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2023 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2023

作者： Wang, Yongshuai Cai, Xiaojun Li, Defeng Sun, Shiwei Chen, Cheng 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

ISBN: (纸本)9798350337488

Tandem mass spectrometry (MS/MS) is a widely used technique for protein identification, post-translational modifications, immunotherapy, and other applications. As the amount of MS/MS spectra data increases, new computational methods are needed to efficiently search through these databases. This study introduces MS2VEC, a novel fingerprint embedding model designed to facilitate large-scale retrieval of peptide mass spectra. MS2VEC captures the relationships between distant peaks and incorporates position-aware fingerprint features from all peaks. To do this, dilated convolutions are used to capture remote relationships, and a novel position-aware multi-head attention pooling mechanism is used to abstract fingerprint features. The results demonstrate that MS2VEC achieves a top-1 retrieval accuracy of 0.810, outperforming existing methods by 5.1%. Interestingly, the precursor charge is not essential for the retrieval task, as the spectra itself contains enough information to accurately predict the charge. Additionally, the results suggest that weight-balanced fragment ions and water losses are important contributors to fingerprint features. © 2023 IEEE.

关键词： deep learning embedding information retrieval peptide mass spectra tandem mass spectrometry

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A prompt-based approach to adversarial example generation and robustness enhancement

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Frontiers of Computer Science 2024年第4期18卷 85-96页

作者： Yuting YANG Pei HUANG Juan CAO Jintao LI Yun LIN Feifei MA Key Lab of Intelligent Information Processing of Chinese Academy of Sciences(CAS) Institute of Computing TechnologyCASBeijing 100190China School of Computer Science and Technology University of Chinese Academy of SciencesBeijing 100049China Department of Computer Science Stanford UniversityCA 94305USA School of Computing National University of SingaporeSingapore 119077Singapore Laboratory of Parallel Software and Computational Science Institute of SoftwareChinese Academy of SciencesBeijing 100190China

Recent years have seen the wide application of natural language processing(NLP)models in crucial areas such as finance,medical treatment,and news media,raising concerns about the model robustness and *** find that prompt paradigm can probe special robust defects of pre-trained language *** prompt texts are first constructed for inputs and a pre-trained language model can generate adversarial examples for victim models via *** results show that prompt paradigm can efficiently generate more diverse adversarial examples besides synonym ***,we propose a novel robust training approach based on prompt paradigm which incorporates prompt texts as the alternatives to adversarial examples and enhances robustness under a lightweight minimax-style optimization *** on three real-world tasks and two deep neural models show that our approach can significantly improve the robustness of models to resist adversarial attacks.

关键词： robustness adversarial example prompt learning pre-trained language model

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Adaptively feature matching via joint transformational-spatial clustering

Adaptively feature matching via joint transformational-spati...

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作者： Wang, Linbo Tan, Li Fang, Xianyong Guo, Yanwen Wan, Shaohua MOE Key Laboratory of Intelligent Computing and Signal Processing School of Computer Science and Technology Anhui University Hefei China National Key Lab for Novel Software Technology Nanjing University Nanjing China School of Information and Safety Engineering Zhongnan University of Economics and Law Wuhan China

The transformational and spatial proximities are important cues for identifying inliers from an appearance based match set because correct matches generally stay close in input images and share similar local transformations. However, most existing approaches only check one type of them or both types consecutively with manually set thresholds, and thus their matching accuracy and flexibility in handling large-scale images are limited. In this paper, we present an efficient clustering based approach to identify match inliers with both proximities simultaneously. It first projects the putative matches into a joint transformational-spatial space, where mismatches tend to scatter all around while correct matches gather together. A mode-seeking process based on joint kernel density estimation is then proposed to obtain significant clusters in the joint space, where each cluster contains matches mapping the same object across images with high accuracy. Moreover, kernel bandwidths for measuring match proximities are adaptively set during density estimation, which enhances its applicability for matching different images. Experiments on three standard datasets show that the proposed approach delivers superior performance on a variety of feature matching tasks, including multi-object matching, duplicate object matching and object retrieval. © 2021, The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.

关键词： Clustering Density estimation Feature matching Mode-seeking

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Graph-Enhanced Dual-Stream Feature Fusion with Pre-Trained Model for Acoustic Traffic Monitoring

Graph-Enhanced Dual-Stream Feature Fusion with Pre-Trained M...

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2025 IEEE International Conference on Acoustics, Speech, and signal processing, ICASSP 2025

作者： Fan, Shitong Xiao, Feiyang Wang, Wenbo Qi, Shuhan Zhu, Qiaoxi Wang, Wenwu Guan, Jian Group of Intelligent Signal Processing Harbin Engineering University Harbin China Faculty of Computing Harbin Institute of Technology Harbin China School of Computer Science and Technology Harbin Institute of Technology Shenzhen China Acoustics Lab University of Technology Sydney Ultimo Australia Centre for Vision Speech and Signal Processing University of Surrey Guildford United Kingdom

ISBN: (纸本)9798350368741

Microphone array techniques are widely used in sound source localization and smart city acoustic-based traffic monitoring, but these applications face significant challenges due to the scarcity of labeled real-world traffic audio data and the complexity and diversity of application scenarios. The DCASE Challenge's Task 10 focuses on using multi-channel audio signals to count vehicles (cars or commercial vehicles) and identify their directions (left-to-right or vice versa). In this paper, we propose a graph-enhanced dual-stream feature fusion network (GEDF-Net) for acoustic traffic monitoring, which simultaneously considers vehicle type and direction to improve detection. We propose a graph-enhanced dual-stream feature fusion strategy which consists of a vehicle type feature extraction (VTFE) branch, a vehicle direction feature extraction (VDFE) branch, and a frame-level feature fusion module to combine the type and direction feature for enhanced performance. A pre-trained model (PANNs) is used in the VTFE branch to mitigate data scarcity and enhance the type features, followed by a graph attention mechanism to exploit temporal relationships and highlight important audio events within these features. The frame-level fusion of direction and type features enables fine-grained feature representation, resulting in better detection performance. Experiments demonstrate the effectiveness of our proposed method. GEDF-Net is our submission that achieved 1st place in the DCASE 2024 Challenge Task 10. © 2025 IEEE.

关键词： Acoustic-based traffic monitoring feature fusion graph attention pre-trained model transfer learning

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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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FastICA based single-channel radar signal separation algorithm

FastICA based single-channel radar signal separation algorit...

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IET International Radar Conference (IRC 2023)

作者： Xinyu Wang Jin Zhao Xianliang Wu Key Lab of Intelligent Computing & Signal Processing Ministry of Education Anhui University Hefei People's Republic of China

ISBN: (数字)9781837240982

Aiming at the traditional blind source separation for the received single-channel mixed radar signal makes it difficult to accurately recover the source signal, a single-channel radar signal comprehensive separation method based on the combination of the FastICA algorithm and the variational modal decomposition (VMD) algorithm is proposed. The method utilizes VMD to first perform modal separation of single-channel mixed Linear Frequency Modulation (LFM) signal, then selects the modal component signal with the largest correlation coefficient with the mixed signal and expands it with single-channel mixed LFM signal into a virtual multi-channel mixed signal, and finally inputs it into FastICA algorithm to obtain the source signal. The simulation experiment results show that the comprehensive separation algorithm can accurately separate the LFM signal, overcoming the limitation that the FastICA algorithm cannot directly separate the single-channel mixed radar signal.

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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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FAE-MSLKNet: Multi-Scale Large Kernel Network With Fourier Adaptive Enhancement for Automatic Modulation Recognition

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IEEE Transactions on Cognitive Communications and Networking 2024年

作者： Lin, Xiaobing Zhang, Jiashu Wang, Hao Zhang, Heying Southwest Jiaotong University Sichuan Province Key Lab of Signal and Information Processing School of Computing and Artificial Intelligence Chengdu611756 China Southwest Jiaotong University Sichuan Province Key Lab of Signal and Information Processing Chengdu611756 China

Automatic Modulation Recognition (AMR) is vital in wireless communication systems. Recently, a number of deep learning(DL) architectures have been developed for AMR. However, existing methods have limitations in frequency analysis and long-range temporal dependencies extraction. Moreover, most models have high computational costs and large model sizes. To overcome these limitations, this paper proposes FAE-MSLKNet, a Multi-Scale Large Kernel Network with Fourier Adaptive Enhancement. First, we introduced a Fourier Adaptive Enhancement (FAE) module to adaptively enhance features and model long-term temporal dependencies in the frequency-domain. Furthermore, a Multi-Scale Large Kernel (MSLK) module is employed to extract local features with small convolution kernels and capture long-range temporal dependencies with large convolution kernels in the time-domain. Experiments on RML2016.10a, RML2016.10b, and RML2018.01a datasets demonstrate that FAE-MSLKNet achieves state-of-the-art performance with improved parameter efficiency and reduced computational complexity, highlighting its potential for practical wireless communication applications. © 2024 IEEE.

关键词： Frequency domain analysis

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Design of Microstrip Type Broadband Directional Coupler

Design of Microstrip Type Broadband Directional Coupler

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International Applied Computational Electromagnetics Society Symposium (ACES)

作者： Hang Yan Xianliang Wu Ruikang Wang Gang Wang Key Laboratory of Intelligent Computing and Signal Processing Ministry of Education Anhui University Hefei China

A microstrip line broadband directional coupler is designed based on microstrip line theory. The bandwidth of the coupler is extended by using a cascade of multiple coupled lines. The isolation of the directional coupler is greatly improved by covering the microstrip line with a dielectric layer [1] and by loading the branching compensation capacitor to compensate for the odd-even mode phase velocity difference. Simulation results of ANSYS HFSS 2019 show that the return loss ( $S_{11}$ ) is greater than 20 dB, the insertion loss ( $S_{21}$ ) is less than 1.7 dB, the coupling degree (S31) is about −6dB(±0.8dB), the isolation degree (S41) is greater than 23.4dB, and the minimum directionality is greater than 17dB during 700 MHz-3700 MHz. The physical size of coupler is $18\text{mm}\times 60\text{mm}$ , which meets the design requirements of 6dB coupler.

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MSCA-UNet: Multi-Scale Channel Adaptive Sensing Module for Medical Image Segmentation

MSCA-UNet: Multi-Scale Channel Adaptive Sensing Module for M...

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2024 International Conference on New Trends in Computational Intelligence, NTCI 2024

作者： Diao, Liangjin Shen, Longfeng Chen, Jiacong Ge, Fangzhen Li, Mengwen College of Computer Science and Technology Huaibei Normal University Anhui Huaibei China Institute of Artificial Intelligence Hefei Comprehensive National Science Center Hefei China Anhui University Key Laboratory of Intelligent Computing & Signal Processing Ministry of Education Anhui Hefei China

ISBN: (纸本)9798331517021

Recent advancements in CNNs for medical image segmentation have focused on the combination of CNN and Transformer architectures to capture both local and global features. However, challenges remain, such as effectively utilizing fused features at the encoder-decoder bottleneck and addressing blurred object edges in datasets. To tackle these issues, we introduce a multi-scale channel adaptive sensing module, enhancing the model's representational and perceptual capabilities by integrating multi-scale and channel-specific information. Additionally, we propose a cross-perception module and multi-scale segmentation head to improve global coordination and multi-scale information gathering. Experiments on the ACDC and Synapse datasets demonstrate our model's superiority. © 2024 IEEE.

关键词： Image segmentation

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