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DMFVAE:miRNA-disease associations prediction based on deep matrix factorization method with variational autoencoder

Frontiers of Computer Science 2024年第6期18卷 259-270页

作者： Pijing WEI Qianqian WANG Zhen GAO Ruifen CAO Chunhou ZHENG Information Materials and Intelligent Sensing Laboratory of Anhui Province Institutes of Physical Science and Information TechnologyAnhui UniversityHefei 230601China Key Lab of Intelligent Computing and Signal Processing of Ministry of Education School of Computer Science and TechnologyAnhui UniversityHefei 230601China Key Lab of Intelligent Computing and Signal Processing of Ministry of Education School of Artificial IntelligenceAnhui UniversityHefei 230601China

MicroRNAs(miRNAs)are closely related to numerous complex human diseases,therefore,exploring miRNA-disease associations(MDAs)can help people gain a better understanding of complex disease *** increasing number of computational methods have been developed to predict ***,the sparsity of the MDAs may hinder the performance of many *** addition,many methods fail to capture the nonlinear relationships of miRNA-disease network and inadequately leverage the features of network and neighbor *** this study,we propose a deep matrix factorization model with variational autoencoder(DMFVAE)to predict potential *** first decomposes the original association matrix and the enhanced association matrix,in which the enhanced association matrix is enhanced by self-adjusting the nearest neighbor method,to obtain sparse vectors and dense vectors,***,the variational encoder is employed to obtain the nonlinear latent vectors of miRNA and disease for the sparse vectors,and meanwhile,node2vec is used to obtain the network structure embedding vectors of miRNA and disease for the dense ***,sample features are acquired by combining the latent vectors and network structure embedding vectors,and the final prediction is implemented by convolutional neural network with channel *** evaluate the performance of DMFVAE,we conduct five-fold cross validation on the HMDD v2.0 and HMDD v3.2 datasets and the results show that DMFVAE performs ***,case studies on lung neoplasms,colon neoplasms,and esophageal neoplasms confirm the ability of DMFVAE in identifying potential miRNAs for human diseases.

关键词： miRNA-disease association deep matrix factorization self-adjusted nearest neighbor variational encoder network structure

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Non-uniform Compressive Sensing Imaging Based on Image Saliency

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Chinese Journal of Electronics 2023年第1期32卷 159-165页

作者： LI Hongliang DAI Feng ZHAO Qiang MA Yike CAO Juan ZHANG Yongdong University of Chinese Academy of Sciences Key Lab of Intelligent Information Processing of Chinese Academy of Sciences Institute of Computing Technology Chinese Academy of Sciences University of Science and Technology of China

For more effective image sampling, compressive sensing(CS) imaging methods based on image saliency have been proposed in recent years. Those methods assign higher measurement rates to salient regions,but lower measurement rate to non-salient regions to improve the performance of CS imaging. However, those methods are block-based, which are difficult to apply to actual CS sampling, as each photodiode should strictly correspond to a block of the scene. In our work, we propose a non-uniform CS imaging method based on image saliency, which assigns higher measurement density to salient regions and lower density to non-salient regions,where measurement density is the number of pixels measured in a unit size. As the dimension of the signal is reduced, the quality of reconstructed image will be improved theoretically, which is confirmed by our experiments. Since the scene is sampled as a whole, our method can be easily applied to actual CS sampling. To verify the feasibility of our approach, we design and implement a hardware sampling system, which can apply our non-uniform sampling method to obtain measurements and reconstruct the images. To our best knowledge, this is the first CS hardware sampling system based on image saliency.

关键词： Measurement units Density measurement Imaging Image sampling Size measurement Hardware Sensors

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Retrieval Augmented Recipe Generation

Retrieval Augmented Recipe Generation

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2025 IEEE/CVF Winter Conference on Applications of Computer Vision, WACV 2025

作者： Liu, Guoshan Yin, Hailong Zhu, Bin Chen, Jingjing Ngo, Chong-Wah Jiang, Yu-Gang School of Computer Science Fudan University Shanghai Key Lab of Intelligent Information Processing China Shanghai Collaborative Innovation Center on Intelligent Visual Computing China Singapore Management University Singapore

ISBN: (纸本)9798331510831

The growing interest in generating recipes from food images has drawn substantial research attention in recent years. Existing works for recipe generation primarily utilize a two-stage training method - first predicting ingredients from a food image and then generating instructions from both the image and ingredients. Large Multi-modal Models (LMMs), which have achieved notable success across a variety of vision and language tasks, shed light on generating both ingredients and instructions directly from images. Nevertheless, LMMs still face the common issue of hallu-cinations during recipe generation, leading to suboptimal performance. To tackle this issue, we propose a retrieval augmented large multimodal model for recipe generation. We first introduce Stochastic Diversified Retrieval Augmentation (SDRA) to retrieve recipes semantically related to the image from an existing datastore as a supplement, integrating them into the prompt to add diverse and rich context to the input image. Additionally, Self-Consistency Ensemble Voting mechanism is proposed to determine the most confident prediction recipes as the final output. It calculates the consistency among generated recipe candidates, which use different retrieval recipes as context for generation. Extensive experiments validate the effectiveness of our proposed method, which demonstrates state-of-the-art (SOTA) performance in recipe generation on the Recipe1M dataset. © 2025 IEEE.

关键词： Food ingredients

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High Contrast Ratio 4-to-2 Plasmonic Encoder Utilizing Cascaded Ring Resonators 6

High Contrast Ratio 4-to-2 Plasmonic Encoder Utilizing Casca...

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6th International Conference on Electronic Engineering and Informatics, EEI 2024

作者： Chen, Yan Xie, Yiyuan Chai, Junxiong Ye, Yichen College of Electronic and Information Engineering Southwest University Chongqing400715 China Chongqing Key Laboratory of Nonlinear Circuits and Intelligent Information Processing Chongqing400715 China Key Laboratory of Networks and Cloud Computing Security of Universities in Chongqing Chongqing400715 China

ISBN: (纸本)9798350353594

In this paper, a novel plasmonic 4-to-2 encoder comprising cascaded ring resonators coated with graphene layers and two metal-insulator-metal (MIM) waveguides. The encoding function operates at 850 nm by modulating the intensity of pump beam focused on the graphene layer to manipulate the state of the plasmonic resonators. The performance of the encoder is analyzed utilizing the finite-difference time-domain method, demonstrating a high contrast ratio of 15.1 dB. Thus, this efficient 4-to-2 optical encoder is well-suited for integration into optical integrated computing devices. © 2024 IEEE.

关键词： Semiconductor insulator boundaries

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Impact of Crosstalk and Loss on the Training Process of Integrated Photonic Neural Networks 6

Impact of Crosstalk and Loss on the Training Process of Inte...

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6th International Conference on Electronic Engineering and Informatics, EEI 2024

作者： Pang, Jing Su, Ye Xie, Yiyuan College of Electronic and Information Engineering Southwest University Chongqing400715 China Chongqing Key Laboratory of Nonlinear Circuits and Intelligent Information Processing Chongqing400715 China Key Laboratory of Networks and Cloud Computing Security of Universities in Chongqing Chongqing400715 China

ISBN: (纸本)9798350353594

Integrated photonic neural networks (IPNNs), with their ability to process large-scale data and parallelize multiple computational tasks, have shown impressive promise for applications in the field of artificial intelligence. However, due to some hard-to-ignore non-ideal characteristics of the underlying silicon photonic MZI devices constituting the IPNN, these non-ideal characteristics can cause the input signal to be affected by crosstalk noise and optical loss during transmission, thus affecting the training and inference accuracy of the IPNN. In order to solve these problems, this paper establishes an analytical model of IPNN affected by crosstalk noise and loss during the training process, covering component level, layer level and system level. Simulations using this model show that the inference accuracy of IPNN decreases by about 65% when the crosstalk noise in the training phase of IPNN reaches -20 dB, while the inference accuracy of IPNN decreases by about 55% when the optical loss reaches -0.5 dB. © 2024 IEEE.

关键词： Crosstalk

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Relation Reconstructive Binarization of word embeddings

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Frontiers of Computer Science 2022年第2期16卷 47-54页

作者： Feiyang PAN Shuokai LI Xiang AO Qing HE Key Lab of Intelligent Information Processing of Chinese Academy of Sciences(CAS) Institute of Computing TechnologyCASBeijing 100190China University of Chinese Academy of Sciences Beijing 100049China

Word-embedding acts as one of the backbones of modern natural language processing(NLP).Recently,with the need for deploying NLP models to low-resource devices,there has been a surge of interest to compress word embeddings into hash codes or binary vectors so as to save the storage and memory ***,existing work learns to encode an embedding into a compressed representation from which the original embedding can be *** these methods aim to preserve most information of every individual word,they often fail to retain the relation between words,thus can yield large loss on certain *** this end,this paper presents Relation Reconstructive Binarization(R2B)to transform word embeddings into binary codes that can preserve the relation between *** its heart,R2B trains an auto-encoder to generate binary codes that allow reconstructing the wordby-word relations in the original embedding *** showed that our method achieved significant improvements over previous methods on a number of tasks along with a space-saving of up to 98.4%.Specifically,our method reached even better results on word similarity evaluation than the uncompressed pre-trained embeddings,and was significantly better than previous compression methods that do not consider word relations.

关键词： embedding compression variational auto-encoder binary word embedding

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Imputation of Compound Property Assay Data Using a Gene Expression Programming-Based Method 1st

Imputation of Compound Property Assay Data Using a Gene Expr...

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1st International Conference on Applied Intelligence, ICAI 2023

作者： Zhou, Hongliang Lin, Yanmei Chen, Nan Peng, Yuzhong Key Lab of Scientific Computing and Intelligent Information Processing Nanning Normal University Guangxi Nanning5300001 China Guangxi Academy of Sciences Guangxi Nanning530007 China

ISBN: (纸本)9789819709021

Compound property assays are an important part of drug development, but incomplete data may occur for a variety of reasons. To deal with these incomplete data and improve the success rate of drug development, researchers often need to effectively impute the missing data. Therefore, this paper proposes a gene expression programming-based method, called GEP-CPI, for imputing missing compound property assay data. In GEP-CPI, the missing data imputation model is expressed by the parse tree of a chromosome, and then the optimal missing data imputation model is mined by iterative evolution of the chromosome population. Experimental results on three compound property assay related datasets demonstrates that the proposed method generally outperforms the state-of-the-art methods in imputing missing data of compound property assays. © The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd. 2024.

关键词： Trees (mathematics)

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Exploring Trial-and-Error in Deep Learning:Initial Application to Isotope Detection in Mass Spectrometry

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Big Data Mining and Analytics 2024年第4期7卷 1251-1261页

作者： Qihong Jiao Yuxiao Wang Yongshuai Wang Shiwei Sun Xuefeng Cui School of Computer Science and Technology Shandong UniversityQingdao 266237China Key Lab of Intelligent Information Processing Institute of Computing TechnologyChinese Academy of SciencesBeijing 100190China

Mass spectrometry plays a crucial role in biomedicine by detecting isotopes,contributing significantly to research,diagnostics,and therapy *** study introduces IsoFusion,a deep learning model designed to address isotope detection in raw mass *** than directly applying convolutional layers to all signal and noise peaks,IsoFusion employs a trial-and-error ***,it investigates all potential charge states(trials)and collects signal peaks around expected m/z values for each ***,convolutional layers extract features from each trial,which are fused to identify the correct ***,the reparameterization trick predicts isotope features based on this correct trial.A key advantage of IsoFusion is shared model parameters across all trials,enhancing feature learning for less common charge states using data from prevalent *** results show a significant accuracy improvement for charge state 5,reaching 99.42%,compared to DeepIso’s 43.36%.Moreover,IsoFusion achieves a 97.33%detection accuracy for isotopes,with 2.4%of detected isotopes previously unidentified by four commonly used methods.

关键词： Liquid Chromatography-Mass Spectrometry(LC-MS) isotope detection retention time prediction charge state prediction deep learning

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REVISITING GRAPH ADVERSARIAL ATTACK AND DEFENSE FROM A DATA DISTRIBUTION PERSPECTIVE 11

REVISITING GRAPH ADVERSARIAL ATTACK AND DEFENSE FROM A DATA ...

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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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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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