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Coordinate denoising is a promising 3D molecular pre-training method, which has achieved remarkable performance in various downstream drug discovery tasks. Theoretically, the objective is equivalent to learning the force field, which is…

Quantitative Methods · Quantitative Biology 2024-02-28 Shikun Feng , Yuyan Ni , Yanyan Lan , Zhi-Ming Ma , Wei-Ying Ma

While molecular pre-training has shown great potential in enhancing drug discovery, the lack of a solid physical interpretation in current methods raises concerns about whether the learned representation truly captures the underlying…

Biomolecules · Quantitative Biology 2023-11-07 Yuyan Ni , Shikun Feng , Wei-Ying Ma , Zhi-Ming Ma , Yanyan Lan

Many important problems involving molecular property prediction from 3D structures have limited data, posing a generalization challenge for neural networks. In this paper, we describe a pre-training technique based on denoising that…

A flexible discriminative image denoiser is introduced in which multi-task learning methods are applied to a densoising FCN based on U-Net. The activations of the U-Net model are modified by affine transforms that are a learned function of…

Image and Video Processing · Electrical Eng. & Systems 2020-11-26 Anthony Kelly

Machine learning approaches have become popular for molecular modeling tasks, including molecular force fields and properties prediction. Traditional supervised learning methods suffer from scarcity of labeled data for particular tasks,…

Chemical Physics · Physics 2022-11-29 Xiang Gao , Weihao Gao , Wenzhi Xiao , Zhirui Wang , Chong Wang , Liang Xiang

Deep neural networks (DNNs) have achieved remarkable success across diverse domains, but their performance can be severely degraded by noisy or corrupted training data. Conventional noise mitigation methods often rely on explicit…

Machine Learning · Computer Science 2025-06-16 Deliang Jin , Gang Chen , Shuo Feng , Yufeng Ling , Haoran Zhu

Machine-learned coarse-grained (MLCG) molecular dynamics is a promising option for modeling biomolecules. However, MLCG models currently require large amounts of data from reference atomistic molecular dynamics or substantial computation…

Biological Physics · Physics 2024-07-02 Aleksander E. P. Durumeric , Yaoyi Chen , Frank Noé , Cecilia Clementi

Deep learning had already demonstrated its power in medical images, including denoising, classification, segmentation, etc. All these applications are proposed to automatically analyze medical images beforehand, which brings more…

Image and Video Processing · Electrical Eng. & Systems 2020-11-05 Shao-Cheng Wen , Yu-Jen Chen , Zihao Liu , Wujie Wen , Xiaowei Xu , Yiyu Shi , Tsung-Yi Ho , Qianjun Jia , Meiping Huang , Jian Zhuang

A long-standing topic in artificial intelligence is the effective recognition of patterns from noisy images. In this regard, the recent data-driven paradigm considers 1) improving the representation robustness by adding noisy samples in…

Computer Vision and Pattern Recognition · Computer Science 2024-06-21 Shuren Qi , Yushu Zhang , Chao Wang , Tao Xiang , Xiaochun Cao , Yong Xiang

Recently, the mainstream practice for training low-light raw image denoising methods has shifted towards employing synthetic data. Noise modeling, which focuses on characterizing the noise distribution of real-world sensors, profoundly…

Image and Video Processing · Electrical Eng. & Systems 2026-01-16 Hansen Feng , Lizhi Wang , Yiqi Huang , Yuzhi Wang , Lin Zhu , Hua Huang

Coordinate denoising has emerged as a promising method for 3D molecular pretraining due to its theoretical connection to learning molecular force field. However, existing denoising methods rely on oversimplied molecular dynamics that assume…

Machine Learning · Computer Science 2025-10-28 Xixian Liu , Rui Jiao , Zhiyuan Liu , Yurou Liu , Yang Liu , Ziheng Lu , Wenbing Huang , Yang Zhang , Yixin Cao

Pretraining molecular representations from large unlabeled data is essential for molecular property prediction due to the high cost of obtaining ground-truth labels. While there exist various 2D graph-based molecular pretraining approaches,…

Machine Learning · Computer Science 2023-09-11 Sungjun Cho , Dae-Woong Jeong , Sung Moon Ko , Jinwoo Kim , Sehui Han , Seunghoon Hong , Honglak Lee , Moontae Lee

Recently, deep learning methods such as the convolutional neural networks have gained prominence in the area of image denoising. This is owing to their proven ability to surpass state-of-the-art classical image denoising algorithms such as…

Image and Video Processing · Electrical Eng. & Systems 2024-09-02 Basit O. Alawode , Mudassir Masood

The approximation and convergence properties of implicit neural representations (INRs) are known to be highly sensitive to parameter initialization strategies. While several data-driven initialization methods demonstrate significant…

Computer Vision and Pattern Recognition · Computer Science 2026-04-01 Kushal Vyas , Alper Kayabasi , Daniel Kim , Vishwanath Saragadam , Ashok Veeraraghavan , Guha Balakrishnan

The success of speech-image retrieval relies on establishing an effective alignment between speech and image. Existing methods often model cross-modal interaction through simple cosine similarity of the global feature of each modality,…

Computation and Language · Computer Science 2024-09-12 Lifeng Zhou , Yuke Li , Rui Deng , Yuting Yang , Haoqi Zhu

Operando microscopy provides direct insight into the dynamic chemical and physical processes that govern functional materials, yet measurement noise limits the effective resolution and undermines quantitative analysis. Here, we present a…

Computer Vision and Pattern Recognition · Computer Science 2025-11-03 Samuel Degnan-Morgenstern , Alexander E. Cohen , Rajeev Gopal , Megan Gober , George J. Nelson , Peng Bai , Martin Z. Bazant

Image denoising is a fundamental challenge in computer vision, with applications in photography and medical imaging. While deep learning-based methods have shown remarkable success, their reliance on specific noise distributions limits…

Computer Vision and Pattern Recognition · Computer Science 2025-08-28 Dongjin Kim , Jaekyun Ko , Muhammad Kashif Ali , Tae Hyun Kim

Recent research on fine-tuning vision-language models has demonstrated impressive performance in various downstream tasks. However, the challenge of obtaining accurately labeled data in real-world applications poses a significant obstacle…

Machine Learning · Computer Science 2024-10-01 Tong Wei , Hao-Tian Li , Chun-Shu Li , Jiang-Xin Shi , Yu-Feng Li , Min-Ling Zhang

The success of large-scale pretraining in NLP and computer vision has catalyzed growing efforts to develop analogous foundation models for the physical sciences. However, pretraining strategies using atomistic data remain underexplored. To…

Machine Learning · Computer Science 2026-03-19 Tynan Perez , Rafael Gomez-Bombarelli

Despite the indispensable role of X-ray computed tomography (CT) in diagnostic medicine field, the associated ionizing radiation is still a major concern considering that it may cause genetic and cancerous diseases. Decreasing the exposure…

Image and Video Processing · Electrical Eng. & Systems 2021-06-09 Ti Bai , Dan Nguyen , Biling Wang , Steve Jiang
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