iFLAS: positive‐unlabeled learning facilitates full‐length transcriptome‐based identification and functional exploration of alternatively spliced isoforms in maize

F Xu, S Liu, A Zhao, M Shang, Q Wang, S Jiang… - New …, 2024 - Wiley Online Library
The advent of full‐length transcriptome sequencing technologies has accelerated the
discovery of novel splicing isoforms. However, existing alternative splicing (AS) tools are …

ADDI: Recommending alternatives for drug–drug interactions with negative health effects

M Allahgholi, H Rahmani, D Javdani, G Weiss… - Computers in Biology …, 2020 - Elsevier
Investigating the interactions among various drugs is an indispensable issue in the field of
computational biology. Scientific literature represents a rich source for the retrieval of …

Good machine learning practices: Learnings from the modern pharmaceutical discovery enterprise

V Makarov, C Chabbert, E Koletou… - Computers in Biology …, 2024 - Elsevier
Abstract Machine Learning (ML) and Artificial Intelligence (AI) have become an integral part
of the drug discovery and development value chain. Many teams in the pharmaceutical …

Interpretability and accessibility of machine learning in selected food processing, agriculture and health applications

N Ranasinghe, A Ramanan, S Fernando… - arXiv preprint arXiv …, 2022 - arxiv.org
Artificial Intelligence (AI) and its data-centric branch of machine learning (ML) have greatly
evolved over the last few decades. However, as AI is used increasingly in real world use …

A multi-objective evolutionary algorithm for robust positive-unlabeled learning

J Qiu, Q Tang, M Tan, K Li, J Xie, X Cai, F Cheng - Information Sciences, 2024 - Elsevier
Positive and unlabeled (PU) learning is to learn a binary classifier with good generalization
ability from PU data. A variety of PU learning algorithms with promising performance have …

DTIP-TC2A: An analytical framework for drug-target interactions prediction methods

MR Keyvanpour, F Haddadi, S Mehrmolaei - Computational Biology and …, 2022 - Elsevier
Identifying drug-target interactions through computational methods is raised an important
and key step in the process of drug discovery and drug-oriented research during the last …

A loss matrix-based alternating optimization method for sparse PU learning

J Qiu, X Cai, L Zhang, F Cheng - Swarm and Evolutionary Computation, 2022 - Elsevier
Positive and unlabeled (PU) learning is an important research topic in machine learning
area, whose aim is to learn a good classifier from PU data. Due to its wide applications, a …

Sure: screening unlabeled samples for reliable negative samples based on reinforcement learning

Y Li, H Sun, W Fang, Q Ma, S Han, R Wang-Sattler… - Information …, 2023 - Elsevier
For many classification tasks, particularly in the bioinformatics field, only experimentally
validated positive samples are available, and experimentally validated negative samples …

Predicting drug-drug interactions using heterogeneous graph attention networks

F Tanvir, KM Saifuddin, M Ifte Khairul Islam… - Proceedings of the 14th …, 2023 - dl.acm.org
Drug-Drug Interactions (DDIs) can alter a drug's efficacy and lead to adverse effects.
Predicting potential DDIs during clinical trials is challenging; thus, computational methods …

PU‐GNN: A Positive‐Unlabeled Learning Method for Polypharmacy Side‐Effects Detection Based on Graph Neural Networks

A Keshavarz, A Lakizadeh - International Journal of Intelligent …, 2024 - Wiley Online Library
The simultaneous use of multiple drugs, known as polypharmacy, heightens the risks of
harmful side effects due to drug‐drug interactions. Predicting these interactions is crucial in …