Transformer architecture and attention mechanisms in genome data analysis: a comprehensive review

SR Choi, M Lee - Biology, 2023 - mdpi.com
Simple Summary The rapidly advancing field of deep learning, specifically transformer-
based architectures and attention mechanisms, has found substantial applicability in …

[HTML][HTML] Machine learning in the prediction of cancer therapy

R Rafique, SMR Islam, JU Kazi - Computational and Structural …, 2021 - Elsevier
Resistance to therapy remains a major cause of cancer treatment failures, resulting in many
cancer-related deaths. Resistance can occur at any time during the treatment, even at the …

DeepTraSynergy: drug combinations using multimodal deep learning with transformers

F Rafiei, H Zeraati, K Abbasi, JB Ghasemi… - …, 2023 - academic.oup.com
Motivation Screening bioactive compounds in cancer cell lines receive more attention.
Multidisciplinary drugs or drug combinations have a more effective role in treatments and …

CancerGPT for few shot drug pair synergy prediction using large pretrained language models

T Li, S Shetty, A Kamath, A Jaiswal, X Jiang… - NPJ Digital …, 2024 - nature.com
Large language models (LLMs) have been shown to have significant potential in few-shot
learning across various fields, even with minimal training data. However, their ability to …

DSN-DDI: an accurate and generalized framework for drug–drug interaction prediction by dual-view representation learning

Z Li, S Zhu, B Shao, X Zeng, T Wang… - Briefings in …, 2023 - academic.oup.com
Drug–drug interaction (DDI) prediction identifies interactions of drug combinations in which
the adverse side effects caused by the physicochemical incompatibility have attracted much …

DeepDDS: deep graph neural network with attention mechanism to predict synergistic drug combinations

J Wang, X Liu, S Shen, L Deng… - Briefings in …, 2022 - academic.oup.com
Motivation Drug combination therapy has become an increasingly promising method in the
treatment of cancer. However, the number of possible drug combinations is so huge that it is …

DrugComb update: a more comprehensive drug sensitivity data repository and analysis portal

S Zheng, J Aldahdooh, T Shadbahr… - Nucleic acids …, 2021 - academic.oup.com
Combinatorial therapies that target multiple pathways have shown great promises for
treating complex diseases. DrugComb (https://drugcomb. org/) is a web-based portal for the …

AttenSyn: an attention-based deep graph neural network for anticancer synergistic drug combination prediction

T Wang, R Wang, L Wei - Journal of Chemical Information and …, 2023 - ACS Publications
Identifying synergistic drug combinations is fundamentally important to treat a variety of
complex diseases while avoiding severe adverse drug–drug interactions. Although several …

Antibiotic discovery in the artificial intelligence era

T Lluka, JM Stokes - Annals of the New York Academy of …, 2023 - Wiley Online Library
As the global burden of antibiotic resistance continues to grow, creative approaches to
antibiotic discovery are needed to accelerate the development of novel medicines. A rapidly …

Multi-way relation-enhanced hypergraph representation learning for anti-cancer drug synergy prediction

X Liu, C Song, S Liu, M Li, X Zhou, W Zhang - Bioinformatics, 2022 - academic.oup.com
Motivation Drug combinations have exhibited promise in treating cancers with less toxicity
and fewer adverse reactions. However, in vitro screening of synergistic drug combinations is …