Unsupervised feature extraction with autoencoder : for the representation of parkinson´s disease patients

Dissertation presented as partial requirement for obtaining the Master’s degree in Information Management, with a specialization in Knowledge Management and Business IntelligenceData representation is one of the fundamental concepts in machine learning. An appropriate representation is found by discovering a structure and automatic detection of patterns in data. In many domains, representation or feature learning is a critical step in improving the performance of machine learning algorithms due to the multidimensionality of data that feeds the model. Some tasks may have different perspectives and approaches depending on how data is represented. In recent years, deep artificial neural networks have provided better solutions to several pattern recognition problems and classification tasks. Deep architectures have also shown their effectiveness in capturing latent features for data representation. In this document, autoencoders will be examined to obtain the representation of Parkinson's disease patients and compared with conventional representation learning algorithms. The results will show whether the proposed method of feature selection leads to the desired accuracy for predicting the severity of Parkinson’s disease

Deep learning pipeline for quality filtering of MRSI spectra.

With the rise of novel 3D magnetic resonance spectroscopy imaging (MRSI) acquisition protocols in clinical practice, which are capable of capturing a large number of spectra from a subject's brain, there is a need for an automated preprocessing pipeline that filters out bad-quality spectra and identifies contaminated but salvageable spectra prior to the metabolite quantification step. This work introduces such a pipeline based on an ensemble of deep-learning classifiers. The dataset consists of 36,338 spectra from one healthy subject and five brain tumor patients, acquired with an EPSI variant, which implemented a novel type of spectral editing named SLOtboom-Weng (SLOW) editing on a 7T MR scanner. The spectra were labeled manually by an expert into four classes of spectral quality as follows: (i) noise, (ii) spectra greatly influenced by lipid-related artifacts (deemed not to contain clinical information), (iii) spectra containing metabolic information slightly contaminated by lipid signals, and (iv) good-quality spectra. The AI model consists of three pairs of networks, each comprising a convolutional autoencoder and a multilayer perceptron network. In the classification step, the encoding half of the autoencoder is kept as a dimensionality reduction tool, while the fully connected layers are added to its output. Each of the three pairs of networks is trained on different representations of spectra (real, imaginary, or both), aiming at robust decision-making. The final class is assigned via a majority voting scheme. The F1 scores obtained on the test dataset for the four previously defined classes are 0.96, 0.93, 0.82, and 0.90, respectively. The arguably lower value of 0.82 was reached for the least represented class of spectra mildly influenced by lipids. Not only does the proposed model minimise the required user interaction, but it also greatly reduces the computation time at the metabolite quantification step (by selecting a subset of spectra worth quantifying) and enforces the display of only clinically relevant information

PT-Net: A Multi-Model Machine Learning Approach for Smarter Next-Generation Wearable Tremor Suppression Devices for Parkinson\u27s Disease Tremor

According to the World Health Organization (WHO), Parkinson\u27s Disease (PD) is the second most common neurodegenerative condition that can cause tremors and other motor and non motor related symptoms. Medication and deep brain stimulation (DBS) are often used to treat tremor; however, medication is not always effective and has adverse effects, and DBS is invasive and carries a significant risk of complications. Wearable tremor suppression devices (WTSDs) have been proposed as a possible alternative, but their effectiveness is limited by the tremor models they use, which introduce a phase delay that decreases the performance of the devices. Additionally, the availability of tremor datasets is limited, which prevents the rapid advancement of these devices. To address the challenges facing the WTSDs, PD tremor data were collected at the Wearable Biomechatronics Laboratory (WearMe Lab) to develop methods and data-driven models to improve the performance of WTSDs in managing tremor, and potentially to be integrated with the wearable tremor suppression glove that is being developed at the WearMe Lab. A predictive model was introduced and showed improved motion estimation with an average estimation accuracy of 99.2%. The model was also able to predict motion with multiple steps ahead, negating the phase delay introduced by previous models and achieving prediction accuracies of 97%, 94%, 92%, and 90\% for predicting voluntary motion 10, 20, 50, and 100 steps ahead, respectively. Tremor and task classification models were also developed, with mean classification accuracies of 91.2% and 91.1%, respectively. These models can be used to fine-tune the parameters of existing estimators based on the type of tremor and task, increasing their suppression capabilities. To address the absence of a mathematical model for generating tremor data and limited access to existing PD tremor datasets, an open-source generative model was developed to produce data with similar characteristics, distribution, and patterns to real data. The reliability of the generated data was evaluated using four different methods, showing that the generative model can produce data with similar distribution, patterns, and characteristics to real data. The development of data-driven models and methods to improve the performance of wearable tremor suppression devices for Parkinson\u27s disease can potentially offer a noninvasive and effective alternative to medication and deep brain stimulation. The proposed predictive model, classification model, and the open-source generative model provide a promising framework for the advancement of wearable technology for tremor suppression, potentially leading to a significant improvement in the quality of life for individuals with Parkinson\u27s disease

Artificial intelligence within the interplay between natural and artificial computation:Advances in data science, trends and applications

Artificial intelligence and all its supporting tools, e.g. machine and deep learning in computational intelligence-based systems, are rebuilding our society (economy, education, life-style, etc.) and promising a new era for the social welfare state. In this paper we summarize recent advances in data science and artificial intelligence within the interplay between natural and artificial computation. A review of recent works published in the latter field and the state the art are summarized in a comprehensive and self-contained way to provide a baseline framework for the international community in artificial intelligence. Moreover, this paper aims to provide a complete analysis and some relevant discussions of the current trends and insights within several theoretical and application fields covered in the essay, from theoretical models in artificial intelligence and machine learning to the most prospective applications in robotics, neuroscience, brain computer interfaces, medicine and society, in general.BMS - Pfizer(U01 AG024904). Spanish Ministry of Science, projects: TIN2017-85827-P, RTI2018-098913-B-I00, PSI2015-65848-R, PGC2018-098813-B-C31, PGC2018-098813-B-C32, RTI2018-101114-B-I, TIN2017-90135-R, RTI2018-098743-B-I00 and RTI2018-094645-B-I00; the FPU program (FPU15/06512, FPU17/04154) and Juan de la Cierva (FJCI-2017–33022). Autonomous Government of Andalusia (Spain) projects: UMA18-FEDERJA-084. Consellería de Cultura, Educación e Ordenación Universitaria of Galicia: ED431C2017/12, accreditation 2016–2019, ED431G/08, ED431C2018/29, Comunidad de Madrid, Y2018/EMT-5062 and grant ED431F2018/02. PPMI – a public – private partnership – is funded by The Michael J. Fox Foundation for Parkinson’s Research and funding partners, including Abbott, Biogen Idec, F. Hoffman-La Roche Ltd., GE Healthcare, Genentech and Pfizer Inc

Dysarthric speech analysis and automatic recognition using phase based representations

Dysarthria is a neurological speech impairment which usually results in the loss of motor speech control due to muscular atrophy and poor coordination of articulators. Dysarthric speech is more difficult to model with machine learning algorithms, due to inconsistencies in the acoustic signal and to limited amounts of training data. This study reports a new approach for the analysis and representation of dysarthric speech, and applies it to improve ASR performance. The Zeros of Z-Transform (ZZT) are investigated for dysarthric vowel segments. It shows evidence of a phase-based acoustic phenomenon that is responsible for the way the distribution of zero patterns relate to speech intelligibility. It is investigated whether such phase-based artefacts can be systematically exploited to understand their association with intelligibility. A metric based on the phase slope deviation (PSD) is introduced that are observed in the unwrapped phase spectrum of dysarthric vowel segments. The metric compares the differences between the slopes of dysarthric vowels and typical vowels. The PSD shows a strong and nearly linear correspondence with the intelligibility of the speaker, and it is shown to hold for two separate databases of dysarthric speakers. A systematic procedure for correcting the underlying phase deviations results in a significant improvement in ASR performance for speakers with severe and moderate dysarthria. In addition, information encoded in the phase component of the Fourier transform of dysarthric speech is exploited in the group delay spectrum. Its properties are found to represent disordered speech more effectively than the magnitude spectrum. Dysarthric ASR performance was significantly improved using phase-based cepstral features in comparison to the conventional MFCCs. A combined approach utilising the benefits of PSD corrections and phase-based features was found to surpass all the previous performance on the UASPEECH database of dysarthric speech

An Explainable Artificial Intelligence Approach Based on Deep Type-2 Fuzzy Logic System

Artificial intelligence (AI) systems have benefitted from the easy availability of computing power and the rapid increase in the quantity and quality of data which has led to the widespread adoption of AI techniques across a wide variety of fields. However, the use of complex (or Black box) AI systems such as Deep Neural Networks, support vector machines, etc., could lead to a lack of transparency. This lack of transparency is not specific to deep learning or complex AI algorithms; other interpretable AI algorithms such as kernel machines, logistic regressions, decision trees, or rules-based algorithms can also become difficult to interpret for high dimensional inputs. The lack of transparency or explainability reduces the effectiveness of AI models in regulated applications (such as medical, financial, etc.), where it is essential to explain the model operation and how it arrived at a given prediction. The need for explainability in AI has led to a new line of research that focuses on developing Explainable AI techniques. There are three main avenues of research that are being explored to achieve explainability; first, Deep Explanations, which involves the modification of existing Deep learning models to add explainability. The methods proposed to do Deep explanations generally provide details about all the input features that affect the output, generally in a visual format as there might be a large number of features. This type of explanation is useful for tasks such as image recognition, but in other tasks, it might be hard to distinguish the most important features. Second, Model induction, which involves methods that are model agnostic, but these methods might not be suitable for use in regulated applications. The third method is to use existing interpretable models such as decision trees, fuzzy logic, etc., but the problem with them is that they can also become opaque for high dimensional data. Hence, this thesis presents a novel AI system by combining the predictive power of Deep Learning with the interpretability of Interval Type-2 Fuzzy Logic Systems. The advantages of such a system are, first, the ability to be trained via labelled and unlabelled data (i.e., mixing supervised and unsupervised learning). Second, having embedded feature selection abilities (i.e., can be trained by hundreds and thousands of inputs with no need for feature selection) while delivering explainable models with small rules bases composed of short rules to maximize the model’s interpretability. The proposed model was developed with data from British Telecom (BT). It achieved comparable performance to the deep models such as Stacked Autoencoder (SAE) and Convolution Neural Networks (CNN). In categorical datasets, the model outperformed the SAE by 2%, performed within 2-3% of the CNN and outperformed Multi-Layer Perceptron (MLP) and IT2FLS by 4%. In the regression datasets, the model performed slightly worse than the SAE, MLP and CNN models, but it outperformed the IT2FLS with a 15% lower error. The proposed model achieved excellent interpretability in a survey where it was rated within 2% of the highly interpretable IT2FLS. It was also rated 20% and 17% better than Deep learning XAI tools LIME and SHAP, respectively. The proposed model shows a small loss in performance for significantly higher interpretability, making it a suitable replacement for the other AI models in applications with many features where interpretability is paramount

Analysis and automatic identification of spontaneous emotions in speech from human-human and human-machine communication

383 p.This research mainly focuses on improving our understanding of human-human and human-machineinteractions by analysing paricipants¿ emotional status. For this purpose, we have developed andenhanced Speech Emotion Recognition (SER) systems for both interactions in real-life scenarios,explicitly emphasising the Spanish language. In this framework, we have conducted an in-depth analysisof how humans express emotions using speech when communicating with other persons or machines inactual situations. Thus, we have analysed and studied the way in which emotional information isexpressed in a variety of true-to-life environments, which is a crucial aspect for the development of SERsystems. This study aimed to comprehensively understand the challenge we wanted to address:identifying emotional information on speech using machine learning technologies. Neural networks havebeen demonstrated to be adequate tools for identifying events in speech and language. Most of themaimed to make local comparisons between some specific aspects; thus, the experimental conditions weretailored to each particular analysis. The experiments across different articles (from P1 to P19) are hardlycomparable due to our continuous learning of dealing with the difficult task of identifying emotions inspeech. In order to make a fair comparison, additional unpublished results are presented in the Appendix.These experiments were carried out under identical and rigorous conditions. This general comparisonoffers an overview of the advantages and disadvantages of the different methodologies for the automaticrecognition of emotions in speech

Políticas de Copyright de Publicações Científicas em Repositórios Institucionais: O Caso do INESC TEC

A progressiva transformação das práticas científicas, impulsionada pelo desenvolvimento das novas Tecnologias de Informação e Comunicação (TIC), têm possibilitado aumentar o acesso à informação, caminhando gradualmente para uma abertura do ciclo de pesquisa. Isto permitirá resolver a longo prazo uma adversidade que se tem colocado aos investigadores, que passa pela existência de barreiras que limitam as condições de acesso, sejam estas geográficas ou financeiras. Apesar da produção científica ser dominada, maioritariamente, por grandes editoras comerciais, estando sujeita às regras por estas impostas, o Movimento do Acesso Aberto cuja primeira declaração pública, a Declaração de Budapeste (BOAI), é de 2002, vem propor alterações significativas que beneficiam os autores e os leitores. Este Movimento vem a ganhar importância em Portugal desde 2003, com a constituição do primeiro repositório institucional a nível nacional. Os repositórios institucionais surgiram como uma ferramenta de divulgação da produção científica de uma instituição, com o intuito de permitir abrir aos resultados da investigação, quer antes da publicação e do próprio processo de arbitragem (preprint), quer depois (postprint), e, consequentemente, aumentar a visibilidade do trabalho desenvolvido por um investigador e a respetiva instituição. O estudo apresentado, que passou por uma análise das políticas de copyright das publicações científicas mais relevantes do INESC TEC, permitiu não só perceber que as editoras adotam cada vez mais políticas que possibilitam o auto-arquivo das publicações em repositórios institucionais, como também que existe todo um trabalho de sensibilização a percorrer, não só para os investigadores, como para a instituição e toda a sociedade. A produção de um conjunto de recomendações, que passam pela implementação de uma política institucional que incentive o auto-arquivo das publicações desenvolvidas no âmbito institucional no repositório, serve como mote para uma maior valorização da produção científica do INESC TEC.The progressive transformation of scientific practices, driven by the development of new Information and Communication Technologies (ICT), which made it possible to increase access to information, gradually moving towards an opening of the research cycle. This opening makes it possible to resolve, in the long term, the adversity that has been placed on researchers, which involves the existence of barriers that limit access conditions, whether geographical or financial. Although large commercial publishers predominantly dominate scientific production and subject it to the rules imposed by them, the Open Access movement whose first public declaration, the Budapest Declaration (BOAI), was in 2002, proposes significant changes that benefit the authors and the readers. This Movement has gained importance in Portugal since 2003, with the constitution of the first institutional repository at the national level. Institutional repositories have emerged as a tool for disseminating the scientific production of an institution to open the results of the research, both before publication and the preprint process and postprint, increase the visibility of work done by an investigator and his or her institution. The present study, which underwent an analysis of the copyright policies of INESC TEC most relevant scientific publications, allowed not only to realize that publishers are increasingly adopting policies that make it possible to self-archive publications in institutional repositories, all the work of raising awareness, not only for researchers but also for the institution and the whole society. The production of a set of recommendations, which go through the implementation of an institutional policy that encourages the self-archiving of the publications developed in the institutional scope in the repository, serves as a motto for a greater appreciation of the scientific production of INESC TEC