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  1. Book ; Online: Transfer Learning with Random Coefficient Ridge Regression

    Zhang, Hongzhe / Li, Hongzhe

    2023  

    Abstract: Ridge regression with random coefficients provides an important alternative to fixed coefficients regression in high dimensional setting when the effects are expected to be small but not zeros. This paper considers estimation and prediction of random ... ...

    Abstract Ridge regression with random coefficients provides an important alternative to fixed coefficients regression in high dimensional setting when the effects are expected to be small but not zeros. This paper considers estimation and prediction of random coefficient ridge regression in the setting of transfer learning, where in addition to observations from the target model, source samples from different but possibly related regression models are available. The informativeness of the source model to the target model can be quantified by the correlation between the regression coefficients. This paper proposes two estimators of regression coefficients of the target model as the weighted sum of the ridge estimates of both target and source models, where the weights can be determined by minimizing the empirical estimation risk or prediction risk. Using random matrix theory, the limiting values of the optimal weights are derived under the setting when $p/n \rightarrow \gamma$, where $p$ is the number of the predictors and $n$ is the sample size, which leads to an explicit expression of the estimation or prediction risks. Simulations show that these limiting risks agree very well with the empirical risks. An application to predicting the polygenic risk scores for lipid traits shows such transfer learning methods lead to smaller prediction errors than the single sample ridge regression or Lasso-based transfer learning.

    Comment: 16 pages, 5 figures
    Keywords Statistics - Machine Learning ; Computer Science - Machine Learning ; Statistics - Methodology
    Subject code 310
    Publishing date 2023-06-28
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Statistical and Computational Methods for Microbial Strain Analysis.

    Ma, Siyuan / Li, Hongzhe

    Methods in molecular biology (Clifton, N.J.)

    2023  Volume 2629, Page(s) 231–245

    Abstract: Microbial strains are interpreted as a lineage derived from a recent ancestor that have not experienced "too many" recombination events and can be successfully retrieved with culture-independent techniques using metagenomic sequencing. Such a strain ... ...

    Abstract Microbial strains are interpreted as a lineage derived from a recent ancestor that have not experienced "too many" recombination events and can be successfully retrieved with culture-independent techniques using metagenomic sequencing. Such a strain variability has been increasingly shown to display additional phenotypic heterogeneities that affect host health, such as virulence, transmissibility, and antibiotics resistance. New statistical and computational methods have recently been developed to track the strains in samples based on shotgun metagenomics data either based on reference genome sequences or Metagenome-assembled genomes (MAGs). In this paper, we review some recent statistical methods for strain identifications based on frequency counts at a set of single nucleotide variants (SNVs) within a set of single-copy marker genes. These methods differ in terms of whether reference genome sequences are needed, how SNVs are called, what methods of deconvolution are used and whether the methods can be applied to multiple samples. We conclude our review with areas that require further research.
    MeSH term(s) Microbiota/genetics ; Metagenome ; Sequence Analysis, DNA/methods ; Metagenomics/methods
    Language English
    Publishing date 2023-03-16
    Publishing country United States
    Document type Review ; Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-2986-4_11
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Inference of microbial covariation networks using copula models with mixture margins.

    Deek, Rebecca A / Li, Hongzhe

    Bioinformatics (Oxford, England)

    2023  Volume 39, Issue 7

    Abstract: Motivation: Quantification of microbial covariations from 16S rRNA and metagenomic sequencing data is difficult due to their sparse nature. In this article, we propose using copula models with mixed zero-beta margins for the estimation of taxon-taxon ... ...

    Abstract Motivation: Quantification of microbial covariations from 16S rRNA and metagenomic sequencing data is difficult due to their sparse nature. In this article, we propose using copula models with mixed zero-beta margins for the estimation of taxon-taxon covariations using data of normalized microbial relative abundances. Copulas allow for separate modeling of the dependence structure from the margins, marginal covariate adjustment, and uncertainty measurement.
    Results: Our method shows that a two-stage maximum-likelihood approach provides accurate estimation of model parameters. A corresponding two-stage likelihood ratio test for the dependence parameter is derived and is used for constructing covariation networks. Simulation studies show that the test is valid, robust, and more powerful than tests based upon Pearson's and rank correlations. Furthermore, we demonstrate that our method can be used to build biologically meaningful microbial networks based on a dataset from the American Gut Project.
    Availability and implementation: R package for implementation is available at https://github.com/rebeccadeek/CoMiCoN.
    MeSH term(s) Likelihood Functions ; RNA, Ribosomal, 16S/genetics ; Microbial Consortia ; Computer Simulation ; Metagenome
    Chemical Substances RNA, Ribosomal, 16S
    Language English
    Publishing date 2023-06-28
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 1422668-6
    ISSN 1367-4811 ; 1367-4803
    ISSN (online) 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btad413
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Combined spatial and frequency dual stream network for face forgery detection.

    Zhao, Hui / Li, Xin / Xu, Bingxin / Liu, Hongzhe

    PeerJ. Computer science

    2024  Volume 10, Page(s) e1959

    Abstract: With the development of generative model, the cost of facial manipulation and forgery is becoming lower and lower. Fraudulent data has brought numerous hidden threats in politics, privacy, and cybersecurity. Although many methods of face forgery ... ...

    Abstract With the development of generative model, the cost of facial manipulation and forgery is becoming lower and lower. Fraudulent data has brought numerous hidden threats in politics, privacy, and cybersecurity. Although many methods of face forgery detection focus on the learning of high frequency forgery traces and achieve promising performance, these methods usually learn features in spatial and frequency independently. In order to combine the information of the two domains, a combined spatial and frequency dual stream network is proposed for face forgery detection. Concretely, a cross self-attention (CSA) module is designed to improve frequency feature interaction and fusion at different scales. Moreover, to augment the semantic and contextual information, frequency guided spatial feature extraction module is proposed to extract and reconstruct the spatial information. These two modules deeply mine the forgery traces
    Language English
    Publishing date 2024-04-11
    Publishing country United States
    Document type Journal Article
    ISSN 2376-5992
    ISSN (online) 2376-5992
    DOI 10.7717/peerj-cs.1959
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: A hydroxide lock for metallo-β-lactamases.

    Li, Hongyan / Sun, Hongzhe

    Nature chemistry

    2022  Volume 14, Issue 1, Page(s) 6–8

    MeSH term(s) Anti-Bacterial Agents/pharmacology ; Hydroxides ; Microbial Sensitivity Tests ; beta-Lactamases/genetics
    Chemical Substances Anti-Bacterial Agents ; Hydroxides ; beta-Lactamases (EC 3.5.2.6)
    Language English
    Publishing date 2022-01-05
    Publishing country England
    Document type Journal Article ; Comment
    ZDB-ID 2464596-5
    ISSN 1755-4349 ; 1755-4330
    ISSN (online) 1755-4349
    ISSN 1755-4330
    DOI 10.1038/s41557-021-00871-3
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Author Correction: Unraveling the epigenetic code: human kidney DNA methylation and chromatin dynamics in renal disease development.

    Yan, Yu / Liu, Hongbo / Abedini, Amin / Sheng, Xin / Palmer, Matthew / Li, Hongzhe / Susztak, Katalin

    Nature communications

    2024  Volume 15, Issue 1, Page(s) 2537

    Language English
    Publishing date 2024-03-21
    Publishing country England
    Document type Published Erratum
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-024-46661-6
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Editorial: Artificial Intelligence, machine learning and the changing landscape of molecular biology.

    Zou, James / Li, Hongzhe / Plevritis, Sylvia

    Journal of molecular biology

    2022  Volume 434, Issue 15, Page(s) 167712

    MeSH term(s) Artificial Intelligence ; Machine Learning ; Molecular Biology
    Language English
    Publishing date 2022-06-28
    Publishing country Netherlands
    Document type Editorial
    ZDB-ID 80229-3
    ISSN 1089-8638 ; 0022-2836
    ISSN (online) 1089-8638
    ISSN 0022-2836
    DOI 10.1016/j.jmb.2022.167712
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: Editorial: Hearing Loss: Mechanisms and Prevention.

    Chai, Renjie / Li, Hongzhe / Yang, Tao / Sun, Shan / Yuan, Yongyi

    Frontiers in cell and developmental biology

    2022  Volume 10, Page(s) 838271

    Language English
    Publishing date 2022-02-03
    Publishing country Switzerland
    Document type Editorial
    ZDB-ID 2737824-X
    ISSN 2296-634X
    ISSN 2296-634X
    DOI 10.3389/fcell.2022.838271
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: Editorial: The mechanism on development and regeneration of inner ear hair cells.

    Sun, Haojie / Chen, Binjun / Sun, Yu / Li, Hongzhe / Ren, Dongdong

    Frontiers in molecular neuroscience

    2022  Volume 15, Page(s) 974270

    Language English
    Publishing date 2022-08-09
    Publishing country Switzerland
    Document type Editorial
    ZDB-ID 2452967-9
    ISSN 1662-5099
    ISSN 1662-5099
    DOI 10.3389/fnmol.2022.974270
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: DFT-assisted low-dimensional carbon-based electrocatalysts design and mechanism study: a review.

    Han, Yun / Xu, Hongzhe / Li, Qin / Du, Aijun / Yan, Xuecheng

    Frontiers in chemistry

    2023  Volume 11, Page(s) 1286257

    Abstract: Low-dimensional carbon-based (LDC) materials have attracted extensive research attention in electrocatalysis because of their unique advantages such as structural diversity, low cost, and chemical tolerance. They have been widely used in a broad range of ...

    Abstract Low-dimensional carbon-based (LDC) materials have attracted extensive research attention in electrocatalysis because of their unique advantages such as structural diversity, low cost, and chemical tolerance. They have been widely used in a broad range of electrochemical reactions to relieve environmental pollution and energy crisis. Typical examples include hydrogen evolution reaction (HER), oxygen evolution reaction (OER), oxygen reduction reaction (ORR), carbon dioxide reduction reaction (CO
    Language English
    Publishing date 2023-10-17
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2711776-5
    ISSN 2296-2646
    ISSN 2296-2646
    DOI 10.3389/fchem.2023.1286257
    Database MEDical Literature Analysis and Retrieval System OnLINE

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