamics of seizure risk cycling, including validation of several known pharmacologic relationships. We also uncover novel findings characterizing the presence and volatility of risk states in Dravet syndrome, which may directly inform counseling to reduce the unpredictability of seizures for patients with this devastating cause of epilepsy.

Growing evidence supports a role for rest-activity rhythms (RARs) in metabolic health. Epidemiological studies in adolescents and young adults showed that RAR characteristics consistent with weakened rhythmicity were associated with obesity. However, studies in older adults are lacking. The objective of this study was to examine the cross-sectional and prospective associations between RAR and obesity in older men using the Harmonic Hidden Markov Model (HHMM), a novel analytical approach with several advantages over conventional methods for characterizing RAR. The analysis included nearly 3,000 participants in the Osteoporotic Fractures in Men study with 5-day 24-h actigraphy data. The strength of RAR was measured by rhythmic index (RI), a scaled value between 0 and 1 with higher values indicating better RAR. Multiple linear and logistic regression adjusting for multiple confounders were performed to examine the RI in relation to body mass index (BMI) and obesity status at baseline and after ~3.5 years of follow-up. We showed that the HHMM can derive both meaningful visual profile and quantifier of RAR. A lower RI was associated with higher BMI and obesity at baseline, and an elevated likelihood for developing obesity over follow-up. Specifically, when compared with men in the highest quartile of RI, those in the lowest quartile on average had a higher BMI (β [95% confidence interval (CI)], 1.76 [1.39, 2.13]) and were more likely to be obese at baseline (odds ratio (OR) [95% CI], 2.63 [2.03, 3.43]). Moreover, among nonobese men at baseline, those in the lowest quartile of RI were 2.06 times (OR [95% CI], 2.06 [1.02, 4.27]) more likely to develop obesity over follow-up when compared with those in the highest quartile. In conclusion, our study demonstrated the utility of HHMM in characterizing RAR and showed that rhythmicity strength was associated with BMI and risk of obesity in older men.

Human activity recognition (HAR) has become an interesting topic in healthcare. This application is important in various domains, such as health monitoring, supporting elders, and disease diagnosis. Considering the increasing improvements in smart devices, large amounts of data are generated in our daily lives. In this work, we propose unsupervised, scaled, Dirichlet-based hidden Markov models to analyze human activities. Our motivation is that human activities have sequential patterns and hidden Markov models (HMMs) are some of the strongest statistical models used for modeling data with continuous flow. In this paper, we assume that emission probabilities in HMM follow a bounded-scaled Dirichlet distribution, which is a proper choice in modeling proportional data. To learn our model, we applied the variational inference approach. We used a publicly available dataset to evaluate the performance of our proposed model.

β-Lactams are a broad class of antimicrobial agents with a high safety profile, making them the most widely used class in clinical, agricultural, and veterinary setups. The widespread use of β-lactams has induced the extensive spread of β-lactamase hydrolyzing enzymes known as β-lactamases (BLs). To neutralize the effect of β-lactamases, newer generations of β-lactams have been developed, which ultimately led to the evolution of a highly diverse family of BLs. Based on sequence homology, BLs are categorized into four classes: A-D in Ambler's classification system. Further, each class is subdivided into families. Class B is first divided into subclasses B1-B3, and then each subclass is divided into families. The class to which a BL belongs gives a lot of insight into its hydrolytic profile. Traditional methods of determining the hydrolytic profile of BLs and their classification are time-consuming and require resources. Hence we developed a machine-learning-based in silico method, named as β-LacFamPred, for the prediction and annotation of Ambler's class, subclass, and 96 families of BLs. During leave-one-out cross-validation, except one all β-LacFamPred model HMMs showed 100% accuracy. Benchmarking with other BL family prediction methods showed β-LacFamPred to be the most accurate. Out of 60 penicillin-binding proteins (PBPs) and 57 glyoxalase II proteins, β-LacFamPred correctly predicted 56 PBPs and none of the glyoxalase II sequences as non-BLs. Proteome-wide annotation of BLs by β-LacFamPred showed a very less number of false-positive predictions in comparison to the recently developed BL class prediction tool DeepBL. β-LacFamPred is available both as a web-server and standalone tool at http://proteininformatics.org/mkumar/blacfampred and GitHub repository https://github.com/mkubiophysics/B-LacFamPred respectively., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Pandey, Singhal and Kumar.)

The majority of current credit-scoring models, used for loan approval processing, are generally built on the basis of the information from the accepted credit applicants whose ability to repay the loan is known. This situation generates what is called the selection bias, presented by a sample that is not representative of the population of applicants, since rejected applications are excluded. Thus, the impact on the eligibility of those models from a statistical and economic point of view. Especially for the models used in the peer-to-peer lending platforms, since their rejection rate is extremely high. The method of inferring rejected applicants information in the process of construction of the credit scoring models is known as reject inference. This study proposes a semi-supervised learning framework based on hidden Markov models (SSHMM), as a novel method of reject inference. Real data from the Lending Club platform, the most used online lending marketplace in the United States as well as the rest of the world, is used to experiment the effectiveness of our method over existing approaches. The results of this study clearly illustrate the proposed method's superiority, stability, and adaptability., (© The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2022.)

We address two computational issues common to open-population N -mixture models, hidden integer-valued autoregressive models, and some hidden Markov models. The first issue is computation time, which can be dramatically improved through the use of a fast Fourier transform. The second issue is tractability of the model likelihood function for large numbers of hidden states, which can be solved by improving numerical stability of calculations. As an illustrative example, we detail the application of these methods to the open-population N -mixture models. We compare computational efficiency and precision between these methods and standard methods employed by state-of-the-art ecological software. We show faster computing times (a ∼ 6 to ∼ 30 times speed improvement for population size upper bounds of 500 and 1000, respectively) over state-of-the-art ecological software for N -mixture models. We also apply our methods to compute the size of a large elk population using an N -mixture model and show that while our methods converge, previous software cannot produce estimates due to numerical issues. These solutions can be applied to many ecological models to improve precision when logs of sums exist in the likelihood function and to improve computational efficiency when convolutions are present in the likelihood function. Supplementary materials accompanying this paper appear online. Supplementary materials for this article are available at 10.1007/s13253-022-00509-y., Competing Interests: Author ContributionsAll authors contributed to the methodology, and all authors contributed to writing the manuscript. The authors have no conflict of interest to report., (© International Biometric Society 2022, Springer Nature or its licensor holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.)

Wearable sensor data is relatively easily collected and provides direct measurements of movement that can be used to develop useful behavioral biomarkers. Sensitive and specific behavioral biomarkers for neurodegenerative diseases are critical to supporting early detection, drug development efforts, and targeted treatments. In this paper, we use autoregressive hidden Markov models and a time-frequency approach to create meaningful quantitative descriptions of behavioral characteristics of cerebellar ataxias from wearable inertial sensor data gathered during movement. We create a flexible and descriptive set of features derived from accelerometer and gyroscope data collected from wearable sensors worn while participants perform clinical assessment tasks, and use these data to estimate disease status and severity. A short period of data collection (<5 min) yields enough information to effectively separate patients with ataxia from healthy controls with very high accuracy, to separate ataxia from other neurodegenerative diseases such as Parkinson’s disease, and to provide estimates of disease severity.

Non-invasive techniques to electrically stimulate the brain such as transcranial direct and alternating current stimulation (tDCS/tACS) are increasingly used in human neuroscience and offer potential new avenues to treat brain disorders. Previous research has shown that stimulation effects may depend on brain-states. However, this work mostly focused on experimentally induced brain-states over the course of several minutes. Besides such global, long-term changes in brain-states, previous research suggests, that the brain is likely to spontaneously alternate between states in sub-second ranges, which is much closer to the time scale at which it is generally believed to operate. Here, we utilized Hidden Markov Models (HMM) to decompose magnetoencephalography data obtained before and after tACS into spontaneous, transient brain-states with distinct spatial, spectral and connectivity profiles. Only one out of four spontaneous brain-states, likely reflecting default mode network activity, showed evidence for an effect of tACS on the power of spontaneous α-oscillations. The identified state appears to disproportionally drive the overall (non-state resolved) tACS effect. No or only marginal effects were found in the remaining states. We found no evidence that tACS influenced the time spent in each state. Although stimulation was applied continuously, our results indicate that spontaneous brain-states and their underlying functional networks differ in their susceptibility to tACS. Global stimulation aftereffects may be disproportionally driven by distinct time periods during which the susceptible state is active. Our results may pave the ground for future work to understand which features make a specific brain-state susceptible to electrical stimulation., Competing Interests: Declaration of Competing Interest CSH holds a patent on brain stimulation. FHK, declares no competing interests., (Copyright © 2022. Published by Elsevier Inc.)

Background: The evolution of multimorbidity patterns during aging is still an under-researched area. We lack evidence concerning the time spent by older adults within one same multimorbidity pattern, and their transitional probability across different patterns when further chronic diseases arise. The aim of this study is to fill this gap by exploring multimorbidity patterns across decades of age in older adults, and longitudinal dynamics among these patterns., Methods: Longitudinal study based on the Swedish National study on Aging and Care in Kungsholmen (SNAC-K) on adults ≥60 years (N=3,363). Hidden Markov Models were applied to model the temporal evolution of both multimorbidity patterns and individuals' transitions over a 12-year follow-up., Findings: Within the study population (mean age 76.1 years, 66.6% female), 87.2% had ≥2 chronic conditions at baseline. Four longitudinal multimorbidity patterns were identified for each decade. Individuals in all decades showed the shortest permanence time in an Unspecific pattern lacking any overrepresented diseases (range: 4.6-10.9 years), but the pattern with the longest permanence time varied by age. Sexagenarians remained longest in the Psychiatric-endocrine and sensorial pattern (15.4 years); septuagenarians in the Neuro-vascular and skin-sensorial pattern (11.0 years); and octogenarians and beyond in the Neuro-sensorial pattern (8.9 years). Transition probabilities varied across decades, sexagenarians showing the highest levels of stability., Interpretation: Our findings highlight the dynamism and heterogeneity underlying multimorbidity by quantifying the varying permanence times and transition probabilities across patterns in different decades. With increasing age, older adults experience decreasing stability and progressively shorter permanence time within one same multimorbidity pattern.

Automated domain annotation is an important tool for structural informatics. These pipelines typically involve searching query sequences against hidden Markov model (HMM) profiles, yielding matches to profiles for various domains. However, domain annotation can be ambiguous or inaccurate when proteins contain domains with non-contiguous residue ranges, and especially when insertional domains are hosted within them. Here, we present DomainMapper, an algorithm that accurately assigns a unique domain structure annotation to a query sequence, including those with complex topologies. We validate our domain assignments using the AlphaFold database and confirm that non-contiguity is pervasive (10.74% of all domains in yeast and 4.52% in human). Using this resource, we find that certain folds have strong propensities to be non-contiguous or insertional across the Tree of Life. DomainMapper is freely available and can be ran as a single command-line function., (© 2022 The Protein Society.)

Mentalizing impairment is one of the core features of schizophrenia, and bias judgement of others' gaze as self-directing is common to schizophrenia patients. In this case-control study, 30 patients with first-episode schizophrenia (FES) and 30 matched healthy controls were assigned gaze perception tasks with variable stimulus presentation times (300 ms and no time limit) to determine the presence of self-referential gaze perception (SRGP) bias. The eye movement pattern during the task were tracked and data were analysed using hidden Markov models (HMMs). The SRGP involves reporting of others' gaze intent and was used as a measurement of explicit mentalizing process. Eye movement measurement represents automated visual attention pattern and was considered as a measurement of implicit mentalizing process. The patients with FES had significantly more SRGP bias than the controls in the 300 ms condition but not in the no-time-limit condition. Social cognitive function was related to SRGP bias in the patient group. Two distinct eye movement patterns were identified: eye-focused and nose-focused. Significant group differences in eye movement patterns in the 300 ms condition were found with more controls had eye-focused pattern. Social anxiety symptoms were related to the nose-focused pattern, positive psychotic symptoms were related to the eye-focused pattern, and depressive symptoms were related to less consistent eye movement patterns. No significant relationship was found between SRGP bias and eye movement patterns. The dissociation between explicit and implicit mentalizing processes with different cognitive and symptom dimensions associated with the two processes suggests the presence of different mechanisms., (© 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany.)

Animal behavioural responses to the environment ultimately affect their survival. Monitoring animal fine-scale behaviour may improve understanding of animal functional response to the environment and provide an important indicator of the welfare of both wild and domesticated species. In this study, we illustrate the application of collar-attached acceleration sensors for investigating reindeer fine-scale behaviour. Using data from 19 reindeer, we tested the supervised machine learning algorithms Random forests, Support vector machines, and hidden Markov models to classify reindeer behaviour into seven classes: grazing, browsing low from shrubs or browsing high from trees, inactivity, walking, trotting, and other behaviours. We implemented leave-one-subject-out cross-validation to assess generalizable results on new individuals. Our main results illustrated that hidden Markov models were able to classify collar-attached accelerometer data into all our pre-defined behaviours of reindeer with reasonable accuracy while Random forests and Support vector machines were biased towards dominant classes. Random forests using 5-s windows had the highest overall accuracy (85%), while hidden Markov models were able to best predict individual behaviours and handle rare behaviours such as trotting and browsing high. We conclude that hidden Markov models provide a useful tool to remotely monitor reindeer and potentially other large herbivore species behaviour. These methods will allow us to quantify fine-scale behavioural processes in relation to environmental events., (© 2022. The Author(s).)

Motivated by the analysis of behavioral data taken from an economic experiment based on the Hawk-and-Dove game, this article describes a multilevel hidden Markov model, that includes covariates, autoregression, and endogenous initial conditions under a unified framework. The data at hand are affected by multiple sources of latent heterogeneity, due to multilevel unobserved factors that operate in conjunction with observed covariates at all the levels of the data hierarchy. We fit a multilevel logistic regression model for repeated measurements of player behaviors, nested within groups of interacting players. The model integrates discrete random effects at the group level and Markovian sequences of discrete random effects at the player level. Parameters are estimated by a computationally feasible expectation-maximization algorithm. We model the probability of playing the Hawk strategy, which implies fighting aggressively for controlling an asset, and test the role played by initial possession, property, and other player-specific characteristics in driving hawkish behaviors. The results from our study suggest that crucial factors in determining hawkish behavior are both the way possession is achieved - which depends on our treatment manipulation- and possession itself. Furthermore, a clear time-dependence is observed in the data at the player level as accounted for by the Markovian random effects.

Background: The decreasing cost of DNA sequencing has led to a great increase in our knowledge about genetic variation. While population-scale projects bring important insight into genotype-phenotype relationships, the cost of performing whole-genome sequencing on large samples is still prohibitive. In-silico genotype imputation coupled with genotyping-by-arrays is a cost-effective and accurate alternative for genotyping of common and uncommon variants. Imputation methods compare the genotypes of the typed variants with the large population-specific reference panels and estimate the genotypes of untyped variants by making use of the linkage disequilibrium patterns. Most accurate imputation methods are based on the Li-Stephens hidden Markov model, HMM, that treats the sequence of each chromosome as a mosaic of the haplotypes from the reference panel., Results: Here we assess the accuracy of vicinity-based HMMs, where each untyped variant is imputed using the typed variants in a small window around itself (as small as 1 centimorgan). Locality-based imputation is used recently by machine learning-based genotype imputation approaches. We assess how the parameters of the vicinity-based HMMs impact the imputation accuracy in a comprehensive set of benchmarks and show that vicinity-based HMMs can accurately impute common and uncommon variants., Conclusions: Our results indicate that locality-based imputation models can be effectively used for genotype imputation. The parameter settings that we identified can be used in future methods and vicinity-based HMMs can be used for re-structuring and parallelizing new imputation methods. The source code for the vicinity-based HMM implementations is publicly available at https://github.com/harmancilab/LoHaMMer ., (© 2022. The Author(s).)

There are different ways contaminants can interact and enhance the effects of habitat fragmentation, such as modifying the movement of organisms. The present study tested the hypothesis that mercury exacerbates the effects of fragmentation by affecting the movement of the marsh periwinkle Littoraria irrorata and reducing the probability of snails crossing fragmented microlandscape experimental systems. How these changes could affect the search efficiency of organisms in the long term was assessed using hidden Markov models and random walks simulations. Bayesian nonlinear models were used to analyze the effects of fragmentation and contamination on the mean speed and mean directional change of organisms. Snail movement for control and two mercury-exposure treatments were recorded in microlandscapes with six different levels of habitat cover and three landscape replicates. The results indicated that exposed organisms had lower probabilities of crossing the landscape, reduced speed, and shifts in step length distributions. Both mercury exposure and habitat fragmentation affected the movement of the marsh periwinkle. Mercury exacerbated the effects of habitat fragmentation by affecting the cognition (e.g., route planning, orientation, and spatial learning) and movement of L. irrorata. Hence, the interaction of these stressors could further reduce the functional connectivity of landscapes and reduce the search efficiency of organisms. Environ Toxicol Chem 2022;41:1742-1753. © 2022 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC., (© 2022 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.)

Receptor-binding proteins (RBPs) of bacteriophages initiate the infection of their corresponding bacterial host and act as the primary determinant for host specificity. The ever-increasing amount of sequence data enables the development of predictive models for the automated identification of RBP sequences. However, the development of such models is challenged by the inconsistent or missing annotation of many phage proteins. Recently developed tools have started to bridge this gap but are not specifically focused on RBP sequences, for which many different annotations are available. We have developed two parallel approaches to alleviate the complex identification of RBP sequences in phage genomic data. The first combines known RBP-related hidden Markov models (HMMs) from the Pfam database with custom-built HMMs to identify phage RBPs based on protein domains. The second approach consists of training an extreme gradient boosting classifier that can accurately discriminate between RBPs and other phage proteins. We explained how these complementary approaches can reinforce each other in identifying RBP sequences. In addition, we benchmarked our methods against the recently developed PhANNs tool. Our best performing model reached a precision-recall area-under-the-curve of 93.8% and outperformed PhANNs on an independent test set, reaching an F1-score of 84.0% compared to 69.8%.

We propose a model based on discrete latent variables, which are spatially associated and time specific, for the analysis of incident cases of SARS-CoV-2 infections. We assume that for each area the sequence of latent variables across time follows a Markov chain with initial and transition probabilities that also depend on latent variables in neighboring areas. The model is estimated by a Markov chain Monte Carlo algorithm based on a data augmentation scheme, in which the latent states are drawn together with the model parameters for each area and time. As an illustration we analyze incident cases of SARS-CoV-2 collected in Italy at regional level for the period from February 24, 2020, to January 17, 2021, corresponding to 48 weeks, where we use number of swabs as an offset. Our model identifies a common trend and, for every week, assigns each region to one among five distinct risk groups., (© 2021 Elsevier B.V. All rights reserved.)

Motivated by the growing availability of personal genomics services, we study an information-theoretic privacy problem that arises when sharing genomic data: a user wants to share his or her genome sequence while keeping the genotypes at certain positions hidden, which could otherwise reveal critical health-related information. A straightforward solution of erasing (masking) the chosen genotypes does not ensure privacy, because the correlation between nearby positions can leak the masked genotypes. We introduce an erasure-based privacy mechanism with perfect information-theoretic privacy, whereby the released sequence is statistically independent of the sensitive genotypes. Our mechanism can be interpreted as a locally-optimal greedy algorithm for a given processing order of sequence positions, where utility is measured by the number of positions released without erasure. We show that finding an optimal order is NP-hard in general and provide an upper bound on the optimal utility. For sequences from hidden Markov models, a standard modeling approach in genetics, we propose an efficient algorithmic implementation of our mechanism with complexity polynomial in sequence length. Moreover, we illustrate the robustness of the mechanism by bounding the privacy leakage from erroneous prior distributions. Our work is a step towards more rigorous control of privacy in genomic data sharing.

From 2018 to 2021, the Sussex-Huawei Locomotion-Transportation Recognition Challenge presented different scenarios in which participants were tasked with recognizing eight different modes of locomotion and transportation using sensor data from smartphones. In 2019, the main challenge was using sensor data from one location to recognize activities with sensors in another location, while in the following year, the main challenge was using the sensor data of one person to recognize the activities of other persons. We use these two challenge scenarios as a framework in which to analyze the effectiveness of different components of a machine-learning pipeline for activity recognition. We show that: (i) selecting an appropriate (location-specific) portion of the available data for training can improve the F1 score by up to 10 percentage points (p. p.) compared to a more naive approach, (ii) separate models for human locomotion and for transportation in vehicles can yield an increase of roughly 1 p. p., (iii) using semi-supervised learning can, again, yield an increase of roughly 1 p. p., and (iv) temporal smoothing of predictions with Hidden Markov models, when applicable, can bring an improvement of almost 10 p. p. Our experiments also indicate that the usefulness of advanced feature selection techniques and clustering to create person-specific models is inconclusive and should be explored separately in each use-case.