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 …

[HTML][HTML] Neural ADMIXTURE for rapid genomic clustering

A Dominguez Mantes, D Mas Montserrat… - Nature computational …, 2023 - nature.com
Characterizing the genetic structure of large cohorts has become increasingly important as
genetic studies extend to massive, increasingly diverse biobanks. Popular methods …

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 …

Deep variational autoencoders for population genetics

M Geleta, D Mas Montserrat, X Giro-i-Nieto… - 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 …

[HTML][HTML] Machine Learning Strategies for Improved Phenotype Prediction in Underrepresented Populations

D Bonet, M Levin, DM Montserrat… - Pacific Symposium on …, 2024 - ncbi.nlm.nih.gov
Precision medicine models often perform better for populations of European ancestry due to
the over-representation of this group in the genomic datasets and large-scale biobanks from …

[HTML][HTML] Estimation of spatial demographic maps from polymorphism data using a neural network

CCR Smith, G Patterson, PL Ralph, AD Kern - bioRxiv, 2024 - ncbi.nlm.nih.gov
A fundamental goal in population genetics is to understand how variation is arrayed over
natural landscapes. From first principles we know that common features such as …

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 …

[HTML][HTML] Fast and accurate local ancestry inference with Recomb-Mix

Y Wei, D Zhi, S Zhang - bioRxiv, 2023 - ncbi.nlm.nih.gov
The availability of large genotyped cohorts brings new opportunities for revealing high-
resolution genetic structure of admixed populations, via local ancestry inference (LAI), the …

Genomic Ancestry Inference of Admixed Population by Identifying Approximate Boundaries of Ancestry Change

F Alizadeh, H Jazayeriy, O Jazayeri, F Vafaee - International Journal of …, 2024 - ije.ir
Admixture is a common phenomenon in human populations, resulting from the mating of
individuals from two or more previously isolated populations. This can lead to the formation …

K-mer-based data structures and pipelines for sequence mapping and analysis

TM Goktas - 2023 - open.library.ubc.ca
The exponential growth of genomic data demands progress and research on scalable
bioinformatics algorithms. A paradigm to improve computational efficiency in bioinformatics …