Elephant Search with Deep Learning for Microarray Data Analysis

Even though there is a plethora of research in Microarray gene expression data analysis, still, it poses challenges for researchers to effectively and efficiently analyze the large yet complex expression of genes. The feature (gene) selection method is of paramount importance for understanding the differences in biological and non-biological variation between samples. In order to address this problem, a novel elephant search (ES) based optimization is proposed to select best gene expressions from the large volume of microarray data. Further, a promising machine learning method is envisioned to leverage such high dimensional and complex microarray dataset for extracting hidden patterns inside to make a meaningful prediction and most accurate classification. In particular, stochastic gradient descent based Deep learning (DL) with softmax activation function is then used on the reduced features (genes) for better classification of different samples according to their gene expression levels. The experiments are carried out on nine most popular Cancer microarray gene selection datasets, obtained from UCI machine learning repository. The empirical results obtained by the proposed elephant search based deep learning (ESDL) approach are compared with most recent published article for its suitability in future Bioinformatics research.Comment: 12 pages, 5 Tabl

Heart Diseases Diagnosis Using Artificial Neural Networks

Information technology has virtually altered every aspect of human life in the present era. The application of informatics in the health sector is rapidly gaining prominence and the benefits of this innovative paradigm are being realized across the globe. This evolution produced large number of patients’ data that can be employed by computer technologies and machine learning techniques, and turned into useful information and knowledge. This data can be used to develop expert systems to help in diagnosing some life-threating diseases such as heart diseases, with less cost, processing time and improved diagnosis accuracy. Even though, modern medicine is generating huge amount of data every day, little has been done to use this available data to solve challenges faced in the successful diagnosis of heart diseases. Highlighting the need for more research into the usage of robust data mining techniques to help health care professionals in the diagnosis of heart diseases and other debilitating disease conditions. Based on the foregoing, this thesis aims to develop a health informatics system for the classification of heart diseases using data mining techniques focusing on Radial Basis functions and emerging Neural Networks approach. The presented research involves three development stages; firstly, the development of a preliminary classification system for Coronary Artery Disease (CAD) using Radial Basis Function (RBF) neural networks. The research then deploys the deep learning approach to detect three different types of heart diseases i.e. Sleep Apnea, Arrhythmias and CAD by designing two novel classification systems; the first adopt a novel deep neural network method (with Rectified Linear unit activation) design as the second approach in this thesis and the other implements a novel multilayer kernel machine to mimic the behaviour of deep learning as the third approach. Additionally, this thesis uses a dataset obtained from patients, and employs normalization and feature extraction means to explore it in a unique way that facilitates its usage for training and validating different classification methods. This unique dataset is useful to researchers and practitioners working in heart disease treatment and diagnosis. The findings from the study reveal that the proposed models have high classification performance that is comparable, or perhaps exceed in some cases, the existing automated and manual methods of heart disease diagnosis. Besides, the proposed deep-learning models provide better performance when applied on large data sets (e.g., in the case of Sleep Apnea), with reasonable performance with smaller data sets. The proposed system for clinical diagnoses of heart diseases, contributes to the accurate detection of such disease, and could serve as an important tool in the area of clinic support system. The outcome of this study in form of implementation tool can be used by cardiologists to help them make more consistent diagnosis of heart diseases

Bioinformatics Applications Based On Machine Learning

The great advances in information technology (IT) have implications for many sectors, such as bioinformatics, and has considerably increased their possibilities. This book presents a collection of 11 original research papers, all of them related to the application of IT-related techniques within the bioinformatics sector: from new applications created from the adaptation and application of existing techniques to the creation of new methodologies to solve existing problems

Implementing decision tree-based algorithms in medical diagnostic decision support systems

As a branch of healthcare, medical diagnosis can be defined as finding the disease based on the signs and symptoms of the patient. To this end, the required information is gathered from different sources like physical examination, medical history and general information of the patient. Development of smart classification models for medical diagnosis is of great interest amongst the researchers. This is mainly owing to the fact that the machine learning and data mining algorithms are capable of detecting the hidden trends between features of a database. Hence, classifying the medical datasets using smart techniques paves the way to design more efficient medical diagnostic decision support systems. Several databases have been provided in the literature to investigate different aspects of diseases. As an alternative to the available diagnosis tools/methods, this research involves machine learning algorithms called Classification and Regression Tree (CART), Random Forest (RF) and Extremely Randomized Trees or Extra Trees (ET) for the development of classification models that can be implemented in computer-aided diagnosis systems. As a decision tree (DT), CART is fast to create, and it applies to both the quantitative and qualitative data. For classification problems, RF and ET employ a number of weak learners like CART to develop models for classification tasks. We employed Wisconsin Breast Cancer Database (WBCD), Z-Alizadeh Sani dataset for coronary artery disease (CAD) and the databanks gathered in Ghaem Hospital’s dermatology clinic for the response of patients having common and/or plantar warts to the cryotherapy and/or immunotherapy methods. To classify the breast cancer type based on the WBCD, the RF and ET methods were employed. It was found that the developed RF and ET models forecast the WBCD type with 100% accuracy in all cases. To choose the proper treatment approach for warts as well as the CAD diagnosis, the CART methodology was employed. The findings of the error analysis revealed that the proposed CART models for the applications of interest attain the highest precision and no literature model can rival it. The outcome of this study supports the idea that methods like CART, RF and ET not only improve the diagnosis precision, but also reduce the time and expense needed to reach a diagnosis. However, since these strategies are highly sensitive to the quality and quantity of the introduced data, more extensive databases with a greater number of independent parameters might be required for further practical implications of the developed models

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

Modeling Human Atrial Patho-Electrophysiology from Ion Channels to ECG - Substrates, Pharmacology, Vulnerability, and P-Waves

Half of the patients suffering from atrial fibrillation (AF) cannot be treated adequately, today. This thesis presents multi-scale computational methods to advance our understanding of patho-mechanisms, to improve the diagnosis of patients harboring an arrhythmogenic substrate, and to tailor therapy. The modeling pipeline ranges from ion channels on the subcellular level up to the ECG on the body surface. The tailored therapeutic approaches carry the potential to reduce the burden of AF

Improving Maternal and Fetal Cardiac Monitoring Using Artificial Intelligence

Early diagnosis of possible risks in the physiological status of fetus and mother during pregnancy and delivery is critical and can reduce mortality and morbidity. For example, early detection of life-threatening congenital heart disease may increase survival rate and reduce morbidity while allowing parents to make informed decisions. To study cardiac function, a variety of signals are required to be collected. In practice, several heart monitoring methods, such as electrocardiogram (ECG) and photoplethysmography (PPG), are commonly performed. Although there are several methods for monitoring fetal and maternal health, research is currently underway to enhance the mobility, accuracy, automation, and noise resistance of these methods to be used extensively, even at home. Artificial Intelligence (AI) can help to design a precise and convenient monitoring system. To achieve the goals, the following objectives are defined in this research: The first step for a signal acquisition system is to obtain high-quality signals. As the first objective, a signal processing scheme is explored to improve the signal-to-noise ratio (SNR) of signals and extract the desired signal from a noisy one with negative SNR (i.e., power of noise is greater than signal). It is worth mentioning that ECG and PPG signals are sensitive to noise from a variety of sources, increasing the risk of misunderstanding and interfering with the diagnostic process. The noises typically arise from power line interference, white noise, electrode contact noise, muscle contraction, baseline wandering, instrument noise, motion artifacts, electrosurgical noise. Even a slight variation in the obtained ECG waveform can impair the understanding of the patient's heart condition and affect the treatment procedure. Recent solutions, such as adaptive and blind source separation (BSS) algorithms, still have drawbacks, such as the need for noise or desired signal model, tuning and calibration, and inefficiency when dealing with excessively noisy signals. Therefore, the final goal of this step is to develop a robust algorithm that can estimate noise, even when SNR is negative, using the BSS method and remove it based on an adaptive filter. The second objective is defined for monitoring maternal and fetal ECG. Previous methods that were non-invasive used maternal abdominal ECG (MECG) for extracting fetal ECG (FECG). These methods need to be calibrated to generalize well. In other words, for each new subject, a calibration with a trustable device is required, which makes it difficult and time-consuming. The calibration is also susceptible to errors. We explore deep learning (DL) models for domain mapping, such as Cycle-Consistent Adversarial Networks, to map MECG to fetal ECG (FECG) and vice versa. The advantages of the proposed DL method over state-of-the-art approaches, such as adaptive filters or blind source separation, are that the proposed method is generalized well on unseen subjects. Moreover, it does not need calibration and is not sensitive to the heart rate variability of mother and fetal; it can also handle low signal-to-noise ratio (SNR) conditions. Thirdly, AI-based system that can measure continuous systolic blood pressure (SBP) and diastolic blood pressure (DBP) with minimum electrode requirements is explored. The most common method of measuring blood pressure is using cuff-based equipment, which cannot monitor blood pressure continuously, requires calibration, and is difficult to use. Other solutions use a synchronized ECG and PPG combination, which is still inconvenient and challenging to synchronize. The proposed method overcomes those issues and only uses PPG signal, comparing to other solutions. Using only PPG for blood pressure is more convenient since it is only one electrode on the finger where its acquisition is more resilient against error due to movement. The fourth objective is to detect anomalies on FECG data. The requirement of thousands of manually annotated samples is a concern for state-of-the-art detection systems, especially for fetal ECG (FECG), where there are few publicly available FECG datasets annotated for each FECG beat. Therefore, we will utilize active learning and transfer-learning concept to train a FECG anomaly detection system with the least training samples and high accuracy. In this part, a model is trained for detecting ECG anomalies in adults. Later this model is trained to detect anomalies on FECG. We only select more influential samples from the training set for training, which leads to training with the least effort. Because of physician shortages and rural geography, pregnant women's ability to get prenatal care might be improved through remote monitoring, especially when access to prenatal care is limited. Increased compliance with prenatal treatment and linked care amongst various providers are two possible benefits of remote monitoring. If recorded signals are transmitted correctly, maternal and fetal remote monitoring can be effective. Therefore, the last objective is to design a compression algorithm that can compress signals (like ECG) with a higher ratio than state-of-the-art and perform decompression fast without distortion. The proposed compression is fast thanks to the time domain B-Spline approach, and compressed data can be used for visualization and monitoring without decompression owing to the B-spline properties. Moreover, the stochastic optimization is designed to retain the signal quality and does not distort signal for diagnosis purposes while having a high compression ratio. In summary, components for creating an end-to-end system for day-to-day maternal and fetal cardiac monitoring can be envisioned as a mix of all tasks listed above. PPG and ECG recorded from the mother can be denoised using deconvolution strategy. Then, compression can be employed for transmitting signal. The trained CycleGAN model can be used for extracting FECG from MECG. Then, trained model using active transfer learning can detect anomaly on both MECG and FECG. Simultaneously, maternal BP is retrieved from the PPG signal. This information can be used for monitoring the cardiac status of mother and fetus, and also can be used for filling reports such as partogram

Simplified Cardiodynamic Tissue Electrophysiology Characterization, Reduced Order Modeling with Therapeutic Perspective

Atrial fibrillation (Afib) is the most common cardiac arrhythmia affecting millions of people around the world. Mapping and analysis of electrical activation patterns such as electric rotors during Afib is crucial in understanding arrhythmic mechanisms and assessment of diagnostic measures. To this end, there exists various mapping studies where textit{'quantitative'} features such as local activation time, dominant frequency, wave direction, and conduction velocity are extracted from recorded intracardiac electrograms (EGMs). However, obtaining quantitative features further adds to multiplicity of the data and henceforth does not help interpretation of measured signals as opposed to using a more compressed diagnostic terms such as linking the measurements to reentry mechanisms. Through some techniques it is possible to construct isopotential and phase mappings by the help of monophasic action potential recordings in higher spatial resolution. In those cases, however, both expensive mapping tools performing multi-site simultaneous recordings which are not available to most of electrophysiologists are required. On the other hand, the most commonly used catheters which provide high resolution but local measurements remain rather rudimentary in mapping a spatially more global arrhythmic behaviors in a simultaneous fashion. Spiral waves are tissue level phenomena observed in both clinical and experimental settings. They are the product of electrical rotors which are associated with reentry mechanisms during Afib. They can be reproduced using computer models of cardiac electrical activity. Current computer models vary in complexity, accuracy, and efficiency. One particular type is called biophysical models which are based on detailed ion channel interactions. Besides being computationally demanding, they are exceedingly complex and intractable preventing their use in a systems approach where multilevel events are generally considered together. Phenomenological models, on the other hand, include summarized details of ionic events yet preserve fundamental biophysical accuracy. A particular one of them, a minimal resistor model (MRM), was shown to reproduce relevant basic electrophysiological behaviors such as (action potential) AP and electrical restitution properties for human ventricular tissue. The objective in present thesis is to 'qualitatively' characterize fibrillatory wavefront propagation dynamics in cardiac tissue using simulated intracardiac EGMs obtained from most commonly used and lower cost catheter types providing high resolution but localized readings. Another purpose connected to the previous is to show adequacy of a phenomenological model, MRM, in reproducing biophysically related behaviors for human atria. In this respect, two category of problems are handled throughout the thesis: (1) parameter estimation of MRM and (2) discrimination of spiral wave behaviors through intracardiac EGMs simulated using MRM. In the first part, representativeness of MRM for human atrial electrophysiology is established through adaptation of it to a biophysically detailed model originated from experimental data. Specifically, a method is proposed for parameter estimation of the simple model, MRM, to match a targeted behavior such as AP and electrical restitutions first generated from a complex model, by using extended Kalman filter (EKF). In the second part, a method that receives intracardiac EGMs and returns corresponding wavefront propagation patterns classified in terms of electric rotor dynamics is introduced. The method incorporates an information theoretical distance which is called normalized compression distance (NCD) used for assessment of distance measure between simulated behaviors. Achieving outstanding performance together with robustness in discrimination through usage of simulated data enables a theoretical validation of the method. Proposed frameworks collectively yield (1) potential usability of a computationally efficient and easier in analysis model for tissue level cardiac events and (2) simplicity and practicality in clinics through a mapping from a multiple, complex EGM signals to electric rotor behaviors, symptoms more relevant to the diagnosis.Ph.D., Electrical Engineering -- Drexel University, 201

Computational Intelligence in Healthcare

This book is a printed edition of the Special Issue Computational Intelligence in Healthcare that was published in Electronic

Modeling Human Atrial Patho-Electrophysiology from Ion Channels to ECG - Substrates, Pharmacology, Vulnerability, and P-Waves

Half of the patients suffering from atrial fibrillation (AF) cannot be treated adequately, today. This book presents multi-scale computational methods to advance our understanding of patho-mechanisms, to improve the diagnosis of patients harboring an arrhythmogenic substrate, and to tailor therapy. The modeling pipeline ranges from ion channels on the subcellular level up to the ECG on the body surface. The tailored therapeutic approaches carry the potential to reduce the burden of AF