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11th International Conference on Learning Representations, ICLR 2023

作者： Li, Kuan Liu, Yang Ao, Xiang He, Qing Key Lab of Intelligent Information Processing of Chinese Academy of Sciences Institute of Computing Technology Chinese Academy of Sciences University of Chinese Academy of Sciences China

Recent studies have shown that structural perturbations are significantly effective in degrading the accuracy of Graph Neural Networks (GNNs) in the semi-supervised node classification (SSNC) task. However, the reasons for the destructive nature of gradient-based methods have not been explored in-depth. In this work, we discover an interesting phenomenon: the adversarial edges are not uniformly distributed on the graph, and a majority of perturbations are generated around the training nodes in poisoning attacks. Combined with this phenomenon, we provide an explanation for the effectiveness of the gradient-based attack method from a data distribution perspective and revisit both poisoning attack and evasion attack in SSNC. From this new perspective, we empirically and theoretically discuss some other attack tendencies. Based on the analysis, we provide nine practical tips on both attack and defense and meanwhile leverage them to improve existing attack and defense methods. Moreover, we design a fast attack method and a self-training defense method, which outperform the state-of-the-art methods and can effectively scale to large graphs like ogbn-arxiv. We validate our claims through extensive experiments on four benchmark datasets. © 2023 11th International Conference on Learning Representations, ICLR 2023. All rights reserved.

关键词： Graph neural networks

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Learned Fingerprint Embedding for Large-Scale Peptide Mass Spectra Retrieval

Learned Fingerprint Embedding for Large-Scale Peptide Mass S...

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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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Lightweight Food Image Recognition With Global Shuffle Convolution

IEEE Transactions on AgriFood Electronics

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IEEE Transactions on AgriFood Electronics 2024年第2期2卷 392-402页

作者： Sheng, Guorui Min, Weiqing Yao, Tao Song, Jingru Yang, Yancun Wang, Lili Jiang, Shuqiang Ludong University Department of Information and Electrical Engineering Yantai264025 China Institute of Computing Technology Chinese Academy of Sciences Key Laboratory of Intelligent Information Processing Beijing100190 China University of Chinese Academy of Sciences Beijing100049 China

Consumer behaviors and habits in food choices impact their physical health and have implications for climate change and global warming. Efficient food image recognition can assist individuals in making more environmentally friendly and healthier dietary choices using end devices, such as smartphones. Simultaneously, it can enhance the efficiency of server-side training, thereby reducing carbon emissions. We propose a lightweight deep neural network named Global Shuffle Net (GSNet) that can efficiently recognize food images. In GSNet, we develop a novel convolution method called global shuffle convolution, which captures the dependence between long-range pixels. Merging global shuffle convolution with classic local convolution yields a framework that works as the backbone of GSNet. Through GSNet's ability to capture the dependence between long-range pixels at the start of the network, by restricting the number of layers in the middle and rear, the parameters and floating operation operations (FLOPs) can be minimized without compromising the performance, thus permitting a lightweight goal to be achieved. Experimental results on four popular food recognition datasets demonstrate that our approach achieves state-of-the-art performance with higher accuracy and fewer FLOPs and parameters. For example, in comparison to the current state-of-the-art model of MobileViTv2, GSNet achieved 87.9% accuracy of the top-1 level on the Eidgenössische Technische Hochschule Zürich (ETHZ) Food-101 dataset with 28% reduction in the parameters, 37% reduction in the FLOPs, but a 0.7% more accuracy. © 2024 IEEE.

关键词： Carbon dioxide

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Leveraging Knowledge Distillation for Improved Event Extraction in QA Models 6

Leveraging Knowledge Distillation for Improved Event Extract...

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6th International Conference on Frontier Technologies of information and Computer, ICFTIC 2024

作者： Zhou, Peiyao Hu, Zhikui Zi, Kangli Zhang, Dawei School of Computer Science Jiangsu University of Science and Technology Zhenjiang China Institute of Computing Technology Chinese Academy of Sciences Key Laboratory of Intelligent Information Processing Beijing China

ISBN: (纸本)9798331541750

Event extraction is an important task in natural language processing, and it is widely utilized in intelligence domains such as business and military for information extraction. Recently, many works have successfully transformed document-level event extraction into Question-answering (QA) tasks with remarkable results. This approach embeds event argument information within the questions, introducing prior knowledge into the process. Jin et al. highlighted the importance of high-quality QA pairs for practical QA tasks, emphasizing that constructing these pairs remains a key challenge[1]. In this study, we propose a Prompt-based question generation method to automatically generate questions containing event arguments, which converts event extraction into a QA task. We introduce an event ontology-based information retrieval module to enhance answer accuracy and select the most relevant document segments as input text. Additionally, we employ knowledge distillation to build the QA model, transferring knowledge from a large pre-trained model to a more compact and efficient one, improving the student model's performance. Experiments show that our model performs strongly in mainstream benchmarks, with 4.8 improvements on WikiEvents. © 2024 IEEE.

关键词： Question answering

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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 availab.e on Github (https://***/xfcui/EI-MS2VEC). © 2024 IEEE.

关键词： Embeddings

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A Semantic Overlay on Blockchain for Supporting Traceability in Cross-border Logistics 2

A Semantic Overlay on Blockchain for Supporting Traceability...

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2nd IEEE International Conference on Digital Twins and Parallel Intelligence, DTPI 2022

作者： Sun, Xiaoping Institute of Computing Technology Chinese Academy of Sciences Key Lab of Intelligent Information Processing Beijing China

ISBN: (纸本)9781665492270

Traceability is important for maintaining quality of logistics transactions and improving logistics efficiency. Implementing traceability for cross-border logistics is facing challenges when it lacks global centralized logistics information management services. Blockchain techniques enable a decentralized cross-border logistics management by publishing logistics transaction on blockchain transactions to support privacy protection and traceability. Logistics transactions involves complex interactions among participants. How to publish those interactions on a blockchain platform is a challenge. We propose a semantic overlay model that publishes a logistics transaction as a semantic link on a blockchain platform for supporting traceability. A semantic link schema model is designed and published on the blockchain platform to validate semantics links for ensuring the correctness of logistics transaction execution. The proposed semantic overlay on blockchain supports further extension of semantic computing in decentralized applications. © 2022 IEEE.

关键词： Blockchain

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Hybrid particle swarm optimization with adaptive learning strategy

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Soft computing 2024年第17-18期28卷 9759-9784页

作者： Wang, Lanyu Tian, Dongping Gou, Xiaorui Shi, Zhongzhi School of Mathematics and Information Sciences Baoji University of Arts and Science Shaanxi Baoji721007 China Institute of Computer Software Baoji University of Arts and Sciences Shaanxi Baoji721007 China Key Laboratory of Intelligent Information Processing Institute of Computing Technology Chinese Academy of Sciences Beijing100190 China

Particle swarm optimization (PSO) is a meta-heuristic algorithm that can be used to solve different real-world optimization problems. However, PSO suffers from some intrinsic drawbacks, including falling into local optimal and slow convergence in the latter evolution process. To deal with these issues, a hybrid PSO with adaptive learning strategy (abbreviated as HPSO-ALS) is proposed in this paper. To start with, the chaotic opposition-learning method is employed to generate the uniformly distributed particles so as to enhance the quality of the initial swarm. Next, a self-logical mapping-based nonlinear decreasing inertia weight is formulated to trade off the global search and local search abilities. Meanwhile, different adaptive position updating strategies are leveraged to achieve better convergence according to different evolution status. In addition, inspired by the cask effect, the global worst particle (gworst) is introduced into the velocity updating to make full use of the potential information of the particles. Finally, extensive experiments on sixteen benchmark functions and CEC’13 test suite have verified the promising performance of HPSO-ALS proposed in this paper. Alternatively, HPSO-ALS is also applied to the classical traveling salesman problem (TSP) and the experimental results have further validated the effectiveness and efficiency of our proposal. © The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2024.

关键词： Traveling salesman problem

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Speculative Decoding with CTC-based Draft Model for LLM Inference Acceleration 38

Speculative Decoding with CTC-based Draft Model for LLM Infe...

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38th Conference on Neural information processing Systems, NeurIPS 2024

作者： Wen, Zhuofan Gui, Shangtong Feng, Yang Key Laboratory of Intelligent Information Processing Institute of Computing Technology Chinese Academy of Sciences China State Key Lab of Processors Institute of Computing Technology Chinese Academy of Sciences China Key Laboratory of Al Safety Chinese Academy of Sciences China University of Chinese Academy of Sciences Beijing China

Inference acceleration of large language models (LLMs) has been put forward in many application scenarios and speculative decoding has shown its advantage in addressing inference acceleration. Speculative decoding usually introduces a draft model to assist the base LLM where the draft model produces drafts and the base LLM verifies the draft for acceptance or rejection. In this framework, the final inference speed is decided by the decoding speed of the draft model and the acceptance rate of the draft provided by the draft model. Currently the widely used draft models usually generate draft tokens for the next several positions in a non-autoregressive way without considering the correlations between draft tokens. Therefore, it has a high decoding speed but an unsatisfactory acceptance rate. In this paper, we focus on how to improve the performance of the draft model and aim to accelerate inference via a high acceptance rate. To this end, we propose a CTC-based draft model which strengthens the correlations between draft tokens during the draft phase, thereby generating higher-quality draft candidate sequences. Experiment results show that compared to strong baselines, the proposed method can achieve a higher acceptance rate and hence a faster inference speed. © 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 availab.e at https://***/xfcui/ctMSNovelist. © 2024 IEEE.

关键词： Neural networks

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DMSS:An Attention-Based Deep Learning Model for High-Quality Mass Spectrometry Prediction

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Big Data Mining and Analytics 2024年第3期7卷 577-589页

作者： Yihui Ren Yu Wang Wenkai Han Yikang Huang Xiaoyang Hou Chunming Zhang Dongbo Bu Xin Gao Shiwei Sun Key Lab of Intelligent Information Processing Institute of Computing TechnologyChinese Academy of SciencesBeijing 100190Chinaand with University of Chinese Academy of SciencesBeijing 100049China Syneron Technology Guangzhou 510000China College of Information and Electrical Engineering China Agricultural UniversityBeijing 100083China Computer Science Program ComputerElectrical and Mathematical Sciences and Engineering DivisionKing Abdullah University of Science and Technology(KAUST)Thuwal 23955-6900Kingdom of Saudi Arabia Insitute of Computing Technology Chinese Academy of SciencesBeijing 100190China with Western Institute of Computing Technology Chongqing 400000China

Accurate prediction of peptide spectra is crucial for improving the efficiency and reliability of proteomic analysis,as well as for gaining insight into various biological *** this study,we introduce Deep MS Simulator(DMSS),a novel attention-based model tailored for forecasting theoretical spectra in mass *** has undergone rigorous validation through a series of experiments,consistently demonstrating superior performance compared to current methods in forecasting theoretical *** superior ability of DMSS to distinguish extremely similar peptides highlights the potential application of incorporating our predicted intensity information into mass spectrometry search engines to enhance the accuracy of protein *** findings contribute to the advancement of proteomics analysis and highlight the potential of the DMSS as a valuable tool in the field.

关键词： mass spectrometry proteomics machine learning deep learning

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