Attention is all you need: utilizing attention in AI-enabled drug discovery

Y Zhang, C Liu, M Liu, T Liu, H Lin… - Briefings in …, 2024 - academic.oup.com
Recently, attention mechanism and derived models have gained significant traction in drug
development due to their outstanding performance and interpretability in handling complex …

[HTML][HTML] Machine learning for perturbational single-cell omics

Y Ji, M Lotfollahi, FA Wolf, FJ Theis - Cell Systems, 2021 - cell.com
Cell biology is fundamentally limited in its ability to collect complete data on cellular
phenotypes and the wide range of responses to perturbation. Areas such as computer vision …

DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome

Y Ji, Z Zhou, H Liu, RV Davuluri - Bioinformatics, 2021 - academic.oup.com
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 …

[HTML][HTML] Automating the design-build-test-learn cycle towards next-generation bacterial cell factories

N Gurdo, DC Volke, D McCloskey, PI Nikel - New Biotechnology, 2023 - Elsevier
Automation is playing an increasingly significant role in synthetic biology. Groundbreaking
technologies, developed over the past 20 years, have enormously accelerated the …

Representation learning applications in biological sequence analysis

H Iuchi, T Matsutani, K Yamada, N Iwano… - Computational and …, 2021 - Elsevier
Although remarkable advances have been reported in high-throughput sequencing, the
ability to aptly analyze a substantial amount of rapidly generated biological …

Transformers in healthcare: A survey

S Nerella, S Bandyopadhyay, J Zhang… - arXiv preprint arXiv …, 2023 - arxiv.org
With Artificial Intelligence (AI) increasingly permeating various aspects of society, including
healthcare, the adoption of the Transformers neural network architecture is rapidly changing …

Recent advances in deep learning models: a systematic literature review

R Malhotra, P Singh - Multimedia Tools and Applications, 2023 - Springer
In recent years, deep learning has evolved as a rapidly growing and stimulating field of
machine learning and has redefined state-of-the-art performances in a variety of …

Explainability in transformer models for functional genomics

J Clauwaert, G Menschaert… - Briefings in …, 2021 - academic.oup.com
The effectiveness of deep learning methods can be largely attributed to the automated
extraction of relevant features from raw data. In the field of functional genomics, this …

Artificial intelligence and the future of life sciences

ML Leite, LS de Loiola Costa, VA Cunha, V Kreniski… - Drug discovery today, 2021 - Elsevier
Over the past few decades, the number of health and 'omics-related data'generated and
stored has grown exponentially. Patient information can be collected in real time and …

Transformer models in biomedicine

S Madan, M Lentzen, J Brandt, D Rueckert… - BMC Medical Informatics …, 2024 - Springer
Deep neural networks (DNN) have fundamentally revolutionized the artificial intelligence
(AI) field. The transformer model is a type of DNN that was originally used for the natural …