Deep learning as a tool for ecology and evolution

ML Borowiec, RB Dikow, PB Frandsen… - Methods in Ecology …, 2022 - Wiley Online Library
Deep learning is driving recent advances behind many everyday technologies, including
speech and image recognition, natural language processing and autonomous driving. It is …

Navigating the temporal continuum of effective population size

K Nadachowska‐Brzyska, M Konczal… - Methods in Ecology …, 2022 - Wiley Online Library
Effective population size, Ne, is a key evolutionary parameter that determines the levels of
genetic variation and efficacy of selection. Estimation and interpretation of Ne are essential …

Extending approximate Bayesian computation with supervised machine learning to infer demographic history from genetic polymorphisms using DIYABC Random …

F Collin, G Durif, L Raynal, E Lombaert… - Molecular Ecology …, 2021 - Wiley Online Library
Simulation‐based methods such as approximate Bayesian computation (ABC) are well‐
adapted to the analysis of complex scenarios of populations and species genetic history. In …

Harnessing deep learning for population genetic inference

X Huang, A Rymbekova, O Dolgova, O Lao… - Nature Reviews …, 2024 - nature.com
In population genetics, the emergence of large-scale genomic data for various species and
populations has provided new opportunities to understand the evolutionary forces that drive …

Toward an integrated machine learning model of a proteomics experiment

BA Neely, V Dorfer, L Martens, I Bludau… - Journal of proteome …, 2023 - ACS Publications
In recent years machine learning has made extensive progress in modeling many aspects of
mass spectrometry data. We brought together proteomics data generators, repository …

[PDF][PDF] Deep learning in population genetics

K Korfmann, OE Gaggiotti… - Genome Biology and …, 2023 - academic.oup.com
Population genetics is transitioning into a data-driven discipline thanks to the availability of
large-scale genomic data and the need to study increasingly complex evolutionary …

Recent advances in generative adversarial networks for gene expression data: a comprehensive review

M Lee - Mathematics, 2023 - mdpi.com
The evolving field of generative artificial intelligence (GenAI), particularly generative deep
learning, is revolutionizing a host of scientific and technological sectors. One of the pivotal …

Detecting adaptive introgression in human evolution using convolutional neural networks

G Gower, PI Picazo, M Fumagalli, F Racimo - Elife, 2021 - elifesciences.org
Studies in a variety of species have shown evidence for positively selected variants
introduced into a population via introgression from another, distantly related population—a …

On the prospect of achieving accurate joint estimation of selection with population history

P Johri, A Eyre-Walker, RN Gutenkunst… - Genome biology and …, 2022 - academic.oup.com
As both natural selection and population history can affect genome-wide patterns of
variation, disentangling the contributions of each has remained as a major challenge in …

An overview of deep generative models in functional and evolutionary genomics

B Yelmen, F Jay - Annual Review of Biomedical Data Science, 2023 - annualreviews.org
Following the widespread use of deep learning for genomics, deep generative modeling is
also becoming a viable methodology for the broad field. Deep generative models (DGMs) …