Machine Learning and Integrative Analysis of Biomedical Big Data.

Recent developments in high-throughput technologies have accelerated the accumulation of massive amounts of omics data from multiple sources: genome, epigenome, transcriptome, proteome, metabolome, etc. Traditionally, data from each source (e.g., genome) is analyzed in isolation using statistical and machine learning (ML) methods. Integrative analysis of multi-omics and clinical data is key to new biomedical discoveries and advancements in precision medicine. However, data integration poses new computational challenges as well as exacerbates the ones associated with single-omics studies. Specialized computational approaches are required to effectively and efficiently perform integrative analysis of biomedical data acquired from diverse modalities. In this review, we discuss state-of-the-art ML-based approaches for tackling five specific computational challenges associated with integrative analysis: curse of dimensionality, data heterogeneity, missing data, class imbalance and scalability issues

Big Data Analytics for Complex Systems

The evolution of technology in all fields led to the generation of vast amounts of data by modern systems. Using data to extract information, make predictions, and make decisions is the current trend in artificial intelligence. The advancement of big data analytics tools made accessing and storing data easier and faster than ever, and machine learning algorithms help to identify patterns in and extract information from data. The current tools and machines in health, computer technologies, and manufacturing can generate massive raw data about their products or samples. The author of this work proposes a modern integrative system that can utilize big data analytics, machine learning, super-computer resources, and industrial health machines’ measurements to build a smart system that can mimic the human intelligence skills of observations, detection, prediction, and decision-making. The applications of the proposed smart systems are included as case studies to highlight the contributions of each system. The first contribution is the ability to utilize big data revolutionary and deep learning technologies on production lines to diagnose incidents and take proper action. In the current digital transformational industrial era, Industry 4.0 has been receiving researcher attention because it can be used to automate production-line decisions. Reconfigurable manufacturing systems (RMS) have been widely used to reduce the setup cost of restructuring production lines. However, the current RMS modules are not linked to the cloud for online decision-making to take the proper decision; these modules must connect to an online server (super-computer) that has big data analytics and machine learning capabilities. The online means that data is centralized on cloud (supercomputer) and accessible in real-time. In this study, deep neural networks are utilized to detect the decisive features of a product and build a prediction model in which the iFactory will make the necessary decision for the defective products. The Spark ecosystem is used to manage the access, processing, and storing of the big data streaming. This contribution is implemented as a closed cycle, which for the best of our knowledge, no one in the literature has introduced big data analysis using deep learning on real-time applications in the manufacturing system. The code shows a high accuracy of 97% for classifying the normal versus defective items. The second contribution, which is in Bioinformatics, is the ability to build supervised machine learning approaches based on the gene expression of patients to predict proper treatment for breast cancer. In the trial, to personalize treatment, the machine learns the genes that are active in the patient cohort with a five-year survival period. The initial condition here is that each group must only undergo one specific treatment. After learning about each group (or class), the machine can personalize the treatment of a new patient by diagnosing the patients’ gene expression. The proposed model will help in the diagnosis and treatment of the patient. The future work in this area involves building a protein-protein interaction network with the selected genes for each treatment to first analyze the motives of the genes and target them with the proper drug molecules. In the learning phase, a couple of feature-selection techniques and supervised standard classifiers are used to build the prediction model. Most of the nodes show a high-performance measurement where accuracy, sensitivity, specificity, and F-measure ranges around 100%. The third contribution is the ability to build semi-supervised learning for the breast cancer survival treatment that advances the second contribution. By understanding the relations between the classes, we can design the machine learning phase based on the similarities between classes. In the proposed research, the researcher used the Euclidean matrix distance among each survival treatment class to build the hierarchical learning model. The distance information that is learned through a non-supervised approach can help the prediction model to select the classes that are away from each other to maximize the distance between classes and gain wider class groups. The performance measurement of this approach shows a slight improvement from the second model. However, this model reduced the number of discriminative genes from 47 to 37. The model in the second contribution studies each class individually while this model focuses on the relationships between the classes and uses this information in the learning phase. Hierarchical clustering is completed to draw the borders between groups of classes before building the classification models. Several distance measurements are tested to identify the best linkages between classes. Most of the nodes show a high-performance measurement where accuracy, sensitivity, specificity, and F-measure ranges from 90% to 100%. All the case study models showed high-performance measurements in the prediction phase. These modern models can be replicated for different problems within different domains. The comprehensive models of the newer technologies are reconfigurable and modular; any newer learning phase can be plugged-in at both ends of the learning phase. Therefore, the output of the system can be an input for another learning system, and a newer feature can be added to the input to be considered for the learning phase

High-Performance Modelling and Simulation for Big Data Applications

This open access book was prepared as a Final Publication of the COST Action IC1406 “High-Performance Modelling and Simulation for Big Data Applications (cHiPSet)“ project. Long considered important pillars of the scientific method, Modelling and Simulation have evolved from traditional discrete numerical methods to complex data-intensive continuous analytical optimisations. Resolution, scale, and accuracy have become essential to predict and analyse natural and complex systems in science and engineering. When their level of abstraction raises to have a better discernment of the domain at hand, their representation gets increasingly demanding for computational and data resources. On the other hand, High Performance Computing typically entails the effective use of parallel and distributed processing units coupled with efficient storage, communication and visualisation systems to underpin complex data-intensive applications in distinct scientific and technical domains. It is then arguably required to have a seamless interaction of High Performance Computing with Modelling and Simulation in order to store, compute, analyse, and visualise large data sets in science and engineering. Funded by the European Commission, cHiPSet has provided a dynamic trans-European forum for their members and distinguished guests to openly discuss novel perspectives and topics of interests for these two communities. This cHiPSet compendium presents a set of selected case studies related to healthcare, biological data, computational advertising, multimedia, finance, bioinformatics, and telecommunications

High-Performance Modelling and Simulation for Big Data Applications

This open access book was prepared as a Final Publication of the COST Action IC1406 “High-Performance Modelling and Simulation for Big Data Applications (cHiPSet)“ project. Long considered important pillars of the scientific method, Modelling and Simulation have evolved from traditional discrete numerical methods to complex data-intensive continuous analytical optimisations. Resolution, scale, and accuracy have become essential to predict and analyse natural and complex systems in science and engineering. When their level of abstraction raises to have a better discernment of the domain at hand, their representation gets increasingly demanding for computational and data resources. On the other hand, High Performance Computing typically entails the effective use of parallel and distributed processing units coupled with efficient storage, communication and visualisation systems to underpin complex data-intensive applications in distinct scientific and technical domains. It is then arguably required to have a seamless interaction of High Performance Computing with Modelling and Simulation in order to store, compute, analyse, and visualise large data sets in science and engineering. Funded by the European Commission, cHiPSet has provided a dynamic trans-European forum for their members and distinguished guests to openly discuss novel perspectives and topics of interests for these two communities. This cHiPSet compendium presents a set of selected case studies related to healthcare, biological data, computational advertising, multimedia, finance, bioinformatics, and telecommunications

Systems Analytics and Integration of Big Omics Data

A “genotype"" is essentially an organism's full hereditary information which is obtained from its parents. A ""phenotype"" is an organism's actual observed physical and behavioral properties. These may include traits such as morphology, size, height, eye color, metabolism, etc. One of the pressing challenges in computational and systems biology is genotype-to-phenotype prediction. This is challenging given the amount of data generated by modern Omics technologies. This “Big Data” is so large and complex that traditional data processing applications are not up to the task. Challenges arise in collection, analysis, mining, sharing, transfer, visualization, archiving, and integration of these data. In this Special Issue, there is a focus on the systems-level analysis of Omics data, recent developments in gene ontology annotation, and advances in biological pathways and network biology. The integration of Omics data with clinical and biomedical data using machine learning is explored. This Special Issue covers new methodologies in the context of gene–environment interactions, tissue-specific gene expression, and how external factors or host genetics impact the microbiome

Empirical study of dimensionality reduction methodologies for classification problems

Cuando hablamos de “Dimensionality Reduction” en Informática o “Big Data” nos referimos al proceso de reducción de variables previamente examinadas de un conjunto de datos para poder así obtener un conjunto de variables menor que nos permitirá construir un modelo de datos igual o con mejor precisión y menor cantidad de datos. Con este propósito se aplican técnicas de “Feature Selection” y “Feature Extraction”, con la primera de ellas extraemos un conjunto de características importantes de un dataset mediante el uso de distintos algoritmos de “machine learning”, mientras que con la segunda obtendremos un nuevo conjunto de características obtenidas a partir de las características originales. En este trabajo de fin de grado hacemos un estudio empírico sobre las distintas metodologías para clasificación de problemas utilizando un dataset médico llamado NCS-1 de pacientes clínicos con distintas patologías médicas, estudiamos los distintos algoritmos que se pueden aplicar a cada caso determinado con dicho dataset, y finalmente con los datos obtenidos realizamos un benchmark que nos permite entender mejor los distintos modelos estudiados.When we speak about Dimensionality reduction in informatics or big data, we refer to the process of reducing the number of random variables under consideration, and so, obtaining a set of principle variables which allow us to build a data model with the same or similar accuracy and a lower amount of data. For this purpose, we apply feature selection and feature extraction techniques. With feature selection we select a subset of the original feature set using techniques of machine learning, and with feature extraction we are going to build a new set of features from the original feature set. In this Project, we are going to make an empirical study about the different methodologies for classification problems using a medical dataset called NCS-1 of clinical patients with different medical pathologies, we study the different algorithms that can be applied for each case with this dataset, and finally with obtained data developing a Benchmark to understand the different applied models.Grado en Ingeniería Informátic

The Convergence of Human and Artificial Intelligence on Clinical Care - Part I

This edited book contains twelve studies, large and pilots, in five main categories: (i) adaptive imputation to increase the density of clinical data for improving downstream modeling; (ii) machine-learning-empowered diagnosis models; (iii) machine learning models for outcome prediction; (iv) innovative use of AI to improve our understanding of the public view; and (v) understanding of the attitude of providers in trusting insights from AI for complex cases. This collection is an excellent example of how technology can add value in healthcare settings and hints at some of the pressing challenges in the field. Artificial intelligence is gradually becoming a go-to technology in clinical care; therefore, it is important to work collaboratively and to shift from performance-driven outcomes to risk-sensitive model optimization, improved transparency, and better patient representation, to ensure more equitable healthcare for all

Towards clinical translation of raman spectroscopy for tumor cell identification

In the modern world, cancer is one of the leading causes of death, and its early diagnostics remains one of the big challenges. Since cancer starts as a malfunction on the cellular level, the diagnostic techniques have to deal with single cells. Detection of circulating tumor cells (CTCs), which are present in the patient's blood, holds promise for the future theranostic applications, as CTCs represent the actual state of the primary tumor. Raman spectroscopy is a label-free technique capable of non-destructive and chemically-specific characterization of individual cells. In contrast to marker-based methods, the CTCs detected by Raman can be reused for more specific single-cells biochemical analysis methods. This thesis focuses on technological developments for Raman-based CTC identification, and encompasses the whole chain of involved methods and processes, including instrumentation and microfluidic cell handling, automation of spectra acquisition and storage, and chemometric data analysis. It starts with a design of custom application-specific instruments that we used to evaluate and optimize different experimental parameters. A major part is software development for automated acquisition and organized storage of spectral data in a database. With the automated measurement systems and the database in place, we were able to collect about 40.000 Raman spectra of more than 15 incubated cancer cell lines, healthy donor leukocytes, as well as samples originating from clinical patients. Additionally, the thesis gives an overview of data analysis methods and provides an insight into the underlying trends of the dataset. Although the cell identification models could not reliably differentiate between individual cancer cell lines, they were able to recognize tumor cells among healthy leukocytes with prediction accuracy of more than 95%. This work demonstrated an increase in the throughput of Raman-based CTC detection, and provides a basis for its clinical translation

Data Science in Healthcare

Data science is an interdisciplinary field that applies numerous techniques, such as machine learning, neural networks, and deep learning, to create value based on extracting knowledge and insights from available data. Advances in data science have a significant impact on healthcare. While advances in the sharing of medical information result in better and earlier diagnoses as well as more patient-tailored treatments, information management is also affected by trends such as increased patient centricity (with shared decision making), self-care (e.g., using wearables), and integrated care delivery. The delivery of health services is being revolutionized through the sharing and integration of health data across organizational boundaries. Via data science, researchers can deliver new approaches to merge, analyze, and process complex data and gain more actionable insights, understanding, and knowledge at the individual and population levels. This Special Issue focuses on how data science is used in healthcare (e.g., through predictive modeling) and on related topics, such as data sharing and data management