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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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Predicting compositional time series via autoregressive Dirichlet estimation

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Science China(information Sciences) 2018年第9期61卷 300-305页

作者： Ganbin ZHOU Ping LUO Qing HE Key Lab of Intelligent Information Processing of Chinese Academy of Sciences Institute of Computing TechnologyChinese Academy of Sciences University of Chinese Academy of Sciences

In recent years,compositional time series(CTS)prediction has become a widely applied data analysis method for modeling tactile sequence data[1],hydrological time series data using a four-

关键词： CTS Predicting compositional time series via autoregressive Dirichlet estimation

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TOP: Towards Better Toxicity Prediction by Deep Molecular Representation Learning

TOP: Towards Better Toxicity Prediction by Deep Molecular Re...

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IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

作者： Yuzhong Peng Ziqiao Zhang Qizhi Jiang Jihong Guan Shuigeng Zhou Key Lab of Scientific Computing Intelligent Information Processing in Universities of Guangxi Nanning Normal University Nanning China Shanghai Key Lab of Intelligent Information Processing School of Computer Science Fudan University Shanghai China Tongji University Shanghai China

At the early stages of the drug discovery, molecule toxicity prediction is crucial to excluding drug candidates that are likely to fail in clinical trials. In this paper, we presented a novel molecular representation method and developed a corresponding deep learning-based framework called TOP (the abbreviation of TOxicity Prediction). TOP integrated a serial special data processing methods, a bidirectional gated recurrent unit-based RNN (BiGRU) and a fully connected neural network for end-to-end molecular representation learning and chemical toxicity prediction. TOP can automatically learn a mixed molecular representation from not only SMILES contextual information that describes the molecule structure, but also physiochemical properties. Therefore, TOP can overcome the drawbacks of existing methods that use either of them, thus greatly promotes toxicity prediction. We conducted extensive experiments over 14 classic toxicity prediction tasks on three different benchmark datasets, including balanced and imbalanced ones. The results show that, with the help of the novel molecular representation method, TOP significantly outperforms not only three baseline machine learning methods, but also five state-of-the-art methods.

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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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A Low SAR, Small size, High gain, Circularly polarized Antenna for Wearable Application 2

A Low SAR, Small size, High gain, Circularly polarized Anten...

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2020 2nd International Conference on Artificial Intelligence Technologies and Application, ICAITA 2020

作者： Wang, Chao Zhang, Liang Cheng, Yi Li, XueMei Wu, Xianliang Key Lab of Ministry of Education of Intelligent Computing and Signal Processing Anhui University Hefei Anhui230601 China AnHui Province Key Laboratory of Simulation and Design for Electronic Information System Hefei Normal University Hefei Anhui230601 China

A planar, small size, high gain, low specific absorption rate (SAR) and circularly-polarized (CP) wearable antenna is proposed in this paper. The antenna is fabricated on a substrate with a dielectric constant of 3.5 with a thickness of 0.5 mm and sized at 42×42 mm only. Both the simulation results show that the overlap bandwidth of impedance and axial ratio of the proposed antenna is 13.7% (5.15-5.91 GHz). To isolate the antenna against the influence of the human body, a artificial magnetic conductor (AMC) plane is added on the reverse side of the radiator. The AMC structure effectively isolates the human body from the radiation of the antenna and reduces the specific absorption rate (SAR) of it by more than 96.1% at 5.5 GHz, which improves the antenna gain and the peak gain reaches 5.09 dBi at 5.5 GHz. The wearable performance of the antenna was analyzed, and it is observed that it can sustain good performance even under human body loading. Beside, the antenna has a small size, which makes it ideal for wearable applications. © 2020 Published under licence by IOP Publishing Ltd.

关键词： Wearable antennas

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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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A survey on context-aware mobile visual recognition

A survey on context-aware mobile visual recognition

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作者： Min, Weiqing Jiang, Shuqiang Wang, Shuhui Xu, Ruihan Cao, Yushan Herranz, Luis He, Zhiqiang Key Lab of Intelligent Information Processing Institute of Computing Technology CAS Beijing100190 China Higher Education Institution Teacher Online Training Center Beijing China Lenovo Corporate Research Beijing100085 China

The phenomenal growth of the usage of mobile devices (e.g., mobile phones and tablet PCs) opens up a new service, namely mobile visual recognition, which has been widely used in many areas, such as mobile shopping and augmented reality. The rich contextual information (e.g., location, time and direction information), easily acquired by the mobile devices, provides useful clues to facilitate mobile visual recognition, including speeding up the recognition time and improving the recognition performance. This survey focuses on recent advances in Context-Aware Mobile Visual Recognition (CAMVR) and reviews related work regarding to different contextual information, recognition methods, recognition types, and various application scenarios. Finally, we discuss future research directions in this field. © 2016, Springer-Verlag Berlin Heidelberg.

关键词： Surveys

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Mining dynamical frequent itemsets based on ant colony algorithm

Mining dynamical frequent itemsets based on ant colony algor...

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IEEE International Conference on Computer Science and Automation Engineering (CSAE)

作者： Chen, Shengbing Wang, Xiaofeng Wang, Xiaofang Key Lab of Network and Intelligent Information Processing Hefei University Hefei 230601 China Department of Computer Science and Technology Hefei University Hefei 230601 China Intelligent Computing Lab Institute of Intelligent Machines Chinese Academy of Sciences Hefei 230031 China Department of Computer Artillery Academy Hefei 230031 China

ISBN: (纸本)9781424487257

Mining frequent itemsets is a core problem in many data mining tasks, most existing works on mining frequent itemsets can only capture the long-term and static frequency itemsets, they do not suit the task whose frequent itemsets often change. Using the theory of ant colony algorithm, we proposed a new method for mining dynamical frequent itemset(called AC-MFI). The method considers the item of transaction as a node in the path, takes the itemset as a path, and takes each transaction as a foraging behavior. According to the pheromone updating policy of ant colony algorithm, AC-MFI mines dynamical frequent itemsets from transaction data stream. Experiment results show that the method is valid and practicable. © 2011 IEEE.

关键词： Data mining

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A sample pre-mapping method enhancing boosting for object detection

A sample pre-mapping method enhancing boosting for object de...

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International Conference on Pattern Recognition

作者： Ren, Haoyu Hong, Xiaopeng Heng, Cher-Keng Liang, Luhong Chen, Xilin Key Lab. of Intelligent Information Processing of Chinese Academy of Sciences Institute of Computing Technology CAS China School of Computer Science and Technology Harbin Institute of Technology Panasonic Singapore Laboratories Pte Ltd.

ISBN: (纸本)9780769541099

We propose a novel method to improve the training efficiency and accuracy of boosted classifiers for object detection. The key step of the proposed method is a sample pre-mapping on original space by referring to the selected 'reference sample' before feeding into weak classifiers. The reference sample corresponds to an approximation of the optimal separating hyper-plane in an implicit high-dimensional space, so that the resulting classifier could achieve the performance similar to kernel method, while spending the computation cost of linear classifier in both training and detection. We employ two different non-linear mappings to verify the proposed method under boosting framework. Experimental results show that the proposed approach achieves performance comparable with the common-used methods on public datasets in both pedestrian detection and car detection. © 2010 IEEE.

关键词： Object detection

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Boosted sigma set for pedestrian detection

Boosted sigma set for pedestrian detection

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International Conference on Pattern Recognition

作者： Hong, Xiaopeng Chang, Hong Chen, Xilin Gao, Wen School of Computer Science and Technology Harbin Institute of Technology China Key Lab. of Intelligent Information Processing Chinese Academy of Sciences Institute of Computing Technology China Institute of Digital Media Peking University China

ISBN: (纸本)9780769541099

This paper presents a new method to detect pedestrian in still image using Sigma sets as image region descriptors in the boosting framework. Sigma set encodes second order statistics of an image region implicitly in the form of a point set. Compared with the covariance matrix, the traditional second order statistics based region descriptor, which requires computationally demanding operations based on Riemannian manifold, Sigma set preserves similar robustness and discriminative power more efficiently because the classification on Sigma sets can be directly performed in vector space. Experimental results on the INRIA and the Daimler Chrysler pedestrian datasets show the effectiveness and efficiency of the proposed method. © 2010 IEEE.

关键词： Covariance matrix

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