Affinity2Vec: drug-target binding affinity prediction through representation learning, graph mining, and machine learning

MA Thafar, M Alshahrani, S Albaradei, T Gojobori… - Scientific reports, 2022 - nature.com
Drug-target interaction (DTI) prediction plays a crucial role in drug repositioning and virtual
drug screening. Most DTI prediction methods cast the problem as a binary classification task …

DTi2Vec: Drug–target interaction prediction using network embedding and ensemble learning

MA Thafar, RS Olayan, S Albaradei, VB Bajic… - Journal of …, 2021 - Springer
Drug–target interaction (DTI) prediction is a crucial step in drug discovery and repositioning
as it reduces experimental validation costs if done right. Thus, developing in-silico methods …

[PDF][PDF] Application and evaluation of knowledge graph embeddings in biomedical data

M Alshahrani, MA Thafar, M Essack - PeerJ Computer Science, 2021 - peerj.com
Linked data and bio-ontologies enabling knowledge representation, standardization, and
dissemination are an integral part of developing biological and biomedical databases. That …

OncoRTT: Predicting novel oncology-related therapeutic targets using BERT embeddings and omics features

MA Thafar, S Albaradei, M Uludag, M Alshahrani… - Frontiers in …, 2023 - frontiersin.org
Late-stage drug development failures are usually a consequence of ineffective targets. Thus,
proper target identification is needed, which may be possible using computational …

How natural language processing derived techniques are used on biological data: a systematic review

ED Oikonomou, P Karvelis, N Giannakeas… - … Modeling Analysis in …, 2024 - Springer
The decoding of the human genome, completed two decades ago, marked a revolutionary
moment in biology by introducing a vast amount of data. This avalanche of information …

Artificial Intelligence in Drug Identification and Validation: A Scoping Review

ML Abubakar, N Kapoor, A Sharma, L Gambhir… - Drug …, 2024 - thieme-connect.com
The end-to-end process in the discovery of drugs involves therapeutic candidate
identification, validation of identified targets, identification of hit compound series, lead …

Drug–target interaction prediction based on improved heterogeneous graph representation learning and feature projection classification

D Yu, H Liu, S Yao - Expert Systems with Applications, 2024 - Elsevier
Drug–target interaction (DTI) identification is a complex process that is time-consuming,
costly and frequently inefficient, with a low success rate, especially with wet-experimental …

Combining biomedical knowledge graphs and text to improve predictions for drug-target interactions and drug-indications

M Alshahrani, A Almansour, A Alkhaldi, MA Thafar… - PeerJ, 2022 - peerj.com
Biomedical knowledge is represented in structured databases and published in biomedical
literature, and different computational approaches have been developed to exploit each type …

Drug‐Target Interaction Prediction via Dual Laplacian Graph Regularized Logistic Matrix Factorization

A Wang, M Wang - BioMed research international, 2021 - Wiley Online Library
Drug‐target interactions provide useful information for biomedical drug discovery as well as
drug development. However, it is costly and time consuming to find drug‐target interactions …

[HTML][HTML] FutureCite: Predicting Research Articles' Impact Using Machine Learning and Text and Graph Mining Techniques

MA Thafar, MM Alsulami, S Albaradei - Mathematical and Computational …, 2024 - mdpi.com
The growth in academic and scientific publications has increased very rapidly. Researchers
must choose a representative and significant literature for their research, which has become …