Obtaining genetics insights from deep learning via explainable artificial intelligence

G Novakovsky, N Dexter, MW Libbrecht… - Nature Reviews …, 2023 - nature.com
Artificial intelligence (AI) models based on deep learning now represent the state of the art
for making functional predictions in genomics research. However, the underlying basis on …

A unifying review of deep and shallow anomaly detection

L Ruff, JR Kauffmann, RA Vandermeulen… - Proceedings of the …, 2021 - ieeexplore.ieee.org
Deep learning approaches to anomaly detection (AD) have recently improved the state of
the art in detection performance on complex data sets, such as large collections of images or …

A survey on generative diffusion models

H Cao, C Tan, Z Gao, Y Xu, G Chen… - IEEE Transactions on …, 2024 - ieeexplore.ieee.org
Deep generative models have unlocked another profound realm of human creativity. By
capturing and generalizing patterns within data, we have entered the epoch of all …

[HTML][HTML] Graph neural networks and their current applications in bioinformatics

XM Zhang, L Liang, L Liu, MJ Tang - Frontiers in genetics, 2021 - frontiersin.org
Graph neural networks (GNNs), as a branch of deep learning in non-Euclidean space,
perform particularly well in various tasks that process graph structure data. With the rapid …

A roadmap for multi-omics data integration using deep learning

M Kang, E Ko, TB Mersha - Briefings in Bioinformatics, 2022 - academic.oup.com
High-throughput next-generation sequencing now makes it possible to generate a vast
amount of multi-omics data for various applications. These data have revolutionized …

[HTML][HTML] The language of proteins: NLP, machine learning & protein sequences

D Ofer, N Brandes, M Linial - Computational and Structural Biotechnology …, 2021 - Elsevier
Natural language processing (NLP) is a field of computer science concerned with automated
text and language analysis. In recent years, following a series of breakthroughs in deep and …

Deep learning: new computational modelling techniques for genomics

G Eraslan, Ž Avsec, J Gagneur, FJ Theis - Nature Reviews Genetics, 2019 - nature.com
As a data-driven science, genomics largely utilizes machine learning to capture
dependencies in data and derive novel biological hypotheses. However, the ability to extract …

Deep learning for anomaly detection: A survey

R Chalapathy, S Chawla - arXiv preprint arXiv:1901.03407, 2019 - arxiv.org
Anomaly detection is an important problem that has been well-studied within diverse
research areas and application domains. The aim of this survey is two-fold, firstly we present …

Ensemble deep learning in bioinformatics

Y Cao, TA Geddes, JYH Yang, P Yang - Nature Machine Intelligence, 2020 - nature.com
The remarkable flexibility and adaptability of ensemble methods and deep learning models
have led to the proliferation of their application in bioinformatics research. Traditionally …

[HTML][HTML] A review on deep learning approaches in healthcare systems: Taxonomies, challenges, and open issues

S Shamshirband, M Fathi, A Dehzangi… - Journal of Biomedical …, 2021 - Elsevier
In the last few years, the application of Machine Learning approaches like Deep Neural
Network (DNN) models have become more attractive in the healthcare system given the …