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Hidden markov

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https://www.readbyqxmd.com/read/28815918/a-model-based-approach-to-characterize-individual-inbreeding-at-both-global-and-local-genomic-scales
#1
T Druet, M Gautier
Inbreeding results from the mating of related individuals and may be associated with reduced fitness because it brings together deleterious variants in one individual. In general, inbreeding is estimated with respect to an arbitrary base population consisting of ancestors that are assumed unrelated. We herein propose a model-based approach to estimate and characterize individual inbreeding at both global and local genomic scales by assuming the individual genome is a mosaic of HBD (Homozygous-By-Descent) and non-HBD segments...
August 16, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28814035/decoding-of-individual-finger-movements-from-surface-emg-signals-using-vector-autoregressive-hierarchical-hidden-markov-models-varhhmm
#2
Nebojsa Malesevic, Dimitrije Markovic, Gunter Kanitz, Marco Controzzi, Christian Cipriani, Christian Antfolk
In this paper we present a novel method for predicting individual fingers movements from surface electromyography (EMG). The method is intended for real-time dexterous control of a multifunctional prosthetic hand device. The EMG data was recorded using 16 single-ended channels positioned on the forearm of healthy participants. Synchronously with the EMG recording, the subjects performed consecutive finger movements based on the visual cues. Our algorithm could be described in following steps: extracting mean average value (MAV) of the EMG to be used as the feature for classification, piece-wise linear modeling of EMG feature dynamics, implementation of hierarchical hidden Markov models (HHMM) to capture transitions between linear models, and implementation of Bayesian inference as the classifier...
July 2017: IEEE ... International Conference on Rehabilitation Robotics: [proceedings]
https://www.readbyqxmd.com/read/28813877/capture-learning-and-classification-of-upper-extremity-movement-primitives-in-healthy-controls-and-stroke-patients
#3
Jorge Guerra, Jasim Uddin, Dawn Nilsen, James Mclnerney, Ammarah Fadoo, Isirame B Omofuma, Shatif Hughes, Sunil Agrawal, Peter Allen, Heidi M Schambra
There currently exist no practical tools to identify functional movements in the upper extremities (UEs). This absence has limited the precise therapeutic dosing of patients recovering from stroke. In this proof-of-principle study, we aimed to develop an accurate approach for classifying UE functional movement primitives, which comprise functional movements. Data were generated from inertial measurement units (IMUs) placed on upper body segments of older healthy individuals and chronic stroke patients. Subjects performed activities commonly trained during rehabilitation after stroke...
July 2017: IEEE ... International Conference on Rehabilitation Robotics: [proceedings]
https://www.readbyqxmd.com/read/28808080/characterization-of-the-human-thyroid-epigenome
#4
Celia Siu, Sam Michael Wiseman, Sitanshu Gakkhar, Alireza Heravi-Moussavi, Misha Bilenky, Annaick Carles, Thomas Sierocinski, Angela Tam, Eric Yang Zhao, Katayoon Kasaian, Richard A Moore, Andrew J Mungall, Blair Walker, Thomas Thomson, Marco A Marra, Martin Hirst, Steven Jones
The thyroid gland, necessary for normal human growth and development, functions as an essential regulator of metabolism by the production and secretion of appropriate levels of thyroid hormone. However, assessment of abnormal thyroid function may be challenging suggesting a more fundamental understanding of normal function is needed. One way to characterize normal gland function is to study the epigenome and resulting transcriptome within its constituent cells. This study generates the first published reference epigenomes for human thyroid from four individuals using ChIP-seq and RNA-seq...
August 14, 2017: Journal of Endocrinology
https://www.readbyqxmd.com/read/28807860/hidden-markov-modeling-of-frequency-following-responses-to-mandarin-lexical-tones
#5
Fernando Llanos, Zilong Xie, Bharath Chandrasekaran
BACKGROUND: The frequency-following response (FFR) is a scalp-recorded electrophysiological potential reflecting phase-locked activity from neural ensembles in the auditory system. The FFR is often used to assess the robustness of subcortical pitch processing. Due to low signal-to-noise ratio at the single-trial level, FFRs are typically averaged across thousands of stimulus repetitions. Prior work using this approach has shown that subcortical encoding of linguistically-relevant pitch patterns is modulated by long-term language experience...
August 11, 2017: Journal of Neuroscience Methods
https://www.readbyqxmd.com/read/28782702/preferences-for-life-sustaining-treatments-examined-by-hidden-markov-modeling-are-mostly-stable-in-terminally-ill-cancer-patients-last-6-months-of-life
#6
Siew Tzuh Tang, Fur-Hsing Wen, Wen-Cheng Chang, Chia-Hsun Hsieh, Wen-Chi Chou, Jen-Shi Chen, Ming-Mo Hou
BACKGROUND/OBJECTIVE: Stability of life-sustaining treatment (LST) preferences at end of life (EOL) has not been well established for terminally ill cancer patients nor have transition probabilities been explored between different types of preferences. We assessed the stability of cancer patients' LST preferences at EOL by identifying distinct LST-preference states and examining the probability of each state transitioning to other states between consecutive time points. METHODS: Stability of LST preferences (cardio-pulmonary resuscitation, intensive care unit [ICU] care, cardiac massage, intubation with mechanical ventilation, intravenous nutrition support, and nasogastric tube feeding) was examined among 303 cancer patients in their last 6 months by hidden Markov modeling...
August 3, 2017: Journal of Pain and Symptom Management
https://www.readbyqxmd.com/read/28771616/quantification-of-transplant-derived-circulating-cell-free-dna-in-absence-of-a-donor-genotype
#7
Eilon Sharon, Hao Shi, Sandhya Kharbanda, Winston Koh, Lance R Martin, Kiran K Khush, Hannah Valantine, Jonathan K Pritchard, Iwijn De Vlaminck
Quantification of cell-free DNA (cfDNA) in circulating blood derived from a transplanted organ is a powerful approach to monitoring post-transplant injury. Genome transplant dynamics (GTD) quantifies donor-derived cfDNA (dd-cfDNA) by taking advantage of single-nucleotide polymorphisms (SNPs) distributed across the genome to discriminate donor and recipient DNA molecules. In its current implementation, GTD requires genotyping of both the transplant recipient and donor. However, in practice, donor genotype information is often unavailable...
August 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28764262/relationship-between-automated-coronary-calcium-volumes-and-a-set-of-manual-coronary-lumen-volume-vessel-volume-and-atheroma-volume-in-japanese-diabetic-cohort
#8
Sumit K Banchhor, Narendra D Londhe, Luca Saba, Petia Radeva, John R Laird, Jasjit S Suri
INTRODUCTION: A high degree of correlation exists between Coronary Artery Diseases (CAD) and calcification of the vessel wall. For Percutaneous Coronary Interventional (PCI) planning, it is essential to have an exact understanding of the extent to which calcium volume is correlated to the lumen, vessel, and atheroma volume regions in the coronary artery, which is unclear in recent studies. AIM: Four automated Coronary Calcium Volume (aCCV) measurement methods {threshold, Fuzzy c-Means (FCM), K-means, and Hidden Markov Random Field (HMRF)} and its correlation with three manual (experts) coronary parameters namely: Coronary Vessel Volume (mCVV), Coronary Lumen Volume (mCLV), and Coronary Atheroma Volume (mCAV), was determined in a Japanese diabetic cohort...
June 2017: Journal of Clinical and Diagnostic Research: JCDR
https://www.readbyqxmd.com/read/28762336/performance-of-an-open-source-heart-sound-segmentation-algorithm-on-eight-independent-databases
#9
Chengyu Liu, David Springer, Gari D Clifford
OBJECTIVE: Heart sound segmentation is a prerequisite step for the automatic analysis of heart sound signals, facilitating the subsequent identification and classification of pathological events. Recently, hidden Markov model-based algorithms have received increased interest due to their robustness in processing noisy recordings. In this study we aim to evaluate the performance of the recently published logistic regression based hidden semi-Markov model (HSMM) heart sound segmentation method, by using a wider variety of independently acquired data of varying quality...
August 1, 2017: Physiological Measurement
https://www.readbyqxmd.com/read/28758641/dropconnected-neural-networks-trained-on-time-frequency-and-inter-beat-features-for-classifying-heart-sounds
#10
Edmund Kay, Anurag Agarwal
OBJECTIVE: Automatic heart sound analysis has the potential to improve the diagnosis of valvular heart diseases in the primary care phase, as well as in countries where there is neither the expertise nor the equipment to perform echocardiograms. An algorithm has been trained, on the PhysioNet open-access heart sounds database, to classify heart sounds as normal or abnormal. APPROACH: The heart sounds are segmented using an open-source algorithm based on a hidden semi-Markov model...
July 31, 2017: Physiological Measurement
https://www.readbyqxmd.com/read/28753360/mode-selection-in-compressible-active-flow-networks
#11
Aden Forrow, Francis G Woodhouse, Jörn Dunkel
Coherent, large-scale dynamics in many nonequilibrium physical, biological, or information transport networks are driven by small-scale local energy input. Here, we introduce and explore an analytically tractable nonlinear model for compressible active flow networks. In contrast to thermally driven systems, we find that active friction selects discrete states with a limited number of oscillation modes activated at distinct fixed amplitudes. Using perturbation theory, we systematically predict the stationary states of noisy networks and find good agreement with a Bayesian state estimation based on a hidden Markov model applied to simulated time series data...
July 14, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28751746/extreme-quantum-advantage-when-simulating-classical-systems-with-long-range-interaction
#12
Cina Aghamohammadi, John R Mahoney, James P Crutchfield
Classical stochastic processes can be generated by quantum simulators instead of the more standard classical ones, such as hidden Markov models. One reason for using quantum simulators has recently come to the fore: they generally require less memory than their classical counterparts. Here, we examine this quantum advantage for strongly coupled spin systems-in particular, the Dyson one-dimensional Ising spin chain with variable interaction length. We find that the advantage scales with both interaction range and temperature, growing without bound as interaction range increases...
July 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28744863/classification-of-changes-occurring-in-lung-patient-during-radiotherapy-using-relative-%C3%AE-analysis-and-hidden-markov-models
#13
Nicolas Varfalvy, Ophelie Piron, Marc François Cyr, Anne Dagnault, Louis Archambault
PURPOSE: to present a new automated patient classification method based on relative gamma analysis and hidden Markov models (HMM) to identify patients undergoing important anatomical changes during radiation therapy. METHODS: daily EPID images of every treatment field were acquired for 52 patients treated for lung cancer. In addition, CBCT were acquired on a regular basis. Gamma analysis was performed relative to the first fraction given that no significant anatomical change was observed on the CBCT of the first fraction compared to the planning CT...
July 26, 2017: Medical Physics
https://www.readbyqxmd.com/read/28734092/disentangling-the-role-of-seed-bank-and-dispersal-in-plant-metapopulation-dynamics-using-patch-occupancy-surveys
#14
F Manna, R Pradel, R Choquet, H Fréville, P-O Cheptou
In plants, the presence of a seed bank challenges the application of classical metapopulation models to above-ground presence surveys; ignoring seed bank leads to overestimated extinction and colonization rates. In this article, we explore the possibility to detect seed bank using hidden Markov models in the analysis of above-ground patch occupancy surveys of an annual plant with limited dispersal. Patch occupancy data were generated by simulation under two metapopulation sizes (N = 200 and N = 1000 patches) and different metapopulation scenarios, each scenario being a combination of the presence/absence of a one-year seed bank and the presence/absence of limited dispersal in a circular 1-dimension configuration of patches...
July 22, 2017: Ecology
https://www.readbyqxmd.com/read/28726751/an-adaptive-feature-learning-model-for-sequential-radar-high-resolution-range-profile-recognition
#15
Xuan Peng, Xunzhang Gao, Yifan Zhang, Xiang Li
This paper proposes a new feature learning method for the recognition of radar high resolution range profile (HRRP) sequences. HRRPs from a period of continuous changing aspect angles are jointly modeled and discriminated by a single model named the discriminative infinite restricted Boltzmann machine (Dis-iRBM). Compared with the commonly used hidden Markov model (HMM)-based recognition method for HRRP sequences, which requires efficient preprocessing of the HRRP signal, the proposed method is an end-to-end method of which the input is the raw HRRP sequence, and the output is the label of the target...
July 20, 2017: Sensors
https://www.readbyqxmd.com/read/28720084/sequence-based-identification-of-inositol-monophosphatase-like-histidinol-phosphate-phosphatases-hisn-in-corynebacterium-glutamicum-actinobacteria-and-beyond
#16
Robert Kasimir Kulis-Horn, Christian Rückert, Jörn Kalinowski, Marcus Persicke
BACKGROUND: The eighth step of L-histidine biosynthesis is carried out by an enzyme called histidinol-phosphate phosphatase (HolPase). Three unrelated HolPase families are known so far. Two of them are well studied: HAD-type HolPases known from Gammaproteobacteria like Escherichia coli or Salmonella enterica and PHP-type HolPases known from yeast and Firmicutes like Bacillus subtilis. However, the third family of HolPases, the inositol monophosphatase (IMPase)-like HolPases, present in Actinobacteria like Corynebacterium glutamicum (HisN) and plants, are poorly characterized...
July 18, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28715501/diversity-and-distribution-of-nuclease-bacteriocins-in-bacterial-genomes-revealed-using-hidden-markov-models
#17
Connor Sharp, James Bray, Nicholas G Housden, Martin C J Maiden, Colin Kleanthous
Bacteria exploit an arsenal of antimicrobial peptides and proteins to compete with each other. Three main competition systems have been described: type six secretion systems (T6SS); contact dependent inhibition (CDI); and bacteriocins. Unlike T6SS and CDI systems, bacteriocins do not require contact between bacteria but are diffusible toxins released into the environment. Identified almost a century ago, our understanding of bacteriocin distribution and prevalence in bacterial populations remains poor. In the case of protein bacteriocins, this is because of high levels of sequence diversity and difficulties in distinguishing their killing domains from those of other competition systems...
July 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28709213/when-memory-pays-discord-in-hidden-markov-models
#18
Emma Lathouwers, John Bechhoefer
When is keeping a memory of observations worthwhile? We use hidden Markov models to look at phase transitions that emerge when comparing state estimates in systems with discrete states and noisy observations. We infer the underlying state of the hidden Markov models from the observations in two ways: through naive observations, which take into account only the current observation, and through Bayesian filtering, which takes the history of observations into account. Defining a discord order parameter to distinguish between the different state estimates, we explore hidden Markov models with various numbers of states and symbols and varying transition-matrix symmetry...
June 2017: Physical Review. E
https://www.readbyqxmd.com/read/28696334/recent-advances-in-heart-sound-analysis
#19
Gari D Clifford, Chengyu Liu, Benjamin E Moody, José Millet Roig, Samuel E Schmidt, Qiao Li, Ikaro Silva, Roger G Mark
Heart sounds have been widely studied and have been demonstrated to have value for detecting pathologies in clinical applications. Over the last few decades, the use of heart sound signals has become increasingly uncommon and its practice in modern medicine somewhat diminished, although research into automated analysis has continued. Unfortunately, a comparative analyses of algorithms in the literature have been hindered by the lack of high-quality, rigorously validated, and standardized open databases of heart sound recordings...
July 11, 2017: Physiological Measurement
https://www.readbyqxmd.com/read/28682786/application-of-computational-methods-in-planaria-research-a-current-update
#20
Shyamasree Ghosh
Planaria is a member of the Phylum Platyhelminthes including flatworms. Planarians possess the unique ability of regeneration from adult stem cells or neoblasts and finds importance as a model organism for regeneration and developmental studies. Although research is being actively carried out globally through conventional methods to understand the process of regeneration from neoblasts, biology of development, neurobiology and immunology of Planaria, there are many thought provoking questions related to stem cell plasticity, and uniqueness of regenerative potential in Planarians amongst other members of Phylum Platyhelminthes...
July 6, 2017: Journal of Integrative Bioinformatics
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