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

Performance Analysis Of Data-Driven Algorithms In Detecting Intrusions On Smart Grid

The traditional power grid is no longer a practical solution for power delivery due to several shortcomings, including chronic blackouts, energy storage issues, high cost of assets, and high carbon emissions. Therefore, there is a serious need for better, cheaper, and cleaner power grid technology that addresses the limitations of traditional power grids. A smart grid is a holistic solution to these issues that consists of a variety of operations and energy measures. This technology can deliver energy to end-users through a two-way flow of communication. It is expected to generate reliable, efficient, and clean power by integrating multiple technologies. It promises reliability, improved functionality, and economical means of power transmission and distribution. This technology also decreases greenhouse emissions by transferring clean, affordable, and efficient energy to users. Smart grid provides several benefits, such as increasing grid resilience, self-healing, and improving system performance. Despite these benefits, this network has been the target of a number of cyber-attacks that violate the availability, integrity, confidentiality, and accountability of the network. For instance, in 2021, a cyber-attack targeted a U.S. power system that shut down the power grid, leaving approximately 100,000 people without power. Another threat on U.S. Smart Grids happened in March 2018 which targeted multiple nuclear power plants and water equipment. These instances represent the obvious reasons why a high level of security approaches is needed in Smart Grids to detect and mitigate sophisticated cyber-attacks. For this purpose, the US National Electric Sector Cybersecurity Organization and the Department of Energy have joined their efforts with other federal agencies, including the Cybersecurity for Energy Delivery Systems and the Federal Energy Regulatory Commission, to investigate the security risks of smart grid networks. Their investigation shows that smart grid requires reliable solutions to defend and prevent cyber-attacks and vulnerability issues. This investigation also shows that with the emerging technologies, including 5G and 6G, smart grid may become more vulnerable to multistage cyber-attacks. A number of studies have been done to identify, detect, and investigate the vulnerabilities of smart grid networks. However, the existing techniques have fundamental limitations, such as low detection rates, high rates of false positives, high rates of misdetection, data poisoning, data quality and processing, lack of scalability, and issues regarding handling huge volumes of data. Therefore, these techniques cannot ensure safe, efficient, and dependable communication for smart grid networks. Therefore, the goal of this dissertation is to investigate the efficiency of machine learning in detecting cyber-attacks on smart grids. The proposed methods are based on supervised, unsupervised machine and deep learning, reinforcement learning, and online learning models. These models have to be trained, tested, and validated, using a reliable dataset. In this dissertation, CICDDoS 2019 was used to train, test, and validate the efficiency of the proposed models. The results show that, for supervised machine learning models, the ensemble models outperform other traditional models. Among the deep learning models, densely neural network family provides satisfactory results for detecting and classifying intrusions on smart grid. Among unsupervised models, variational auto-encoder, provides the highest performance compared to the other unsupervised models. In reinforcement learning, the proposed Capsule Q-learning provides higher detection and lower misdetection rates, compared to the other model in literature. In online learning, the Online Sequential Euclidean Distance Routing Capsule Network model provides significantly better results in detecting intrusion attacks on smart grid, compared to the other deep online models

Geometry- and Accuracy-Preserving Random Forest Proximities with Applications

Many machine learning algorithms use calculated distances or similarities between data observations to make predictions, cluster similar data, visualize patterns, or generally explore the data. Most distances or similarity measures do not incorporate known data labels and are thus considered unsupervised. Supervised methods for measuring distance exist which incorporate data labels and thereby exaggerate separation between data points of different classes. This approach tends to distort the natural structure of the data. Instead of following similar approaches, we leverage a popular algorithm used for making data-driven predictions, known as random forests, to naturally incorporate data labels into similarity measures known as random forest proximities. In this dissertation, we explore previously defined random forest proximities and demonstrate their weaknesses in popular proximity-based applications. Additionally, we develop a new proximity definition that can be used to recreate the random forest’s predictions. We call these random forest-geometry-and accuracy-Preserving proximities or RF-GAP. We show by proof and empirical demonstration can be used to perfectly reconstruct the random forest’s predictions and, as a result, we argue that RF-GAP proximities provide a truer representation of the random forest’s learning when used in proximity-based applications. We provide evidence to suggest that RF-GAP proximities improve applications including imputing missing data, detecting outliers, and visualizing the data. We also introduce a new random forest proximity-based technique that can be used to generate 2- or 3-dimensional data representations which can be used as a tool to visually explore the data. We show that this method does well at portraying the relationship between data variables and the data labels. We show quantitatively and qualitatively that this method surpasses other existing methods for this task

Cost-Sensitive Learning-based Methods for Imbalanced Classification Problems with Applications

Analysis and predictive modeling of massive datasets is an extremely significant problem that arises in many practical applications. The task of predictive modeling becomes even more challenging when data are imperfect or uncertain. The real data are frequently affected by outliers, uncertain labels, and uneven distribution of classes (imbalanced data). Such uncertainties create bias and make predictive modeling an even more difficult task. In the present work, we introduce a cost-sensitive learning method (CSL) to deal with the classification of imperfect data. Typically, most traditional approaches for classification demonstrate poor performance in an environment with imperfect data. We propose the use of CSL with Support Vector Machine, which is a well-known data mining algorithm. The results reveal that the proposed algorithm produces more accurate classifiers and is more robust with respect to imperfect data. Furthermore, we explore the best performance measures to tackle imperfect data along with addressing real problems in quality control and business analytics

A survey on online active learning

Online active learning is a paradigm in machine learning that aims to select the most informative data points to label from a data stream. The problem of minimizing the cost associated with collecting labeled observations has gained a lot of attention in recent years, particularly in real-world applications where data is only available in an unlabeled form. Annotating each observation can be time-consuming and costly, making it difficult to obtain large amounts of labeled data. To overcome this issue, many active learning strategies have been proposed in the last decades, aiming to select the most informative observations for labeling in order to improve the performance of machine learning models. These approaches can be broadly divided into two categories: static pool-based and stream-based active learning. Pool-based active learning involves selecting a subset of observations from a closed pool of unlabeled data, and it has been the focus of many surveys and literature reviews. However, the growing availability of data streams has led to an increase in the number of approaches that focus on online active learning, which involves continuously selecting and labeling observations as they arrive in a stream. This work aims to provide an overview of the most recently proposed approaches for selecting the most informative observations from data streams in the context of online active learning. We review the various techniques that have been proposed and discuss their strengths and limitations, as well as the challenges and opportunities that exist in this area of research. Our review aims to provide a comprehensive and up-to-date overview of the field and to highlight directions for future work