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Accurate protein function prediction requires integrating heterogeneous intrinsic signals (e.g., sequence and structure) with noisy extrinsic contexts (e.g., protein-protein interactions and GO term annotations). However, two key challenges…

Machine Learning · Computer Science 2025-10-28 Runjie Zheng , Zhen Wang , Anjie Qiao , Jiancong Xie , Jiahua Rao , Yuedong Yang

Meta learning with multiple objectives can be formulated as a Multi-Objective Bi-Level optimization Problem (MOBLP) where the upper-level subproblem is to solve several possible conflicting targets for the meta learner. However, existing…

Machine Learning · Computer Science 2021-02-16 Feiyang Ye , Baijiong Lin , Zhixiong Yue , Pengxin Guo , Qiao Xiao , Yu Zhang

Feature selection is essential for high-dimensional biomedical data, enabling stronger predictive performance, reduced computational cost, and improved interpretability in precision medicine applications. Existing approaches face notable…

Machine Learning · Computer Science 2026-01-07 Xiaoyan Sun , Qingyu Meng , Yalu Wen

Motivation Protein fold recognition is an important problem in structural bioinformatics. Almost all traditional fold recognition methods use sequence (homology) comparison to indirectly predict the fold of a tar get protein based on the…

Machine Learning · Computer Science 2017-06-06 Jie Hou , Badri Adhikari , Jianlin Cheng

With the emergence of various molecular tasks and massive datasets, how to perform efficient training has become an urgent yet under-explored issue in the area. Data pruning (DP), as an oft-stated approach to saving training burdens,…

Machine Learning · Computer Science 2024-09-04 Dingshuo Chen , Zhixun Li , Yuyan Ni , Guibin Zhang , Ding Wang , Qiang Liu , Shu Wu , Jeffrey Xu Yu , Liang Wang

Protein flexibility is crucial for understanding protein structures, functions, and dynamics, and it can be measured through experimental methods such as X-ray crystallography. Theoretical approaches have also been developed to predict…

Biomolecules · Quantitative Biology 2024-11-06 Hongsong Feng , Jeffrey Y. Zhao , Guo-Wei Wei

Accurate identification of agricultural pests is essential for crop protection but remains challenging due to the large intra-class variance and fine-grained differences among pest species. While deep learning has advanced pest detection,…

Artificial Intelligence · Computer Science 2025-05-06 Jiaqi Zhang , Zhuodong Liu , Kejian Yu

Multi-objective optimization problems (MOPs) require the simultaneous optimization of conflicting objectives. Real-world MOPs often exhibit complex characteristics, including high-dimensional decision spaces, many objectives, or…

Neural and Evolutionary Computing · Computer Science 2025-10-20 Haokai Hong , Liang Feng , Min Jiang , Kay Chen Tan

Prompt learning has become a dominant paradigm for adapting vision-language models (VLMs) such as CLIP to downstream tasks without modifying pretrained weights. While extending prompts to both vision and text encoders across multiple…

Computer Vision and Pattern Recognition · Computer Science 2026-02-26 Sajjad Ghiasvand , Haniyeh Ehsani Oskouie , Mahnoosh Alizadeh , Ramtin Pedarsani

Deep neural networks show great potential for automating various visual quality inspection tasks in manufacturing. However, their applicability is limited in more volatile scenarios, such as remanufacturing, where the inspected products and…

Computer Vision and Pattern Recognition · Computer Science 2026-02-12 Johannes C. Bauer , Paul Geng , Stephan Trattnig , Petr Dokládal , Rüdiger Daub

Many vision-related tasks benefit from reasoning over multiple modalities to leverage complementary views of data in an attempt to learn robust embedding spaces. Most deep learning-based methods rely on a late fusion technique whereby…

Computer Vision and Pattern Recognition · Computer Science 2020-03-04 Austin Reiter , Menglin Jia , Pu Yang , Ser-Nam Lim

Grammar-Guided Genetic Programming (GGGP) employs a variety of insights from evolutionary theory to autonomously design solutions for a given task. Recent insights from evolutionary biology can lead to further improvements in GGGP…

Neural and Evolutionary Computing · Computer Science 2023-07-13 Stefano Tiso , Pedro Carvalho , Nuno Lourenço , Penousal Machado

Fabricating neural models for a wide range of mobile devices demands for a specific design of networks due to highly constrained resources. Both evolution algorithms (EA) and reinforced learning methods (RL) have been dedicated to solve…

Neural and Evolutionary Computing · Computer Science 2019-01-17 Xiangxiang Chu , Bo Zhang , Ruijun Xu , Hailong Ma

The accurate segmentation of medical images is a crucial step in obtaining reliable morphological statistics. However, training a deep neural network for this task requires a large amount of labeled data to ensure high-accuracy results. To…

Image and Video Processing · Electrical Eng. & Systems 2023-07-04 Xianjun Han , Qianqian Chen , Zhaoyang Xie , Xuejun Li , Hongyu Yang

Software fault prediction (SFP) is a critical task in software engineering, enabling early identification of faults in modules to improve software quality and reduce maintenance costs. This research investigates the combined effects of…

Software Engineering · Computer Science 2026-05-19 Ahmad Nauman Ghazi , Nagajyothi Devarapalli , Ashir Javeed , Sadi Alawadi , Fahed Alkhabbas , Khalid AlKharabsheh

The main feature of large-scale multi-objective optimization problems (LSMOP) is to optimize multiple conflicting objectives while considering thousands of decision variables at the same time. An efficient LSMOP algorithm should have the…

Neural and Evolutionary Computing · Computer Science 2021-08-10 Haokai Hong , Kai Ye , Min Jiang , Donglin Cao , Kay Chen Tan

Graph based molecular representation learning is essential for accurately predicting molecular properties in drug discovery and materials science; however, it faces significant challenges due to the intricate relationships among molecules…

Computational Engineering, Finance, and Science · Computer Science 2025-05-28 Zhengyang Zhou , Yunrui Li , Pengyu Hong , Hao Xu

Clinically, automated polyp segmentation techniques have the potential to significantly improve the efficiency and accuracy of medical diagnosis, thereby reducing the risk of colorectal cancer in patients. Unfortunately, existing methods…

Computer Vision and Pattern Recognition · Computer Science 2023-09-26 Junzhuo Liu , Qiaosong Chen , Ye Zhang , Zhixiang Wang , Deng Xin , Jin Wang

Many-Objective Feature Selection (MOFS) approaches use four or more objectives to determine the relevance of a subset of features in a supervised learning task. As a consequence, MOFS typically returns a large set of non-dominated…

Machine Learning · Computer Science 2023-12-01 Uchechukwu F. Njoku , Alberto Abelló , Besim Bilalli , Gianluca Bontempi

Predicting protein secondary structure is a fundamental problem in protein structure prediction. Here we present a new supervised generative stochastic network (GSN) based method to predict local secondary structure with deep hierarchical…

Quantitative Methods · Quantitative Biology 2014-03-07 Jian Zhou , Olga G. Troyanskaya