LIVIVO - The Search Portal for Life Sciences

zur deutschen Oberfläche wechseln
Advanced search

Search results

Result 1 - 7 of total 7

Search options

  1. Article ; Online: Capture-Recapture Models with Heterogeneous Temporary Emigration

    Matechou, Eleni / Argiento, Raffaele

    Journal of the American Statistical Association. 2023 Jan. 2, v. 118, no. 541 p.56-69

    2023  

    Abstract: We propose a novel approach for modeling capture-recapture (CR) data on open populations that exhibit temporary emigration, while also accounting for individual heterogeneity to allow for differences in visit patterns and capture probabilities between ... ...

    Abstract We propose a novel approach for modeling capture-recapture (CR) data on open populations that exhibit temporary emigration, while also accounting for individual heterogeneity to allow for differences in visit patterns and capture probabilities between individuals. Our modeling approach combines changepoint processes—fitted using an adaptive approach—for inferring individual visits, with Bayesian mixture modeling—fitted using a nonparametric approach—for identifying clusters of individuals with similar visit patterns or capture probabilities. The proposed method is extremely flexible as it can be applied to any CR dataset and is not reliant upon specialized sampling schemes, such as Pollock’s robust design. We fit the new model to motivating data on salmon anglers collected annually at the Gaula river in Norway. Our results when analyzing data from the 2017, 2018, and 2019 seasons reveal two clusters of anglers—consistent across years—with substantially different visit patterns. Most anglers are allocated to the “occasional visitors” cluster, making infrequent and shorter visits with mean total length of stay at the river of around seven days, whereas there also exists a small cluster of “super visitors,” with regular and longer visits, with mean total length of stay of around 30 days in a season. Our estimate of the probability of catching salmon whilst at the river is more than three times higher than that obtained when using a model that does not account for temporary emigration, giving us a better understanding of the impact of fishing at the river. Finally, we discuss the effect of the COVID-19 pandemic on the angling population by modeling data from the 2020 season. Supplementary materials for this article are available online.
    Keywords Bayesian theory ; COVID-19 infection ; data collection ; mark-recapture studies ; models ; probability ; rivers ; salmon ; Norway ; Angling ; Chinese restaurant process ; Clustering ; Population size ; Stopover model
    Language English
    Dates of publication 2023-0102
    Size p. 56-69.
    Publishing place Taylor & Francis
    Document type Article ; Online
    ZDB-ID 2064981-2
    ISSN 1537-274X
    ISSN 1537-274X
    DOI 10.1080/01621459.2022.2123332
    Database NAL-Catalogue (AGRICOLA)

    More links

    Kategorien

  2. Article ; Online: Personalized treatment selection via product partition models with covariates.

    Pedone, Matteo / Argiento, Raffaele / Stingo, Francesco C

    Biometrics

    2024  Volume 80, Issue 1

    Abstract: Precision medicine is an approach for disease treatment that defines treatment strategies based on the individual characteristics of the patients. Motivated by an open problem in cancer genomics, we develop a novel model that flexibly clusters patients ... ...

    Abstract Precision medicine is an approach for disease treatment that defines treatment strategies based on the individual characteristics of the patients. Motivated by an open problem in cancer genomics, we develop a novel model that flexibly clusters patients with similar predictive characteristics and similar treatment responses; this approach identifies, via predictive inference, which one among a set of treatments is better suited for a new patient. The proposed method is fully model based, avoiding uncertainty underestimation attained when treatment assignment is performed by adopting heuristic clustering procedures, and belongs to the class of product partition models with covariates, here extended to include the cohesion induced by the normalized generalized gamma process. The method performs particularly well in scenarios characterized by considerable heterogeneity of the predictive covariates in simulation studies. A cancer genomics case study illustrates the potential benefits in terms of treatment response yielded by the proposed approach. Finally, being model based, the approach allows estimating clusters' specific response probabilities and then identifying patients more likely to benefit from personalized treatment.
    MeSH term(s) Humans ; Models, Statistical ; Precision Medicine/methods ; Probability ; Computer Simulation ; Neoplasms/genetics ; Neoplasms/therapy ; Bayes Theorem
    Language English
    Publishing date 2024-01-01
    Publishing country United States
    Document type Journal Article
    ZDB-ID 213543-7
    ISSN 1541-0420 ; 0099-4987 ; 0006-341X
    ISSN (online) 1541-0420
    ISSN 0099-4987 ; 0006-341X
    DOI 10.1093/biomtc/ujad003
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  3. Article ; Online: Clustering blood donors via mixtures of product partition models with covariates.

    Argiento, Raffaele / Corradin, Riccardo / Guglielmi, Alessandra / Lanzarone, Ettore

    Biometrics

    2024  Volume 80, Issue 1

    Abstract: Motivated by the problem of accurately predicting gap times between successive blood donations, we present here a general class of Bayesian nonparametric models for clustering. These models allow for the prediction of new recurrences, accommodating ... ...

    Abstract Motivated by the problem of accurately predicting gap times between successive blood donations, we present here a general class of Bayesian nonparametric models for clustering. These models allow for the prediction of new recurrences, accommodating covariate information that describes the personal characteristics of the sample individuals. We introduce a prior for the random partition of the sample individuals, which encourages two individuals to be co-clustered if they have similar covariate values. Our prior generalizes product partition models with covariates (PPMx) models in the literature, which are defined in terms of cohesion and similarity functions. We assume cohesion functions that yield mixtures of PPMx models, while our similarity functions represent the denseness of a cluster. We show that including covariate information in the prior specification improves the posterior predictive performance and helps interpret the estimated clusters in terms of covariates in the blood donation application.
    MeSH term(s) Humans ; Blood Donors ; Bayes Theorem ; Cluster Analysis
    Language English
    Publishing date 2024-01-01
    Publishing country United States
    Document type Journal Article
    ZDB-ID 213543-7
    ISSN 1541-0420 ; 0099-4987 ; 0006-341X
    ISSN (online) 1541-0420
    ISSN 0099-4987 ; 0006-341X
    DOI 10.1093/biomtc/ujad021
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  4. Article: Gaussian graphical modeling for spectrometric data analysis

    Codazzi, Laura / Colombi, Alessandro / Gianella, Matteo / Argiento, Raffaele / Paci, Lucia / Pini, Alessia

    Computational statistics & data analysis. 2021 Dec. 29,

    2021  

    Abstract: Motivated by the analysis of spectrometric data, a Gaussian graphical model for learning the dependence structure among frequency bands of the infrared absorbance spectrum is introduced. The spectra are modeled as continuous functional data through a B- ... ...

    Abstract Motivated by the analysis of spectrometric data, a Gaussian graphical model for learning the dependence structure among frequency bands of the infrared absorbance spectrum is introduced. The spectra are modeled as continuous functional data through a B-spline basis expansion and a Gaussian graphical model is assumed as a prior specification for the smoothing coefficients to induce sparsity in their precision matrix. Bayesian inference is carried out to simultaneously smooth the curves and to estimate the conditional independence structure between portions of the functional domain. The proposed model is applied to the analysis of infrared absorbance spectra of strawberry purees.
    Keywords Bayesian theory ; absorbance ; data analysis ; models ; normal distribution ; strawberries
    Language English
    Dates of publication 2021-1229
    Publishing place Elsevier B.V.
    Document type Article
    Note Pre-press version
    ZDB-ID 1478763-5
    ISSN 0167-9473
    ISSN 0167-9473
    DOI 10.1016/j.csda.2021.107416
    Database NAL-Catalogue (AGRICOLA)

    More links

    Kategorien

  5. Article: Hierarchical Normalized Completely Random Measures for Robust Graphical Modeling.

    Cremaschi, Andrea / Argiento, Raffaele / Shoemaker, Katherine / Peterson, Christine / Vannucci, Marina

    Bayesian analysis

    2019  Volume 14, Issue 4, Page(s) 1271–1301

    Abstract: Gaussian graphical models are useful tools for exploring network structures in multivariate normal data. In this paper we are interested in situations where data show departures from Gaussianity, therefore requiring alternative modeling distributions. ... ...

    Abstract Gaussian graphical models are useful tools for exploring network structures in multivariate normal data. In this paper we are interested in situations where data show departures from Gaussianity, therefore requiring alternative modeling distributions. The multivariate
    Language English
    Publishing date 2019-03-28
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2201249-7
    ISSN 1931-6690 ; 1936-0975
    ISSN (online) 1931-6690
    ISSN 1936-0975
    DOI 10.1214/19-ba1153
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  6. Article ; Online: Erratum to: An integrative Bayesian Dirichlet-multinomial regression model for the analysis of taxonomic abundances in microbiome data.

    Wadsworth, W Duncan / Argiento, Raffaele / Guindani, Michele / Galloway-Pena, Jessica / Shelburne, Samuel A / Vannucci, Marina

    BMC bioinformatics

    2017  Volume 18, Issue 1, Page(s) 185

    Language English
    Publishing date 2017-03-23
    Publishing country England
    Document type Journal Article ; Published Erratum
    ZDB-ID 2041484-5
    ISSN 1471-2105 ; 1471-2105
    ISSN (online) 1471-2105
    ISSN 1471-2105
    DOI 10.1186/s12859-017-1606-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  7. Article ; Online: An integrative Bayesian Dirichlet-multinomial regression model for the analysis of taxonomic abundances in microbiome data.

    Wadsworth, W Duncan / Argiento, Raffaele / Guindani, Michele / Galloway-Pena, Jessica / Shelburne, Samuel A / Vannucci, Marina

    BMC bioinformatics

    2017  Volume 18, Issue 1, Page(s) 94

    Abstract: Background: The Human Microbiome has been variously associated with the immune-regulatory mechanisms involved in the prevention or development of many non-infectious human diseases such as autoimmunity, allergy and cancer. Integrative approaches which ... ...

    Abstract Background: The Human Microbiome has been variously associated with the immune-regulatory mechanisms involved in the prevention or development of many non-infectious human diseases such as autoimmunity, allergy and cancer. Integrative approaches which aim at associating the composition of the human microbiome with other available information, such as clinical covariates and environmental predictors, are paramount to develop a more complete understanding of the role of microbiome in disease development.
    Results: In this manuscript, we propose a Bayesian Dirichlet-Multinomial regression model which uses spike-and-slab priors for the selection of significant associations between a set of available covariates and taxa from a microbiome abundance table. The approach allows straightforward incorporation of the covariates through a log-linear regression parametrization of the parameters of the Dirichlet-Multinomial likelihood. Inference is conducted through a Markov Chain Monte Carlo algorithm, and selection of the significant covariates is based upon the assessment of posterior probabilities of inclusions and the thresholding of the Bayesian false discovery rate. We design a simulation study to evaluate the performance of the proposed method, and then apply our model on a publicly available dataset obtained from the Human Microbiome Project which associates taxa abundances with KEGG orthology pathways. The method is implemented in specifically developed R code, which has been made publicly available.
    Conclusions: Our method compares favorably in simulations to several recently proposed approaches for similarly structured data, in terms of increased accuracy and reduced false positive as well as false negative rates. In the application to the data from the Human Microbiome Project, a close evaluation of the biological significance of our findings confirms existing associations in the literature.
    MeSH term(s) Algorithms ; Bacteria/classification ; Bayes Theorem ; Computer Simulation ; Humans ; Linear Models ; Markov Chains ; Microbiota ; Monte Carlo Method
    Language English
    Publishing date 2017-02-08
    Publishing country England
    Document type Journal Article
    ZDB-ID 2041484-5
    ISSN 1471-2105 ; 1471-2105
    ISSN (online) 1471-2105
    ISSN 1471-2105
    DOI 10.1186/s12859-017-1516-0
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

To top