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

Comparative Study of Classification Techniques on Breast Cancer FNA Biopsy Data

Accurate diagnostic detection of the cancerous cells in a patient is critical and may alter the subsequent treatment and increase the chances of survival rate. Machine learning techniques have been instrumental in disease detection and are currently being used in various classification problems due to their accurate prediction performance. Various techniques may provide different desired accuracies and it is therefore imperative to use the most suitable method which provides the best desired results. This research seeks to provide comparative analysis of Support Vector Machine, Bayesian classifier and other Artificial neural network classifiers (Backpropagation, linear programming, Learning vector quantization, and K nearest neighborhood) on the Wisconsin breast cancer classification problem

Boosting the concordance index for survival data - a unified framework to derive and evaluate biomarker combinations

The development of molecular signatures for the prediction of time-to-event outcomes is a methodologically challenging task in bioinformatics and biostatistics. Although there are numerous approaches for the derivation of marker combinations and their evaluation, the underlying methodology often suffers from the problem that different optimization criteria are mixed during the feature selection, estimation and evaluation steps. This might result in marker combinations that are only suboptimal regarding the evaluation criterion of interest. To address this issue, we propose a unified framework to derive and evaluate biomarker combinations. Our approach is based on the concordance index for time-to-event data, which is a non-parametric measure to quantify the discrimatory power of a prediction rule. Specifically, we propose a component-wise boosting algorithm that results in linear biomarker combinations that are optimal with respect to a smoothed version of the concordance index. We investigate the performance of our algorithm in a large-scale simulation study and in two molecular data sets for the prediction of survival in breast cancer patients. Our numerical results show that the new approach is not only methodologically sound but can also lead to a higher discriminatory power than traditional approaches for the derivation of gene signatures.Comment: revised manuscript - added simulation study, additional result

Asterias: a parallelized web-based suite for the analysis of expression and aCGH data

Asterias (\url{http://www.asterias.info}) is an integrated collection of freely-accessible web tools for the analysis of gene expression and aCGH data. Most of the tools use parallel computing (via MPI). Most of our applications allow the user to obtain additional information for user-selected genes by using clickable links in tables and/or figures. Our tools include: normalization of expression and aCGH data; converting between different types of gene/clone and protein identifiers; filtering and imputation; finding differentially expressed genes related to patient class and survival data; searching for models of class prediction; using random forests to search for minimal models for class prediction or for large subsets of genes with predictive capacity; searching for molecular signatures and predictive genes with survival data; detecting regions of genomic DNA gain or loss. The capability to send results between different applications, access to additional functional information, and parallelized computation make our suite unique and exploit features only available to web-based applications.Comment: web based application; 3 figure

Medical Internet-of-Things Based Breast Cancer Diagnosis Using Hyperparameter-Optimized Neural Networks

In today’s healthcare setting, the accurate and timely diagnosis of breast cancer is critical for recovery and treatment in the early stages. In recent years, the Internet of Things (IoT) has experienced a transformation that allows the analysis of real-time and historical data using artificial intelligence (AI) and machine learning (ML) approaches. Medical IoT combines medical devices and AI applications with healthcare infrastructure to support medical diagnostics. The current state-of-the-art approach fails to diagnose breast cancer in its initial period, resulting in the death of most women. As a result, medical professionals and researchers are faced with a tremendous problem in early breast cancer detection. We propose a medical IoT-based diagnostic system that competently identifies malignant and benign people in an IoT environment to resolve the difficulty of identifying early-stage breast cancer. The artificial neural network (ANN) and convolutional neural network (CNN) with hyperparameter optimization are used for malignant vs. benign classification, while the Support Vector Machine (SVM) and Multilayer Perceptron (MLP) were utilized as baseline classifiers for comparison. Hyperparameters are important for machine learning algorithms since they directly control the behaviors of training algorithms and have a significant effect on the performance of machine learning models. We employ a particle swarm optimization (PSO) feature selection approach to select more satisfactory features from the breast cancer dataset to enhance the classification performance using MLP and SVM, while grid-based search was used to find the best combination of the hyperparameters of the CNN and ANN models. The Wisconsin Diagnostic Breast Cancer (WDBC) dataset was used to test the proposed approach. The proposed model got a classification accuracy of 98.5% using CNN, and 99.2% using ANN.publishedVersio

Detection of Breast Cancer using AI Techniques – A Survey

Cancer refers to any one of a large number of diseases characterized by the development of abnormal cells that divide uncontrollably and have the ability to infiltrate and destroy normal body tissue.Without treatment, it can cause serious health issues andresult in a loss of life. Breast cancer is the most common cancer among women around the world. Despite enormous medical progress, breast cancer has still remained the second leading cause of death worldwide. Early detection of cancer may reduce mortality and morbidity. This paper presents a review of the detection methods for cancer through Artificial Intelligence (AI) in different ways. Previously Microscopic reviews of tissues on glass slides are used for cancer diagnostics to improve diagnostic accuracy. We can use different techniques such as digital imaging and artificial intelligence algorithm. Cancer care is also advancing thanks to AI’s ability to collect and process data. Due to the nature of processing this information, the task is often a time-consuming and tedious job for doctors. This process may be made much easier, quicker and efficient through the advancement as well as by using modified technologies

Predicting breast cancer risk, recurrence and survivability

This thesis focuses on predicting breast cancer at early stages by using machine learning algorithms based on biological datasets. The accuracy of those algorithms has been improved to enable the physicians to enhance the success of treatment, thus saving lives and avoiding several further medical tests