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Spatially proximate amino acids in a protein tend to coevolve. A protein's three-dimensional (3D) structure hence leaves an echo of correlations in the evolutionary record. Reverse engineering 3D structures from such correlations is an open…

Quantitative Methods · Quantitative Biology 2013-01-15 Magnus Ekeberg , Cecilia Lövkvist , Yueheng Lan , Martin Weigt , Erik Aurell

Given the vastness of chemical space and the ongoing emergence of previously uncharacterized proteins, zero-shot compound-protein interaction (CPI) prediction better reflects the practical challenges and requirements of real-world drug…

Machine Learning · Computer Science 2025-07-29 Hongzhi Zhang , Zhonglie Liu , Kun Meng , Jiameng Chen , Jia Wu , Bo Du , Di Lin , Yan Che , Wenbin Hu

A second-order-based latent factor (SLF) analysis model demonstrates superior performance in graph representation learning, particularly for high-dimensional and incomplete (HDI) interaction data, by incorporating the curvature information…

Machine Learning · Computer Science 2024-09-05 Jialiang Wang , Yan Xia , Ye Yuan

Given the scarcity and cost of high-field MRI, the synthesis of high-field MRI from low-field MRI holds significant potential when there is limited data for training downstream tasks (e.g. segmentation). Low-field MRI often suffers from a…

Image and Video Processing · Electrical Eng. & Systems 2025-03-10 Zhenxuan Zhang , Peiyuan Jing , Coraline Beitone , Jiahao Huang , Zhifan Gao , Guang Yang , Pete Lally

Multimodal protein features play a crucial role in protein function prediction. However, these features encompass a wide range of information, ranging from structural data and sequence features to protein attributes and interaction…

Machine Learning · Computer Science 2025-11-07 Xiaoling Luo , Peng Chen , Chengliang Liu , Xiaopeng Jin , Jie Wen , Yumeng Liu , Junsong Wang

In unsupervised adaptation for vision-language models such as CLIP, pseudo-labels derived from zero-shot predictions often exhibit significant noise, particularly under domain shifts or in visually complex scenarios. Conventional…

Machine Learning · Computer Science 2025-07-31 Eman Ali , Chetan Arora , Muhammad Haris Khan

The recognition of personalized content, such as contact names, remains a challenging problem for end-to-end speech recognition systems. In this work, we demonstrate how first and second-pass rescoring strategies can be leveraged together…

Fine-tuning large pre-trained models on downstream tasks has been adopted in a variety of domains recently. However, it is costly to update the entire parameter set of large pre-trained models. Although recently proposed parameter-efficient…

Computation and Language · Computer Science 2022-11-01 Yi-Lin Sung , Jaemin Cho , Mohit Bansal

The continual learning (CL) ability is vital for deploying large language models (LLMs) in the dynamic world. Existing methods devise the learning module to acquire task-specific knowledge with parameter-efficient tuning (PET) block and the…

Computation and Language · Computer Science 2024-06-07 Weixiang Zhao , Shilong Wang , Yulin Hu , Yanyan Zhao , Bing Qin , Xuanyu Zhang , Qing Yang , Dongliang Xu , Wanxiang Che

Accurate prediction of protein-protein binding affinity is vital for understanding molecular interactions and designing therapeutics. We adapt Boltz-2, a state-of-the-art structure-based protein-ligand affinity predictor, for…

Machine Learning · Computer Science 2025-12-09 James King , Lewis Cornwall , Andrei Cristian Nica , James Day , Aaron Sim , Neil Dalchau , Lilly Wollman , Joshua Meyers

Look-Up Table based methods have emerged as a promising direction for efficient image restoration tasks. Recent LUT-based methods focus on improving their performance by expanding the receptive field. However, they inevitably introduce…

Computer Vision and Pattern Recognition · Computer Science 2026-03-04 Xiaolong Zeng , Yitong Yu , Shiyao Xiong , Jinhua Hao , Ming Sun , Chao Zhou , Bin Wang

A series of modified cognitive-only particle swarm optimization (PSO) algorithms effectively mitigate premature convergence by constructing distinct vectors for different particles. However, the underutilization of these constructed vectors…

Neural and Evolutionary Computing · Computer Science 2025-04-22 Zhenxing Zhang , Tianxian Zhang , Xiangliang Xu

As natural language interfaces enable users to express increasingly complex natural language queries, there is a parallel explosion of user review content that can allow users to better find items such as restaurants, books, or movies that…

We present analysis of a novel tool for protein secondary structure prediction using the recently-investigated Neural Machine Translation framework. The tool provides a fast and accurate folding prediction based on primary structure with…

Quantitative Methods · Quantitative Biology 2021-05-11 Evan Weissburg , Ian Bulovic

Despite the high accuracy of 'black box' deep learning models, drug discovery still relies on protein-ligand interaction principles and heuristics. To improve interpretability of protein-small molecule binding predictions, we developed the…

Machine Learning · Computer Science 2026-04-21 Jingke Chen , Jingrui Zhong , Tazneen Hossain Tani , Zidong Su , Xiaochun Zhang , Boxue Tian

We propose a self-supervised method for partial point set registration. While recent proposed learning-based methods have achieved impressive registration performance on the full shape observations, these methods mostly suffer from…

Computer Vision and Pattern Recognition · Computer Science 2020-09-14 Xiang Li , Lingjing Wang , Yi Fang

In many applications, data can be heterogeneous in the sense of spanning latent groups with different underlying distributions. When predictive models are applied to such data the heterogeneity can affect both predictive performance and…

Machine Learning · Statistics 2022-05-04 Thomas Lartigue , Sach Mukherjee

Fine-tuning the Segment Anything Model (SAM) for infrared small target detection poses significant challenges due to severe domain shifts. Existing adaptation methods often incorporate handcrafted priors to bridge this gap, yet such designs…

Computer Vision and Pattern Recognition · Computer Science 2025-10-14 Guoyi Zhang , Siyang Chen , Guangsheng Xu , Han Wang , Donghe Wang , Xiaohu Zhang

Heterogeneous Face Recognition (HFR) refers to matching face images captured in different domains, such as thermal to visible images (VIS), sketches to visible images, near-infrared to visible, and so on. This is particularly useful in…

Computer Vision and Pattern Recognition · Computer Science 2022-10-14 Anjith George , Amir Mohammadi , Sebastien Marcel

In this paper, we propose a novel method for speaker adaptation in lip reading, motivated by two observations. Firstly, a speaker's own characteristics can always be portrayed well by his/her few facial images or even a single image with…

Computer Vision and Pattern Recognition · Computer Science 2024-05-01 Songtao Luo , Shuang Yang , Shiguang Shan , Xilin Chen