[HTML][HTML] The survey: Text generation models in deep learning

T Iqbal, S Qureshi - Journal of King Saud University-Computer and …, 2022 - Elsevier
Deep learning methods possess many processing layers to understand the stratified
representation of data and have achieved state-of-art results in several domains. Recently …

A review of deep learning applications in human genomics using next-generation sequencing data

WS Alharbi, M Rashid - Human Genomics, 2022 - Springer
Genomics is advancing towards data-driven science. Through the advent of high-throughput
data generating technologies in human genomics, we are overwhelmed with the heap of …

scBERT as a large-scale pretrained deep language model for cell type annotation of single-cell RNA-seq data

F Yang, W Wang, F Wang, Y Fang, D Tang… - Nature Machine …, 2022 - nature.com
Annotating cell types on the basis of single-cell RNA-seq data is a prerequisite for research
on disease progress and tumour microenvironments. Here we show that existing annotation …

Artificial-intelligence-based molecular classification of diffuse gliomas using rapid, label-free optical imaging

T Hollon, C Jiang, A Chowdury, M Nasir-Moin… - Nature medicine, 2023 - nature.com
Molecular classification has transformed the management of brain tumors by enabling more
accurate prognostication and personalized treatment. However, timely molecular diagnostic …

Learning functional properties of proteins with language models

S Unsal, H Atas, M Albayrak, K Turhan… - Nature Machine …, 2022 - nature.com
Data-centric approaches have been used to develop predictive methods for elucidating
uncharacterized properties of proteins; however, studies indicate that these methods should …

cACP-DeepGram: classification of anticancer peptides via deep neural network and skip-gram-based word embedding model

S Akbar, M Hayat, M Tahir, S Khan, FK Alarfaj - Artificial intelligence in …, 2022 - Elsevier
Cancer is a Toxic health concern worldwide, it happens when cellular modifications cause
the irregular growth and division of human cells. Several traditional approaches such as …

Learning interpretable cellular and gene signature embeddings from single-cell transcriptomic data

Y Zhao, H Cai, Z Zhang, J Tang, Y Li - Nature communications, 2021 - nature.com
The advent of single-cell RNA sequencing (scRNA-seq) technologies has revolutionized
transcriptomic studies. However, large-scale integrative analysis of scRNA-seq data remains …

Ten quick tips for effective dimensionality reduction

LH Nguyen, S Holmes - PLoS computational biology, 2019 - journals.plos.org
Dimensionality reduction (DR) is frequently applied during the analysis of high-dimensional
data. Both a means of denoising and simplification, it can be beneficial for the majority of …

GeneCompass: deciphering universal gene regulatory mechanisms with a knowledge-informed cross-species foundation model

X Yang, G Liu, G Feng, D Bu, P Wang, J Jiang, S Chen… - Cell Research, 2024 - nature.com
Deciphering universal gene regulatory mechanisms in diverse organisms holds great
potential for advancing our knowledge of fundamental life processes and facilitating clinical …

GenePT: a simple but effective foundation model for genes and cells built from ChatGPT

Y Chen, J Zou - bioRxiv, 2024 - pmc.ncbi.nlm.nih.gov
There has been significant recent progress in leveraging large-scale gene expression data
to develop foundation models for single-cell biology. Models such as Geneformer and …