From 4edc04e4c0932cdd5d0d3f08904b4452be176a6d Mon Sep 17 00:00:00 2001 From: Leonardo Date: Wed, 12 Jun 2024 15:39:49 +0200 Subject: [PATCH] clean references --- paper/paper.bib | 357 ++---------------------------------------------- paper/paper.md | 1 + 2 files changed, 16 insertions(+), 342 deletions(-) diff --git a/paper/paper.bib b/paper/paper.bib index 1815309..913669e 100644 --- a/paper/paper.bib +++ b/paper/paper.bib @@ -1,34 +1,3 @@ -@article{betancourt2017conceptual, - title={A conceptual introduction to Hamiltonian Monte Carlo}, - author={Betancourt, Michael}, - journal={arXiv preprint arXiv:1701.02434}, - year={2017} -} - - -@incollection{kmeans, - author={Egidi, Leonardo and Pappad{\`a}, Roberta and Pauli, Francesco and Torelli, Nicola}, - title = {K-means seeding via {M}{U}{S} algorithm}, - booktitle = {Book of Short Papers SIS 2018}, - year = 2018, - editor={A. Abbruzzo and E. Brentari and M. Chiodi and D. Piacentino}, - publisher ={Pearson}, - pages={256--262} - } - - -@incollection{egidi2018maxima, -author={Egidi, Leonardo and Pappad{\`a}, Roberta and Pauli, Francesco and Torelli, Nicola}, - title = {Maxima {U}nits {S}earch ({M}{U}{S}) algorithm: methodology and applications}, - booktitle = {Studies in Theoretical and Applied Statistics}, - year = 2018, - editor={C. Perna and M. Pratesi and A. Ruiz-Gazen} , - publisher={Springer}, - pages={71--81}, - doi = {10.1007/978-3-319-73906-9_7} - } - - @article{egidi2018relabelling, title={Relabelling in {B}ayesian mixture models by pivotal units}, @@ -45,60 +14,17 @@ @article{egidi2018relabelling @ARTICLE{JMLR02, -author={Strehl, A. and Ghosh, J.}, -title={Cluster ensembles - A knowledge reuse framework for combining multiple partitions}, -journal={Journal on Machine Learning Research}, -year={2002}, -volume={3}, -pages={583-617}, -doi = {10.1162/153244303321897735} + author={Strehl, A. and Ghosh, J.}, + title={Cluster ensembles - A knowledge reuse framework for combining multiple partitions}, + journal={Journal on Machine Learning Research}, + year={2002}, + volume={3}, + pages={583-617}, + doi = {10.1162/153244303321897735} } -@article{fredJain05, - author = {Fred, Ana L. N. and Jain, Anil K.}, - title = {Combining multiple clusterings using evidence accumulation}, - journal = {IEEE Trans. Pattern Anal. Mach. Intell.}, - volume = {27}, - number = {6}, - year = {2005}, - pages = {835--850}, - doi = {10.1109/TPAMI.2005.113} -} - - -@inproceedings{kmeans07, - title={k-means++: The advantages of careful seeding}, - author={Arthur, David and Vassilvitskii, Sergei}, - booktitle={Proceedings of the eighteenth annual ACM-SIAM symposium on Discrete algorithms}, - pages={1027--1035}, - year={2007}} - - - -@incollection{puolamaki2009bayesian, - title={{B}ayesian solutions to the label switching problem}, - author={Puolam{\"a}ki, Kai and Kaski, Samuel}, - booktitle={Advances in Intelligent Data Analysis VIII}, - pages={381--392}, - year={2009}, - publisher={Springer}, - doi = {10.1007/978-3-642-03915-7_33} -} - -@article{fritsch2009improved, - title={Improved criteria for clustering based on the posterior similarity matrix}, - author={Fritsch, Arno and Ickstadt, Katja}, - journal={{B}ayesian analysis}, - volume={4}, - number={2}, - pages={367--391}, - year={2009}, - publisher={International Society for {B}ayesian Analysis}, - doi = {10.1214/09-BA414} -} - @article{stephens2000dealing, title={Dealing with label switching in mixture models}, author={Stephens, Matthew}, @@ -111,37 +37,6 @@ @article{stephens2000dealing doi = {10.1111/1467-9868.00265} } -@article{yao2012bayesian, - title={{B}ayesian mixture labeling and clustering}, - author={Yao, Weixin}, - journal={Communications in Statistics-Theory and Methods}, - volume={41}, - number={3}, - pages={403--421}, - year={2012}, - publisher={Taylor \& Francis} -} - - -@article{jasra2005markov, - title={{M}arkov chain {M}onte {C}arlo methods and the label switching problem in {B}ayesian mixture modeling}, - author={Jasra, A and Holmes, CC and Stephens, DA}, - journal={Statistical Science}, - volume={20}, - number={1}, - pages={50--67}, - year={2005} -} - - -@article{yao2009bayesian, - title={{B}ayesian mixture labeling by highest posterior density}, - author={Yao, Weixin and Lindsay, Bruce G}, - journal={Journal of the American Statistical Association}, - volume={104}, - number={486}, - year={2009} -} @article{fruhwirth2001markov, @@ -156,36 +51,7 @@ @article{fruhwirth2001markov doi ={10.1198/016214501750333063} } -@article{chung2004difficulties, - title={Difficulties in drawing inferences with finite-mixture models}, - author={Chung, Hwan and Loken, Eric and Schafer, Joseph L}, - journal={The American Statistician}, - volume={58}, - number={2}, - pages={152--158}, - year={2004} -} - -@article{yao2014online, - title={An online {B}ayesian mixture labelling method by minimizing deviance of classification probabilities to reference labels}, - author={Yao, Weixin and Li, Longhai}, - journal={Journal of Statistical Computation and Simulation}, - volume={84}, - number={2}, - pages={310--323}, - year={2014}, - publisher={Taylor \& Francis} -} -@article{papastamoulis2010artificial, - title={An artificial allocations based solution to the label switching problem in {B}ayesian analysis of mixtures of distributions}, - author={Papastamoulis, Panagiotis and Iliopoulos, George}, - journal={Journal of Computational and Graphical Statistics}, - volume={19}, - number={2}, -pages = {313--331}, - year={2010} -} @article{papastamoulis2016label, @@ -199,13 +65,7 @@ @article{papastamoulis2016label doi = {10.18637/jss.v069.c01} } -@Manual{label.switching, - title = {label.switching: Relabelling MCMC Outputs of Mixture Models}, - author = {Panagiotis Papastamoulis}, - year = {2018}, - note = {{R} package version 1.7}, - url = {https://CRAN.R-project.org/package=label.switching}, -} + @Manual{bayesmix, title = {bayesmix: {B}ayesian Mixture Models with JAGS}, @@ -219,95 +79,11 @@ @book{titterington1985statistical title={Statistical analysis of finite mixture distributions}, author={Titterington, D Michael and Smith, Adrian FM and Makov, Udi E}, year={1985}, - publisher={Wiley, New York} + publisher={Wiley, New York}, + doi = {10.2307/2531224} } -@book{McPeel2000, - title={Finite Mixture Models}, - author={McLachlan, J and Peel, D}, - year={2000}, - publisher={John Wiley \& Sons} -} -@article{hubert1985comparing, - title={Comparing partitions}, - author={Hubert, Lawrence and Arabie, Phipps}, - journal={Journal of classification}, - volume={2}, - number={1}, - pages={193--218}, - year={1985}, - publisher={Springer} -} - - -@article{rodriguez2014label, - title={Label switching in {B}ayesian mixture models: {D}eterministic relabeling strategies}, - author={Rodr{\'\i}guez, Carlos E and Walker, Stephen G}, - journal={Journal of Computational and Graphical Statistics}, - volume={23}, - number={1}, - pages={25--45}, - year={2014}, - publisher={Taylor \& Francis} -} - -@book{marin2007bayesian, - title={{B}ayesian core: a practical approach to computational {B}ayesian statistics}, - author={Marin, Jean-Michel and Robert, Christian P}, - year={2007}, - publisher={Springer Science \& Business Media} -} - -@article{marin2005bayesian, - title={{B}ayesian modelling and inference on mixtures of distributions}, - author={Marin, Jean-Michel and Mengersen, Kerrie and Robert, Christian P}, - journal={Handbook of {S}tatistics}, - volume={25}, - pages={459--507}, - year={2005}, - publisher={Elsevier} -} - -@article{celeux2000computational, - title={Computational and inferential difficulties with mixture posterior distributions}, - author={Celeux, Gilles and Hurn, Merrilee and Robert, Christian P}, - journal={Journal of the American Statistical Association}, - volume={95}, - number={451}, - pages={957--970}, - year={2000}, - publisher={Taylor \& Francis Group} -} - -@article{sperrin2010probabilistic, - title={Probabilistic relabelling strategies for the label switching problem in {B}ayesian mixture models}, - author={Sperrin, Matthew and Jaki, Thomas and Wit, Ernst}, - journal={Statistics and Computing}, - volume={20}, - number={3}, - pages={357--366}, - year={2010}, - publisher={Springer} -} - -@phdthesis{jasra2006bayesian, - title={{B}ayesian inference for mixture models via {M}onte {C}arlo computation}, - author={Jasra, Ajay}, - year={2006}, - school={Imperial College London (University of London)} -} - -@article{neal1996sampling, - title={Sampling from multimodal distributions using tempered transitions}, - author={Neal, Radford M}, - journal={Statistics and computing}, - volume={6}, - number={4}, - pages={353--366}, - year={1996}, - publisher={Springer} -} @article{richardson1997bayesian, title={On {B}ayesian analysis of mixtures with an unknown number of components (with discussion)}, @@ -321,42 +97,8 @@ @article{richardson1997bayesian doi ={10.1111/1467-9868.00095} } -@article{roeder1990density, - title={Density estimation with confidence sets exemplified by superclusters and voids in the galaxies}, - author={Roeder, Kathryn}, - journal={Journal of the American Statistical Association}, - volume={85}, - number={411}, - pages={617--624}, - year={1990}, - publisher={Taylor \& Francis} -} -@Manual{foreign, - title = {foreign: Read Data Stored by `Minitab', `S', `SAS', `SPSS', `Stata', -`Systat', `Weka', `dBase', ...}, - author = {{R Core Team}}, - year = {2022}, - note = {{R} package version 0.8-84}, - url = {https://CRAN.R-project.org/package=foreign}, -} - -@Manual{mass, - title = {MASS: Support Functions and Datasets for Venables and Ripley's MASS}, - author = {Brian Ripley}, - year = {2018}, - note = {{R} package version 7.3-51.1}, - url = {https://CRAN.R-project.org/package=MASS}, -} -@Manual{mclust, - title = {mclust: Gaussian Mixture Modelling for Model-Based Clustering, -Classification, and Density Estimation}, - author = {Chris Fraley and Adrian E. Raftery and Luca Scrucca}, - year = {2022}, - note = {{R} package version 6.0.0}, - url = {https://CRAN.R-project.org/package=mclust}, -} @Manual{pivmet, title = {pivmet: {P}ivotal {M}ethods for {B}ayesian {R}elabelling and k-Means {C}lustering}, @@ -372,7 +114,7 @@ @Misc{rstan note = {{R} package version 2.21.7}, year = {2022}, url = {http://mc-stan.org/}, - } +} @Manual{rjags, title = {rjags: {B}ayesian graphical models using MCMC}, @@ -380,51 +122,9 @@ @Manual{rjags year = {2022}, note = {{R} package version 4-13}, url = {https://CRAN.R-project.org/package=rjags}, - } - -@article{denwood2016, - title = {{runjags}: An {R} package providing interface utilities, model templates, parallel computing methods and additional distributions for {MCMC} models in {JAGS}}, - author = {Matthew J. Denwood}, - journal = {Journal of {S}tatistical {S}oftware}, - year = {2016}, - volume = {71}, - number = {9}, - pages = {1--25} } - -@article{gelman2008weakly, - title={A weakly informative default prior distribution for logistic and other regression models}, - author={Gelman, Andrew and Jakulin, Aleks and Pittau, Maria Grazia and Su, Yu-Sung and others}, - journal={The {A}nnals of {A}pplied {S}tatistics}, - volume={2}, - number={4}, - pages={1360--1383}, - year={2008}, - publisher={Institute of Mathematical Statistics} -} - -@article{gelman2006prior, - title={Prior distributions for variance parameters in hierarchical models (comment on article by Browne and Draper)}, - author={Gelman, Andrew}, - journal={{B}ayesian {A}nalysis}, - volume={1}, - number={3}, - pages={515--534}, - year={2006}, - publisher={International Society for {B}ayesian Analysis} -} -@article{spike, - title={Spike and slab variable selection: frequentist and {B}ayesian strategies}, - author={Ishwaran, Hemant and Rao, J Sunil}, - journal={The Annals of Statistics}, - volume={33}, - number={2}, - pages={730--773}, - year={2005}, - publisher={Institute of Mathematical Statistics} -} @article{neal2000markov, title={Markov {C}hain sampling methods for {D}irichlet process mixture models}, @@ -438,14 +138,7 @@ @article{neal2000markov doi ={10.1080/10618600.2000.10474879} } -@incollection{ferguson1983bayesian, - title={Bayesian density estimation by mixtures of normal distributions}, - author={Ferguson, Thomas S}, - booktitle={Recent advances in statistics}, - pages={287--302}, - year={1983}, - publisher={Elsevier} -} + @article{escobar1995bayesian, title={Bayesian density estimation and inference using mixtures}, @@ -459,13 +152,7 @@ @article{escobar1995bayesian doi = {10.1080/01621459.1995.10476550} } -@misc{ross2018dirichletprocess, - title={dirichletprocess: An R Package for {F}itting {C}omplex {B}ayesian {N}onparametric {M}odels}, - author={Ross, Gordon J and Markwick, Dean}, - year={2018}, - note = {{R} package version 0.4.0}, - url={https://cloud.r-project.org/web/packages/dirichletprocess/} -} + @article{ferguson1973bayesian, title={A {B}ayesian analysis of some nonparametric problems}, @@ -501,20 +188,6 @@ @article{malsiner2016model doi = {10.1007/s11222-014-9500-2} } -@article{greve2020spying, - title={Spying on the prior of the number of data clusters and the partition distribution in {B}ayesian cluster analysis}, - author={Greve, Jan and Gr{\"u}n, Bettina and Malsiner-Walli, Gertraud and Fr{\"u}hwirth-Schnatter, Sylvia}, - journal={arXiv preprint arXiv:2012.12337}, - year={2020} -} -@article{fraley2002model, - title={Model-based clustering, discriminant analysis, and density estimation}, - author={Fraley, Chris and Raftery, Adrian E}, - journal={Journal of the American statistical Association}, - volume={97}, - number={458}, - pages={611--631}, - year={2002}, - publisher={Taylor \& Francis} -} + + diff --git a/paper/paper.md b/paper/paper.md index 7c5f852..f6719a8 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -40,6 +40,7 @@ We introduce the `R` package `pivmet`, a software that performs different pivota the so-called pivotal units that are chosen from a partition of data points to represent the groups to which they belong. Such units turn out be very useful in both unsupervised and supervised learning frameworks such as clustering, classification and mixture modelling. + More specifically, applications of pivotal methods include, among the others: a Markov-Chain Monte Carlo (MCMC) relabelling procedure to deal with the well-known label-switching problem occurring during Bayesian estimation of mixture models [@stephens2000dealing; @richardson1997bayesian; @fruhwirth2001markov; @egidi2018relabelling];