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 …

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 …

Efficient ancestry and mutation simulation with msprime 1.0

F Baumdicker, G Bisschop, D Goldstein, G Gower… - Genetics, 2022 - academic.oup.com
Stochastic simulation is a key tool in population genetics, since the models involved are
often analytically intractable and simulation is usually the only way of obtaining ground-truth …

fastsimcoal2: demographic inference under complex evolutionary scenarios

L Excoffier, N Marchi, DA Marques… - …, 2021 - academic.oup.com
Motivation fastsimcoal2 extends fastsimcoal, a continuous time coalescent-based genetic
simulation program, by enabling the estimation of demographic parameters under very …

[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 …

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 …

Tree sequences as a general-purpose tool for population genetic inference

LS Whitehouse, DD Ray… - Molecular Biology and …, 2024 - academic.oup.com
As population genetic data increase in size, new methods have been developed to store
genetic information in efficient ways, such as tree sequences. These data structures are …

Neural typographical error modeling via generative adversarial networks

JR Bellegarda, G Pagallo - US Patent 11,170,166, 2021 - Google Patents
the tasks can then be performed by executing one or more services of the electronic device,
and a relevant output responsive to the user request can be returned to the user.intelligent …

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 …

Deep convolutional and conditional neural networks for large-scale genomic data generation

B Yelmen, A Decelle, LL Boulos… - PLOS Computational …, 2023 - journals.plos.org
Applications of generative models for genomic data have gained significant momentum in
the past few years, with scopes ranging from data characterization to generation of genomic …