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SinCWIm: An imputation method for single-cell RNA sequence dropouts using weighted alternating least squares

Computers in Biology and Medicine 2024年 171卷 108225-108225页

作者： Gong, Lejun Cui, Xiong Liu, Yang Lin, Cai Gao, Zhihong Jiangsu Key Lab of Big Data Security & Intelligent Processing School of Computer Science Nanjing University of Posts and Telecommunications Nanjing China Department of Burn Wound Repair and Regenerative Medicine Center The First Affiliated Hospital of Wenzhou Medical University Zhejiang Wenzhou325000 China Zhejiang Engineering Research Center of Intelligent Medicine The First Affiliated Hospital of Wenzhou Medical University Wenzhou325000 China

Background and objectives: Single-cell RNA sequencing (scRNA-seq) provides a powerful tool for exploring cellular heterogeneity, discovering novel or rare cell types, distinguishing between tissue-specific cellular composition, and understanding cell differentiation during development. However, due to technological limitations, dropout events in scRNA-seq can mistakenly convert some entries in the real data to zero. This is equivalent to introducing noise into the data of cell gene expression entries. The data is contaminated, which affects the performance of downstream analyses, including clustering, cell annotation, differential gene expression analysis, and so on. Therefore, it is a crucial work to accurately determine which zeros are due to dropout events and perform imputation operations on them. Methods: Considering the different confidence levels of different zeros in the gene expression matrix, this paper proposes a SinCWIm method for dropout events in scRNA-seq based on weighted alternating least squares (WALS). The method utilizes Pearson correlation coefficient and hierarchical clustering to quantify the confidence of zero entries. It is then combined with WALS for matrix decomposition. And the imputation result is made close to the actual number by outlier removal and data correction operations. Results: A total of eight single-cell sequencing datasets were used for comparative experiments to demonstrate the overall superiority of SinCWIm over state-of-the-art models. SinCWIm was applied to cluster the data to obtain an adjusted RAND index evaluation, and the Usoskin, Pollen and Bladder datasets scored 94.46%, 96.48% and 76.74%, respectively. In addition, significant improvements were made in the retention of differential expression genes and visualization. Conclusions: SinCWIm provides a valuable imputation method for handling dropout events in single-cell sequencing data. In comparison to advanced methods, SinCWIm demonstrates excellent performance in

关键词： RNA

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Throughput Maximization for UAV-Enabled data Collection

Throughput Maximization for UAV-Enabled Data Collection

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International Conference on Mobile Ad-hoc and Sensor Networks, MSN

作者： Junchao Gong Xiaojun Zhu Lijie Xu College of Computer Science and Technology Nanjing University of Aeronautics and Astronautics Nanjing China Jiangsu Key Laboratory of Big Data Security & Intelligent Processing Nanjing University of Posts and Telecommunications Nanjing China Collaborative Innovation Center of Novel Software Technology and Industrialization Nanjing China

ISBN: (数字)9781728199160

ISBN: (纸本)9781728192369

In this paper, we consider a scenario where an unmanned aerial vehicle (UAV) collects data from a set of nodes placed on a two-dimensional (2-D) plane. The UAV flies along a given line to collect data. To prevent transmission collisions, only one node is allowed to transmit data to the UAV at any time, and the number of nodes that can transmit data to the UAV cannot exceed a specified number to avoid frequent switches. The problem is to select a subset of nodes and schedule their transmission time to maximize the UAV's throughput. After formulating the problem, we find that it is difficult to solve due to mixture of real variables and integer variables. We then propose to decompose the problem into subproblems, and give a polynomial time algorithm to solve each subproblem to optimality. We then get an exact algorithm by solving all subproblems. Unfortunately, due to an exponential number of subproblems, the overall running time is exponential with respect to the input size. We then propose two polynomial-time suboptimal algorithms to solve the problem, both of which explore a polynomial number of subproblems. Simulations show that the suboptimal algorithms perform comparably with the exponential-time exact algorithm, while the running time is much smaller.

关键词： Schedules Heuristic algorithms Two dimensional displays data collection Throughput Unmanned aerial vehicles Sensors

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Pptcdr: Personalized Preference Transfer Cross-Domain Recommendation Based on Heterogeneous Graph Neural Networks

SSRN

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SSRN 2023年

作者： Zhu, Fan Xu, Xiaolong Jiangsu Key Laboratory of Big Data Security and Intelligent Processing Nanjing University of Posts and Telecommunications No. 9 Wenyuan Road Nanjing210023 China School of Computer Science Nanjing University of Posts and Telecommunications No. 9 Wenyuan Road Nanjing210023 China

Cross-domain recommendation methods aim to solve the problems of data sparsity and cold start by leveraging rich information from the source domain to enhance the recommendation accuracy of the target domain. Many methods ignore auxiliary information, which is often structured. Therefore, based on the above issue, we propose a method called PPTCDR (Personalized Preference Transfer Cross-Domain Recommendation) based on heterogeneous graph neural networks. PPTCDR introduces auxiliary information to enrich the information of the source and target domains, alleviates the problem of inaccurate embedding caused by data sparsity, and performs feature embedding of users and items separately in the source and target domains. In addition, for user preference transfer, in order to achieve personalization, a personalized bridging function is provided for each user. PPTCDR first constructs heterogeneous graphs separately in the source and target domains, and learns the latent embeddings of users and items using heterogeneous graph neural networks. Then, a meta-network is used to generate a personalized bridging function for each user. Through the personalized bridging function, the user's embedding in the source domain can be transformed to the target domain, and the transformed user embedding is used as the initial embedding of cold start users in the target domain. In this paper, we set up three cross-domain tasks on the Amazon dataset to verify and compare the performance of the experiment. PPTCDR achieves MAE and RMSE performances of 0.67 and 0.94 respectively, which are respectively improved by 23% and 18% compared to the state-of-the-art works EMCDR and PTUPCDR. © 2023, The Authors. All rights reserved.

关键词： Embeddings

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Dual-Correction Adaptation Network for Noisy Knowledge Transfer

arXiv

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arXiv 2022年

作者： Wang, Yunyun Zheng, Weiwen Chen, Songcan The Jiangsu Key Laboratory of Big Data Security & Intelligent Processing Computer Science and Engineering Nanjing University of Posts & Telecommunications Nanjing210046 China The MIIT Key Laboratory of Pattern Analysis and Machine Intelligence Computer Science & Technology/AI Nanjing University of Aeronautics & Astronautics Nanjing210023 China

Previous unsupervised domain adaptation (UDA) methods aim to promote target learning via a single-directional knowledge transfer from label-rich source domain to unlabeled target domain, while its reverse adaption from target to source has not jointly been considered yet so far. In fact, in some real teaching practice, a teacher helps students learn while also gets promotion from students to some extent, which inspires us to explore a dual-directional knowledge transfer between domains, and thus propose a Dual-Correction Adaptation Network (DualCAN) in this paper. However, due to the asymmetrical label knowledge across domains, transfer from unlabeled target to labeled source poses a more difficult challenge than the common source-to-target counterpart. First, the target pseudo-labels predicted by source commonly involve noises due to model bias, hence in the reverse adaptation, they may hurt the source performance and bring a negative target-to-source transfer. Secondly, source domain usually contains innate noises, which will inevitably aggravate the target noises, leading to noise amplification across domains. To this end, we further introduce a Noise Identification and Correction (NIC) module to correct and recycle noises in both domains. To our best knowledge, this is the first naive attempt of dual-directional adaptation for noisy UDA, and naturally applicable to noise-free UDA. A theory justification is given to state the rationality of our intuition. Empirical results confirm the effectiveness of DualCAN with remarkable performance gains over state-of-the-arts, particularly for extreme noisy tasks (e.g., ∼+ 15% on Pw→Pr and Pr→Rw of Office-Home). Copyright © 2022, The Authors. All rights reserved.

关键词： Knowledge management

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Sindiff: Spoken-to-Sign Language Generation Based Transformer Diffusion Model

SSRN

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SSRN 2023年

作者： Liang, Wuyan Xu, Xiaolong Jiangsu Key Laboratory of Big Data Security & Intelligent Processing Nanjing University of Posts and Telecommunications No. 9 Wenyuan Road Nanjing210023 China School of Computer Science Nanjing University of Posts and Telecommunications No. 9 Wenyuan Road Nanjing210023 China

Sign language generation (SLG) is meaningful in facilitating the communication between deaf and healthy people. Recently, transformer-based diffusion models have been achieved success in human motion generation. However, it is still under-explored how to generate long-term sign language with diffusion model. Here, we propose a transformer-based diffusion framework, SinDiff, that explore all the advantages of transformer (i.e., dynamic attention and global context) for spoken-driven SLG. To meet the goal, we develop a linear biased multi-head self-attention with periodic position encoding to generalize longer-term sign language, and a linear biased cross-modal multi-head attention function to align the spoken and sign language modalities. Besides, a transformer-based spoken encoder is introduced to solve the limitations of sign data and learn the global spoken semantics. By experimental results on our testbed, we show that the word accuracy of the SinDiff for the back-translated spoken translation with ground truth spoken reach 21.02%, which has a 2.8% improvement over the 18.22% accuracy of the typical SLG method (GEN-OBT) on PHOENIX14T test set. And the generative visualization results further verify the feasibility of the proposed method. © 2023, The Authors. All rights reserved.

关键词： Semantics

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Optimizing Location Quality in Privacy Preserving Crowdsensing

Optimizing Location Quality in Privacy Preserving Crowdsensi...

引用

2019 IEEE Global Communications Conference (GLOBECOM)

作者： Yuhui Zhang Ming Li Dejun Yang Jian Tang Guoliang Xue Colorado School of Mines Golden CO Colorado School of Mines Golden CO USA Jiangsu Key Laboratory of Big Data Security and Intelligent Processing Nanjing University of Posts and Telecommunications Nanjing China Syracuse University Syracuse NY Arizona State University Tempe AZ

ISBN: (数字)9781728109626

ISBN: (纸本)9781728109633

Crowdsensing enables a wide range of data collection, where the data are usually tagged with private locations. Protecting users' location privacy has been a central issue. The study of various location perturbation techniques for protecting users' location privacy has received widespread attention. Despite the huge promise and considerable attention, the location perturbation operation causes inevitable location errors, which can diminish the location quality of the crowdsensing results. Provable good algorithms that consider location quality in privacy preserving crowdsensing from optimization perspectives are still lacking in the literature. In this paper, we investigate the problem of location quality optimization in privacy preserving crowdsensing, which is to minimize the location quality desegregation, while protecting all users' location privacy. We present an optimal algorithm OLQDM for this problem. Extensive simulations demonstrate that OLQDM significantly outperforms an existing algorithm in terms of the location quality and SSE.

关键词： Privacy Degradation Sensors Perturbation methods Optimization Minimization Mobile handsets

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Consistent and Complementary Graph Regularized Multi-view Subspace Clustering

arXiv

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arXiv 2020年

作者： Zheng, Qinghai Zhu, Jihua Li, Zhongyu Pang, Shanmin Wang, Jun Chen, Lei School of Software Engineering Xi’an Jiaotong University Xi’an710049 China Shanghai Institute for Advanced Communication and Data Science School of Communication and Information Engineering Shanghai University Shanghai200444 China Jiangsu Key Laboratory of Big Data Security and Intelligent Processing Nanjing University of Posts and Telecommunications Nanjing210023 China

This study investigates the problem of multi-view clustering, where multiple views contain consistent information and each view also includes complementary information. Exploration of all information is crucial for good multi-view clustering. However, most traditional methods blindly or crudely combine multiple views for clustering and are unable to fully exploit the valuable information. Therefore, we propose a method that involves consistent and complementary graph-regularized multi-view subspace clustering (GRMSC), which simultaneously integrates a consistent graph regularizer with a complementary graph regularizer into the objective function. In particular, the consistent graph regularizer learns the intrinsic affinity relationship of data points shared by all views. The complementary graph regularizer investigates the specific information of multiple views. It is noteworthy that the consistent and complementary regularizers are formulated by two different graphs constructed from the first-order proximity and second-order proximity of multiple views, respectively. The objective function is optimized by the augmented Lagrangian multiplier method in order to achieve multi-view clustering. Extensive experiments on six benchmark datasets serve to validate the effectiveness of the proposed method over other state-of-the-art multi-view clustering methods. Copyright © 2020, The Authors. All rights reserved.

关键词： Clustering algorithms

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WISERNet: Wider Separate-then-reunion Network for Steganalysis of Color Images

arXiv

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arXiv 2018年

作者： Zeng, Jishen Tan, Shunquan Liu, Guangqing Li, Bin Huang, Jiwu Guangdong Key Laboratory of Intelligent Information Processing National Engineering Laboratory for Big Data System Computing Technology Shenzhen University Shenzhen518060 China College of Computer Science and Software Engineering Shenzhen University Guangdong Key Lab. of Intelligent Info. Processing and Shenzhen Key Laboratory of Media Security Shenzhen University Shenzhen518060 China Peng Cheng Laboratory Shenzhen518052 China

Until recently, deep steganalyzers in spatial domain have been all designed for gray-scale images. In this paper, we propose WISERNet (the wider separate-then-reunion network) for steganalysis of color images. We provide theoretical rationale to claim that the summation in normal convolution is one sort of "linear collusion attack" which reserves strong correlated patterns while impairs uncorrelated noises. Therefore in the bottom convolutional layer which aims at suppressing correlated image contents, we adopt separate channel-wise convolution without summation instead. Conversely, in the upper convolutional layers we believe that the summation in normal convolution is beneficial. Therefore we adopt united normal convolution in those layers and make them remarkably wider to reinforce the effect of "linear collusion attack". As a result, our proposed wide-and-shallow, separate-then-reunion network structure is specifically suitable for color image steganalysis. We have conducted extensive experiments on color image datasets generated from BOSSBase raw images and another large-scale dataset which contains 100,000 raw images, with di_erent demosaicking algorithms and downsampling algorithms. The experimental results show that our proposed network outperforms other state-of-the-art color image steganalytic models either hand-crafted or learned using deep networks in the literature by a clear margin. Specifically, it is noted that the detection performance gain is achieved with less than half the complexity compared to the most advanced deeplearning steganalyzer as far as we know, which is scarce in the literature. Copyright © 2018, The Authors. All rights reserved.

关键词： Steganography

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Network-coding-based video transmission via WiFi direct in local mobile networks

Network-coding-based video transmission via WiFi direct in l...

引用

International Conference on intelligent System and Knowledge Engineering, ISKE

作者： Lei Wang Qing Wang Zhongwei Sun Jun Yin Lijie Xu Yuwang Yang Jiangsu Key Laboratory of Big Data Security and Intelligent Processing Nanjing P.R. China School of Computer Nanjing University of Posts and Telecommunications Nanjing P.R. China School of Computer Science and Engineering Nanjing University of Science and Technology Nanjing P.R. China

It will incur high expense by sharing large-scale files (such as video) with others through commercial 4G networks. When the users are located at the same area, the traffic cost could be saved via the technology of WiFi direct. In this paper, a network-coding-based video transmission scheme is proposed for such scenario. In the scheme, when a source user needs to transmit a video to others, it equally splits the original file into multiple segments. When a neighbour connects to it and requests a segment, the user will linearly generate a new segment with all the segments it buffers, and then send the re-encoded segment to other neighbours. After the neighbours receive all or part of the segments, they could become a new source and send data to their own neighbours through the technology of WiFi direct. The results show that compared with the traditional scheme, the transmission scheme based on network coding could be used to complete transmission at a higher rate.

关键词： Switches Analytical models Network coding Streaming media Wireless fidelity Mobile handsets Mobile computing

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VFL: A Verifiable Federated Learning with Privacy-Preserving for big data in Industrial IoT

arXiv

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arXiv 2020年

作者： Fu, Anmin Zhang, Xianglong Xiong, Naixue Gao, Yansong Wang, Huaqun School of Computer Science and Engineering Nanjing University of Science and Technology Nanjing210094 China Northeastern State University Department of Mathematics and Computer Science TahlequahOK United States Jiangsu Key Laboratory of Big Data Security and Intelligent Processing Nanjing University of Posts and Telecommunications Nanjing210023 China

Due to the strong analytical ability of big data, deep learning has been widely applied to model the collected data in industrial IoT. However, for privacy issues, traditional data-gathering centralized learning is not applicable to industrial scenarios sensitive to training sets. Recently, federated learning has received widespread attention, since it trains a model by only relying on gradient aggregation without accessing training sets. But existing researches reveal that the shared gradient still retains the sensitive information of the training set. Even worse, a malicious aggregation server may return forged aggregated gradients. In this paper, we propose the VFL, verifiable federated learning with privacy-preserving for big data in industrial IoT. Specifically, we use Lagrange interpolation to elaborately set interpolation points for verifying the correctness of the aggregated gradients. Compared with existing schemes, the verification overhead of VFL remains constant regardless of the number of participants. Moreover, we employ the blinding technology to protect the privacy of the gradients submitted by the participants. If no more than n-2 of n participants collude with the aggregation server, VFL could guarantee the encrypted gradients of other participants not being inverted. Experimental evaluations corroborate the practical performance of the presented VFL framework with high accuracy and efficiency. Copyright © 2020, The Authors. All rights reserved.

关键词： Deep learning

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