Using machine learning approaches for multi-omics data analysis: A review

PS Reel, S Reel, E Pearson, E Trucco… - Biotechnology advances, 2021 - Elsevier
With the development of modern high-throughput omic measurement platforms, it has
become essential for biomedical studies to undertake an integrative (combined) approach to …

Multimodal data fusion for cancer biomarker discovery with deep learning

S Steyaert, M Pizurica, D Nagaraj… - Nature machine …, 2023 - nature.com
Technological advances have made it possible to study a patient from multiple angles with
high-dimensional, high-throughput multiscale biomedical data. In oncology, massive …

On the opportunities and risks of foundation models

R Bommasani, DA Hudson, E Adeli, R Altman… - arXiv preprint arXiv …, 2021 - arxiv.org
AI is undergoing a paradigm shift with the rise of models (eg, BERT, DALL-E, GPT-3) that are
trained on broad data at scale and are adaptable to a wide range of downstream tasks. We …

Multi‐Omics Factor Analysis—a framework for unsupervised integration of multi‐omics data sets

R Argelaguet, B Velten, D Arnol, S Dietrich… - Molecular systems …, 2018 - embopress.org
Multi‐omics studies promise the improved characterization of biological processes across
molecular layers. However, methods for the unsupervised integration of the resulting …

Machine learning for integrating data in biology and medicine: Principles, practice, and opportunities

M Zitnik, F Nguyen, B Wang, J Leskovec… - Information …, 2019 - Elsevier
New technologies have enabled the investigation of biology and human health at an
unprecedented scale and in multiple dimensions. These dimensions include a myriad of …

More is better: recent progress in multi-omics data integration methods

S Huang, K Chaudhary, LX Garmire - Frontiers in genetics, 2017 - frontiersin.org
Multi-omics data integration is one of the major challenges in the era of precision medicine.
Considerable work has been done with the advent of high-throughput studies, which have …

Network propagation: a universal amplifier of genetic associations

L Cowen, T Ideker, BJ Raphael, R Sharan - Nature Reviews Genetics, 2017 - nature.com
Biological networks are powerful resources for the discovery of genes and genetic modules
that drive disease. Fundamental to network analysis is the concept that genes underlying the …

Machine learning applications in genetics and genomics

MW Libbrecht, WS Noble - Nature Reviews Genetics, 2015 - nature.com
The field of machine learning, which aims to develop computer algorithms that improve with
experience, holds promise to enable computers to assist humans in the analysis of large …

Methods of integrating data to uncover genotype–phenotype interactions

MD Ritchie, ER Holzinger, R Li… - Nature Reviews …, 2015 - nature.com
Recent technological advances have expanded the breadth of available omic data, from
whole-genome sequencing data, to extensive transcriptomic, methylomic and metabolomic …

[PDF][PDF] Multiple kernel learning algorithms

M Gönen, E Alpaydın - The Journal of Machine Learning Research, 2011 - jmlr.org
In recent years, several methods have been proposed to combine multiple kernels instead of
using a single one. These different kernels may correspond to using different notions of …