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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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Interpretable multi-view attention network for drug-drug interaction prediction

Interpretable multi-view attention network for drug-drug int...

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2023 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2023

作者： Lin, Xuan Wen, Qi Yang, Sijie Yu, Zu-Guo Long, Yahui Zeng, Xiangxiang Xiangtan University College of Computer Science China Xiangtan University Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education China Singapore Hunan University College of Information Science and Engineering China

ISBN: (纸本)9798350337488

Drug-drug interaction (DDI) plays an increasingly crucial role in drug discovery. Predicting potential DDI is also essential for clinical research. Given the high cost and risk of wet-lab experiments, in-silico DDI prediction is an alternative choice. Recently, deep learning methods have been developed for DDI prediction. However, most of existing methods focus on feature extraction from either molecular SMILES sequences or drug interactive networks, ignoring the valuable complementary information that can be derived from these two views. In this paper, we propose a novel interpretable Multi-View Attention network (MVA-DDI) for DDI prediction. MVA-DDI can effectively extracts drug representations from different perspectives to improve DDI prediction. Specifically, for a given drug, we design a transformer-based encoder and a graph convolutional networkbased encoder to learn sequence and graph representations from SMILES sequence and molecular graph, respectively. To fully exploit the complementary information between the sequence and molecular views, an attention mechanism is further adopted to adaptively aggregate the sequence and graph representations by taking the importance of different views into accounts, generating the final drug representations. Comparison experiments demonstrated that our MVA-DDI1 model achieved superior performance to state-of-the-art models on DDI prediction. © 2023 IEEE.

关键词： Contrastive learning Drug-drug interaction prediction Interpretable attention network Multi-view learning

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Few-Shot Class-Incremental Semantic Segmentation via Pseudo-Labeling and Knowledge Distillation 4

Few-Shot Class-Incremental Semantic Segmentation via Pseudo-...

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4th International Conference on information Science, Parallel and distributed Systems, ISPDS 2023

作者： Jiang, Chengjia Wang, Tao Li, Sien Wang, Jinyang Wang, Shirui Antoniou, Antonios Minjiang University Fujian Provincial Key Laboratory of Information Processing and Intelligent Control Fuzhou China Fujian Education Institutions Wuyi University The Key Laboratory of Cognitive Computing and Intelligent Information Processing Wuyishan China College of Computer and Data Science Fuzhou University Fuzhou China European University Cyprus Department of Computer Science and Engineering Nicosia Cyprus

ISBN: (纸本)9798350337181

We address the problem of learning new classes for semantic segmentation models from few examples, which is challenging because of the following two reasons. Firstly, it is difficult to learn from limited novel data to capture the underlying class distribution. Secondly, it is challenging to retain knowledge for existing classes and to avoid catastrophic forgetting. For learning from limited data, we propose a pseudo-labeling strategy to augment the few-shot training annotations in order to learn novel classes more effectively. Given only one or a few images labeled with the novel classes and a much larger set of unlabeled images, we transfer the knowledge from labeled images to unlabeled images with a coarse-to-fine pseudo-labeling approach in two steps. Specifically, we first match each labeled image to its nearest neighbors in the unlabeled image set at the scene level, in order to obtain images with a similar scene layout. This is followed by obtaining pseudo-labels within this neighborhood by applying classifiers learned on the few-shot annotations. In addition, we use knowledge distillation on both labeled and unlabeled data to retain knowledge on existing classes. We integrate the above steps into a single convolutional neural network with a unified learning objective. Extensive experiments on the Cityscapes and KITTI datasets validate the efficacy of the proposed approach in the self-driving domain. Code is available from https://***/ChasonJiang/FSCILSS. © 2023 IEEE.

关键词： Distillation

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Privacy protection oriented on data stream computing

Privacy protection oriented on data stream computing

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2022 International Conference on Computer Application and information Security, ICCAIS 2022

作者： He, Renjie Zheng, Xianghan Wang, Gong School of Computer and Big Data Fuzhou University Fujian Fuzhou China The Fujian Key Laboratory of Network Computing and Intelligent Information Processing Fuzhou University Fujian Fuzhou China

ISBN: (纸本)9781510663459

Data security has always been one of the public concerns, and homomorphic encryption technology, as one of the effective means to ensure data security, has always been a hot topic of academic research. Traditional machine learning is trained in a batch environment. In practice, data owners tend to outsource data and model training tasks to third-party clouds with huge computing resources, but data outsourcing carries the risk of privacy leakage. Therefore, in order to prevent this situation, an effective method is to encrypt the data before the outsourcing, and the third-party cloud trains the machine model of the ciphertext data. This method has special requirements for encryption algorithms which should support computation directly on the ciphertext data. This paper presents a novel data flow computing privacy protection framework based on the homomorphic encryption algorithm CKKS and the flow data processing engine Flink, called SDPPF (Streaming Data Privacy Protection on Flink). The proposed framework supports the functions of data stream encryption, decryption and ciphertext computing, and expands the functions of vector point multiplication and array sum operation on the basic simultaneous operation supported by the original CKKS algorithm. This paper also selects a classical machine learning algorithm: KNN algorithm, combined with the homomorphic encryption algorithm CKKS to realize the privacy protection machine learning algorithm. © 2023 SPIE.

关键词： Cryptography

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Efficient DOA Estimation Based on Cauchy Loss Variable Step Size Algorithm 6

Efficient DOA Estimation Based on Cauchy Loss Variable Step ...

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

作者： Xu, Xingchao Li, Yingsong College of Information and Communications Engineering Harbin Engineering University Harbin150001 China Key Laboratory of Intelligent Computing and Signal Processing Ministry of Education Anhui University Hefei China

ISBN: (纸本)9798350399059

The Cauchy loss function is robust to large outliers and has successful applications in signal processing. In this paper, a DOA estimation algorithm based on adaptive zero technology is proposed, which updates the weight of the filter by applying the Cauchy loss function, and further improves the algorithm performance by using the variable step size method. The algorithm step size is adjusted by accumulating errors and establishing a nonlinear function with instantaneous errors. The DOA estimation ability, estimation error and accuracy of the improved Cauchy algorithm in the impulse noise environment are analyzed. The algorithm is verified by simulation experiments. © 2023 IEEE.

关键词： Impulse noise

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FUZZY ALIGNMENTS IN DIRECTED ACYCLIC GRAPH FOR NON-AUTOREGRESSIVE MACHINE TRANSLATION 11

FUZZY ALIGNMENTS IN DIRECTED ACYCLIC GRAPH FOR NON-AUTOREGRE...

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11th International Conference on Learning Representations, ICLR 2023

作者： Ma, Zhengrui Shao, Chenze Gui, Shangtong Zhang, Min Feng, Yang Key Laboratory of Intelligent Information Processing Institute of Computing Technology Chinese Academy of Sciences China University of Chinese Academy of Sciences China Harbin Institute of Technology Shenzhen China

Non-autoregressive translation (NAT) reduces the decoding latency but suffers from performance degradation due to the multi-modality problem. Recently, the structure of directed acyclic graph has achieved great success in NAT, which tackles the multi-modality problem by introducing dependency between vertices. However, training it with negative log-likelihood loss implicitly requires a strict alignment between reference tokens and vertices, weakening its ability to handle multiple translation modalities. In this paper, we hold the view that all paths in the graph are fuzzily aligned with the reference sentence. We do not require the exact alignment but train the model to maximize a fuzzy alignment score between the graph and reference, which takes captured translations in all modalities into account. Extensive experiments on major WMT benchmarks show that our method substantially improves translation performance and increases prediction confidence, setting a new state of the art for NAT on the raw training data. © 2023 11th International Conference on Learning Representations, ICLR 2023. All rights reserved.

关键词： Benchmarking

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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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Few-Shot Object Detection Based on Generalized Features 2

Few-Shot Object Detection Based on Generalized Features

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2nd International Conference on Artificial Intelligence and intelligent information processing, AIIIP 2023

作者： Chen, Qiuqin Ke, Xiao College of Computer and Data Science Fuzhou University Fujian Provincial Key Laboratory of Networking Computing and Intelligent Information Processing Fuzhou350116 China Key Laboratory of Spatial Data Mining & Information Sharing Ministry of Education Fuzhou Fuzhou350003 China

ISBN: (纸本)9798350371451

Few-shot object detection aims to rapidly detect novel classes of objects using a minimal number of annotated instances. Compared to methods such as meta-learning, few-shot object detection based on transfer learning can achieve better performance. However, when training on base-class datasets, the model gradually improves its detection performance on base classes but does not enhance its generalization. A base-class model lacking generalization tends to result in lower detection performance for novel classes during fine-tuning. To address the aforementioned issues, this paper tackles the problem from two aspects: firstly, we introduce the Confusion-Dropblock Module (CDM) to perturb the model's features, thus enhancing feature generalization. Secondly, we incorporate Deformable Convolution Modules to mitigate the impact of object shapes and sizes on detection performance, thereby improving overall detection performance. Experimental results on the COCO dataset demonstrate the effectiveness of the proposed algorithm, outperforming the compared methods. © 2023 IEEE.

关键词： Object detection

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A Novel Approach for State of Health Estimation and Remaining Useful Life Prediction of Supercapacitors Using an Improved Honey Badger Algorithm Assisted Hybrid Neural Network

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Protection and Control of Modern Power Systems 2024年第6期9卷 1-18页

作者： Zhenxiao Yi Shi Wang Zhaoting Li Licheng Wang Kai Wang the School of Electrical Engineering Qingdao UniversityQingdao 266071Chinaand the State Key Laboratory of Reliability and Intelligence of Electrical EquipmentHebei University of TechnologyTianjin 300130China the Key Laboratory of Intelligent Information Processing Institute of Computing TechnologyChinese Academy of SciencesBeijing 100190China the School of Engineering Brown UniversityProvidenceRhode Island 02912USA the School of Information Engineering Zhejiang University of TechnologyHangzhou 310014China the School of Electrical Engineering Qingdao UniversityQingdao 266071China

Supercapacitors(SCs)are widely recognized as excellent clean energy storage *** state of health(SOH)estimation and remaining useful life(RUL)prediction are essential for ensuring their safe and reliable *** paper introduces a novel method for SOH estimation and RUL prediction,based on a hybrid neural network optimized by an improved honey badger algorithm(HBA).The method combines the advantages of convolutional neural network(CNN)and bidirectional long-short-term memory(BiLSTM)neural *** HBA optimizes the hyperparameters of the hybrid neural *** CNN automatically extracts deep features from time series data and reduces dimensionality,which are then used as input for the ***,recurrent dropout is introduced in the recurrent layer to reduce overfitting and facilitate the learning *** approach not only improves the accuracy of estimates and forecasts but also significantly reduces data processing *** under different working conditions are used to validate the proposed *** results show that the proposed hybrid model effectively extracts features,enriches local details,and enhances global perception *** proposed hybrid model outperforms single models,reducing the root mean square error to below 1%,and offers higher prediction accuracy and robustness compared to other methods.

关键词： Supercapacitors state of health remaining useful life honey badger algorithm recurrent dropout.

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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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