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

Coupling different methods for overcoming the class imbalance problem

Many classification problems must deal with imbalanced datasets where one class \u2013 the majority class \u2013 outnumbers the other classes. Standard classification methods do not provide accurate predictions in this setting since classification is generally biased towards the majority class. The minority classes are oftentimes the ones of interest (e.g., when they are associated with pathological conditions in patients), so methods for handling imbalanced datasets are critical. Using several different datasets, this paper evaluates the performance of state-of-the-art classification methods for handling the imbalance problem in both binary and multi-class datasets. Different strategies are considered, including the one-class and dimension reduction approaches, as well as their fusions. Moreover, some ensembles of classifiers are tested, in addition to stand-alone classifiers, to assess the effectiveness of ensembles in the presence of imbalance. Finally, a novel ensemble of ensembles is designed specifically to tackle the problem of class imbalance: the proposed ensemble does not need to be tuned separately for each dataset and outperforms all the other tested approaches. To validate our classifiers we resort to the KEEL-dataset repository, whose data partitions (training/test) are publicly available and have already been used in the open literature: as a consequence, it is possible to report a fair comparison among different approaches in the literature. Our best approach (MATLAB code and datasets not easily accessible elsewhere) will be available at https://www.dei.unipd.it/node/2357

Parameter-Free Extreme Learning Machine for Imbalanced Classification

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A survey on learning from imbalanced data streams: taxonomy, challenges, empirical study, and reproducible experimental framework

Class imbalance poses new challenges when it comes to classifying data streams. Many algorithms recently proposed in the literature tackle this problem using a variety of data-level, algorithm-level, and ensemble approaches. However, there is a lack of standardized and agreed-upon procedures on how to evaluate these algorithms. This work presents a taxonomy of algorithms for imbalanced data streams and proposes a standardized, exhaustive, and informative experimental testbed to evaluate algorithms in a collection of diverse and challenging imbalanced data stream scenarios. The experimental study evaluates 24 state-of-the-art data streams algorithms on 515 imbalanced data streams that combine static and dynamic class imbalance ratios, instance-level difficulties, concept drift, real-world and semi-synthetic datasets in binary and multi-class scenarios. This leads to the largest experimental study conducted so far in the data stream mining domain. We discuss the advantages and disadvantages of state-of-the-art classifiers in each of these scenarios and we provide general recommendations to end-users for selecting the best algorithms for imbalanced data streams. Additionally, we formulate open challenges and future directions for this domain. Our experimental testbed is fully reproducible and easy to extend with new methods. This way we propose the first standardized approach to conducting experiments in imbalanced data streams that can be used by other researchers to create trustworthy and fair evaluation of newly proposed methods. Our experimental framework can be downloaded from https://github.com/canoalberto/imbalanced-streams

DATA-DRIVEN TECHNIQUES FOR DIAGNOSING BEARING DEFECTS IN INDUCTION MOTORS

Induction motors are frequently used in many automated systems as a major driving force, and thus, their reliable performances are of predominant concerns. Induction motors are subject to different types of faults and an early detection of faults can reduce maintenance costs and prevent unscheduled downtime. Motor faults are generally related to three components: the stator, the rotor and/or the bearings. This study focuses on the fault diagnosis of the bearings, which is the major reason for failures in induction motors. Data-driven fault diagnosis systems usually include a classification model which is supported by an efficient pre-processing unit. Various classifiers, which aim to diagnose multiple bearing defects (i.e., ball, inner race and outer race defects of different diameters), require well-processed data. The pre-processing tasks plays a vital role for extracting informative features from the vibration signal, reducing the dimensionality of the features and selecting the best features from the feature pool. Once the vibration signal is perfectly analyzed and a proper feature subset is created, then fault classifiers can be trained. However, classification task can be difficult if the training dataset is not balanced. Induction motors usually operate under healthy condition (than faulty situation), thus the monitored vibration samples relate to the normal state of the system expected to be more than the samples of the faulty state. Here, in this work, this challenge is also considered so that the classification model needs to deal with class imbalance problem