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IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

作者： Shibo Liu Xuan Zhang Anlei Jiao Shiwei Sun Longyang Dian Xuefeng Cui School of Computer Science and Technology Shandong University Qingdao China Key Lab of Intelligent Information Processing Institute of Computing Technology Chinese Academy of Sciences Beijing China State Key Laboratory of Microbial Technology Shandong University Qingdao China

ISBN: (数字)9798350386226

ISBN: (纸本)9798350386233

The task of retrieving and analyzing mass spectra is indispensable for the identification of compounds in mass spectrometry (MS). This methodology is of critical importance as it enables researchers to correlate observed spectra with established databases, thereby precisely determining the chemical composition of samples. The primary challenges to its efficacy lie in optimizing the balance between retrieval accuracy and processing speed. Empirical studies have demonstrated that by converting mass spectra into embeddings via deep learning, it is possible to achieve both high accuracy and speed in retrieval. Nevertheless, there are complex challenges associated with employing deep learning for spectral embedding, particularly within the domain of electron ionization mass spectrometry (EI-MS). In this paper, we introduce a novel representation learning technique termed EI-MS2VEC for EI-MS retrieval. Our spectrum retrieval methodology surpasses current state-of-the-art techniques such as FastEI. For the in-silico library, we attain hit rate@1 and hit rate@10 of 43.6% and 84.5%, respectively, compared to FastEI’s 36.7% and 80.4%. Moreover, our retrieval approach operates with an order of magnitude greater speed than FastEI. The source code is available on Github (https://***/xfcui/EI-MS2VEC).

关键词： Representation learning Deep learning Accuracy Databases Source coding Ionization Predictive models Mass spectroscopy Electrons Software development management

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Learning with Open-world Noisy Data via Class-independent Margin in Dual Representation Space 39

Learning with Open-world Noisy Data via Class-independent Ma...

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39th Annual AAAI Conference on Artificial Intelligence, AAAI 2025

作者： Pan, Linchao Gao, Can Zhou, Jie Wang, Jinbao College of Computer Science and Software Engineering Shenzhen University China Guangdong Provincial Key Laboratory of Intelligent Information Processing China National Engineering Laboratory for Big Data System Computing Technology Shenzhen University China

ISBN: (纸本)157735897X

Learning with Noisy Labels (LNL) aims to improve the model generalization when facing data with noisy labels, and existing methods generally assume that noisy labels come from known classes, called closed-set noise. However, in real-world scenarios, noisy labels from similar unknown classes, i.e., open-set noise, may occur during the training and inference stage. Such open-world noisy labels may significantly impact the performance of LNL methods. In this study, we propose a novel dual-space joint learning method to robustly handle the open-world noise. To mitigate model overfitting on closed-set and open-set noises, a dual representation space is constructed by two networks. One is a projection network that learns shared representations in the prototype space, while the other is a One-Vs-All (OVA) network that makes predictions using unique semantic representations in the class-independent space. Then, bi-level contrastive learning and consistency regularization are introduced in two spaces to enhance the detection capability for data with unknown classes. To benefit from the memorization effects across different types of samples, class-independent margin criteria are designed for sample identification, which selects clean samples, weights closed-set noise, and filters open-set noise effectively. Extensive experiments demonstrate that our method outperforms the state-of-the-art methods and achieves an average accuracy improvement of 4.55% and an AUROC improvement of 6.17% on CIFAR80N. Copyright © 2025, Association for the Advancement of Artificial Intelligence (***). All rights reserved.

关键词： Contrastive Learning

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Forget less,count better:a domain-incremental self-distillation learning benchmark for lifelong crowd counting

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Frontiers of information technology & Electronic Engineering 2023年第2期24卷 187-202页

作者： Jiaqi GAO Jingqi LI Hongming SHAN Yanyun QU James ZWANG Fei-Yue WANG Junping ZHANG Shanghai Key Laboratory of Intelligent Information Processing School of Computer ScienceFudan UniversityShanghai 200433China Institute of Science and Technology for Brain-inspired Intelligence Fudan UniversityShanghai 200433China Shanghai Center for Brain Science and Brain-inspired Technology Shanghai 201210China School of Information Science and Technology Xiamen UniversityXiamen 361005China College of Information Sciences and Technology the Pennsylvania State UniversityUniversity ParkPA 16802USA State Key Laboratory of Management and Control for Complex Systems Institute of AutomationChinese Academy of SciencesBeijing 100190China

Crowd counting has important applications in public safety and pandemic control.A robust and practical crowd counting system has to be capable of continuously learning with the newly incoming domain data in real-world scenarios instead of fitting one domain ***-the-shelf methods have some drawbacks when handling multiple domains:(1)the models will achieve limited performance(even drop dramatically)among old domains after training images from new domains due to the discrepancies in intrinsic data distributions from various domains,which is called catastrophic forgetting;(2)the well-trained model in a specific domain achieves imperfect performance among other unseen domains because of domain shift;(3)it leads to linearly increasing storage overhead,either mixing all the data for training or simply training dozens of separate models for different domains when new ones are *** overcome these issues,we investigate a new crowd counting task in incremental domain training setting called lifelong crowd *** goal is to alleviate catastrophic forgetting and improve the generalization ability using a single model updated by the incremental ***,we propose a self-distillation learning framework as a benchmark(forget less,count better,or FLCB)for lifelong crowd counting,which helps the model leverage previous meaningful knowledge in a sustainable manner for better crowd counting to mitigate the forgetting when new data arrive.A new quantitative metric,normalized Backward Transfer(nBwT),is developed to evaluate the forgetting degree of the model in the lifelong learning *** experimental results demonstrate the superiority of our proposed benchmark in achieving a low catastrophic forgetting degree and strong generalization ability.

关键词： Crowd counting Knowledge distillation Lifelong learning

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Learning with Open-world Noisy Data via Class-independent Margin in Dual Representation Space

arXiv

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arXiv 2025年

关键词： Contrastive Learning

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Shapley Value-based Contrastive Alignment for Multimodal information Extraction

arXiv

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arXiv 2024年

作者： Luo, Wen Tianshu, Shen Xia, Yu Li, Sujian State Key Laboratory of Multimedia Information Processing School of Computer Science Peking University Beijing China Wangxuan Institute of Computer Technology Peking University Beijing China School of Computer Science Peking University Beijing China

The rise of social media and the exponential growth of multimodal communication necessitates advanced techniques for Multimodal information Extraction (MIE). However, existing methodologies primarily rely on direct Image-Text interactions, a paradigm that often faces significant challenges due to semantic and modality gaps between images and text. In this paper, we introduce a new paradigm of Image-Context-Text interaction, where large multimodal models (LMMs) are utilized to generate descriptive textual context to bridge these gaps. In line with this paradigm, we propose a novel Shapley Value-based Contrastive Alignment (Shap-CA) method, which aligns both context-text and context-image pairs. Shap-CA initially applies the Shapley value concept from cooperative game theory to assess the individual contribution of each element in the set of contexts, texts and images towards total semantic and modality overlaps. Following this quantitative evaluation, a contrastive learning strategy is employed to enhance the interactive contribution within context-text/image pairs, while minimizing the influence across these pairs. Furthermore, we design an adaptive fusion module for selective cross-modal fusion. Extensive experiments across four MIE datasets demonstrate that our method significantly outperforms existing state-of-the-art methods. Copyright © 2024, The Authors. All rights reserved.

关键词： Semantics

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PLAYING TECHNIQUE DETECTION BY FUSING NOTE ONSET information IN GUZHENG PERFORMANCE 23

PLAYING TECHNIQUE DETECTION BY FUSING NOTE ONSET INFORMATION...

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23rd International Society for Music information Retrieval Conference, ISMIR 2022

作者： Li, Dichucheng Wu, Yulun Li, Qinyu Zhao, Jiahao Yu, Yi Xia, Fan Li, Wei School of Computer Science and Technology Fudan University Shanghai China College of Experimental Art Sichuan Conservatory of Music Sichuan China Tokyo Japan Shanghai Key Laboratory of Intelligent Information Processing Fudan University China

ISBN: (纸本)9781732729926

The Guzheng is a kind of traditional Chinese instruments with diverse playing techniques. Instrument playing techniques (IPT) play an important role in musical performance. However, most of the existing works for IPT detection show low efficiency for variable-length audio and provide no assurance in the generalization as they rely on a single sound bank for training and testing. In this study, we propose an end-to-end Guzheng playing technique detection system using Fully Convolutional Networks that can be applied to variable-length audio. Because each Guzheng playing technique is applied to a note, a dedicated onset detector is trained to divide an audio into several notes and its predictions are fused with frame-wise IPT predictions. During fusion, we add the IPT predictions frame by frame inside each note and get the IPT with the highest probability within each note as the final output of that note. We create a new dataset named GZ_IsoTech from multiple sound banks and real-world recordings for Guzheng performance analysis. Our approach achieves 87.97% in frame-level accuracy and 80.76% in note-level F1-score, outperforming existing works by a large margin, which indicates the effectiveness of our proposed method in IPT detection. © D. Li, Y. Wu, Q. Li, J. Zhao, Y. Yu, F. Xia, and W. Li.

关键词： Audio acoustics

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How to Train Your Neural Network for Molecular Structure Generation from Mass Spectra?

How to Train Your Neural Network for Molecular Structure Gen...

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IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

作者： Kai Zhao Yanmin Liu Longyang Dian Shiwei Sun Xuefeng Cui School of Computer Science and Technology Shandong University Qingdao China State Key Laboratory of Microbial Technology Shandong University Qingdao China Key Lab of Intelligent Information Processing Institute of Computing Technology Chinese Academy of Sciences Beijing China

ISBN: (数字)9798350386226

ISBN: (纸本)9798350386233

Mass spectrometry serves as a pivotal tool for the analysis of small molecules through an examination of their mass-to-charge ratios. Recent advancements in deep learning have markedly enhanced the analysis of mass spectrometric data, facilitating the prediction of novel small molecule structures without the necessity of extensive databases. Nonetheless, the paucity of annotated datasets impedes the efficacious training of molecular generation models predicated on MS 2 spectra. To mitigate this limitation, we introduce ctMSNovelist, an avant-garde method that amalgamates pre-training, fine-tuning, and co-training techniques to construct a more precise model for the generation of molecular structures from tandem mass spectrometry data. This novel approach augments both the training regimen and the predictive accuracy of the MSNovelist model, thereby surmounting the obstacle of limited data. The methodology commences with the pretraining of a Variational Autoencoder (VAE) to generate molecular fingerprints derived from SMILES strings. Subsequently, it undergoes fine-tuning to emulate noisy fingerprints originating from mass spectrometry (MS) data. Concurrently, MSNovelist is co-trained utilizing these simulated fingerprints, inclusive of the highly noisy variants produced in the early stages of VAE training. The incorporation of a substantial volume of noisy data serves to enhance model accuracy and avert overfitting. We evaluated ctMSNovelist using the GNPS dataset and attained a SMILES prediction accuracy of 48.8%, representing a 4.1% enhancement over MSNovelist. It is pertinent to note that the sole distinction between ctMSNovelist and MSNovelist in this experiment was the training process. The code and models are publicly available at https://***/xfcui/ctMSNovelist.

关键词： Training Solid modeling Accuracy Biological system modeling Fingerprint recognition Predictive models Mass spectroscopy Data models Noise measurement Overfitting

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Big-Moe: Bypassing Isolated Gating For Generalized Multimodal Face Anti-Spoofing

Big-Moe: Bypassing Isolated Gating For Generalized Multimoda...

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International Conference on Acoustics, Speech, and Signal processing (ICASSP)

作者： Yingjie Ma Zitong Yu Xun Lin Weicheng Xie Linlin Shen College of Computer Science and Software Engineering Shenzhen University Great Bay University National Engineering Laboratory for Big Data System Computing Technology Shenzhen University Guangdong Provincial Key Laboratory of Intelligent Information Processing

ISBN: (数字)9798350368741

ISBN: (纸本)9798350368758

In the domain of facial recognition security, multimodal Face Anti-Spoofing (FAS) is essential for countering presentation attacks. However, existing technologies encounter challenges due to modality biases and imbalances, as well as domain shifts. Our research introduces a Mixture of Experts (MoE) model to address these issues effectively. We identified three limitations in traditional MoE approaches to multimodal FAS: (1) Coarse-grained experts’ inability to capture nuanced spoofing indicators; (2) Gated networks’ susceptibility to input noise affecting decision-making; (3) MoE’s sensitivity to prompt tokens leading to overfitting with conventional learning methods. To mitigate these, we propose the Bypass Isolated Gating MoE (BIG-MoE) framework, featuring: (1) Fine-grained experts for enhanced detection of subtle spoofing cues; (2) An isolation gating mechanism to counteract input noise; (3) A novel differential convolutional prompt bypass enriching the gating network with critical local features, thereby improving perceptual capabilities. Extensive experiments on four benchmark datasets demonstrate significant generalization performance improvement in multimodal FAS task. The code is released at https://***/murInJ/BIG-MoE.

关键词： Convolutional codes Sensitivity Convolution Face recognition Noise Logic gates Feature extraction Security Speech processing Overfitting

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Generating Molecules Conditional on 3D Protein Pockets with HGAF

Generating Molecules Conditional on 3D Protein Pockets with ...

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IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

作者： Qinglian Zhu Xiaoli Lin Xiaolong Zhang Hubei Key Laboratory of Intelligent Information Processing and Real-Time Industrial System School of Computer Science and Technology Wuhan University of Science and Technology Wuhan China

Most current representations of protein pockets are the atom-pair graph, which ignore the global structural information of amino acids. Therefore, we propose a new molecular generation model, which uses the hypergraph to represent protein pocket structure, and combines the structural features obtained by atom-pair graph representation. These two levels of graphs are more capable of representing the complex structural information of protein pockets. Then, the graphs of the two levels of the protein pockets are input into the improved network model, which is named Hypergraph Graph Attention Fusion (HGAF), to obtain the embedding representation of the protein pockets, which is used as a condition to constrain the molecule generation. The molecules sampled by HGAF are subjected to quality assessment and docking targeting validation. Experimental results show that the molecules generated by proposed method can achieve better results in both of these assessment approaches.

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Size-Invariance Matters: Rethinking Metrics and Losses for Imbalanced Multi-object Salient Object Detection 41

Size-Invariance Matters: Rethinking Metrics and Losses for I...

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41st International Conference on Machine Learning, ICML 2024

作者： Li, Feiran Xu, Qianqian Bao, Shilong Yang, Zhiyong Cong, Runmin Cao, Xiaochun Huang, Qingming Institute of Information Engineering Chinese Academy of Sciences Beijing China School of Cyber Security University of Chinese Academy of Sciences Beijing China Key Laboratory of Intelligent Information Processing Institute of Computing Technology Chinese Academy of Sciences Beijing China School of Computer Science and Technology University of Chinese Academy of Sciences Beijing China Institute of Information Science Beijing Jiaotong University Beijing China School of Control Science and Engineering Shandong University Jinan China Key Laboratory of Machine Intelligence and System Control Ministry of Education Jinan China School of Cyber Science and Tech. Sun Yat-sen University Shenzhen Campus China Key Laboratory of Big Data Mining and Knowledge Management Chinese Academy of Sciences Beijing China

This paper explores the size-invariance of evaluation metrics in Salient Object Detection (SOD), especially when multiple targets of diverse sizes co-exist in the same image. We observe that current metrics are size-sensitive, where larger objects are focused, and smaller ones tend to be ignored. We argue that the evaluation should be size-invariant because bias based on size is unjustified without additional semantic information. In pursuit of this, we propose a generic approach that evaluates each salient object separately and then combines the results, effectively alleviating the imbalance. We further develop an optimization framework tailored to this goal, achieving considerable improvements in detecting objects of different sizes. Theoretically, we provide evidence supporting the validity of our new metrics and present the generalization analysis of SOD. Extensive experiments demonstrate the effectiveness of our method. The code is available at https://***/Ferry-Li/SI-SOD. Copyright 2024 by the author(s)

关键词： Object detection

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