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Drug-target interaction (DTI) prediction plays a crucial role in drug discovery, and deep learning approaches have achieved state-of-the-art performance in this field. We introduce an ensemble of deep learning models (EnsembleDLM) for DTI…

Biomolecules · Quantitative Biology 2022-01-19 Po-Yu Kao , Shu-Min Kao , Nan-Lan Huang , Yen-Chu Lin

In the treatment of complex diseases, treatment regimens using a single drug often yield limited efficacy and can lead to drug resistance. In contrast, combination drug therapies can significantly improve therapeutic outcomes through…

Machine Learning · Computer Science 2026-04-24 Jiyan Song , Wenyang Wang , Chengcheng Yan , Zhiquan Han , Feifei Zhao

The identification of novel drug-target (DT) interactions is a substantial part of the drug discovery process. Most of the computational methods that have been proposed to predict DT interactions have focused on binary classification, where…

Machine Learning · Statistics 2019-02-06 Hakime Öztürk , Elif Ozkirimli , Arzucan Özgür

Complex or co-existing diseases are commonly treated using drug combinations, which can lead to higher risk of adverse side effects. The detection of polypharmacy side effects is usually done in Phase IV clinical trials, but there are still…

Machine Learning · Statistics 2019-05-03 Andreea Deac , Yu-Hsiang Huang , Petar Veličković , Pietro Liò , Jian Tang

Accurate drug response prediction (DRP) is a crucial yet challenging task in precision medicine. This paper presents a novel Attention-Guided Multi-omics Integration (AGMI) approach for DRP, which first constructs a Multi-edge Graph (MeG)…

Genomics · Quantitative Biology 2022-01-20 Ruiwei Feng , Yufeng Xie , Minshan Lai , Danny Z. Chen , Ji Cao , Jian Wu

Knowledge distillation has become increasingly important in model compression. It boosts the performance of a miniaturized student network with the supervision of the output distribution and feature maps from a sophisticated teacher…

Machine Learning · Computer Science 2020-08-04 Yushuo Guan , Pengyu Zhao , Bingxuan Wang , Yuanxing Zhang , Cong Yao , Kaigui Bian , Jian Tang

The extraction of biomedical data has significant academic and practical value in contemporary biomedical sciences. In recent years, drug repositioning, a cost-effective strategy for drug development by discovering new indications for…

Machine Learning · Computer Science 2025-01-20 Enqiang Zhu , Xiang Li , Chanjuan Liu , Nikhil R. Pal

Hypergraph can capture complex and higher-order dependencies among learners and learning resources in personalized educational recommender systems. Many existing hypergraph-based recommendation approaches underexplored the dynamic…

Information Retrieval · Computer Science 2026-03-17 Tao Xie , Yan Li , Yongpan Sheng , Jian Liao

Drug discovery remains a slow and expensive process that involves many steps, from detecting the target structure to obtaining approval from the Food and Drug Administration (FDA), and is often riddled with safety concerns. Accurate…

Quantitative Methods · Quantitative Biology 2025-08-22 Ali Vefghi , Zahed Rahmati , Mohammad Akbari

Object detection has achieved promising performance on clean datasets, but how to achieve better tradeoff between the adversarial robustness and clean precision is still under-explored. Adversarial training is the mainstream method to…

Computer Vision and Pattern Recognition · Computer Science 2022-10-20 Weipeng Xu , Pengzhi Chu , Renhao Xie , Xiongziyan Xiao , Hongcheng Huang

In the realm of digital pathology, multi-magnification Multiple Instance Learning (multi-mag MIL) has proven effective in leveraging the hierarchical structure of Whole Slide Images (WSIs) to reduce information loss and redundant data.…

Computer Vision and Pattern Recognition · Computer Science 2024-10-11 Yujian Liu , Ruoxuan Wu , Xinjie Shen , Zihuang Lu , Lingyu Liang , Haiyu Zhou , Shipu Xu , Shaoai Cai , Shidang Xu

In this paper, an advanced fracture detection framework, FracDetNet, is proposed to address challenges in medical imaging, as accurate fracture detection is essential for enhancing diagnostic efficiency in clinical practice. Despite recent…

Computer Vision and Pattern Recognition · Computer Science 2025-09-30 Yuyang Sun , Cuiming Zou

Examining Drug-Drug Interactions (DDIs) is a pivotal element in the process of drug development. DDIs occur when one drug's properties are affected by the inclusion of other drugs. Detecting favorable DDIs has the potential to pave the way…

Machine Learning · Computer Science 2026-03-20 Azmine Toushik Wasi , Taki Hasan Rafi , Raima Islam , Serbetar Karlo , Dong-Kyu Chae

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

Adverse drug interactions are largely preventable causes of medical accidents, which frequently result in physician and emergency room encounters. The detection of drug interactions in a lab, prior to a drug's use in medical practice, is…

Machine Learning · Computer Science 2023-02-08 Bar Vered , Guy Shtar , Lior Rokach , Bracha Shapira

Recent visual object tracking methods have witnessed a continuous improvement in the state-of-the-art with the development of efficient discriminative correlation filters (DCF) and robust deep neural network features. Despite the…

Computer Vision and Pattern Recognition · Computer Science 2020-06-02 Tianyang Xu , Zhen-Hua Feng , Xiao-Jun Wu , Josef Kittler

Recently, representation learning over graph networks has gained popularity, with various models showing promising results. Despite this, several challenges persist: 1) most methods are designed for static or discrete-time dynamic graphs;…

Machine Learning · Computer Science 2024-04-25 Xiaobo Zhu , Yan Wu , Zhipeng Li , Hailong Su , Jin Che , Zhanheng Chen , Liying Wang

Accurate and real-time surgical instrument segmentation is important in the endoscopic vision of robot-assisted surgery, and significant challenges are posed by frequent instrument-tissue contacts and continuous change of observation…

Computer Vision and Pattern Recognition · Computer Science 2020-08-12 Fangbo Qin , Shan Lin , Yangming Li , Randall A. Bly , Kris S. Moe , Blake Hannaford

Background: Drug-drug interactions (DDIs) refer to processes triggered by the administration of two or more drugs leading to side effects beyond those observed when drugs are administered by themselves. Due to the massive number of possible…

Quantitative Methods · Quantitative Biology 2020-12-25 Kyriakos Schwarz , Ahmed Allam , Nicolas Andres Perez Gonzalez , Michael Krauthammer

Diffusion-based data augmentation (DiffDA) has emerged as a promising approach to improving classification performance under data scarcity. However, existing works vary significantly in task configurations, model choices, and experimental…

Computer Vision and Pattern Recognition · Computer Science 2026-03-10 Zekun Li , Yinghuan Shi , Yang Gao , Dong Xu