Algorithms for time series clustering applied to biomedical signals

Thesis submitted in the fulfillment of the requirements for the Degree of Master in Biomedical EngineeringThe increasing number of biomedical systems and applications for human body understanding creates a need for information extraction tools to use in biosignals. It’s important to comprehend the changes in the biosignal’s morphology over time, as they often contain critical information on the condition of the subject or the status of the experiment. The creation of tools that automatically analyze and extract relevant attributes from biosignals, providing important information to the user, has a significant value in the biosignal’s processing field. The present dissertation introduces new algorithms for time series clustering, where we are able to separate and organize unlabeled data into different groups whose signals are similar to each other. Signal processing algorithms were developed for the detection of a meanwave, which represents the signal’s morphology and behavior. The algorithm designed computes the meanwave by separating and averaging all cycles of a cyclic continuous signal. To increase the quality of information given by the meanwave, a set of wave-alignment techniques was also developed and its relevance was evaluated in a real database. To evaluate our algorithm’s applicability in time series clustering, a distance metric created with the information of the automatic meanwave was designed and its measurements were given as input to a K-Means clustering algorithm. With that purpose, we collected a series of data with two different modes in it. The produced algorithm successfully separates two modes in the collected data with 99.3% of efficiency. The results of this clustering procedure were compared to a mechanism widely used in this area, which models the data and uses the distance between its cepstral coefficients to measure the similarity between the time series.The algorithms were also validated in different study projects. These projects show the variety of contexts in which our algorithms have high applicability and are suitable answers to overcome the problems of exhaustive signal analysis and expert intervention. The algorithms produced are signal-independent, and therefore can be applied to any type of signal providing it is a cyclic signal. The fact that this approach doesn’t require any prior information and the preliminary good performance make these algorithms powerful tools for biosignals analysis and classification

Algorithms for information extraction and signal annotation on long-term biosignals using clustering techniques

Dissertação para obtenção do Grau de Mestre em Engenharia BiomédicaOne of the biggest challenges when analysing data is to extract information from it, especially if we dealing with very large sized data, which brings a new set of barriers to be overcome. The extracted information can be used to aid physicians in their diagnosis since biosignals often carry vital information on the subjects. In this research work, we present a signal-independent algorithm with two main goals: perform events detection in biosignals and, with those events, extract information using a set of distance measures which will be used as input to a parallel version of the k-means clustering algorithm. The first goal is achieved by using two different approaches. Events can be found based on peaks detection through an adaptive threshold defined as the signal’s root mean square (RMS) or by morphological analysis through the computation of the signal’s meanwave. The final goal is achieved by dividing the distance measures into n parts and by performing k-means individually. In order to improve speed performance, parallel computing techniques were applied. For this study, a set of different types of signals was acquired and annotated by our algorithm. By visual inspection, the L1 and L2 Minkowski distances returned an output that allowed clustering signals’ cycles with an efficiency of 97:5% and 97:3%, respectively. Using the meanwave distance, our algorithm achieved an accuracy of 97:4%. For the downloaded ECGs from the Physionet databases, the developed algorithm detected 638 out of 644 manually annotated events provided by physicians. The fact that this algorithm can be applied to long-term raw biosignals and without requiring any prior information about them makes it an important contribution in biosignals’ information extraction and annotation

Human activity recognition for an intelligent knee orthosis

Dissertação para obtenção do Grau de Mestre em Engenharia BiomédicaActivity recognition with body-worn sensors is a large and growing field of research. In this thesis we evaluate the possibility to recognize human activities based on data from biosignal sensors solely placed on or under an existing passive knee orthosis, which will produce the needed information to integrate sensors into the orthosis in the future. The development of active orthotic knee devices will allow population to ambulate in a more natural, efficient and less painful manner than they might with a traditional orthosis. Thus, the term ’active orthosis’ refers to a device intended to increase the ambulatory ability of a person suffering from a knee pathology by applying forces to correct the position only when necessary and thereby make usable over longer periods of time. The contribution of this work is the evaluation of the ability to recognize activities with these restrictions on sensor placement as well as providing a proof-of-concept for the development of an activity recognition system for an intelligent orthosis. We use accelerometers and a goniometer placed on the orthosis and Electromyography (EMG) sensors placed on the skin under the orthosis to measure motion and muscle activity respectively. We segment signals in motion primitives semi-automatically and apply Hidden-Markov-Models (HMM) to classify the isolated motion primitives. We discriminate between seven activities like for example walking stairs up and ascend a hill. In a user study with six participants, we evaluate the systems performance for each of the different biosignal modalities alone as well as the combinations of them. For the best performing combination, we reach an average person-dependent accuracy of 98% and a person-independent accuracy of 79%

Long-term biosignals visualization and processing

Thesis submitted in the fulfillment of the requirements for the Degree of Master in Biomedical EngineeringLong-term biosignals acquisitions are an important source of information about the patients’state and its evolution. However, long-term biosignals monitoring involves managing extremely large datasets, which makes signal visualization and processing a complex task. To overcome these problems, a new data structure to manage long-term biosignals was developed. Based on this new data structure, dedicated tools for long-term biosignals visualization and processing were implemented. A multilevel visualization tool for any type of biosignals, based on subsampling is presented, focused on four representative signal parameters (mean, maximum, minimum and standard deviation error). The visualization tool enables an overview of the entire signal and a more detailed visualization in specific parts which we want to highlight, allowing an user friendly interaction that leads to an easier signal exploring. The ”map” and ”reduce” concept is also exposed for long-term biosignal processing. A processing tool (ECG peak detection) was adapted for long-term biosignals. In order to test the developed algorithm, long-term biosignals acquisitions (approximately 8 hours each) were carried out. The visualization tool has proven to be faster than the standard methods, allowing a fast navigation over the different visualization levels of biosignals. Regarding the developed processing algorithm, it detected the peaks of long-term ECG signals with fewer time consuming than the nonparalell processing algorithm. The non-specific characteristics of the new data structure, visualization tool and the speed improvement in signal processing introduced by these algorithms makes them powerful tools for long-term biosignals visualization and processing

Modulation of electrical stimulation applied to human physiology and clinical diagnostic

The use, manipulation and application of electrical currents, as a controlled interference mechanism in the human body system, is currently a strong source of motivation to researchers in areas such as clinical, sports, neuroscience, amongst others. In electrical stimulation (ES), the current applied to tissue is traditionally controlled concerning stimulation amplitude, frequency and pulse-width. The main drawbacks of the transcutaneous ES are the rapid fatigue induction and the high discomfort induced by the non-selective activation of nervous fibers. There are, however, electrophysiological parameters whose response, like the response to different stimulation waveforms, polarity or a personalized charge control, is still unknown. The study of the following questions is of great importance: What is the physiological effect of the electric pulse parametrization concerning charge, waveform and polarity? Does the effect change with the clinical condition of the subjects? The parametrization influence on muscle recruitment can retard fatigue onset? Can parametrization enable fiber selectivity, optimizing the motor fibers recruitment rather than the nervous fibers, reducing contraction discomfort? Current hardware solutions lack flexibility at the level of stimulation control and physiological response assessment. To answer these questions, a miniaturized, portable and wireless controlled device with ES functions and full integration with a generic biosignals acquisition platform has been created. Hardware was also developed to provide complete freedom for controlling the applied current with respect to the waveform, polarity, frequency, amplitude, pulse-width and duration. The impact of the methodologies developed is successfully applied and evaluated in the contexts of fundamental electrophysiology, psycho-motor rehabilitation and neuromuscular disorders diagnosis. This PhD project was carried out in the Physics Department of Faculty of Sciences and Technology (FCT-UNL), in straight collaboration with PLUX - Wireless Biosignals S.A. company and co-funded by the Foundation for Science and Technology.Fundação para a Ciência e Tecnologia (FCT); PLUX - Wireless Biosignals, S.A.; FCT-UNL- CEFITE

Data-driven methods for analyzing ballistocardiograms in longitudinal cardiovascular monitoring

Cardiovascular disease (CVD) is the leading cause of death in the US; about 48% of American adults have one or more types of CVD. The importance of continuous monitoring of the older population, for early detection of changes in health conditions, has been shown in the literature, as the key to a successful clinical intervention. We have been investigating environmentally-embedded in-home networks of non-invasive sensing modalities. This dissertation concentrates on the signal processing techniques required for the robust extraction of morphological features from the ballistocardiographs (BCG), and machine learning approaches to utilize these features in non-invasive monitoring of cardiovascular conditions. At first, enhancements in the time domain detection of the cardiac cycle are addressed due to its importance in the estimation of heart rate variability (HRV) and sleep stages. The proposed enhancements in the energy-based algorithm for BCG beat detection have shown at least 50% improvement in the root mean square error (RMSE) of the beat to beat heart rate estimations compared to the reference estimations from the electrocardiogram (ECG) R to R intervals. These results are still subject to some errors, primarily due to the contamination of noise and motion artifacts caused by floor vibration, unconstrained subject movements, or even the respiratory activities. Aging, diseases, breathing, and sleep disorders can also affect the quality of estimation as they slightly modify the morphology of the BCG waveform.Includes bibliographical reference

Wavelet transform methods for identifying onset of SEMG activity

Quantifying improvements in motor control is predicated on the accurate identification of the onset of surface electromyograpic (sEMG) activity. Applying methods from wavelet theory developed in the past decade to digitized signals, a robust algorithm has been designed for use with sEMG collected during reaching tasks executed with the less-affected arm of stroke patients. The method applied both Discretized Continuous Wavelet Transforms (CWT) and Discrete Wavelet Transforms (DWT) for event detection and no-lag filtering, respectively. Input parameters were extracted from the assessed signals. The onset times found in the sEMG signals using the wavelet method were compared with physiological instants of motion onset, determined from video data. Robustness was evaluated by considering the response in onset time with variations of input parameter values. The wavelet method found physiologically relevant onset times in all signals, averaging 147 ms prior to motion onset, compared to predicted onset latencies of 90-110 ins. Latency exhibited slight dependence on subject, but no other variables

Nonlinear and factorization methods for the non-invasive investigation of the central nervous system

This thesis focuses on the functional study of the Central Nervous System (CNS) with non-invasive techniques. Two different aspects are investigated: nonlinear aspects of the cerebrovascular system, and the muscle synergies model for motor control strategies. The main objective is to propose novel protocols, post-processing procedures or indices to enhance the analysis of cerebrovascular system and human motion analysis with noninvasive devices or wearable sensors in clinics and rehabilitation. We investigated cerebrovascular system with Near-infrared Spectroscopy (NIRS), a technique measuring blood oxygenation at the level of microcirculation, whose modification reflects cerebrovascular response to neuronal activation. NIRS signal was analyzed with nonlinear methods, because some physiological systems, such as neurovascular coupling, are characterized by nonlinearity. We adopted Empirical Mode Decomposition (EMD) to decompose signal into a finite number of simple functions, called Intrinsic Mode Functions (IMF). For each IMF, we computed entropy-based features to characterize signal complexity and variability. Nonlinear features of the cerebrovascular response were employed to characterize two treatments. Firstly, we administered a psychotherapy called eye movement desensitization and reprocessing (EMDR) to two groups of patients. The first group performed therapy with eye movements, the second without. NIRS analysis with EMD and entropy-based features revealed a different cerebrovascular pattern between the two groups, that may indicate the efficacy of the psychotherapy when administered with eye movements. Secondly, we administered ozone autohemotherapy to two groups of subjects: a control group of healthy subjects and a group of patients suffering by multiple sclerosis (MS). We monitored the microcirculation with NIRS from oxygen-ozone injection up 1.5 hours after therapy, and 24 hours after therapy. We observed that, after 1.5 hours after the ozonetherapy, oxygenation levels improved in both groups, that may indicate that ozonetherapy reduced oxidative stress level in MS patients. Furthermore, we observed that, after ozonetherapy, autoregulation improved in both groups, and that the beneficial effects of ozonetherapy persisted up to 24 hours after the treatment in MS patients. Due to the complexity of musculoskeletal system, CNS adopts strategies to efficiently control the execution of motor tasks. A model of motor control are muscle synergies, defined as functional groups of muscles recruited by a unique central command. Human locomotion was the object of investigation, due to its importance for daily life and the cyclicity of the movement. Firstly, by exploiting features provided from statistical gait analysis, we investigated consistency of muscle synergies. We demonstrated that synergies are highly repeatable within-subjects, reinforcing the hypothesis of modular control in motor performance. Secondly, in locomotion, we distinguish principal from secondary activations of electromyography. Principal activations are necessary for the generation of the movement. Secondary activations generate supplement movements, for instance slight balance correction. We investigated the difference in the motor control strategies underlying muscle synergies of principal (PS) and secondary (SS) activations. We found that PS are constituted by a few modules with many muscles each, whereas SS are described by more modules than PS with one or two muscles each. Furthermore, amplitude of activation signals of PS is higher than SS. Finally, muscle synergies were adopted to investigate the efficacy of rehabilitation of stiffed-leg walking in lower back pain (LBP). We recruited a group of patients suffering from non-specific LBP stiffening the leg at initial contact. Muscle synergies during gait were extracted before and after rehabilitation. Our results showed that muscles recruitment and consistency of synergies improved after the treatment, showing that the rehabilitation may affect motor control strategies