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

SMOTE for Learning from Imbalanced Data: Progress and Challenges, Marking the 15-year Anniversary

The Synthetic Minority Oversampling Technique (SMOTE) preprocessing algorithm is considered \de facto" standard in the framework of learning from imbalanced data. This is due to its simplicity in the design of the procedure, as well as its robustness when applied to di erent type of problems. Since its publication in 2002, SMOTE has proven successful in a variety of applications from several di erent domains. SMOTE has also inspired several approaches to counter the issue of class imbalance, and has also signi cantly contributed to new supervised learning paradigms, including multilabel classi cation, incremental learning, semi-supervised learning, multi-instance learning, among others. It is standard benchmark for learning from imbalanced data. It is also featured in a number of di erent software packages | from open source to commercial. In this paper, marking the fteen year anniversary of SMOTE, we re ect on the SMOTE journey, discuss the current state of a airs with SMOTE, its applications, and also identify the next set of challenges to extend SMOTE for Big Data problems.This work have been partially supported by the Spanish Ministry of Science and Technology under projects TIN2014-57251-P, TIN2015-68454-R and TIN2017-89517-P; the Project 887 BigDaP-TOOLS - Ayudas Fundaci on BBVA a Equipos de Investigaci on Cient ca 2016; and the National Science Foundation (NSF) Grant IIS-1447795

Handling Imbalanced Data through Re-sampling: Systematic Review

Handling imbalanced data is an important issue that can affect the validity and reliability of the results. One common approach to addressing this issue is through re-sampling the data. Re-sampling is a technique that allows researchers to balance the class distribution of their dataset by either over-sampling the minority class or under-sampling the majority class. Over-sampling involves adding more copies of the minority class examples to the dataset in order to balance out the class distribution. On the other hand, under-sampling involves removing some of the majority class examples from the dataset in order to balance out the class distribution. It's also common to combine both techniques, usually called hybrid sampling. It is important to note that re-sampling techniques can have an impact on the model's performance, and it is essential to evaluate the model using different evaluation metrics and to consider other techniques such as cost-sensitive learning and anomaly detection. In addition, it is important to keep in mind that increasing the sample size is always a good idea to improve the performance of the model. In this systematic review, we aim to provide an overview of existing methods for re-sampling imbalanced data. We will focus on methods that have been proposed in the literature and evaluate their effectiveness through a thorough examination of experimental results. The goal of this review is to provide practitioners with a comprehensive understanding of the different re-sampling methods available, as well as their strengths and weaknesses, to help them make informed decisions when dealing with imbalanced data