Machine Learning Models for High-dimensional Biomedical Data

abstract: The recent technological advances enable the collection of various complex, heterogeneous and high-dimensional data in biomedical domains. The increasing availability of the high-dimensional biomedical data creates the needs of new machine learning models for effective data analysis and knowledge discovery. This dissertation introduces several unsupervised and supervised methods to help understand the data, discover the patterns and improve the decision making. All the proposed methods can generalize to other industrial fields. The first topic of this dissertation focuses on the data clustering. Data clustering is often the first step for analyzing a dataset without the label information. Clustering high-dimensional data with mixed categorical and numeric attributes remains a challenging, yet important task. A clustering algorithm based on tree ensembles, CRAFTER, is proposed to tackle this task in a scalable manner. The second part of this dissertation aims to develop data representation methods for genome sequencing data, a special type of high-dimensional data in the biomedical domain. The proposed data representation method, Bag-of-Segments, can summarize the key characteristics of the genome sequence into a small number of features with good interpretability. The third part of this dissertation introduces an end-to-end deep neural network model, GCRNN, for time series classification with emphasis on both the accuracy and the interpretation. GCRNN contains a convolutional network component to extract high-level features, and a recurrent network component to enhance the modeling of the temporal characteristics. A feed-forward fully connected network with the sparse group lasso regularization is used to generate the final classification and provide good interpretability. The last topic centers around the dimensionality reduction methods for time series data. A good dimensionality reduction method is important for the storage, decision making and pattern visualization for time series data. The CRNN autoencoder is proposed to not only achieve low reconstruction error, but also generate discriminative features. A variational version of this autoencoder has great potential for applications such as anomaly detection and process control.Dissertation/ThesisDoctoral Dissertation Industrial Engineering 201

Multi-sensor data fusion in mobile devices for the identification of Activities of Daily Living

Following the recent advances in technology and the growing use of mobile devices such as smartphones, several solutions may be developed to improve the quality of life of users in the context of Ambient Assisted Living (AAL). Mobile devices have different available sensors, e.g., accelerometer, gyroscope, magnetometer, microphone and Global Positioning System (GPS) receiver, which allow the acquisition of physical and physiological parameters for the recognition of different Activities of Daily Living (ADL) and the environments in which they are performed. The definition of ADL includes a well-known set of tasks, which include basic selfcare tasks, based on the types of skills that people usually learn in early childhood, including feeding, bathing, dressing, grooming, walking, running, jumping, climbing stairs, sleeping, watching TV, working, listening to music, cooking, eating and others. On the context of AAL, some individuals (henceforth called user or users) need particular assistance, either because the user has some sort of impairment, or because the user is old, or simply because users need/want to monitor their lifestyle. The research and development of systems that provide a particular assistance to people is increasing in many areas of application. In particular, in the future, the recognition of ADL will be an important element for the development of a personal digital life coach, providing assistance to different types of users. To support the recognition of ADL, the surrounding environments should be also recognized to increase the reliability of these systems. The main focus of this Thesis is the research on methods for the fusion and classification of the data acquired by the sensors available in off-the-shelf mobile devices in order to recognize ADL in almost real-time, taking into account the large diversity of the capabilities and characteristics of the mobile devices available in the market. In order to achieve this objective, this Thesis started with the review of the existing methods and technologies to define the architecture and modules of the method for the identification of ADL. With this review and based on the knowledge acquired about the sensors available in off-the-shelf mobile devices, a set of tasks that may be reliably identified was defined as a basis for the remaining research and development to be carried out in this Thesis. This review also identified the main stages for the development of a new method for the identification of the ADL using the sensors available in off-the-shelf mobile devices; these stages are data acquisition, data processing, data cleaning, data imputation, feature extraction, data fusion and artificial intelligence. One of the challenges is related to the different types of data acquired from the different sensors, but other challenges were found, including the presence of environmental noise, the positioning of the mobile device during the daily activities, the limited capabilities of the mobile devices and others. Based on the acquired data, the processing was performed, implementing data cleaning and feature extraction methods, in order to define a new framework for the recognition of ADL. The data imputation methods were not applied, because at this stage of the research their implementation does not have influence in the results of the identification of the ADL and environments, as the features are extracted from a set of data acquired during a defined time interval and there are no missing values during this stage. The joint selection of the set of usable sensors and the identifiable set of tasks will then allow the development of a framework that, considering multi-sensor data fusion technologies and context awareness, in coordination with other information available from the user context, such as his/her agenda and the time of the day, will allow to establish a profile of the tasks that the user performs in a regular activity day. The classification method and the algorithm for the fusion of the features for the recognition of ADL and its environments needs to be deployed in a machine with some computational power, while the mobile device that will use the created framework, can perform the identification of the ADL using a much less computational power. Based on the results reported in the literature, the method chosen for the recognition of the ADL is composed by three variants of Artificial Neural Networks (ANN), including simple Multilayer Perceptron (MLP) networks, Feedforward Neural Networks (FNN) with Backpropagation, and Deep Neural Networks (DNN). Data acquisition can be performed with standard methods. After the acquisition, the data must be processed at the data processing stage, which includes data cleaning and feature extraction methods. The data cleaning method used for motion and magnetic sensors is the low pass filter, in order to reduce the noise acquired; but for the acoustic data, the Fast Fourier Transform (FFT) was applied to extract the different frequencies. When the data is clean, several features are then extracted based on the types of sensors used, including the mean, standard deviation, variance, maximum value, minimum value and median of raw data acquired from the motion and magnetic sensors; the mean, standard deviation, variance and median of the maximum peaks calculated with the raw data acquired from the motion and magnetic sensors; the five greatest distances between the maximum peaks calculated with the raw data acquired from the motion and magnetic sensors; the mean, standard deviation, variance, median and 26 Mel- Frequency Cepstral Coefficients (MFCC) of the frequencies obtained with FFT based on the raw data acquired from the microphone data; and the distance travelled calculated with the data acquired from the GPS receiver. After the extraction of the features, these will be grouped in different datasets for the application of the ANN methods and to discover the method and dataset that reports better results. The classification stage was incrementally developed, starting with the identification of the most common ADL (i.e., walking, running, going upstairs, going downstairs and standing activities) with motion and magnetic sensors. Next, the environments were identified with acoustic data, i.e., bedroom, bar, classroom, gym, kitchen, living room, hall, street and library. After the environments are recognized, and based on the different sets of sensors commonly available in the mobile devices, the data acquired from the motion and magnetic sensors were combined with the recognized environment in order to differentiate some activities without motion, i.e., sleeping and watching TV. The number of recognized activities in this stage was increased with the use of the distance travelled, extracted from the GPS receiver data, allowing also to recognize the driving activity. After the implementation of the three classification methods with different numbers of iterations, datasets and remaining configurations in a machine with high processing capabilities, the reported results proved that the best method for the recognition of the most common ADL and activities without motion is the DNN method, but the best method for the recognition of environments is the FNN method with Backpropagation. Depending on the number of sensors used, this implementation reports a mean accuracy between 85.89% and 89.51% for the recognition of the most common ADL, equals to 86.50% for the recognition of environments, and equals to 100% for the recognition of activities without motion, reporting an overall accuracy between 85.89% and 92.00%. The last stage of this research work was the implementation of the structured framework for the mobile devices, verifying that the FNN method requires a high processing power for the recognition of environments and the results reported with the mobile application are lower than the results reported with the machine with high processing capabilities used. Thus, the DNN method was also implemented for the recognition of the environments with the mobile devices. Finally, the results reported with the mobile devices show an accuracy between 86.39% and 89.15% for the recognition of the most common ADL, equal to 45.68% for the recognition of environments, and equal to 100% for the recognition of activities without motion, reporting an overall accuracy between 58.02% and 89.15%. Compared with the literature, the results returned by the implemented framework show only a residual improvement. However, the results reported in this research work comprehend the identification of more ADL than the ones described in other studies. The improvement in the recognition of ADL based on the mean of the accuracies is equal to 2.93%, but the maximum number of ADL and environments previously recognized was 13, while the number of ADL and environments recognized with the framework resulting from this research is 16. In conclusion, the framework developed has a mean improvement of 2.93% in the accuracy of the recognition for a larger number of ADL and environments than previously reported. In the future, the achievements reported by this PhD research may be considered as a start point of the development of a personal digital life coach, but the number of ADL and environments recognized by the framework should be increased and the experiments should be performed with different types of devices (i.e., smartphones and smartwatches), and the data imputation and other machine learning methods should be explored in order to attempt to increase the reliability of the framework for the recognition of ADL and its environments.Após os recentes avanços tecnológicos e o crescente uso dos dispositivos móveis, como por exemplo os smartphones, várias soluções podem ser desenvolvidas para melhorar a qualidade de vida dos utilizadores no contexto de Ambientes de Vida Assistida (AVA) ou Ambient Assisted Living (AAL). Os dispositivos móveis integram vários sensores, tais como acelerómetro, giroscópio, magnetómetro, microfone e recetor de Sistema de Posicionamento Global (GPS), que permitem a aquisição de vários parâmetros físicos e fisiológicos para o reconhecimento de diferentes Atividades da Vida Diária (AVD) e os seus ambientes. A definição de AVD inclui um conjunto bem conhecido de tarefas que são tarefas básicas de autocuidado, baseadas nos tipos de habilidades que as pessoas geralmente aprendem na infância. Essas tarefas incluem alimentar-se, tomar banho, vestir-se, fazer os cuidados pessoais, caminhar, correr, pular, subir escadas, dormir, ver televisão, trabalhar, ouvir música, cozinhar, comer, entre outras. No contexto de AVA, alguns indivíduos (comumente chamados de utilizadores) precisam de assistência particular, seja porque o utilizador tem algum tipo de deficiência, seja porque é idoso, ou simplesmente porque o utilizador precisa/quer monitorizar e treinar o seu estilo de vida. A investigação e desenvolvimento de sistemas que fornecem algum tipo de assistência particular está em crescente em muitas áreas de aplicação. Em particular, no futuro, o reconhecimento das AVD é uma parte importante para o desenvolvimento de um assistente pessoal digital, fornecendo uma assistência pessoal de baixo custo aos diferentes tipos de pessoas. pessoas. Para ajudar no reconhecimento das AVD, os ambientes em que estas se desenrolam devem ser reconhecidos para aumentar a fiabilidade destes sistemas. O foco principal desta Tese é o desenvolvimento de métodos para a fusão e classificação dos dados adquiridos a partir dos sensores disponíveis nos dispositivos móveis, para o reconhecimento quase em tempo real das AVD, tendo em consideração a grande diversidade das características dos dispositivos móveis disponíveis no mercado. Para atingir este objetivo, esta Tese iniciou-se com a revisão dos métodos e tecnologias existentes para definir a arquitetura e os módulos do novo método de identificação das AVD. Com esta revisão da literatura e com base no conhecimento adquirido sobre os sensores disponíveis nos dispositivos móveis disponíveis no mercado, um conjunto de tarefas que podem ser identificadas foi definido para as pesquisas e desenvolvimentos desta Tese. Esta revisão também identifica os principais conceitos para o desenvolvimento do novo método de identificação das AVD, utilizando os sensores, são eles: aquisição de dados, processamento de dados, correção de dados, imputação de dados, extração de características, fusão de dados e extração de resultados recorrendo a métodos de inteligência artificial. Um dos desafios está relacionado aos diferentes tipos de dados adquiridos pelos diferentes sensores, mas outros desafios foram encontrados, sendo os mais relevantes o ruído ambiental, o posicionamento do dispositivo durante a realização das atividades diárias, as capacidades limitadas dos dispositivos móveis. As diferentes características das pessoas podem igualmente influenciar a criação dos métodos, escolhendo pessoas com diferentes estilos de vida e características físicas para a aquisição e identificação dos dados adquiridos a partir de sensores. Com base nos dados adquiridos, realizou-se o processamento dos dados, implementando-se métodos de correção dos dados e a extração de características, para iniciar a criação do novo método para o reconhecimento das AVD. Os métodos de imputação de dados foram excluídos da implementação, pois não iriam influenciar os resultados da identificação das AVD e dos ambientes, na medida em que são utilizadas as características extraídas de um conjunto de dados adquiridos durante um intervalo de tempo definido. A seleção dos sensores utilizáveis, bem como das AVD identificáveis, permitirá o desenvolvimento de um método que, considerando o uso de tecnologias para a fusão de dados adquiridos com múltiplos sensores em coordenação com outras informações relativas ao contexto do utilizador, tais como a agenda do utilizador, permitindo estabelecer um perfil de tarefas que o utilizador realiza diariamente. Com base nos resultados obtidos na literatura, o método escolhido para o reconhecimento das AVD são as diferentes variantes das Redes Neuronais Artificiais (RNA), incluindo Multilayer Perceptron (MLP), Feedforward Neural Networks (FNN) with Backpropagation and Deep Neural Networks (DNN). No final, após a criação dos métodos para cada fase do método para o reconhecimento das AVD e ambientes, a implementação sequencial dos diferentes métodos foi realizada num dispositivo móvel para testes adicionais. Após a definição da estrutura do método para o reconhecimento de AVD e ambientes usando dispositivos móveis, verificou-se que a aquisição de dados pode ser realizada com os métodos comuns. Após a aquisição de dados, os mesmos devem ser processados no módulo de processamento de dados, que inclui os métodos de correção de dados e de extração de características. O método de correção de dados utilizado para sensores de movimento e magnéticos é o filtro passa-baixo de modo a reduzir o ruído, mas para os dados acústicos, a Transformada Rápida de Fourier (FFT) foi aplicada para extrair as diferentes frequências. Após a correção dos dados, as diferentes características foram extraídas com base nos tipos de sensores usados, sendo a média, desvio padrão, variância, valor máximo, valor mínimo e mediana de dados adquiridos pelos sensores magnéticos e de movimento, a média, desvio padrão, variância e mediana dos picos máximos calculados com base nos dados adquiridos pelos sensores magnéticos e de movimento, as cinco maiores distâncias entre os picos máximos calculados com os dados adquiridos dos sensores de movimento e magnéticos, a média, desvio padrão, variância e 26 Mel-Frequency Cepstral Coefficients (MFCC) das frequências obtidas com FFT com base nos dados obtidos a partir do microfone, e a distância calculada com os dados adquiridos pelo recetor de GPS. Após a extração das características, as mesmas são agrupadas em diferentes conjuntos de dados para a aplicação dos métodos de RNA de modo a descobrir o método e o conjunto de características que reporta melhores resultados. O módulo de classificação de dados foi incrementalmente desenvolvido, começando com a identificação das AVD comuns com sensores magnéticos e de movimento, i.e., andar, correr, subir escadas, descer escadas e parado. Em seguida, os ambientes são identificados com dados de sensores acústicos, i.e., quarto, bar, sala de aula, ginásio, cozinha, sala de estar, hall, rua e biblioteca. Com base nos ambientes reconhecidos e os restantes sensores disponíveis nos dispositivos móveis, os dados adquiridos dos sensores magnéticos e de movimento foram combinados com o ambiente reconhecido para diferenciar algumas atividades sem movimento (i.e., dormir e ver televisão), onde o número de atividades reconhecidas nesta fase aumenta com a fusão da distância percorrida, extraída a partir dos dados do recetor GPS, permitindo também reconhecer a atividade de conduzir. Após a implementação dos três métodos de classificação com diferentes números de iterações, conjuntos de dados e configurações numa máquina com alta capacidade de processamento, os resultados relatados provaram que o melhor método para o reconhecimento das atividades comuns de AVD e atividades sem movimento é o método DNN, mas o melhor método para o reconhecimento de ambientes é o método FNN with Backpropagation. Dependendo do número de sensores utilizados, esta implementação reporta uma exatidão média entre 85,89% e 89,51% para o reconhecimento das AVD comuns, igual a 86,50% para o reconhecimento de ambientes, e igual a 100% para o reconhecimento de atividades sem movimento, reportando uma exatidão global entre 85,89% e 92,00%. A última etapa desta Tese foi a implementação do método nos dispositivos móveis, verificando que o método FNN requer um alto poder de processamento para o reconhecimento de ambientes e os resultados reportados com estes dispositivos são inferiores aos resultados reportados com a máquina com alta capacidade de processamento utilizada no desenvolvimento do método. Assim, o método DNN foi igualmente implementado para o reconhecimento dos ambientes com os dispositivos móveis. Finalmente, os resultados relatados com os dispositivos móveis reportam uma exatidão entre 86,39% e 89,15% para o reconhecimento das AVD comuns, igual a 45,68% para o reconhecimento de ambientes, e igual a 100% para o reconhecimento de atividades sem movimento, reportando uma exatidão geral entre 58,02% e 89,15%. Com base nos resultados relatados na literatura, os resultados do método desenvolvido mostram uma melhoria residual, mas os resultados desta Tese identificam mais AVD que os demais estudos disponíveis na literatura. A melhoria no reconhecimento das AVD com base na média das exatidões é igual a 2,93%, mas o número máximo de AVD e ambientes reconhecidos pelos estudos disponíveis na literatura é 13, enquanto o número de AVD e ambientes reconhecidos com o método implementado é 16. Assim, o método desenvolvido tem uma melhoria de 2,93% na exatidão do reconhecimento num maior número de AVD e ambientes. Como trabalho futuro, os resultados reportados nesta Tese podem ser considerados um ponto de partida para o desenvolvimento de um assistente digital pessoal, mas o número de ADL e ambientes reconhecidos pelo método deve ser aumentado e as experiências devem ser repetidas com diferentes tipos de dispositivos móveis (i.e., smartphones e smartwatches), e os métodos de imputação e outros métodos de classificação de dados devem ser explorados de modo a tentar aumentar a confiabilidade do método para o reconhecimento das AVD e ambientes

Artificial Intelligence and COVID-19: Deep Learning Approaches for Diagnosis and Treatment

COVID-19 outbreak has put the whole world in an unprecedented difficult situation bringing life around the world to a frightening halt and claiming thousands of lives. Due to COVID-19’s spread in 212 countries and territories and increasing numbers of infected cases and death tolls mounting to 5,212,172 and 334,915 (as of May 22 2020), it remains a real threat to the public health system. This paper renders a response to combat the virus through Artificial Intelligence (AI). Some Deep Learning (DL) methods have been illustrated to reach this goal, including Generative Adversarial Networks (GANs), Extreme Learning Machine (ELM), and Long/Short Term Memory (LSTM). It delineates an integrated bioinformatics approach in which different aspects of information from a continuum of structured and unstructured data sources are put together to form the user-friendly platforms for physicians and researchers. The main advantage of these AI-based platforms is to accelerate the process of diagnosis and treatment of the COVID-19 disease. The most recent related publications and medical reports were investigated with the purpose of choosing inputs and targets of the network that could facilitate reaching a reliable Artificial Neural Network-based tool for challenges associated with COVID-19. Furthermore, there are some specific inputs for each platform, including various forms of the data, such as clinical data and medical imaging which can improve the performance of the introduced approaches toward the best responses in practical applications

Cybersecurity in Industrial Networks: Artificial Intelligence Techniques Applied to Intrusion Detection Systems

Industrial control systems (ICS) operate on serial based networks which lack proper security safeguards by design. They are also becoming more integrated to corporate networks, creating new vulnerabilities which expose ICS networks to increasing levels of risk with potentially significant impact. Despite those risks, only a few mechanisms have been suggested and are available in practice as cybersecurity safeguards for the ICS network layer, maybe because they might not be commercially viable. Intrusion detection systems (IDS) are typically deployed in the corporate networks to protect against attacks since they are based on TCP/IP. However, IDS are not used in serial based ICS networks yet. This study examines and compares modern Artificial Intelligence (AI) techniques applied in IDS that are potentially useful for serial-based ICS networks. The results showed that current AI-based IDS methods are viable in such networks. A mix of AI techniques would be the best way forward to detect known attacks via rules and novel attacks, not previously mapped, via supervised and unsupervised techniques. Despite these strategies’ limited use in serial-based networks, their adoption could significantly strengthen cybersecurity of ICS networks

Space-partitioning with cascade-connected ANN structures for positioning in mobile communication systems

The world around us is getting more connected with each day passing by – new portable devices employing wireless connections to various networks wherever one might be. Locationaware computing has become an important bit of telecommunication services and industry. For this reason, the research efforts on new and improved localisation algorithms are constantly being performed. Thus far, the satellite positioning systems have achieved highest popularity and penetration regarding the global position estimation. In spite the numerous investigations aimed at enabling these systems to equally procure the position in both indoor and outdoor environments, this is still a task to be completed. This research work presented herein aimed at improving the state-of-the-art positioning techniques through the use of two highly popular mobile communication systems: WLAN and public land mobile networks. These systems already have widely deployed network structures (coverage) and a vast number of (inexpensive) mobile clients, so using them for additional, positioning purposes is rational and logical. First, the positioning in WLAN systems was analysed and elaborated. The indoor test-bed, used for verifying the models’ performances, covered almost 10,000m2 area. It has been chosen carefully so that the positioning could be thoroughly explored. The measurement campaigns performed therein covered the whole of test-bed environment and gave insight into location dependent parameters available in WLAN networks. Further analysis of the data lead to developing of positioning models based on ANNs. The best single ANN model obtained 9.26m average distance error and 7.75m median distance error. The novel positioning model structure, consisting of cascade-connected ANNs, improved those results to 8.14m and 4.57m, respectively. To adequately compare the proposed techniques with other, well-known research techniques, the environment positioning error parameter was introduced. This parameter enables to take the size of the test environment into account when comparing the accuracy of the indoor positioning techniques. Concerning the PLMN positioning, in-depth analysis of available system parameters and signalling protocols produced a positioning algorithm, capable of fusing the system received signal strength parameters received from multiple systems and multiple operators. Knowing that most of the areas are covered by signals from more than one network operator and even more than one system from one operator, it becomes easy to note the great practical value of this novel algorithm. On the other hand, an extensive drive-test measurement campaign, covering more than 600km in the central areas of Belgrade, was performed. Using this algorithm and applying the single ANN models to the recorded measurements, a 59m average distance error and 50m median distance error were obtained. Moreover, the positioning in indoor environment was verified and the degradation of performances, due to the crossenvironment model use, was reported: 105m average distance error and 101m median distance error. When applying the new, cascade-connected ANN structure model, distance errors were reduced to 26m and 2m, for the average and median distance errors, respectively. The obtained positioning accuracy was shown to be good enough for the implementation of a broad scope of location based services by using the existing and deployed, commonly available, infrastructure

Efficient Learning Machines

Computer scienc

Capacity Analysis of Vector Symbolic Architectures

Hyperdimensional computing (HDC) is a biologically-inspired framework which represents symbols with high-dimensional vectors, and uses vector operations to manipulate them. The ensemble of a particular vector space and a prescribed set of vector operations (including one addition-like for "bundling" and one outer-product-like for "binding") form a *vector symbolic architecture* (VSA). While VSAs have been employed in numerous applications and have been studied empirically, many theoretical questions about VSAs remain open. We analyze the *representation capacities* of four common VSAs: MAP-I, MAP-B, and two VSAs based on sparse binary vectors. "Representation capacity' here refers to bounds on the dimensions of the VSA vectors required to perform certain symbolic tasks, such as testing for set membership $i \in S$ and estimating set intersection sizes $|X \cap Y|$ for two sets of symbols $X$ and $Y$, to a given degree of accuracy. We also analyze the ability of a novel variant of a Hopfield network (a simple model of associative memory) to perform some of the same tasks that are typically asked of VSAs. In addition to providing new bounds on VSA capacities, our analyses establish and leverage connections between VSAs, "sketching" (dimensionality reduction) algorithms, and Bloom filters

Image and Video Forensics

Nowadays, images and videos have become the main modalities of information being exchanged in everyday life, and their pervasiveness has led the image forensics community to question their reliability, integrity, confidentiality, and security. Multimedia contents are generated in many different ways through the use of consumer electronics and high-quality digital imaging devices, such as smartphones, digital cameras, tablets, and wearable and IoT devices. The ever-increasing convenience of image acquisition has facilitated instant distribution and sharing of digital images on digital social platforms, determining a great amount of exchange data. Moreover, the pervasiveness of powerful image editing tools has allowed the manipulation of digital images for malicious or criminal ends, up to the creation of synthesized images and videos with the use of deep learning techniques. In response to these threats, the multimedia forensics community has produced major research efforts regarding the identification of the source and the detection of manipulation. In all cases (e.g., forensic investigations, fake news debunking, information warfare, and cyberattacks) where images and videos serve as critical evidence, forensic technologies that help to determine the origin, authenticity, and integrity of multimedia content can become essential tools. This book aims to collect a diverse and complementary set of articles that demonstrate new developments and applications in image and video forensics to tackle new and serious challenges to ensure media authenticity