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RBP-Former: Joint Prediction of RNA-protein Binding Sites on Full-length RNA Transcripts for Multiple RBPs

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RBP-Former: Joint Prediction of RNA-protein Binding Sites on...

2024 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2024

作者： Li, Yichong Liu, Xiaojian Cheng, Fan Pan, Xiaoyong Yang, Yang Shanghai Jiao Tong University Department of Computer Science and Engineering Shanghai200240 China Shanghai Jiao Tong University Institute of Image Processing and Pattern Recognition Shanghai200240 China Ministry of Education of China Key Laboratory of System Control and Information Processing Shanghai200240 China Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering Shanghai200240 China

ISBN: (纸本)9798350386226

RNA-binding proteins (RBPs) are essential for gene expression, and the complex RNA-protein interaction mechanisms require analysis of global RNA information. Therefore, accurate prediction of RBP binding sites on full-length RNA transcripts is crucial for understanding these mechanisms and their roles in diseases. While machine learning methods can predict RBP binding to RNA fragments, extending this to full-length transcripts presents challenges due to sequence length and data imbalance. In this paper, we introduce RBP-Former, a binding site joint prediction model designed specifically for full-length RNA transcripts that can be used for multiple RBPs. This model processes information at both coarse and fine-grained levels to fully exploit sequence data and its interactions with multiple RBPs. We develop multi-level imbalance learning strategies, achieving favorable results on imbalanced data. Our method outperforms existing methods in predicting binding sites on full-length RNA transcripts for multiple RBPs, demonstrating its effectiveness in handling imbalanced label and sample distributions. © 2024 IEEE.

关键词： Binding sites

FADE: A Task-Agnostic Upsampling Operator for Encoder-Decoder Architectures

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arXiv 2024年

作者： Lu, Hao Liu, Wenze Fu, Hongtao Cao, Zhiguo The Key Laboratory of Image Processing and Intelligent Control Ministry of Education School of Artificial Intelligence and Automation Huazhong University of Science and Technology Wuhan430074 China

The goal of this work is to develop a task-agnostic feature upsampling operator for dense prediction where the operator is required to facilitate not only region-sensitive tasks like semantic segmentation but also detail-sensitive tasks such as image matting. Prior upsampling operators often can work well in either type of the tasks, but not both. We argue that task-agnostic upsampling should dynamically trade off between semantic preservation and detail delineation, instead of having a bias between the two properties. In this paper, we present FADE, a novel, plug-and-play, lightweight, and task-agnostic upsampling operator by fusing the assets of decoder and encoder features at three levels: i) considering both the encoder and decoder feature in upsampling kernel generation;ii) controlling the per-point contribution of the encoder/decoder feature in upsampling kernels with an efficient semi-shift convolutional operator;and iii) enabling the selective pass of encoder features with a decoder-dependent gating mechanism for compensating details. To improve the practicality of FADE, we additionally study parameter- and memory-efficient implementations of semi-shift convolution. We analyze the upsampling behavior of FADE on toy data and show through large-scale experiments that FADE is task-agnostic with consistent performance improvement on a number of dense prediction tasks with little extra cost. For the first time, we demonstrate robust feature upsampling on both region- and detail-sensitive tasks successfully. Code is made available at: https://***/poppinace/fade Copyright © 2024, The Authors. All rights reserved.

关键词： Object detection

Late Better than Early: A Decision-Level Information Fusion Approach for Rgb-Thermal Crowd Counting with Illumination Awareness

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SSRN

SSRN 2024年

作者： Cheng, Jian Feng, Chen Xiao, Yang Cao, Zhiguo Key Laboratory of Image Processing and Intelligent Control Ministry of Education School of Artificial Intelligence and Automation Huazhong University of Science and Technology Wuhan430074 China

In this paper, we make the first research effort to address the RGB-Thermal (RGB-T) crowd counting problem with decision-level late fusion manner. Being different from the existing pixel-level or feature-level fusion methods, our proposition chooses to fuse the density maps yielded by RGB and thermal counterparts via spatially adaptive weighting with RGB illumination-aware attention. Our key intuition to conduct RGB-T density map fusion lies in 3 main folders. First, compared with the raw RGB-T images or convolutional feature maps, RGB-T density maps contain stronger counting-wise semantic meanings. Secondly, they are also of high spatial resolution for revealing fine local details. Thirdly, RGB-T density maps are complementary to each other for effective counting pattern characterization. To fuse them adaptively, a spatial weighting map is generated concerning the issues of RGB illumination awareness and local counting pattern characterization ability jointly. To the best of our knowledge, we are the first to leverage RGB-T crowd counting via concerning these 2 issues in a unified way. Meanwhile, cross-modality feature interaction is conducted between RGB and thermal modalities to facilitate spatial weighting map generation. The experiments on 2 well-established RGB-T crowd counting datasets, i.e., RGBT-CC and DroneRGBT) verify the superiority of our proposition. The source code and pretrained models will be released upon acceptance at https://***/hustaia/DLF-IA. © 2024, The Authors. All rights reserved.

关键词： Semantics

Pseudo-Labeling by Multi-Policy Viewfinder Network for image Cropping

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arXiv 2024年

作者： Pan, Zhiyu Wang, Kewei Wu, Yizheng Xiao, Liwen Cui, Jiahao Wang, Zhicheng Cao, Zhiguo Key Laboratory of Image Processing and Intelligent Control Ministry of Education School of Artificial Intelligence and Automation Huazhong University of Science and Technology Wuhan430074 China

Automatic image cropping models predict reframing boxes to enhance image aesthetics. Yet, the scarcity of labeled data hinders the progress of this task. To overcome this limitation, we explore the possibility of utilizing both labeled and unlabeled data together to expand the scale of training data for image cropping models. This idea can be implemented in a pseudo-labeling way: producing pseudo labels for unlabeled data by a teacher model and training a student model with these pseudo labels. However, the student may learn from teacher's mistakes. To address this issue, we propose the multi-policy viewfinder network (MPV-Net) that offers diverse refining policies to rectify the mistakes in original pseudo labels from the teacher. The most reliable policy is selected to generate trusted pseudo labels. The reliability of policies is evaluated via the robustness against box jittering. The efficacy of our method can be evaluated by the improvement compared to the supervised baseline which only uses labeled data. Notably, our MPV-Net outperforms off-the-shelf pseudo-labeling methods, yielding the most substantial improvement over the supervised baseline. Furthermore, our approach achieves state-of-the-art results on both the FCDB and FLMS datasets, signifying the superiority of our approach. Copyright © 2024, The Authors. All rights reserved.

关键词： Distillation

A Comparison of Large-Scale MOEAs with Informed Initialization for Voltage Transformer Ratio Error Estimation 1

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17th International Conference on Bio-Inspired Computing: Theories and Applications, BIC-TA 2022

作者： Li, Lianghao He, Cheng Li, Hongbin Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China School of Artificial Intelligence and Automation Huazhong University of Science and Technology Wuhan430074 China School of Electrical and Electronic Engineering Huazhong University of Science and Technology Wuhan430074 China

ISBN: (数字)9789819915491

ISBN: (纸本)9789819915484

Large-scale multiobjective optimization problems (LSMOPs) exist widely in real-world applications. The large number of decision variables in LSMOP leads to a tremendous high-dimensional search space, which is still challenging for existing multiobjective evolutionary algorithms (MOEAs). The voltage transformer ratio error estimation (TREE) problem is a typical LSMOP in real-world applications. A number of large-scale multiobjective evolutionary algorithms (LSMOEAs) have been adopted for solving the TREE problem, but so far there is still considerable potential for improvement in their results. In this paper, we propose a informed initialization for solving the TREE problem. The physical properties of the TREE problem are used to construct an initial set of solutions with specific characteristics. The proposed initialization method is tested against the default initialization method on five TREE problems by being applied on six state-of-the-art LSMOEAs and a classical MOEA. The experimental results demonstrate that the initialization method has a significant effect on the performance of LSMOEAs in solving the TREE problems. © 2023, The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.

关键词： Multiobjective optimization

Cross-Task Inconsistency Based Active Learning (CTIAL) for Emotion Recognition

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arXiv 2024年

作者： Xu, Yifan Jiang, Xue Wu, Dongrui Key Laboratory of the Ministry of Education for Image Processing and Intelligent Control School of Artificial Intelligence and Automation Huazhong University of Science and Technology Wuhan430074 China

Emotion recognition is a critical component of affective computing. Training accurate machine learning models for emotion recognition typically requires a large amount of labeled data. Due to the subtleness and complexity of emotions, multiple evaluators are usually needed for each affective sample to obtain its ground-truth label, which is expensive. To save the labeling cost, this paper proposes an inconsistency-based active learning approach for cross-task transfer between emotion classification and estimation. Affective norms are utilized as prior knowledge to connect the label spaces of categorical and dimensional emotions. Then, the prediction inconsistency on the two tasks for the unlabeled samples is used to guide sample selection in active learning for the target task. Experiments on within-corpus and cross-corpus transfers demonstrated that cross-task inconsistency could be a very valuable metric in active learning. To our knowledge, this is the first work that utilizes prior knowledge on affective norms and data in a different task to facilitate active learning for a new task, even the two tasks are from different datasets. © 2024, CC BY.

关键词： Active learning

A Point Cloud Segmentation Method Based on Ground Point Cloud Removal and Multi-Scale Twin Range image 42

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A Point Cloud Segmentation Method Based on Ground Point Clou...

42nd Chinese control Conference, CCC 2023

作者： Zhou, Yicheng Peng, Gang Duan, Hangqi Wu, Zhangang Zhu, Xukang School of Artificial Intelligence and Automation Huazhong University of Science and Technology Wuhan430074 China Key Laboratory of Image Processing and Intelligent Control Ministry of Education Wuhan430074 China Shantui Construction Machinery Co. Ltd. Jining272073 China

ISBN: (纸本)9789887581543

Aiming at the shortcomings of traditional point cloud segmentation algorithms, this paper proposes a 3D lidar point cloud segmentation method combining ground filtering and multi-scale twin range image construction. This method fully considers the geometric space distribution characteristics of the point cloud and the randomness of the positions between objects. Based on the assumption of multi plane model, the point cloud is divided into sectors. The ground points are removed through region ground plane fitting and growth, and then the multi-scale twin range image is constructed according to non-ground points. On the basis of the twin range image, the Breadth First Search algorithm is improved, the depth-breadth joint search strategy is proposed, all the points to be clustered are traversed, and the adaptive clustering threshold is used for point cloud clustering, which realizes a point cloud segmentation method with higher accuracy and robustness. Through the experimental analysis of KITTI dataset and collected campus outdoor scene dataset, compared with the traditional point cloud segmentation algorithm, the method proposed in this paper can effectively improve the point cloud segmentation accuracy and robustness of mobile robots in complex environments. © 2023 Technical Committee on control Theory, Chinese Association of Automation.

关键词： image enhancement

Knowledge-Data Fusion Based Source-Free Semi-Supervised Domain Adaptation for Seizure Subtype Classification

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arXiv 2024年

作者： Peng, Ruimin An, Jiayu Wu, Dongrui Key Laboratory of the Ministry of Education for Image Processing and Intelligent Control School of Artificial Intelligence and Automation Huazhong University of Science and Technology Wuhan430074 China

Electroencephalogram (EEG)-based seizure subtype classification enhances clinical diagnosis efficiency. Source-free semi-supervised domain adaptation (SF-SSDA), which transfers a pre-trained model to a new dataset with no source data and limited labeled target data, can be used for privacy-preserving seizure subtype classification. This paper considers two challenges in SF-SSDA for EEG-based seizure subtype classification: 1) How to effectively fuse both raw EEG data and expert knowledge in classifier design? 2) How to align the source and target domain distributions for SF-SSDA? We propose a Knowledge-Data Fusion based SF-SSDA approach, KDF-MutualSHOT, for EEG-based seizure subtype classification. In source model training, KDF uses Jensen-Shannon Divergence to facilitate mutual learning between a feature-driven Decision Tree-based model and a data-driven Transformer-based model. To adapt KDF to a new target dataset, an SF-SSDA algorithm, MutualSHOT, is developed, which features a consistency-based pseudo-label selection strategy. Experiments on the public TUSZ and CHSZ datasets demonstrated that KDF-MutualSHOT outperformed other supervised and source-free domain adaptation approaches in cross-subject seizure subtype classification. © 2024, CC BY.

关键词： Self-supervised learning

A3E: Aligned and Augmented Adversarial Ensemble for Accurate, Robust and Privacy-Preserving EEG Decoding

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arXiv 2024年

作者： Chen, Xiaoqing Jia, Tianwang Wu, Dongrui Key Laboratory of Image Processing and Intelligent Control Ministry of Education School of Artificial Intelligence and Automation Huazhong University of Science and Technology Wuhan430074 China

An electroencephalogram (EEG) based brain-computer interface (BCI) enables direct communication between the brain and external devices. However, EEG-based BCIs face at least three major challenges in real-world applications: data scarcity and individual differences, adversarial vulnerability, and data privacy. While previous studies have addressed one or two of these issues, simultaneous accommodation of all three challenges remains challenging and unexplored. This paper fills this gap, by proposing an Aligned and Augmented Adversarial Ensemble (A3E) algorithm and integrating it into three privacy protection scenarios (centralized source-free transfer, federated source-free transfer, and source data perturbation), achieving simultaneously accurate decoding, adversarial robustness, and privacy protection of EEG-based BCIs. Experiments on three public EEG datasets demonstrated that our proposed approach outperformed over 10 classic and state-of-the-art approaches in both accuracy and robustness in all three privacy-preserving scenarios, even outperforming state-of-the-art transfer learning approaches that do not consider privacy protection at all. This is the first time that three major challenges in EEG-based BCIs can be addressed simultaneously, significantly improving the practicalness of EEG decoding in real-world BCIs. © 2024, CC BY.

关键词： Transfer learning