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 …

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) …

Adversarial learning for feature shift detection and correction

M Barrabés, D Mas Montserrat… - Advances in …, 2024 - proceedings.neurips.cc
Data shift is a phenomenon present in many real-world applications, and while there are
multiple methods attempting to detect shifts, the task of localizing and correcting the features …

SALAI-Net: species-agnostic local ancestry inference network

B Oriol Sabat, D Mas Montserrat, X Giro-i-Nieto… - …, 2022 - academic.oup.com
Motivation Local ancestry inference (LAI) is the high resolution prediction of ancestry labels
along a DNA sequence. LAI is important in the study of human history and migrations, and it …

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 …

Deep variational autoencoders for population genetics

M Geleta, DM Montserrat, X Giro-i-Nieto, AG Ioannidis - biorxiv, 2023 - biorxiv.org
Motivation Modern biobanks provide numerous high-resolution genomic sequences of
diverse populations. These datasets enable a better understanding of genotype-phenotype …

Towards creating longer genetic sequences with GANs: Generation in principal component space

A Szatkownik, C Furtlehner… - Machine Learning …, 2024 - proceedings.mlr.press
Synthetic data generation via generative modeling has recently become a prominent
research field in genomics, with applications ranging from functional sequence design to …

Adversarial attacks on genotype sequences

DM Montserrat, AG Ioannidis - ICASSP 2023-2023 IEEE …, 2023 - ieeexplore.ieee.org
Adversarial attacks can drastically change the output of a method by small alterations to its
input. While this can be a useful framework to analyze worst-case robustness, it can also be …

Generating Synthetic Genotypes using Diffusion Models

P Kenneweg, R Dandinasivara, X Luo… - arXiv preprint arXiv …, 2024 - arxiv.org
In this paper, we introduce the first diffusion model designed to generate complete synthetic
human genotypes, which, by standard protocols, one can straightforwardly expand into full …

Genomic Databases Homogenization with Machine Learning

M Barrabés, D Bonet, VN Moriano… - 2023 IEEE …, 2023 - ieeexplore.ieee.org
Large-scale and increasingly diverse datasets power modern genomic studies, yet robust
data integration and homogenization across varying sources remains a challenge. The …