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  1. Article ; Online: Adaptive Diffusion Pairwise Fused Lasso LMS Algorithm Over Networks.

    Huang, Wei / Shan, Haojie / Xu, Jinshan / Yao, Xinwei

    IEEE transactions on neural networks and learning systems

    2023  Volume 34, Issue 9, Page(s) 5816–5827

    Abstract: The topic of identification for sparse vector in a distributed way has triggered great interest in the area of adaptive filtering. Grouping components in the sparse vector has been validated to be an efficient way for enhancing identification performance ...

    Abstract The topic of identification for sparse vector in a distributed way has triggered great interest in the area of adaptive filtering. Grouping components in the sparse vector has been validated to be an efficient way for enhancing identification performance for sparse parameter. The technique of pairwise fused lasso, which can promote similarity between each possible pair of nonnegligible components in the sparse vector, does not require that the nonnegligible components have to be distributed in one or multiple clusters. In other words, the nonnegligible components may be randomly scattered in the unknown sparse vector. In this article, based on the technique of pairwise fused lasso, we propose the novel pairwise fused lasso diffusion least mean-square (PFL-DLMS) algorithm, to identify sparse vector. The objective function we construct consists of three terms, i.e., the mean-square error (MSE) term, the regularizing term promoting the sparsity of all components, and the regularizing term promoting the sparsity of difference between each pair of components in the unknown sparse vector. After investigating mean stability condition of mean-square behavior in theoretical analysis, we propose the strategy of variable regularizing coefficients to overcome the difficulty that the optimal regularizing coefficients are usually unknown. Finally, numerical experiments are conducted to verify the effectiveness of the PFL-DLMS algorithm in identifying and tracking sparse parameter vector.
    Language English
    Publishing date 2023-09-01
    Publishing country United States
    Document type Journal Article
    ISSN 2162-2388
    ISSN (online) 2162-2388
    DOI 10.1109/TNNLS.2021.3131335
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Slot Self-Allocation Based MAC Protocol for Energy Harvesting Nano-Networks.

    Wang, Wan-Liang / Wang, Chao-Chao / Yao, Xin-Wei

    Sensors (Basel, Switzerland)

    2019  Volume 19, Issue 21

    Abstract: Nano-networks are composed of interconnected nano-nodes and can enable unprecedented applications in various fields. Due to the peculiarities of nano-networks, such as high density, extremely limited energy and computational resources, traditional ... ...

    Abstract Nano-networks are composed of interconnected nano-nodes and can enable unprecedented applications in various fields. Due to the peculiarities of nano-networks, such as high density, extremely limited energy and computational resources, traditional carrier-sensing based Media Access Control (MAC) protocols are not suitable for nano-networks. In this paper, a Slot Self-Allocation based MAC protocol (SSA-MAC) is proposed for energy harvesting nano-networks. Two transmission schemes for centralized and distributed nano-networks are designed, respectively. In centralized nano-networks, nano-nodes can only send packets to the nano-controller in their Self-Allocation Slots (SASs), while, in distributed nano-networks, nano-nodes can only receive packets from surrounding nano-nodes in their SASs. Extensive simulations were conducted to compare the proposed SSA-MAC with PHysical LAyer aware MAC (PHLAME), Receiver-Initiated Harvesting-aware MAC (RIH-MAC) and Energy Efficient Wireless NanoSensor Network MAC (EEWNSN). From the results, it can be concluded that the proposed SSA-MAC achieves better performance and can reduce the collision probability, while improving the energy efficiency of nano-networks.
    Language English
    Publishing date 2019-10-25
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2052857-7
    ISSN 1424-8220 ; 1424-8220
    ISSN (online) 1424-8220
    ISSN 1424-8220
    DOI 10.3390/s19214646
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Gold Nanostars Combined with the Searched Antibody for Targeted Oral Squamous Cell Carcinoma Therapy.

    Cai, Lingling / Wang, Yanxing / Peng, Xiangrong / Li, Wenjing / Yuan, Ying / Tao, Xiaofeng / Yao, Xinwei / Lv, Ruichan

    ACS biomaterials science & engineering

    2022  Volume 8, Issue 6, Page(s) 2664–2675

    Abstract: Oral squamous cell carcinoma (OSCC) is the most common cancer in the oral and maxillofacial region. Due to the special physiological and anatomical position of the oral cavity, the disease often has a significant impact on the chewing, swallowing, ... ...

    Abstract Oral squamous cell carcinoma (OSCC) is the most common cancer in the oral and maxillofacial region. Due to the special physiological and anatomical position of the oral cavity, the disease often has a significant impact on the chewing, swallowing, language, and breathing functions of patients. In recent years, with the development of medical molecular biology, molecular targeted therapy has received increasing clinical attention and has gradually become a new method for the treatment of malignant tumors. In this research, gold nanostars with a high photothermal effect combined with the searched targeted antibody were used for OSCC therapy. We use the data set in the public database and construct a gene co-expression module by weighted gene co-expression network analysis (WGCNA). It was found that the turquoise module and the midnight blue module had the greatest connection to tumorigenesis. Cytoscape software was used to analyze the important modules, and the top 10 genes of each module were selected; the survival analysis of the top 10 genes was carried out by gene expression profiling interactive analysis (GEPIA), which indicated that these genes (SERPINH1, MMP11, ADAM12, FADS3, SLC36A2, C1QTNF7, SCRG1, and APOBEC2) have statistical significance as key genes that are related to the tumorigenesis of OSCC. Then, the anti-SERPINH1 antibody targeted to SERPINH1 was chosen as the inhibitor and combined with gold nanostars for photothermal assisted targeted therapy. Thus, the searched key genes can be regarded as biomarkers and therapeutic targets for further precise diagnosis.
    MeSH term(s) Carcinogenesis ; Carcinoma, Squamous Cell/genetics ; Carcinoma, Squamous Cell/metabolism ; Carcinoma, Squamous Cell/therapy ; Gold ; Head and Neck Neoplasms ; Humans ; Mouth Neoplasms/genetics ; Mouth Neoplasms/metabolism ; Mouth Neoplasms/therapy ; Squamous Cell Carcinoma of Head and Neck
    Chemical Substances Gold (7440-57-5)
    Language English
    Publishing date 2022-05-22
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2373-9878
    ISSN (online) 2373-9878
    DOI 10.1021/acsbiomaterials.2c00276
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Dense GAN and multi-layer attention based lesion segmentation method for COVID-19 CT images.

    Zhang, Ju / Yu, Lundun / Chen, Decheng / Pan, Weidong / Shi, Chao / Niu, Yan / Yao, Xinwei / Xu, Xiaobin / Cheng, Yun

    Biomedical signal processing and control

    2021  Volume 69, Page(s) 102901

    Abstract: As the COVID-19 virus spreads around the world, testing and screening of patients have become a headache for governments. With the accumulation of clinical diagnostic data, the imaging big data features of COVID-19 are gradually clear, and CT imaging ... ...

    Abstract As the COVID-19 virus spreads around the world, testing and screening of patients have become a headache for governments. With the accumulation of clinical diagnostic data, the imaging big data features of COVID-19 are gradually clear, and CT imaging diagnosis results become more important. To obtain clear lesion information from the CT images of patients' lungs is helpful for doctors to adopt effective medical methods, and at the same time, is helpful to screen the patients with real infection. Deep learning image segmentation is widely used in the field of medical image segmentation. However, there are some challenges in using deep learning to segment the lung lesions of COVID-19 patients. Since image segmentation requires the labeling of lesion information on a pixel by pixel basis, most professional radiologists need to screen and diagnose patients on the front line, and they do not have enough energy to label a large amount of image data. In this paper, an improved Dense GAN to expand data set is developed, and a multi-layer attention mechanism method, combined with U-Net's COVID-19 pulmonary CT image segmentation, is proposed. The experimental results showed that the segmentation method proposed in this paper improved the segmentation accuracy of COVID-19 pulmonary medical CT image by comparing with other image segmentation methods.
    Language English
    Publishing date 2021-06-23
    Publishing country England
    Document type Journal Article
    ZDB-ID 2241886-6
    ISSN 1746-8108 ; 1746-8094
    ISSN (online) 1746-8108
    ISSN 1746-8094
    DOI 10.1016/j.bspc.2021.102901
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: GenoWAP: GWAS signal prioritization through integrated analysis of genomic functional annotation

    Lu, Qiongshi / Yao, Xinwei / Hu, Yiming / Zhao, Hongyu

    Bioinformatics. 2016 Feb. 15, v. 32, no. 4

    2016  

    Abstract: Motivation: Genome-wide association study (GWAS) has been a great success in the past decade. However, significant challenges still remain in both identifying new risk loci and interpreting results. Bonferroni-corrected significance level is known to be ... ...

    Abstract Motivation: Genome-wide association study (GWAS) has been a great success in the past decade. However, significant challenges still remain in both identifying new risk loci and interpreting results. Bonferroni-corrected significance level is known to be conservative, leading to insufficient statistical power when the effect size is moderate at risk locus. Complex structure of linkage disequilibrium also makes it challenging to separate causal variants from nonfunctional ones in large haplotype blocks. Under such circumstances, a computational approach that may increase signal replication rate and identify potential functional sites among correlated markers is urgently needed. Results: We describe GenoWAP, a GWAS signal prioritization method that integrates genomic functional annotation and GWAS test statistics. The effectiveness of GenoWAP is demonstrated through its applications to Crohn’s disease and schizophrenia using the largest studies available, where highly ranked loci show substantially stronger signals in the whole dataset after prioritization based on a subset of samples. At the single nucleotide polymorphism (SNP) level, top ranked SNPs after prioritization have both higher replication rates and consistently stronger enrichment of eQTLs. Within each risk locus, GenoWAP may be able to distinguish functional sites from groups of correlated SNPs. Availability and implementation: GenoWAP is freely available on the web at http://genocanyon.med.yale.edu/GenoWAP Contact: hongyu.zhao@yale.edu Supplementary information: Supplementary data are available at Bioinformatics online.
    Keywords Crohn disease ; bioinformatics ; data collection ; genome-wide association study ; genomics ; haplotypes ; linkage disequilibrium ; loci ; prioritization ; risk ; schizophrenia ; single nucleotide polymorphism
    Language English
    Dates of publication 2016-0215
    Size p. 542-548.
    Publishing place Oxford University Press
    Document type Article
    ZDB-ID 1468345-3
    ISSN 1460-2059 ; 1367-4811 ; 1367-4803
    ISSN (online) 1460-2059 ; 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btv610
    Database NAL-Catalogue (AGRICOLA)

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  6. Article ; Online: GenoWAP: GWAS signal prioritization through integrated analysis of genomic functional annotation.

    Lu, Qiongshi / Yao, Xinwei / Hu, Yiming / Zhao, Hongyu

    Bioinformatics (Oxford, England)

    2015  Volume 32, Issue 4, Page(s) 542–548

    Abstract: Motivation: Genome-wide association study (GWAS) has been a great success in the past decade. However, significant challenges still remain in both identifying new risk loci and interpreting results. Bonferroni-corrected significance level is known to be ...

    Abstract Motivation: Genome-wide association study (GWAS) has been a great success in the past decade. However, significant challenges still remain in both identifying new risk loci and interpreting results. Bonferroni-corrected significance level is known to be conservative, leading to insufficient statistical power when the effect size is moderate at risk locus. Complex structure of linkage disequilibrium also makes it challenging to separate causal variants from nonfunctional ones in large haplotype blocks. Under such circumstances, a computational approach that may increase signal replication rate and identify potential functional sites among correlated markers is urgently needed.
    Results: We describe GenoWAP, a GWAS signal prioritization method that integrates genomic functional annotation and GWAS test statistics. The effectiveness of GenoWAP is demonstrated through its applications to Crohn's disease and schizophrenia using the largest studies available, where highly ranked loci show substantially stronger signals in the whole dataset after prioritization based on a subset of samples. At the single nucleotide polymorphism (SNP) level, top ranked SNPs after prioritization have both higher replication rates and consistently stronger enrichment of eQTLs. Within each risk locus, GenoWAP may be able to distinguish functional sites from groups of correlated SNPs.
    Availability and implementation: GenoWAP is freely available on the web at http://genocanyon.med.yale.edu/GenoWAP.
    MeSH term(s) Biomarkers/analysis ; Crohn Disease/genetics ; Genome-Wide Association Study ; Genomics/methods ; Haplotypes/genetics ; Humans ; Linkage Disequilibrium ; Polymorphism, Single Nucleotide/genetics ; Quantitative Trait Loci ; Schizophrenia/genetics ; Software
    Chemical Substances Biomarkers
    Language English
    Publishing date 2015-10-25
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 1422668-6
    ISSN 1367-4811 ; 1367-4803
    ISSN (online) 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btv610
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Leveraging functional annotations in genetic risk prediction for human complex diseases.

    Hu, Yiming / Lu, Qiongshi / Powles, Ryan / Yao, Xinwei / Yang, Can / Fang, Fang / Xu, Xinran / Zhao, Hongyu

    PLoS computational biology

    2017  Volume 13, Issue 6, Page(s) e1005589

    Abstract: Genetic risk prediction is an important goal in human genetics research and precision medicine. Accurate prediction models will have great impacts on both disease prevention and early treatment strategies. Despite the identification of thousands of ... ...

    Abstract Genetic risk prediction is an important goal in human genetics research and precision medicine. Accurate prediction models will have great impacts on both disease prevention and early treatment strategies. Despite the identification of thousands of disease-associated genetic variants through genome wide association studies (GWAS), genetic risk prediction accuracy remains moderate for most diseases, which is largely due to the challenges in both identifying all the functionally relevant variants and accurately estimating their effect sizes in the presence of linkage disequilibrium. In this paper, we introduce AnnoPred, a principled framework that leverages diverse types of genomic and epigenomic functional annotations in genetic risk prediction for complex diseases. AnnoPred is trained using GWAS summary statistics in a Bayesian framework in which we explicitly model various functional annotations and allow for linkage disequilibrium estimated from reference genotype data. Compared with state-of-the-art risk prediction methods, AnnoPred achieves consistently improved prediction accuracy in both extensive simulations and real data.
    MeSH term(s) Chromosome Mapping/methods ; Data Interpretation, Statistical ; Data Mining/methods ; Databases, Genetic ; Epigenomics/methods ; Genetic Association Studies/methods ; Genetic Predisposition to Disease/epidemiology ; Genetic Predisposition to Disease/genetics ; Genetic Variation/genetics ; Genome, Human/genetics ; Humans ; Linkage Disequilibrium/genetics ; Polymorphism, Single Nucleotide/genetics ; Proportional Hazards Models ; Quantitative Trait Loci/genetics ; Risk Assessment/methods
    Language English
    Publishing date 2017-06-08
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2193340-6
    ISSN 1553-7358 ; 1553-734X
    ISSN (online) 1553-7358
    ISSN 1553-734X
    DOI 10.1371/journal.pcbi.1005589
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Book ; Online: Analyzing Who and What Appears in a Decade of US Cable TV News

    Hong, James / Crichton, Will / Zhang, Haotian / Fu, Daniel Y. / Ritchie, Jacob / Barenholtz, Jeremy / Hannel, Ben / Yao, Xinwei / Murray, Michaela / Moriba, Geraldine / Agrawala, Maneesh / Fatahalian, Kayvon

    2020  

    Abstract: Cable TV news reaches millions of U.S. households each day, meaning that decisions about who appears on the news and what stories get covered can profoundly influence public opinion and discourse. We analyze a data set of nearly 24/7 video, audio, and ... ...

    Abstract Cable TV news reaches millions of U.S. households each day, meaning that decisions about who appears on the news and what stories get covered can profoundly influence public opinion and discourse. We analyze a data set of nearly 24/7 video, audio, and text captions from three U.S. cable TV networks (CNN, FOX, and MSNBC) from January 2010 to July 2019. Using machine learning tools, we detect faces in 244,038 hours of video, label each face's presented gender, identify prominent public figures, and align text captions to audio. We use these labels to perform screen time and word frequency analyses. For example, we find that overall, much more screen time is given to male-presenting individuals than to female-presenting individuals (2.4x in 2010 and 1.9x in 2019). We present an interactive web-based tool, accessible at https://tvnews.stanford.edu, that allows the general public to perform their own analyses on the full cable TV news data set.

    Comment: 14 pages, 22 figures (15 pages, 16 figures in supplemental materials)
    Keywords Computer Science - Computers and Society ; Computer Science - Multimedia
    Subject code 420
    Publishing date 2020-08-13
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Book ; Online: Rekall

    Fu, Daniel Y. / Crichton, Will / Hong, James / Yao, Xinwei / Zhang, Haotian / Truong, Anh / Narayan, Avanika / Agrawala, Maneesh / Ré, Christopher / Fatahalian, Kayvon

    Specifying Video Events using Compositions of Spatiotemporal Labels

    2019  

    Abstract: Many real-world video analysis applications require the ability to identify domain-specific events in video, such as interviews and commercials in TV news broadcasts, or action sequences in film. Unfortunately, pre-trained models to detect all the events ...

    Abstract Many real-world video analysis applications require the ability to identify domain-specific events in video, such as interviews and commercials in TV news broadcasts, or action sequences in film. Unfortunately, pre-trained models to detect all the events of interest in video may not exist, and training new models from scratch can be costly and labor-intensive. In this paper, we explore the utility of specifying new events in video in a more traditional manner: by writing queries that compose outputs of existing, pre-trained models. To write these queries, we have developed Rekall, a library that exposes a data model and programming model for compositional video event specification. Rekall represents video annotations from different sources (object detectors, transcripts, etc.) as spatiotemporal labels associated with continuous volumes of spacetime in a video, and provides operators for composing labels into queries that model new video events. We demonstrate the use of Rekall in analyzing video from cable TV news broadcasts, films, static-camera vehicular video streams, and commercial autonomous vehicle logs. In these efforts, domain experts were able to quickly (in a few hours to a day) author queries that enabled the accurate detection of new events (on par with, and in some cases much more accurate than, learned approaches) and to rapidly retrieve video clips for human-in-the-loop tasks such as video content curation and training data curation. Finally, in a user study, novice users of Rekall were able to author queries to retrieve new events in video given just one hour of query development time.
    Keywords Computer Science - Databases ; Computer Science - Computation and Language ; Computer Science - Computer Vision and Pattern Recognition ; Computer Science - Information Retrieval
    Subject code 004
    Publishing date 2019-10-07
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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