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The first step in drug discovery is finding drug molecule moieties with medicinal activity against specific targets. Therefore, it is crucial to investigate the interaction between drug-target proteins and small chemical molecules. However,…

Biomolecules · Quantitative Biology 2022-11-15 Boyuan Liu

Drug combinations are essential in cancer therapy, leveraging synergistic drug-drug interactions (DDI) to enhance efficacy and combat resistance. However, the vast combinatorial space makes experimental screening impractical, and existing…

Machine Learning · Computer Science 2026-03-26 Yuxuan Nie , Yutong Song , Jinjie Yang , Yupeng Song , Yujue Zhou , Hong Peng

Computational protein-protein interaction (PPI) prediction techniques can contribute greatly in reducing time, cost and false-positive interactions compared to experimental approaches. Sequence is one of the key and primary information of…

Machine Learning · Computer Science 2022-03-29 Soumyadeep Debnath , Ayatullah Faruk Mollah

Biological networks provide insight into the complex organization of biological processes in a cell at the system level. They are an effective tool for understanding the comprehensive map of functional interactions, finding the functional…

Molecular Networks · Quantitative Biology 2017-09-14 Somaye Hashemifar

Multi-interest candidate matching plays a pivotal role in personalized recommender systems, as it captures diverse user interests from their historical behaviors. Most existing methods utilize attention mechanisms to generate interest…

Information Retrieval · Computer Science 2025-02-14 Yankun Le , Haoran Li , Baoyuan Ou , Yingjie Qin , Zhixuan Yang , Ruilong Su , Fu Zhang

Predicting drug-target affinity is fundamental to virtual screening and lead optimization. However, existing deep models often suffer from representation collapse in stringent cold-start regimes, where the scarcity of labels and domain…

Machine Learning · Statistics 2026-03-13 Yining Qian , Pengjie Wang , Yixiao Li , An-Yang Lu , Cheng Tan , Shuang Li , Lijun Liu

Recent advances and achievements of artificial intelligence (AI) as well as deep and graph learning models have established their usefulness in biomedical applications, especially in drug-drug interactions (DDIs). DDIs refer to a change in…

Feature interaction has been recognized as an important problem in machine learning, which is also very essential for click-through rate (CTR) prediction tasks. In recent years, Deep Neural Networks (DNNs) can automatically learn implicit…

Background: Discovering potential drug-drug interactions (DDIs) is a long-standing challenge in clinical treatments and drug developments. Recently, deep learning techniques have been developed for DDI prediction. However, they generally…

Machine Learning · Computer Science 2024-03-20 Yaqing Wang , Zaifei Yang , Quanming Yao

Drug-drug interactions (DDIs) represent a critical challenge in pharmacology, often leading to adverse drug reactions with significant implications for patient safety and healthcare outcomes. While graph-based methods have achieved strong…

Machine Learning · Computer Science 2025-07-15 Mengjie Chen , Ming Zhang , Cunquan Qu

Aberrant protein-protein interactions (PPIs) underpin a plethora of human diseases, and disruption of these harmful interactions constitute a compelling treatment avenue. Advances in computational approaches to PPI prediction have closely…

Biomolecules · Quantitative Biology 2025-07-29 François Charih , James R. Green , Kyle K. Biggar

Pain is a significant global health issue, and the current treatment options for pain management have limitations in terms of effectiveness, side effects, and potential for addiction. There is a pressing need for improved pain treatments…

Biomolecules · Quantitative Biology 2023-07-13 Long Chen , Jian Jiang , Bozheng Dou , Hongsong Feng , Jie Liu , Yueying Zhu , Bengong Zhang , Tianshou Zhou , Guo-Wei Wei

Drug combinations can cause adverse drug-drug interactions(DDIs). Identifying specific effects is crucial for developing safer therapies. Previous works on DDI event prediction have typically been limited to using labels of specific events…

Biomolecules · Quantitative Biology 2024-11-05 Yingying Wang , Yun Xiong , Xixi Wu , Xiangguo Sun , Jiawei Zhang

Multimodal fusion leverages information across modalities to learn better feature representations with the goal of improving performance in fusion-based tasks. However, multimodal datasets, especially in medical settings, are typically…

Machine Learning · Computer Science 2025-02-05 Alejandro Guerra-Manzanares , Farah E. Shamout

Identifying and discovering drug-target interactions(DTIs) are vital steps in drug discovery and development. They play a crucial role in assisting scientists in finding new drugs and accelerating the drug development process. Recently,…

Quantitative Methods · Quantitative Biology 2023-11-15 Wenting Ye , Chen Li , Yang Xie , Wen Zhang , Hong-Yu Zhang , Bowen Wang , Debo Cheng , Zaiwen Feng

Predicting drug-target binding affinity (DTA) is essential for identifying potential therapeutic candidates in drug discovery. However, most existing models rely heavily on static protein structures, often overlooking the dynamic nature of…

Robotics · Computer Science 2025-05-20 Dan Luo , Jinyu Zhou , Le Xu , Sisi Yuan , Xuan Lin

Click-through rate (CTR) Prediction is a crucial task in personalized information retrievals, such as industrial recommender systems, online advertising, and web search. Most existing CTR Prediction models utilize explicit feature…

Information Retrieval · Computer Science 2024-02-19 Honghao Li , Lei Sang , Yi Zhang , Xuyun Zhang , Yiwen Zhang

Standard decoding approaches rely on model-based channel estimation methods to compensate for varying channel effects, which degrade in performance whenever there is a model mismatch. Recently proposed Deep learning based neural decoders…

Signal Processing · Electrical Eng. & Systems 2019-03-07 Yihan Jiang , Hyeji Kim , Himanshu Asnani , Sreeram Kannan

Accurate prediction of drug-target binding affinity can accelerate drug discovery by prioritizing promising compounds before costly wet-lab screening. While deep learning has advanced this task, most models fuse ligand and protein…

Machine Learning · Computer Science 2025-09-26 Mohammadsaleh Refahi , Bahrad A. Sokhansanj , James R. Brown , Gail Rosen

Drug discovery remains time-consuming, labor-intensive, and expensive, often requiring years and substantial investment per drug candidate. Predicting compound-protein interactions (CPIs) is a critical component in this process, enabling…

Artificial Intelligence · Computer Science 2026-02-06 Zhe Wang , Zijing Liu , Chencheng Xu , Yuan Yao