Clinical Gait Analysis: Characterizing Normal Gait and Pathological Deviations Due to Neurological Diseases

This study addresses the characterization of normal gait and pathological deviations induced by neurological diseases, considering knee angular kinematics in the sagittal plane. We propose an unsupervised approach based on Dynamic Time Warping (DTW) to identify different normal gait profiles (NGPs) corresponding to real cycles representing the overall behavior of healthy subjects, instead of considering an average reference, as done in the literature. The obtained NGPs are then used to measure the deviations of pathological gait cycles from normal gait with DTW. Hierarchical Clustering is applied to stratify deviations into clusters. Results show that three NGPs are necessary to finely characterize the heterogeneity of normal gait and accurately quantify pathological deviations. In particular, we automatically identify which lower limb is affected for Hemiplegic patients and characterize the severity of motor impairment for Paraplegic patients. Concerning Tetraplegic patients, different profiles appear in terms of impairment severity. These promising results are obtained by considering the raw description of gait signals. Indeed, we have shown that normalizing signals removes the temporal properties of signals, inducing a loss of dynamic information that is crucial for accurately measuring pathological deviations. Our methodology could be exploited to quantify the impact of therapies on gait rehabilitation.

The effects of curve registration on linear models of jump performance and classification based on vertical ground reaction forces

Functional principal components define modes of variation in time series, which represent characteristic movement patterns in biomechanical data. Their usefulness however depends on the prior choices made in data processing. Recent research showed that better curve alignment achieved with registration (dynamic time warping) reduces errors in linear models predicting jump height. However, the efficacy of registration in different preprocessing combinations, including time normalisation, padding and feature extraction, is largely unknown. A more comprehensive analysis is needed, given the potential value of registration to machine learning in biomechanics. We evaluated popular preprocessing methods combined with registration, creating 512 models based on ground reaction force data from 385 countermovement jumps. The models either predicted jump height or classified jumps into those performed with or without arm swing. Our results show that the classification models benefited from registration in various forms, particularly when landmarks were placed at critical points. The best classifier achieved a 5.5 percentage point improvement over the equivalent unregistered model. However, registration was detrimental to the jump height models, although this performance variable may be a special case given its direct relationship with impulse. Our meta-models revealed the relative contributions made by various preprocessing operations, highlighting that registration does not generalise so well to new data. Nonetheless, our analysis shows the potential for registration in further biomechanical applications, particularly in classification, when combined with the other appropriate preprocessing operations.

Quality zones automatically identified in water distribution networks by applying data clustering methods to conductivity measurements

This paper presents a clustering study showing how conductivity measured every five minutes by 215 probes over four years can be used to determine specific quality zones for a large Water Distribution Network (WDN): 8500 km of pipes, 4.6 M customers. Conductivity time-series are compared using Dynamic Time Warping. Then, probes are ordered using a density-based method, and probe clusters are extracted automatically. The clusters are a sound representation of water quality in the WDN, both in terms of water origin and water residence time. More specifically, zones directly impacted by plants or by external water imports, mixing zones and zones influenced by tanks, can be isolated and analyzed. Globally, 82% of the probes were found to be clustered, consistent with expert knowledge on the WDN operation; 13% were unclassified; 3% were erroneously clustered; and 1% seemed to be reasonably clustered, without any physical understanding yet. Besides providing users with an increased understanding of water quality in WDNs, conductivity-based clusters offer an interesting prior tool for contamination warning systems.

NUVA: A Naming Utterance Verifier for Aphasia Treatment

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NUVA automatically assesses online word naming attempts in aphasia therapy.

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Significantly more accurate and faster than leading commercial speech recognition.

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Accuracies between 83.6% and 93.6% validate use in clinical research.

Anomia (word-finding difficulties) is the hallmark of aphasia, an acquired language disorder most commonly caused by stroke. Assessment of speech performance using picture naming tasks is a key method for both diagnosis and monitoring of responses to treatment interventions by people with aphasia (PWA). Currently, this assessment is conducted manually by speech and language therapists (SLT). Surprisingly, despite advancements in automatic speech recognition (ASR) and artificial intelligence with technologies like deep learning, research on developing automated systems for this task has been scarce. Here we present NUVA, an utterance verification system incorporating a deep learning element that classifies 'correct' versus' incorrect' naming attempts from aphasic stroke patients. When tested on eight native British-English speaking PWA the system's performance accuracy ranged between 83.6% to 93.6%, with a 10-fold cross-validation mean of 89.5%. This performance was not only significantly better than a baseline created for this study using one of the leading commercially available ASRs (Google speech-to-text service) but also comparable in some instances with two independent SLT ratings for the same dataset.

A Novel Acceleration Signal Processing Procedure for Cycling Safety Assessment

With the growing rate of urban population and transport congestion, it is important for a city to have bike riding as an attractive travel choice but one of its biggest barriers for people is the perceived lack of safety. To improve the safety of urban cycling, identification of high-risk location and routes are major obstacles for safety countermeasures. Risk assessment is performed by crash data analysis, but the lack of data makes that approach less effective when applied to cyclist safety. Furthermore, the availability of data collected with the modern technologies opens the way to different approaches. This research aim is to analyse data needs and capability to identify critical cycling safety events for urban context where bicyclist behaviour can be recorded with different equipment and bicycle used as a probe vehicle to collect data. More specifically, three different sampling frequencies have been investigated to define the minimum one able to detect and recognize hard breaking. In details, a novel signal processing procedure has been proposed to correctly deal with speed and acceleration signals. Besides common signal filtering approaches, wavelet transformation and Dynamic Time Warping (DTW) techniques have been applied to remove more efficiently the instrument noise and align the signals with respect to the reference. The Euclidean distance of the DTW has been introduced as index to get the best filter parameters configuration. Obtained results, both during the calibration and the investigated real scenario, confirm that at least a GPS signal with a sampling frequency of 1Hz is needed to track the rider’s behaviour to detect events. In conclusion, with a very cheap hardware setup is possible to monitor riders’ speed and acceleration.

Gait-cycle segmentation method based on lower-trunk acceleration signals and dynamic time warping

Gait analysis is the systematic study of human walking. The analysis of gait signals from the lower trunk, acquired through accelerometers, begins with the proper identification of gait cycles. The goal of this work is to supplement gait-event based segmentation methods, tested for unimpaired and impaired populations, so that their need to calibrate or rely on pre-defined thresholds is overcome, and to implement strategies that reduce step-detection errors. A new system for the automatic extraction and analysis of gait cycles from acceleration signals of the lower trunk, combining knowledge from previous strategies with a dynamic time warping function, is presented. Performance was tested on gait signals from public databases. Sensitivities in step detection above 99.95% were achieved, with a positive predictive value of 100.00%. Step-correction strategies reduced the number of incorrect detections from 57 to 3 of 7056 steps. Bland-Altman plots and equivalence tests performed on cycle times by the proposed method and selected references showed good agreement, with mean differences below 0.003 s, and percent errors of 2%. This method may give place to a research tool for the automatic analysis of signals from subjects in a variety of cases.

Non-Linear Template-Based Approach for the Study of Locomotion

The automatic detection of gait events (i.e., Initial Contact (IC) and Final Contact (FC)) is crucial for the characterisation of gait from Inertial Measurements Units. In this article, we present a method for detecting steps (i.e., IC and FC) from signals of gait sequences of individuals recorded with a gyrometer. The proposed approach combines the use of a dictionary of templates and a Dynamic Time Warping (DTW) measure of fit to retrieve these templates into input signals. Several strategies for choosing and learning the adequate templates from annotated data are also described. The method is tested on thirteen healthy subjects and compared to gold standard. Depending of the template choice, the proposed algorithm achieves average errors from 0.01 to 0.03 s for the detection of IC, FC and step duration. Results demonstrate that the use of DTW allows achieving these performances with only one single template. DTW is a convenient tool to perform pattern recognition on gait gyrometer signals. This study paves the way for new step detection methods: it shows that using one single template associated with non-linear deformations may be sufficient to model the gait of healthy subjects.

Resting State fMRI Functional Connectivity-Based Classification Using a Convolutional Neural Network Architecture

Machine learning techniques have become increasingly popular in the field of resting state fMRI (functional magnetic resonance imaging) network based classification. However, the application of convolutional networks has been proposed only very recently and has remained largely unexplored. In this paper we describe a convolutional neural network architecture for functional connectome classification called connectome-convolutional neural network (CCNN). Our results on simulated datasets and a publicly available dataset for amnestic mild cognitive impairment classification demonstrate that our CCNN model can efficiently distinguish between subject groups. We also show that the connectome-convolutional network is capable to combine information from diverse functional connectivity metrics and that models using a combination of different connectivity descriptors are able to outperform classifiers using only one metric. From this flexibility follows that our proposed CCNN model can be easily adapted to a wide range of connectome based classification or regression tasks, by varying which connectivity descriptor combinations are used to train the network.

Resting State fMRI Functional Connectivity Analysis Using Dynamic Time Warping

Traditional resting-state network concept is based on calculating linear dependence of spontaneous low frequency fluctuations of the BOLD signals of different brain areas, which assumes temporally stable zero-lag synchrony across regions. However, growing amount of experimental findings suggest that functional connectivity exhibits dynamic changes and a complex time-lag structure, which cannot be captured by the static zero-lag correlation analysis. Here we propose a new approach applying Dynamic Time Warping (DTW) distance to evaluate functional connectivity strength that accounts for non-stationarity and phase-lags between the observed signals. Using simulated fMRI data we found that DTW captures dynamic interactions and it is less sensitive to linearly combined global noise in the data as compared to traditional correlation analysis. We tested our method using resting-state fMRI data from repeated measurements of an individual subject and showed that DTW analysis results in more stable connectivity patterns by reducing the within-subject variability and increasing robustness for preprocessing strategies. Classification results on a public dataset revealed a superior sensitivity of the DTW analysis to group differences by showing that DTW based classifiers outperform the zero-lag correlation and maximal lag cross-correlation based classifiers significantly. Our findings suggest that analysing resting-state functional connectivity using DTW provides an efficient new way for characterizing functional networks.

DGW: an exploratory data analysis tool for clustering and visualisation of epigenomic marks

Background

Functional genomic and epigenomic research relies fundamentally on sequencing based methods like ChIP-seq for the detection of DNA-protein interactions. These techniques return large, high dimensional data sets with visually complex structures, such as multi-modal peaks extended over large genomic regions. Current tools for visualisation and data exploration represent and leverage these complex features only to a limited extent.

Results

We present DGW, an open source software package for simultaneous alignment and clustering of multiple epigenomic marks. DGW uses Dynamic Time Warping to adaptively rescale and align genomic distances which allows to group regions of interest with similar shapes, thereby capturing the structure of epigenomic marks. We demonstrate the effectiveness of the approach in a simulation study and on a real epigenomic data set from the ENCODE project.

Conclusions

Our results show that DGW automatically recognises and aligns important genomic features such as transcription start sites and splicing sites from histone marks. DGW is available as an open source Python package.

A new method to analyze protein sequence similarity using Dynamic Time Warping

Sequences similarity analysis is one of the major topics in bioinformatics. It helps researchers to reveal evolution relationships of different species. In this paper, we outline a new method to analyze the similarity of proteins by Discrete Fourier Transform (DFT) and Dynamic Time Warping (DTW). The original symbol sequences are converted to numerical sequences according to their physico-chemical properties. We obtain the power spectra of sequences from DFT and extend the spectra to the same length to calculate the distance between different sequences by DTW. Our method is tested in different datasets and the results are compared with that of other software algorithms. In the comparison we find our scheme could amend some wrong classifications appear in other software. The comparison shows our approach is reasonable and effective.

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We propose a novel method to extract the features of the sequences based on physicochemical property of proteins.

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We apply the Discrete Fourier Transform (DFT) and Dynamic Time Warping (DTW) to analyze the similarity of proteins.

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Different datasets are used to prove our model's effectiveness.

Rapid annotation of interictal epileptiform discharges via template matching under Dynamic Time Warping

BACKGROUND

EEG interpretation relies on experts who are in short supply. There is a great need for automated pattern recognition systems to assist with interpretation. However, attempts to develop such systems have been limited by insufficient expert-annotated data. To address these issues, we developed a system named NeuroBrowser for EEG review and rapid waveform annotation.

NEW METHODS

At the core of NeuroBrowser lies on ultrafast template matching under Dynamic Time Warping, which substantially accelerates the task of annotation.

RESULTS

Our results demonstrate that NeuroBrowser can reduce the time required for annotation of interictal epileptiform discharges by EEG experts by 20-90%, with an average of approximately 70%.

COMPARISON WITH EXISTING METHOD(S)

In comparison with conventional manual EEG annotation, NeuroBrowser is able to save EEG experts approximately 70% on average of the time spent in annotating interictal epileptiform discharges. We have already extracted 19,000+ interictal epileptiform discharges from 100 patient EEG recordings. To our knowledge this represents the largest annotated database of interictal epileptiform discharges in existence.

CONCLUSION

NeuroBrowser is an integrated system for rapid waveform annotation. While the algorithm is currently tailored to annotation of interictal epileptiform discharges in scalp EEG recordings, the concepts can be easily generalized to other waveforms and signal types.

Impact of Sensor Misplacement on Dynamic Time Warping Based Human Activity Recognition using Wearable Computers

Daily living activity monitoring is important for early detection of the onset of many diseases and for improving quality of life especially in elderly. A wireless wearable network of inertial sensor nodes can be used to observe daily motions. Continuous stream of data generated by these sensor networks can be used to recognize the movements of interest. Dynamic Time Warping (DTW) is a widely used signal processing method for time-series pattern matching because of its robustness to variations in time and speed as opposed to other template matching methods. Despite this flexibility, for the application of activity recognition, DTW can only find the similarity between the template of a movement and the incoming samples, when the location and orientation of the sensor remains unchanged. Due to this restriction, small sensor misplacements can lead to a decrease in the classification accuracy. In this work, we adopt DTW distance as a feature for real-time detection of human daily activities like sit to stand in the presence of sensor misplacement. To measure this performance of DTW, we need to create a large number of sensor configurations while the sensors are rotated or misplaced. Creating a large number of closely spaced sensors is impractical. To address this problem, we use the marker based optical motion capture system and generate simulated inertial sensor data for different locations and orientations on the body. We study the performance of the DTW under these conditions to determine the worst-case sensor location variations that the algorithm can accommodate.