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Deep Representation Learning for Electron Ionization Mass Spectra Retrieval

Deep Representation Learning for Electron Ionization Mass Sp...

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2024 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2024

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

ISBN: (纸本)9798350386226

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). © 2024 IEEE.

关键词： Embeddings

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Machine Learning Based FDTD Method for 3D Electromagnetic Simulation

Machine Learning Based FDTD Method for 3D Electromagnetic Si...

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2024 IEEE International Conference on Computational Electromagnetics, ICCEM 2024

作者： Dai, Jinpeng Xie, Guoda Hou, Guilin Zhang, Liyuan Huang, Zhixiang Anhui University The Key Laboratory of Intelligent Computing and Signal Processing Hefei China Education of Anhui Province Anhui Province Key Laboratory of Target Recognition and Feature Extraction Anhui Luan237000 China Ministry of Education The Key Laboratory of Intelligent Computing and Signal Processing Hefei China Institute of Energy Hefei Comprehensive National Science Center Hefei230031 China Institute of Plasma Physics Hefei Institutes of Physical Science Chinese Academy of Sciences Hefei230031 China Anhui Province Anhui University Key Laboratory of Electromagnetic Environmental Sensing Hefei230601 China Anhui University Hefei China

ISBN: (纸本)9798350383317

This article introduces an innovative and efficient deep learning-assisted Finite-Difference Time-Domain (DL-FDTD) method in the field of computational electromagnetics. This method ingeniously integrates the Gated Recurrent Unit (GRU) network and Particle Swarm Optimization (PSO) algorithm into the traditional FDTD framework, termed as the PSO-GRU-FDTD model. A key innovation of this model is the application of the particle swarm algorithm, which significantly simplifies the parameter tuning process, thereby accelerating model development. This advancement represents a notable breakthrough from the complex parameter adjustment process typical in traditional neural network models. Moreover, compared to the traditional Long Short-Term Memory (LSTM) networks, the GRU network excels in simplicity, convenience, and efficiency, while also ensuring accuracy. Ultimately, this method is applied to three-dimensional electromagnetic simulation and emulation. Numerical results demonstrate that this approach exhibits outstanding performance in both simulation accuracy and efficiency. © 2024 IEEE.

关键词： Electromagnetic simulation

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Accelerating Unsupervised Federated Graph Neural Networks via Semi-asynchronous Communication 18th

Accelerating Unsupervised Federated Graph Neural Networks vi...

引用

18th CCF Conference on Computer Supported Cooperative Work and Social computing, ChineseCSCW 2023

作者： Liao, Yuanming Wu, Duanji Lin, Pengyu Guo, Kun College of Computer and Data Science Fuzhou University Fuzhou350108 China Fujian Key Laboratory of Network Computing and Intelligent Information Processing Fuzhou University Fuzhou350108 China Key Laboratory of Spatial Data Mining and Information Sharing Ministry of Education Fuzhou350108 China

ISBN: (纸本)9789819996360

Graph neural networks have shown excellent performance in many fields owing to their powerful processing ability of graph data. In recent years, federated graph neural network has become a reasonable solution due to the enactment of privacy-related regulations. However, frequent communication between the coordinator and participants in federated graph neural network results in longer model training time and consumes many communication resources. To address this challenge, in this paper, we propose a novel semi-asynchronous federated graph learning communication protocol that simultaneously alleviates the negative impact of stragglers(slow participants) and accelerate the training process in the unsupervised federated graph neural network scenario. First, the weighted enforced synchronization strategy is intended to preserve the information carried by stragglers while preventing their stale models from harming the global model update. Second, the adaptive local update strategy is developed to make the local model of the participant with poor computing performance as close as possible to the global model. Experiments combine federated learning with graph contrastive learning. The results demonstrate that our proposed protocol outperforms the existing protocols in real-world networks. © 2024, The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.

关键词： Internet protocols

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Nonnegative Matrix Factorization Based on Topology-and-Attribute-Matching Degree for Community Detection 18th

Nonnegative Matrix Factorization Based on Topology-and-Attr...

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18th CCF Conference on Computer Supported Cooperative Work and Social computing, ChineseCSCW 2023

作者： Zeng, Ruolan Liu, Zhanghui Guo, Kun College of Computer and Data Science Fuzhou University Fuzhou350108 China Fujian Key Laboratory of Network Computing and Intelligent Information Processing Fuzhou University Fuzhou350108 China Key Laboratory of Spatial Data Mining and Information Sharing Ministry of Education Fuzhou350108 China

ISBN: (纸本)9789819996360

Community detection is widely used in network analysis, which seeks to divide network nodes into distinct communities based on the topology structure and attribute information of the network. Due to its interpretability, nonnegative matrix factorization becomes an essential method for community detection. However, it decomposes the adjacency matrix and attribute matrix separately, which do not tightly incorporate topology and attributes. And in the problem of division inconsistency based on topology and attributes caused by the mismatch between the topology similarity and attribute similarity of paired nodes, it ignores the difference in the matching degree of each attribute and each node. In this paper, we propose a nonnegative matrix factorization algorithm for community detection (MTACD) based on the matching degree between topology and attribute. First, we employ an attribute embedding mechanism to enhance the node-attribute relationship. Second, we design an attribute matching degree and a node topology-and-attribute matching degree in order to resolve the mismatch between topology and attribute similarity. Experiments on both real-world and synthetic networks demonstrate the effectiveness of our algorithm. © 2024, The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.

关键词： Topology

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AUCSeg: AUC-oriented Pixel-level Long-tail Semantic Segmentation 38

AUCSeg: AUC-oriented Pixel-level Long-tail Semantic Segmenta...

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38th Conference on Neural Information processing Systems, NeurIPS 2024

作者： Han, Boyu Xu, Qianqian Yang, Zhiyong Bao, Shilong Wen, Peisong Jiang, Yangbangyan Huang, Qingming Key Lab. of Intelligent Information Processing Institute of Computing Technology CAS China School of Computer Science and Tech. University of Chinese Academy of Sciences China Peng Cheng Laboratory China Key Laboratory of Big Data Mining and Knowledge Management CAS China

The Area Under the ROC Curve (AUC) is a well-known metric for evaluating instance-level long-tail learning problems. In the past two decades, many AUC optimization methods have been proposed to improve model performance under long-tail distributions. In this paper, we explore AUC optimization methods in the context of pixel-level long-tail semantic segmentation, a much more complicated scenario. This task introduces two major challenges for AUC optimization techniques. On one hand, AUC optimization in a pixel-level task involves complex coupling across loss terms, with structured inner-image and pairwise inter-image dependencies, complicating theoretical analysis. On the other hand, we find that mini-batch estimation of AUC loss in this case requires a larger batch size, resulting in an unaffordable space complexity. To address these issues, we develop a pixel-level AUC loss function and conduct a dependency-graph-based theoretical analysis of the algorithm's generalization ability. Additionally, we design a Tail-Classes Memory Bank (T-Memory Bank) to manage the significant memory demand. Finally, comprehensive experiments across various benchmarks confirm the effectiveness of our proposed AUCSeg method. The code is available at https://***/boyuh/AUCSeg. © 2024 Neural information processing systems foundation. All rights reserved.

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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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2024 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2024

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

ISBN: (纸本)9798350386226

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 MS2 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. © 2024 IEEE.

关键词： Neural networks

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DisenGCD: a meta multigraph-assisted disentangled graph learning framework for cognitive diagnosis 24

DisenGCD: a meta multigraph-assisted disentangled graph lear...

引用

Proceedings of the 38th International Conference on Neural Information processing Systems

作者： Shangshang Yang Mingyang Chen Ziwen Wang Xiaoshan Yu Panpan Zhang Haiping Ma Xingyi Zhang Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education Anhui University Hefei Anhui P. R. China and Anhui Province Key Laboratory of Intelligent Computing and Applications Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education Anhui University Hefei Anhui P. R. China and Department of Information Materials and Intelligent Sensing Laboratory of Anhui Province Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education Anhui University Hefei Anhui P. R. China

ISBN: (纸本)9798331314385

Existing graph learning-based cognitive diagnosis (CD) methods have made relatively good results, but their student, exercise, and concept representations are learned and exchanged in an implicit unified graph, which makes the interaction-agnostic exercise and concept representations be learned poorly, failing to provide high robustness against noise in students' interactions. Besides, lower-order exercise latent representations obtained in shallow layers are not well explored when learning the student representation. To tackle the issues, this paper suggests a meta multigraph-assisted disentangled graph learning framework for CD (DisenGCD), which learns three types of representations on three disentangled graphs: student-exercise-concept interaction, exercise-concept relation, and concept dependency graphs, respectively. Specifically, the latter two graphs are first disentangled from the interaction graph. Then, the student representation is learned from the interaction graph by a devised meta multigraph learning module; multiple learnable propagation paths in this module enable current student latent representation to access lower-order exercise latent representations, which can lead to more effective nad robust student representations learned; the exercise and concept representations are learned on the relation and dependency graphs by graph attention modules. Finally, a novel diagnostic function is devised to handle three disentangled representations for prediction. Experiments show better performance and robustness of DisenGCD than state-of-the-art CD methods and demonstrate the effectiveness of the disentangled learning framework and meta multigraph module. The source code is available at https://***/BIMK/intelligent-Education/tree/main/DisenGCD.

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Semi-supervised PolSAR image classification method based on contrastive learning 6

Semi-supervised PolSAR image classification method based on ...

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6th International Conference on Artificial Intelligence and Pattern Recognition, AIPR 2023

作者： Hua, Wenqiang Sun, Nan Liu, Lin The Shaanxi Key Laboratory of Network Data Analysis and Intelligent Processing Xi'an Key Laboratory of Big Data and Intelligent Computing School of Computer Science and Technology Xi'an University of Posts and Telecommunications Xi'an China School of Computer Technology Xi'an University of Posts and Telecommunications Xi'an China

ISBN: (纸本)9798400707674

Polarimetric synthetic aperture radar (PolSAR) image classification has important application value and a wide range of application scenarios in many fields. Supervised classification methods, which need to use a large amount of labeled data to improve classification accuracy, have achieved satisfactory classification performance. However, it is difficult and expensive to obtain sufficient labeled data for PolSAR images. The problem to be solved is how to obtain high classification accuracy with a limited number of labeled samples. Semi-supervised PolSAR image classification method based on contrastive learning is proposed. Firstly, a supervised PolSAR image classification method based on meta-learning is introduced. Prototypical network based on meta-learning ideas is used as the basic classification model, and a prototypical representation is created for each category. Classification is performed by computing the similarity between the prototypical representation and samples to be classified. Secondly, a method of training feature extractor based on contrastive learning is designed. By maintaining the consistency of features between the same data and distinguishing the differences between different data after data augmentation, the method enables the feature extractor to obtain accurate feature representation. By co-training with meta-learning, so as to improve the classification performance. Finally, experiments on real PolSAR data prove the effectiveness of the proposed method. © 2023 ACM.

关键词： Image classification

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Broadband external rejection miniaturized SIW filter based on C-shaped symmetric structure

Broadband external rejection miniaturized SIW filter based o...

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2022 International Applied Computational Electromagnetics Society Symposium, ACES-China 2022

作者： Xiao, Shuang Li, Minquan Qu, Xin Li, Chen Zhang, Zufeng Anhui University Key Laboratory of Intelligent Computing & Signal Processing Ministry of Education Liaoyang Province Hefei230601 China

ISBN: (纸本)9781665452366

To effectively improve the frequency selectivity of the filter, a substrate integrated waveguide (SIW) filter with miniaturization and out-of-band rejection was designed. To achieve the desired filter response, symmetrical C-shaped resonators are etched on the top and bottom layers of the SIW filter. The C-shaped resonator etched on the top layer of SIW achieves miniaturization and filtering characteristics. In order to improve the frequency response, a two-stage SIW filter and a SIW filter with coupled gap-ring defected ground structure (CGRDGS) are proposed, and an equivalent circuit is given to verify the transmission response. The simulation results show that the filter achieves miniaturization, out-of-band rejection and low insertion loss, which can be used in 5G wireless communication The simulation results show that the filter achieves miniaturization, out-of-band rejection and low insertion loss, which can be used in 5G wireless communication. © 2022 IEEE.

关键词： Resonators

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DOA Estimation for RIS Assisted Multi-User Wireless Communication System with Squared-Sine Error Criterion and Lawson Norm Constraint 6

DOA Estimation for RIS Assisted Multi-User Wireless Communic...

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6th IEEE International Conference on Electronic Information and Communication Technology, ICEICT 2023

作者： Yu, Canping Li, Li Li, Yingsong Sun, Dazhi Li, Liping Huang, Zhixiang Loh, Tian Hong Anhui University Key Laboratory of Intelligent Computing and Signal Processing Ministry of Education China Beijing101399 China National Physical Laboratory Electromagnetic and Eletrochemical Technologies Department Middlesex Teddington United Kingdom

ISBN: (纸本)9798350399059

Reconfigurable intelligent surface (RIS) can control the phase of reflected signals, and has become a hotspot in the field of wireless communication. In this paper, we propose a direction-of-arrival (DOA) estimation algorithm for RIS assisted multi-user wireless communication systems with squared-sine error criterion and Lawson norm constraint. This algorithm utilizes the sparsity of the signal and can achieve fast and accurate DOA estimation under the interference of impulsive noises. To suppress the line-of-sight (LOS) interference and thus to maximize the received signal-to-interference-plus-noise ratio (SINR), we also propose a random optimal phase selection (ROPS) technique to design the control matrix of RIS elements. The simulation results show that the proposed algorithm performs better than the existing methods. © 2023 IEEE.

关键词： Impulse noise

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