Ten quick tips for deep learning in biology

Systematic misestimation of machine learning performance in neuroimaging studies of depression

(2021) Claas Flint et al.   NEUROPSYCHOPHARMACOLOGY

Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences

(2021) Alexander Rives et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Privacy preserving distributed learning classifiers – Sequential learning with small sets of data

(2021) Fadila Zerka et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Reproducibility standards for machine learning in the life sciences

(2021) Benjamin J. Heil et al.   NATURE METHODS

Standard machine learning approaches outperform deep representation learning on phenotype prediction from transcriptomics data

(2020) Aaron M. Smith et al.   BMC BIOINFORMATICS

Backpropagation and the brain

(2020) Timothy P. Lillicrap et al.   NATURE REVIEWS NEUROSCIENCE

Machine learning and AI-based approaches for bioactive ligand discovery and GPCR-ligand recognition

(2020) Sebastian Raschka et al.   METHODS

Responsible, practical genomic data sharing that accelerates research

(2020) James Brian Byrd et al.   NATURE REVIEWS GENETICS

Deep learning‐based methods for individual recognition in small birds

(2020) André C. Ferreira et al.   Methods in Ecology and Evolution

Deep Ethical Learning: Taking the Interplay of Human and Artificial Intelligence Seriously

(2019) Anita Ho   HASTINGS CENTER REPORT

The Kipoi repository accelerates community exchange and reuse of predictive models for genomics

(2019) Žiga Avsec et al.   NATURE BIOTECHNOLOGY

Reconciling modern machine-learning practice and the classical bias–variance trade-off

(2019) Mikhail Belkin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Optimization of Molecules via Deep Reinforcement Learning

(2019) Zhenpeng Zhou et al.   Scientific Reports

Open collaborative writing with Manubot

(2019) Daniel S. Himmelstein et al.   PLoS Computational Biology

Deep learning with convolutional neural network in radiology

(2018) Koichiro Yasaka et al.   JAPANESE JOURNAL OF RADIOLOGY

Opportunities and obstacles for deep learning in biology and medicine

(2018) Travers Ching et al.   Journal of the Royal Society Interface

Fast and robust segmentation of white blood cell images by self-supervised learning

(2018) Xin Zheng et al.   MICRON

Deep learning with convolutional neural network in radiology

(2018) Koichiro Yasaka et al.   Japanese Journal of Radiology

VAMPnets for deep learning of molecular kinetics

(2018) Andreas Mardt et al.   Nature Communications

A Deep Learning Approach for Predicting Antidepressant Response in Major Depression Using Clinical and Genetic Biomarkers

(2018) Eugene Lin et al.   Frontiers in Psychiatry

Deep learning to predict the lab-of-origin of engineered DNA

(2018) Alec A. K. Nielsen et al.   Nature Communications

SIG-DB: Leveraging homomorphic encryption to securely interrogate privately held genomic databases

(2018) Alexander J. Titus et al.   PLoS Computational Biology

Adversarial Controls for Scientific Machine Learning

(2018) Kangway V. Chuang et al.   ACS Chemical Biology

Identifying facial phenotypes of genetic disorders using deep learning

(2018) Yaron Gurovich et al.   NATURE MEDICINE

Variable generalization performance of a deep learning model to detect pneumonia in chest radiographs: A cross-sectional study

(2018) John R. Zech et al.   PLOS MEDICINE

Towards trustable machine learning

(2018)   Nature Biomedical Engineering

Deep learning for pharmacovigilance: recurrent neural network architectures for labeling adverse drug reactions in Twitter posts

(2017) Anne Cocos et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Comparison of Deep Learning With Multiple Machine Learning Methods and Metrics Using Diverse Drug Discovery Data Sets

(2017) Alexandru Korotcov et al.   MOLECULAR PHARMACEUTICS

Reproducibility of computational workflows is automated using continuous analysis

(2017) Brett K Beaulieu-Jones et al.   NATURE BIOTECHNOLOGY

Efficient Processing of Deep Neural Networks: A Tutorial and Survey

(2017) Vivienne Sze et al.   PROCEEDINGS OF THE IEEE

Deep-learning: investigating deep neural networks hyper-parameters and comparison of performance to shallow methods for modeling bioactivity data

(2017) Alexios Koutsoukas et al.   Journal of Cheminformatics

Ten simple rules for responsible big data research

(2017) Matthew Zook et al.   PLoS Computational Biology

Ten quick tips for machine learning in computational biology

(2017) Davide Chicco   BioData Mining

Deep Learning for Health Informatics

(2017) Daniele Ravi et al.   IEEE Journal of Biomedical and Health Informatics

Deep learning microscopy

(2017) Yair Rivenson et al.   Optica

High-Throughput Classification of Radiographs Using Deep Convolutional Neural Networks

(2016) Alvin Rajkomar et al.   JOURNAL OF DIGITAL IMAGING

Ten Simple Rules for Taking Advantage of Git and GitHub

(2016) Yasset Perez-Riverol et al.   PLoS Computational Biology

Correct machine learning on protein sequences: a peer-reviewing perspective

(2015) Ian Walsh et al.   BRIEFINGS IN BIOINFORMATICS

ImageNet Large Scale Visual Recognition Challenge

(2015) Olga Russakovsky et al.   INTERNATIONAL JOURNAL OF COMPUTER VISION

Deep learning

(2015) Yann LeCun et al.   NATURE

The Precision-Recall Plot Is More Informative than the ROC Plot When Evaluating Binary Classifiers on Imbalanced Datasets

(2015) Takaya Saito et al.   PLoS One

The Legal And Ethical Concerns That Arise From Using Complex Predictive Analytics In Health Care

(2014) I. Glenn Cohen et al.   HEALTH AFFAIRS

Ten Simple Rules for Reproducible Computational Research

(2013) Geir Kjetil Sandve et al.   PLoS Computational Biology

Tackling the widespread and critical impact of batch effects in high-throughput data

(2010) Jeffrey T. Leek et al.   NATURE REVIEWS GENETICS