scholarly journals Hidden Markov Model based stride segmentation on unsupervised free-living gait data in Parkinson’s disease patients

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Nils Roth ◽  
Arne Küderle ◽  
Martin Ullrich ◽  
Till Gladow ◽  
Franz Marxreiter ◽  
...  
Keyword(s):  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Markov Model ◽  
Hidden Markov Model ◽  
Gait Analysis ◽  
Large Scale ◽  
Hidden Markov ◽  
Inertial Sensor ◽  
Training Data ◽  
Free Living

Abstract Background To objectively assess a patient’s gait, a robust identification of stride borders is one of the first steps in inertial sensor-based mobile gait analysis pipelines. While many different methods for stride segmentation have been presented in the literature, an out-of-lab evaluation of respective algorithms on free-living gait is still missing. Method To address this issue, we present a comprehensive free-living evaluation dataset, including 146.574 semi-automatic labeled strides of 28 Parkinson’s Disease patients. This dataset was used to evaluate the segmentation performance of a new Hidden Markov Model (HMM) based stride segmentation approach compared to an available dynamic time warping (DTW) based method. Results The proposed HMM achieved a mean F1-score of 92.1% and outperformed the DTW approach significantly. Further analysis revealed a dependency of segmentation performance to the number of strides within respective walking bouts. Shorter bouts ($$< 30$$ < 30 strides) resulted in worse performance, which could be related to more heterogeneous gait and an increased diversity of different stride types in short free-living walking bouts. In contrast, the HMM reached F1-scores of more than 96.2% for longer bouts ($$> 50$$ > 50 strides). Furthermore, we showed that an HMM, which was trained on at-lab data only, could be transferred to a free-living context with a negligible decrease in performance. Conclusion The generalizability of the proposed HMM is a promising feature, as fully labeled free-living training data might not be available for many applications. To the best of our knowledge, this is the first evaluation of stride segmentation performance on a large scale free-living dataset. Our proposed HMM-based approach was able to address the increased complexity of free-living gait data, and thus will help to enable a robust assessment of stride parameters in future free-living gait analysis applications.

scholarly journals Hidden Markov Model based Stride Segmentation on Unsupervised Free-living Gait Data in Parkinson’s Disease Patients

2021 ◽  
Author(s):  
Nils Roth ◽  
Arne Küderle ◽  
Martin Ullrich ◽  
Till Gladow ◽  
Franz Marxreiter ◽  
...  
Keyword(s):  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Markov Model ◽  
Hidden Markov Model ◽  
Gait Analysis ◽  
Large Scale ◽  
Hidden Markov ◽  
Inertial Sensor ◽  
Training Data ◽  
Free Living

Abstract Background: To objectively assess a patient's gait, a robust identification of stride borders is one of the first steps in inertial sensor-based mobile gait analysis pipelines. While many different methods for stride segmentation have been presented in the literature, an out-of-lab evaluation of respective algorithms on free-living gait is still missing. Method : To address this issue, we present a comprehensive free-living evaluation dataset, including 146.574 semi-automatic labeled strides of 28 Parkinson's Disease patients. This dataset was used to evaluate the segmentation performance of a new Hidden Markov Model (HMM) based stride segmentation approach compared to an available dynamic time warping (DTW) based method. Results: The proposed HMM achieved a mean F1-score of 92.1% and outperformed the DTW approach significantly. Further analysis revealed a dependency of segmentation performance to the number of strides within respective walking bouts. Shorter bouts (<30 strides) resulted in worse performance, which could be related to more heterogeneous gait and an increased diversity of different stride types in short free-living walking bouts. In contrast, the HMM reached F1-scores of more than 96.2% for longer bouts (>50 strides). Furthermore, we showed that an HMM, which was trained on at-lab data only, could be transferred to a free-living context with a negligible decrease in performance. Conclusion: The generalizability of the proposed HMM is a promising feature, as fully labeled free-living training data might not be available for many applications. To the best of our knowledge, this is the first evaluation of stride segmentation performance on a large scale free-living dataset. Our proposed HMM-based approach was able to address the increased complexity of free-living gait data, and thus will help to enable a robust assessment of stride parameters in future free-living gait analysis applications

scholarly journals Ambulatory Human Gait Phase Detection Using Wearable Inertial Sensors and Hidden Markov Model

Sensors ◽  
2021 ◽  
Vol 21 (4) ◽  
pp. 1347
Author(s):  
Long Liu ◽  
Huihui Wang ◽  
Haorui Li ◽  
Jiayi Liu ◽  
Sen Qiu ◽  
...  
Keyword(s):  
Markov Model ◽  
Hidden Markov Model ◽  
Gait Analysis ◽  
Hidden Markov ◽  
Inertial Sensor ◽  
Outdoor Environment ◽  
Human Gait ◽  
Velocity Signal ◽  
Inspection Method ◽  
Gait Phase

Gait analysis, as a common inspection method for human gait, can provide a series of kinematics, dynamics and other parameters through instrumental measurement. In recent years, gait analysis has been gradually applied to the diagnosis of diseases, the evaluation of orthopedic surgery and rehabilitation progress, especially, gait phase abnormality can be used as a clinical diagnostic indicator of Alzheimer Disease and Parkinson Disease, which usually show varying degrees of gait phase abnormality. This research proposed an inertial sensor based gait analysis method. Smoothed and filtered angular velocity signal was chosen as the input data of the 15-dimensional temporal characteristic feature. Hidden Markov Model and parameter adaptive model are used to segment gait phases. Experimental results show that the proposed model based on HMM and parameter adaptation achieves good recognition rate in gait phases segmentation compared to other classification models, and the recognition results of gait phase are consistent with ground truth. The proposed wearable device used for data collection can be embedded on the shoe, which can not only collect patients’ gait data stably and reliably, ensuring the integrity and objectivity of gait data, but also collect data in daily scene and ambulatory outdoor environment.

scholarly journals Detection of structural variations in densely-labelled optical DNA barcodes: A hidden Markov model approach

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0259670
Author(s):  
Albertas Dvirnas ◽  
Callum Stewart ◽  
Vilhelm Müller ◽  
Santosh Kumar Bikkarolla ◽  
Karolin Frykholm ◽  
...  
Keyword(s):  
Markov Model ◽  
Hidden Markov Model ◽  
Large Scale ◽  
Hidden Markov ◽  
Sequence Information ◽  
True Positive ◽  
Dna Barcodes ◽  
Structural Variations ◽  
Genomic Alterations ◽  
Data Set

Large-scale genomic alterations play an important role in disease, gene expression, and chromosome evolution. Optical DNA mapping (ODM), commonly categorized into sparsely-labelled ODM and densely-labelled ODM, provides sequence-specific continuous intensity profiles (DNA barcodes) along single DNA molecules and is a technique well-suited for detecting such alterations. For sparsely-labelled barcodes, the possibility to detect large genomic alterations has been investigated extensively, while densely-labelled barcodes have not received as much attention. In this work, we introduce HMMSV, a hidden Markov model (HMM) based algorithm for detecting structural variations (SVs) directly in densely-labelled barcodes without access to sequence information. We evaluate our approach using simulated data-sets with 5 different types of SVs, and combinations thereof, and demonstrate that the method reaches a true positive rate greater than 80% for randomly generated barcodes with single variations of size 25 kilobases (kb). Increasing the length of the SV further leads to larger true positive rates. For a real data-set with experimental barcodes on bacterial plasmids, we successfully detect matching barcode pairs and SVs without any particular assumption of the types of SVs present. Instead, our method effectively goes through all possible combinations of SVs. Since ODM works on length scales typically not reachable with other techniques, our methodology is a promising tool for identifying arbitrary combinations of genomic alterations.

scholarly journals Continuous Hidden Markov Model for Pedestrian Activity Classification and Gait Analysis

2013 ◽  
Vol 62 (5) ◽  
pp. 1073-1083 ◽  
Author(s):  
Ghazaleh Panahandeh ◽  
Nasser Mohammadiha ◽  
Arne Leijon ◽  
Peter Handel
Keyword(s):  
Markov Model ◽  
Hidden Markov Model ◽  
Gait Analysis ◽  
Hidden Markov ◽  
Activity Classification

Bidirectional LSTM Recurrent Neural Network Plus Hidden Markov Model for Wearable Sensor-Based Dynamic State Estimation

2020 ◽  
Vol 1 (2) ◽  
Author(s):  
Ritika Sibal ◽  
Ding Zhang ◽  
Julie Rocho-Levine ◽  
K. Alex Shorter ◽  
Kira Barton
Keyword(s):  
Markov Model ◽  
Hidden Markov Model ◽  
State Estimation ◽  
Short Term Memory ◽  
Hidden Markov ◽  
Training Data ◽  
Dynamic State ◽  
Support Vector ◽  
Similar Amount ◽  
Dynamic State Estimation

Abstract Behavior of animals living in the wild is often studied using visual observations made by trained experts. However, these observations tend to be used to classify behavior during discrete time periods and become more difficult when used to monitor multiple individuals for days or weeks. In this work, we present automatic tools to enable efficient behavior and dynamic state estimation/classification from data collected with animal borne bio-logging tags, without the need for statistical feature engineering. A combined framework of an long short-term memory (LSTM) network and a hidden Markov model (HMM) was developed to exploit sequential temporal information in raw motion data at two levels: within and between windows. Taking a moving window data segmentation approach, LSTM estimates the dynamic state corresponding to each window by parsing the contiguous raw data points within the window. HMM then links all of the individual window estimations and further improves the overall estimation. A case study with bottlenose dolphins was conducted to demonstrate the approach. The combined LSTM–HMM method achieved a 6% improvement over conventional methods such as K-nearest neighbor (KNN) and support vector machine (SVM), pushing the accuracy above 90%. In addition to performance improvements, the proposed method requires a similar amount of training data to traditional machine learning methods, making the method easily adaptable to new tasks.

scholarly journals Development of Vietnamese Speech Synthesis System using Deep Neural Networks

2019 ◽  
Vol 34 (4) ◽  
pp. 349-363 ◽  
Author(s):  
Thinh Van Nguyen ◽  
Bao Quoc Nguyen ◽  
Kinh Huy Phan ◽  
Hai Van Do
Keyword(s):  
Neural Networks ◽  
Markov Model ◽  
Hidden Markov Model ◽  
Speech Synthesis ◽  
Deep Neural Networks ◽  
Hidden Markov ◽  
Experimental Results ◽  
Training Data ◽  
The Internet ◽  
Synthesis System

In this paper, we present our first Vietnamese speech synthesis system based on deep neural networks. To improve the training data collected from the Internet, a cleaning method is proposed. The experimental results indicate that by using deeper architectures we can achieve better performance for the TTS than using shallow architectures such as hidden Markov model. We also present the effect of using different amounts of data to train the TTS systems. In the VLSP TTS challenge 2018, our proposed DNN-based speech synthesis system won the first place in all three subjects including naturalness, intelligibility, and MOS.

scholarly journals Increasing the Efficiency of Genome-wide Association Mapping via Hidden Markov Models

2016 ◽  
Author(s):  
Hong Gao ◽  
Hua Tang ◽  
Carlos Bustamante
Keyword(s):  
Markov Model ◽  
Hidden Markov Model ◽  
Large Scale ◽  
Hidden Markov ◽  
Association Studies ◽  
Genome Wide Association ◽  
Trend Test ◽  
Genome Wide Association Studies ◽  
Data Set ◽  
Genome Wide

With the rapid production of high dimensional genetic data, one major challenge in genome-wide association studies is to develop effective and efficient statistical tools to resolve the low power problem of detecting causal SNPs with low to moderate susceptibility, whose effects are often obscured by substantial background noises. Here we present a novel method that serves as an optimal technique for reducing background noises and improving detection power in genome-wide association studies. The approach uses hidden Markov model and its derivate Markov hidden Markov model to estimate the posterior probabilities of a markers being in an associated state. We conducted extensive simulations based on the human whole genome genotype data from the GlaxoSmithKline-POPRES project to calibrate the sensitivity and specificity of our method and compared with many popular approaches for detecting positive signals including the χ^2 test for association and the Cochran-Armitage trend test. Our simulation results suggested that at very low false positive rates (<10^-6), our method reaches the power of 0.9, and is more powerful than any other approaches, when the allelic effect of the causal variant is non-additive or unknown. Application of our method to the data set generated by Welcome Trust Case Control Consortium using 14,000 cases and 3,000 controls confirmed its powerfulness and efficiency under the context of the large-scale genome-wide association studies.

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