Error-based Analysis of VEP EEG Signal using LMS

Electroencephalography (EEG) involves the usage of electrodes placed on the human scalp to record electrical impulses generated by the brain. One of the many components that are present in EEG signals is the Visually Evoked Potential (VEP), whereby brief electrical impulses are generated as a result of the presence of visual stimuli. The aim of this project is to analyse EEG signals that contain VEP using the least-mean squares (LMS) method and differentiate between alcoholic and non-alcoholic subjects based on the resultant error signal. This LMS method is a form of adaptive filter that minimizes the mean square of the cost function for every iteration it undergoes and is widely used in many signal imaging applications due to its simplicity in implementation and low computational complexity. The EEG recording with VEP components is already available so the scope of the project only covers the adaptation of the LMS adaptive filter and the analysis of the VEP EEG error signals for 5 alcoholic and non-alcoholic subjects. The analysis of the results indicate that there is a certain range of standard deviation values in which it is possible to classify the condition of the subject into either alcoholic or non-alcoholic condition. vi

Performance Evaluation of Smart Decision Support Systems on Healthcare

Medical activity requires responsibility not only from clinical knowledge and skill but also on the management of an enormous amount of information related to patient care. It is through proper treatment of information that experts can consistently build a healthy wellness policy. The primary objective for the development of decision support systems (DSSs) is to provide information to specialists when and where they are needed. These systems provide information, models, and data manipulation tools to help experts make better decisions in a variety of situations. Most of the challenges that smart DSSs face come from the great difficulty of dealing with large volumes of information, which is continuously generated by the most diverse types of devices and equipment, requiring high computational resources. This situation makes this type of system susceptible to not recovering information quickly for the decision making. As a result of this adversity, the information quality and the provision of an infrastructure capable of promoting the integration and articulation among different health information systems (HIS) become promising research topics in the field of electronic health (e-health) and that, for this same reason, are addressed in this research. The work described in this thesis is motivated by the need to propose novel approaches to deal with problems inherent to the acquisition, cleaning, integration, and aggregation of data obtained from different sources in e-health environments, as well as their analysis. To ensure the success of data integration and analysis in e-health environments, it is essential that machine-learning (ML) algorithms ensure system reliability. However, in this type of environment, it is not possible to guarantee a reliable scenario. This scenario makes intelligent SAD susceptible to predictive failures, which severely compromise overall system performance. On the other hand, systems can have their performance compromised due to the overload of information they can support. To solve some of these problems, this thesis presents several proposals and studies on the impact of ML algorithms in the monitoring and management of hypertensive disorders related to pregnancy of risk. The primary goals of the proposals presented in this thesis are to improve the overall performance of health information systems. In particular, ML-based methods are exploited to improve the prediction accuracy and optimize the use of monitoring device resources. It was demonstrated that the use of this type of strategy and methodology contributes to a significant increase in the performance of smart DSSs, not only concerning precision but also in the computational cost reduction used in the classification process. The observed results seek to contribute to the advance of state of the art in methods and strategies based on AI that aim to surpass some challenges that emerge from the integration and performance of the smart DSSs. With the use of algorithms based on AI, it is possible to quickly and automatically analyze a larger volume of complex data and focus on more accurate results, providing high-value predictions for a better decision making in real time and without human intervention.A atividade médica requer responsabilidade não apenas com base no conhecimento e na habilidade clínica, mas também na gestão de uma enorme quantidade de informações relacionadas ao atendimento ao paciente. É através do tratamento adequado das informações que os especialistas podem consistentemente construir uma política saudável de bem-estar. O principal objetivo para o desenvolvimento de sistemas de apoio à decisão (SAD) é fornecer informações aos especialistas onde e quando são necessárias. Esses sistemas fornecem informações, modelos e ferramentas de manipulação de dados para ajudar os especialistas a tomar melhores decisões em diversas situações. A maioria dos desafios que os SAD inteligentes enfrentam advêm da grande dificuldade de lidar com grandes volumes de dados, que é gerada constantemente pelos mais diversos tipos de dispositivos e equipamentos, exigindo elevados recursos computacionais. Essa situação torna este tipo de sistemas suscetível a não recuperar a informação rapidamente para a tomada de decisão. Como resultado dessa adversidade, a qualidade da informação e a provisão de uma infraestrutura capaz de promover a integração e a articulação entre diferentes sistemas de informação em saúde (SIS) tornam-se promissores tópicos de pesquisa no campo da saúde eletrônica (e-saúde) e que, por essa mesma razão, são abordadas nesta investigação. O trabalho descrito nesta tese é motivado pela necessidade de propor novas abordagens para lidar com os problemas inerentes à aquisição, limpeza, integração e agregação de dados obtidos de diferentes fontes em ambientes de e-saúde, bem como sua análise. Para garantir o sucesso da integração e análise de dados em ambientes e-saúde é importante que os algoritmos baseados em aprendizagem de máquina (AM) garantam a confiabilidade do sistema. No entanto, neste tipo de ambiente, não é possível garantir um cenário totalmente confiável. Esse cenário torna os SAD inteligentes suscetíveis à presença de falhas de predição que comprometem seriamente o desempenho geral do sistema. Por outro lado, os sistemas podem ter seu desempenho comprometido devido à sobrecarga de informações que podem suportar. Para tentar resolver alguns destes problemas, esta tese apresenta várias propostas e estudos sobre o impacto de algoritmos de AM na monitoria e gestão de transtornos hipertensivos relacionados com a gravidez (gestação) de risco. O objetivo das propostas apresentadas nesta tese é melhorar o desempenho global de sistemas de informação em saúde. Em particular, os métodos baseados em AM são explorados para melhorar a precisão da predição e otimizar o uso dos recursos dos dispositivos de monitorização. Ficou demonstrado que o uso deste tipo de estratégia e metodologia contribui para um aumento significativo do desempenho dos SAD inteligentes, não só em termos de precisão, mas também na diminuição do custo computacional utilizado no processo de classificação. Os resultados observados buscam contribuir para o avanço do estado da arte em métodos e estratégias baseadas em inteligência artificial que visam ultrapassar alguns desafios que advêm da integração e desempenho dos SAD inteligentes. Como o uso de algoritmos baseados em inteligência artificial é possível analisar de forma rápida e automática um volume maior de dados complexos e focar em resultados mais precisos, fornecendo previsões de alto valor para uma melhor tomada de decisão em tempo real e sem intervenção humana

Deep Cellular Recurrent Neural Architecture for Efficient Multidimensional Time-Series Data Processing

Efficient processing of time series data is a fundamental yet challenging problem in pattern recognition. Though recent developments in machine learning and deep learning have enabled remarkable improvements in processing large scale datasets in many application domains, most are designed and regulated to handle inputs that are static in time. Many real-world data, such as in biomedical, surveillance and security, financial, manufacturing and engineering applications, are rarely static in time, and demand models able to recognize patterns in both space and time. Current machine learning (ML) and deep learning (DL) models adapted for time series processing tend to grow in complexity and size to accommodate the additional dimensionality of time. Specifically, the biologically inspired learning based models known as artificial neural networks that have shown extraordinary success in pattern recognition, tend to grow prohibitively large and cumbersome in the presence of large scale multi-dimensional time series biomedical data such as EEG. Consequently, this work aims to develop representative ML and DL models for robust and efficient large scale time series processing. First, we design a novel ML pipeline with efficient feature engineering to process a large scale multi-channel scalp EEG dataset for automated detection of epileptic seizures. With the use of a sophisticated yet computationally efficient time-frequency analysis technique known as harmonic wavelet packet transform and an efficient self-similarity computation based on fractal dimension, we achieve state-of-the-art performance for automated seizure detection in EEG data. Subsequently, we investigate the development of a novel efficient deep recurrent learning model for large scale time series processing. For this, we first study the functionality and training of a biologically inspired neural network architecture known as cellular simultaneous recurrent neural network (CSRN). We obtain a generalization of this network for multiple topological image processing tasks and investigate the learning efficacy of the complex cellular architecture using several state-of-the-art training methods. Finally, we develop a novel deep cellular recurrent neural network (CDRNN) architecture based on the biologically inspired distributed processing used in CSRN for processing time series data. The proposed DCRNN leverages the cellular recurrent architecture to promote extensive weight sharing and efficient, individualized, synchronous processing of multi-source time series data. Experiments on a large scale multi-channel scalp EEG, and a machine fault detection dataset show that the proposed DCRNN offers state-of-the-art recognition performance while using substantially fewer trainable recurrent units

Error-based Analysis of VEP EEG Signal using LMS

Electroencephalography (EEG) involves the usage of electrodes placed on the human scalp to record electrical impulses generated by the brain. One of the many components that are present in EEG signals is the Visually Evoked Potential (VEP), whereby brief electrical impulses are generated as a result of the presence of visual stimuli. The aim of this project is to analyse EEG signals that contain VEP using the least-mean squares (LMS) method and differentiate between alcoholic and non-alcoholic subjects based on the resultant error signal. This LMS method is a form of adaptive filter that minimizes the mean square of the cost function for every iteration it undergoes and is widely used in many signal imaging applications due to its simplicity in implementation and low computational complexity. The EEG recording with VEP components is already available so the scope of the project only covers the adaptation of the LMS adaptive filter and the analysis of the VEP EEG error signals for 5 alcoholic and non-alcoholic subjects. The analysis of the results indicate that there is a certain range of standard deviation values in which it is possible to classify the condition of the subject into either alcoholic or non-alcoholic condition. vi

생물학적 서열 데이터에 대한 표현 학습

학위논문(박사) -- 서울대학교대학원 : 공과대학 전기·정보공학부, 2021.8. 윤성로.As we are living in the era of big data, the biomedical domain is not an exception. With the advent of technologies such as next-generation sequencing, developing methods to capitalize on the explosion of biomedical data is one of the most major challenges in bioinformatics. Representation learning, in particular deep learning, has made significant advancements in diverse fields where the artificial intelligence community has struggled for many years. However, although representation learning has also shown great promises in bioinformatics, it is not a silver bullet. Off-the-shelf applications of representation learning cannot always provide successful results for biological sequence data. There remain full of challenges and opportunities to be explored. This dissertation presents a set of representation learning methods to address three issues in biological sequence data analysis. First, we propose a two-stage training strategy to address throughput and information trade-offs within wet-lab CRISPR-Cpf1 activity experiments. Second, we propose an encoding scheme to model interaction between two sequences for functional microRNA target prediction. Third, we propose a self-supervised pre-training method to bridge the exponentially growing gap between the numbers of unlabeled and labeled protein sequences. In summary, this dissertation proposes a set of representation learning methods that can derive invaluable information from the biological sequence data.우리는 빅데이터의 시대를 맞이하고 있으며, 의생명 분야 또한 예외가 아니다. 차세대 염기서열 분석과 같은 기술들이 도래함에 따라, 폭발적인 의생명 데이터의 증가를 활용하기 위한 방법론의 개발은 생물정보학 분야의 주요 과제 중의 하나이다. 심층 학습을 포함한 표현 학습 기법들은 인공지능 학계가 오랫동안 어려움을 겪어온 다양한 분야에서 상당한 발전을 이루었다. 표현 학습은 생물정보학 분야에서도 많은 가능성을 보여주었다. 하지만 단순한 적용으로는 생물학적 서열 데이터 분석의 성공적인 결과를 항상 얻을 수는 않으며, 여전히 연구가 필요한 많은 문제들이 남아있다. 본 학위논문은 생물학적 서열 데이터 분석과 관련된 세 가지 사안을 해결하기 위해, 표현 학습에 기반한 일련의 방법론들을 제안한다. 첫 번째로, 유전자가위 실험 데이터에 내재된 정보와 수율의 균형에 대처할 수 있는 2단계 학습 기법을 제안한다. 두 번째로, 두 염기 서열 간의 상호 작용을 학습하기 위한 부호화 방식을 제안한다. 세 번째로, 기하급수적으로 증가하는 특징되지 않은 단백질 서열을 활용하기 위한 자기 지도 사전 학습 기법을 제안한다. 요약하자면, 본 학위논문은 생물학적 서열 데이터를 분석하여 중요한 정보를 도출할 수 있는 표현 학습에 기반한 일련의 방법론들을 제안한다.1 Introduction 1 1.1 Motivation 1 1.2 Contents of Dissertation 4 2 Background 8 2.1 Representation Learning 8 2.2 Deep Neural Networks 12 2.2.1 Multi-layer Perceptrons 12 2.2.2 Convolutional Neural Networks 14 2.2.3 Recurrent Neural Networks 16 2.2.4 Transformers 19 2.3 Training of Deep Neural Networks 23 2.4 Representation Learning in Bioinformatics 26 2.5 Biological Sequence Data Analyses 29 2.6 Evaluation Metrics 32 3 CRISPR-Cpf1 Activity Prediction 36 3.1 Methods 39 3.1.1 Model Architecture 39 3.1.2 Training of Seq-deepCpf1 and DeepCpf1 41 3.2 Experiment Results 44 3.2.1 Datasets 44 3.2.2 Baselines 47 3.2.3 Evaluation of Seq-deepCpf1 49 3.2.4 Evaluation of DeepCpf1 51 3.3 Summary 55 4 Functional microRNA Target Prediction 56 4.1 Methods 62 4.1.1 Candidate Target Site Selection 63 4.1.2 Input Encoding 64 4.1.3 Residual Network 67 4.1.4 Post-processing 68 4.2 Experiment Results 70 4.2.1 Datasets 70 4.2.2 Classification of Functional and Non-functional Targets 71 4.2.3 Distinguishing High-functional Targets 73 4.2.4 Ablation Studies 76 4.3 Summary 77 5 Self-supervised Learning of Protein Representations 78 5.1 Methods 83 5.1.1 Pre-training Procedure 83 5.1.2 Fine-tuning Procedure 86 5.1.3 Model Architecturen 87 5.2 Experiment Results 90 5.2.1 Experiment Setup 90 5.2.2 Pre-training Results 92 5.2.3 Fine-tuning Results 93 5.2.4 Comparison with Larger Protein Language Models 97 5.2.5 Ablation Studies 100 5.2.6 Qualitative Interpreatation Analyses 103 5.3 Summary 106 6 Discussion 107 6.1 Challenges and Opportunities 107 7 Conclusion 111 Bibliography 113 Abstract in Korean 130박

CNN-LSTM-based models to predict the heart rate using PPG signal from wearables during physical exercise

Atrial fibrillation, or AFib is the most common form of arrhythmia, in fact, 3\% of people over the age of 20 suffer from this condition and more shockingly, it is found that patients with arrhythmias are 5 times more likely to have a stroke [1]. These events of irregularity in the heart beat occur briefly and can be very sporadic which leads their detection to be rather cumbersome, with the standard diagnostic procedure being a long term continuous ECG. This leads to multiple problems, first of all, the ECG is commonly performed as the person is laying down in a hospital bed, which immediately distances the test environment from the real world scenario of living with AFib or another kind of arrhythmia, especially since arrhythmias are more likely to manifest during the practice of physical exercise. From this need arises the alternative of using a PPG (Photoplethysmography) signal, which is an optical method of measuring the blood volume in surfaces such as the finger tip, wrist or ear lobe[2] and can be present in many portable devices like fitness bands and smartwatches, therefore enabling it to be used during the practice of physical exercise [3]. This alternative heart rate monitor is substantially less invasive and more mobile but it is also much more susceptible to motion artifacts. However the motion artifacts that create this noise can be quantified through the pairing of an accelerometer to this device, which provides us with data regarding the acceleration of the devices over the 3 axis. Data like this is available and we will be using the dataset from the IEEE Signal Processing Cup 2015, with which, a plethora of different approaches to remove the noise becomes available, from more traditional filtering methods to the more modern Artificial Intelligence approaches, like the neural networks and support vector machines that have been used in the related work. We believe this multimodal approach will provide us with substantially better results than traditional methods that used the signal itself as the only input of the model

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

Smart Distributed Generation System Event Classification using Recurrent Neural Network-based Long Short-term Memory

High penetration of distributed generation (DG) sources into a decentralized power system causes several disturbances, making the monitoring and operation control of the system complicated. Moreover, because of being passive, modern DG systems are unable to detect and inform about these disturbances related to power quality in an intelligent approach. This paper proposed an intelligent and novel technique, capable of making real-time decisions on the occurrence of different DG events such as islanding, capacitor switching, unsymmetrical faults, load switching, and loss of parallel feeder and distinguishing these events from the normal mode of operation. This event classification technique was designed to diagnose the distinctive pattern of the time-domain signal representing a measured electrical parameter, like the voltage, at DG point of common coupling (PCC) during such events. Then different power system events were classified into their root causes using long short-term memory (LSTM), which is a deep learning algorithm for time sequence to label classification. A total of 1100 events showcasing islanding, faults, and other DG events were generated based on the model of a smart distributed generation system using a MATLAB/Simulink environment. Classifier performance was calculated using 5-fold cross-validation. The genetic algorithm (GA) was used to determine the optimum value of classification hyper-parameters and the best combination of features. The simulation results indicated that the events were classified with high precision and specificity with ten cycles of occurrences while achieving a 99.17% validation accuracy. The performance of the proposed classification technique does not degrade with the presence of noise in test data, multiple DG sources in the model, and inclusion of motor starting event in training samples