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The last few years have seen the development of numerous deep learning-based protein-ligand docking methods. They offer huge promise in terms of speed and accuracy. However, despite claims of state-of-the-art performance in terms of…

Quantitative Methods · Quantitative Biology 2025-05-05 Martin Buttenschoen , Garrett M. Morris , Charlotte M. Deane

This paper evaluates DINOv3, a recent large-scale self-supervised vision backbone, for visuomotor diffusion policy learning in robotic manipulation. We investigate whether a purely self-supervised encoder can match or surpass conventional…

Computer Vision and Pattern Recognition · Computer Science 2025-09-23 ThankGod Egbe , Peng Wang , Zhihao Guo , Zidong Chen

Designing compounds with desired properties is a key element of the drug discovery process. However, measuring progress in the field has been challenging due to the lack of realistic retrospective benchmarks, and the large cost of…

Biomolecules · Quantitative Biology 2023-06-16 Tobiasz Cieplinski , Tomasz Danel , Sabina Podlewska , Stanislaw Jastrzebski

Purpose: Visual perception enables robots to perceive the environment. Visual data is processed using computer vision algorithms that are usually time-expensive and require powerful devices to process the visual data in real-time, which is…

Computer Vision and Pattern Recognition · Computer Science 2022-11-22 Sandro Costa Magalhães , Filipe Neves Santos , Pedro Machado , António Paulo Moreira , Jorge Dias

Previous evaluations on 6DoF object pose tracking have presented obvious limitations along with the development of this area. In particular, the evaluation protocols are not unified for different methods, the widely-used YCBV dataset…

Computer Vision and Pattern Recognition · Computer Science 2023-09-18 Yang Li , Fan Zhong , Xin Wang , Shuangbing Song , Jiachen Li , Xueying Qin , Changhe Tu

In drug discovery, molecular docking aims at characterizing the binding of a drug-like molecule to a macromolecule. AutoDock-GPU, a state-of-the-art docking software, estimates the geometrical conformation of a docked ligand-protein complex…

Distributed, Parallel, and Cluster Computing · Computer Science 2024-10-15 Gabin Schieffer , Ivy Peng

Drug discovery is the most expensive, time demanding and challenging project in biopharmaceutical companies which aims at the identification and optimization of lead compounds from large-sized chemical libraries. The lead compounds should…

Distributed, Parallel, and Cluster Computing · Computer Science 2021-12-02 Natarajan Arul Murugan , Artur Podobas , Davide Gadioli , Emanuele Vitali , Gianluca Palermo , Stefano Markidis

Deep neural networks (DNNs) are typically evaluated under the assumption that each image has a single correct label. However, many images in benchmarks like ImageNet contain multiple valid labels, creating a mismatch between evaluation…

Computer Vision and Pattern Recognition · Computer Science 2025-05-29 Esla Timothy Anzaku , Seyed Amir Mousavi , Arnout Van Messem , Wesley De Neve

Automated document classification is a trending topic in Natural Language Processing (NLP) due to the extensive growth in digital databases. However, a model that fits well for a specific classification task might perform weakly for another…

Machine Learning · Computer Science 2025-10-03 Uvini Ranaweera , Bawun Mawitagama , Sanduni Liyanage , Sandupa Keshan , Tiloka de Silva , Supun Hewawalpita

This study investigates the effectiveness of several machine learning algorithms for static malware detection using the EMBER dataset, which contains feature representations of Portable Executable (PE) files. We evaluate eight…

Cryptography and Security · Computer Science 2025-07-28 Md Min-Ha-Zul Abedin , Tazqia Mehrub

In recent years, machine learning (ML) methods have emerged as promising alternatives for molecular docking, offering the potential for high accuracy without incurring prohibitive computational costs. However, recent studies have indicated…

Biomolecules · Quantitative Biology 2024-05-21 Eric Alcaide , Zhifeng Gao , Guolin Ke , Yaqi Li , Linfeng Zhang , Hang Zheng , Gengmo Zhou

Deep learning promises to dramatically improve scoring functions for molecular docking, leading to substantial advances in binding pose prediction and virtual screening. To train scoring functions-and to perform molecular docking-one must…

Biomolecules · Quantitative Biology 2023-12-04 Patricia Suriana , Ron O. Dror

Reranking is a critical component in many information retrieval pipelines. Despite remarkable progress in text-only settings, multimodal reranking remains challenging, particularly when the candidate set contains hybrid text and image…

Information Retrieval · Computer Science 2026-05-26 Yupei Yang , Lin Yang , Wanxi Deng , Lin Qu , Shikui Tu , Lei Xu

Datasets used for molecular docking, such as PDBBind, contain technical variability - they are noisy. Although the origins of the noise have been discussed, a comprehensive analysis of the physical, chemical, and bioactivity characteristics…

Machine Learning · Computer Science 2024-10-02 Ahmet Sarigun , Vedran Franke , Bora Uyar , Altuna Akalin

Virtual screening, which identifies potential drugs from vast compound databases to bind with a particular protein pocket, is a critical step in AI-assisted drug discovery. Traditional docking methods are highly time-consuming, and can only…

Machine Learning · Computer Science 2023-10-11 Bowen Gao , Bo Qiang , Haichuan Tan , Minsi Ren , Yinjun Jia , Minsi Lu , Jingjing Liu , Weiying Ma , Yanyan Lan

Molecular docking is a cornerstone of drug discovery to unveil the mechanism of ligand-receptor interactions. With the recent development of deep learning in the field of artificial intelligence, innovative methods were developed for…

Chemical Physics · Physics 2025-10-29 Xuhan Liu , Baohua Zhang , Hong Zhang , Yi Qin Gao

This study examines credit default prediction by comparing three techniques, namely SMOTE, SMOTE-Tomek, and ADASYN, that are commonly used to address the class imbalance problem in credit default situations. Recognizing that credit default…

Machine Learning · Computer Science 2025-09-25 Obu-Amoah Ampomah , Edmund Agyemang , Kofi Acheampong , Louis Agyekum

By leveraging contrastive learning, clustering, and other pretext tasks, unsupervised methods for learning image representations have reached impressive results on standard benchmarks. The result has been a crowded field - many methods with…

Computer Vision and Pattern Recognition · Computer Science 2022-06-17 Matthew Gwilliam , Abhinav Shrivastava

Semiconductor quantum dots (QDs) are a leading platform for scalable quantum processors. However, scaling to large arrays requires reliable, automated tuning strategies for devices' bootstrapping, calibration, and operation, with many…

Computer Vision and Pattern Recognition · Computer Science 2025-12-02 Valeria Díaz Moreno , Ryan P Khalili , Daniel Schug , Patrick J. Walsh , Justyna P. Zwolak

Medical data poses a daunting challenge for AI algorithms: it exists in many different modalities, experiences frequent distribution shifts, and suffers from a scarcity of examples and labels. Recent advances, including transformers and…