Obtaining genetics insights from deep learning via explainable artificial intelligence
Artificial intelligence (AI) models based on deep learning now represent the state of the art
for making functional predictions in genomics research. However, the underlying basis on …
for making functional predictions in genomics research. However, the underlying basis on …
A guide to machine learning for biologists
The expanding scale and inherent complexity of biological data have encouraged a growing
use of machine learning in biology to build informative and predictive models of the …
use of machine learning in biology to build informative and predictive models of the …
Effective gene expression prediction from sequence by integrating long-range interactions
How noncoding DNA determines gene expression in different cell types is a major unsolved
problem, and critical downstream applications in human genetics depend on improved …
problem, and critical downstream applications in human genetics depend on improved …
The evolution, evolvability and engineering of gene regulatory DNA
Mutations in non-coding regulatory DNA sequences can alter gene expression, organismal
phenotype and fitness,–. Constructing complete fitness landscapes, in which DNA …
phenotype and fitness,–. Constructing complete fitness landscapes, in which DNA …
DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome
Motivation Deciphering the language of non-coding DNA is one of the fundamental
problems in genome research. Gene regulatory code is highly complex due to the existence …
problems in genome research. Gene regulatory code is highly complex due to the existence …
Hopfield networks is all you need
We introduce a modern Hopfield network with continuous states and a corresponding
update rule. The new Hopfield network can store exponentially (with the dimension of the …
update rule. The new Hopfield network can store exponentially (with the dimension of the …
Identification of LZTFL1 as a candidate effector gene at a COVID-19 risk locus
The severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) disease (COVID-19)
pandemic has caused millions of deaths worldwide. Genome-wide association studies …
pandemic has caused millions of deaths worldwide. Genome-wide association studies …
A roadmap for multi-omics data integration using deep learning
High-throughput next-generation sequencing now makes it possible to generate a vast
amount of multi-omics data for various applications. These data have revolutionized …
amount of multi-omics data for various applications. These data have revolutionized …
[HTML][HTML] Chromatin and gene-regulatory dynamics of the developing human cerebral cortex at single-cell resolution
Genetic perturbations of cortical development can lead to neurodevelopmental disease,
including autism spectrum disorder (ASD). To identify genomic regions crucial to …
including autism spectrum disorder (ASD). To identify genomic regions crucial to …
Wilds: A benchmark of in-the-wild distribution shifts
Distribution shifts—where the training distribution differs from the test distribution—can
substantially degrade the accuracy of machine learning (ML) systems deployed in the wild …
substantially degrade the accuracy of machine learning (ML) systems deployed in the wild …