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Stopping Criteria in Contrastive Divergence: Alternatives to the Reconstruction Error [article]

David Buchaca, Enrique Romero, Ferran Mazzanti, Jordi Delgado
2014 arXiv   pre-print
However, not many alternatives to the reconstruction error have been used in the literature.  ...  In this manuscript we investigate simple alternatives to the reconstruction error in order to detect as soon as possible the decrease in the log-likelihood during learning.  ...  and discussed as an alternative to the reconstruction error.  ... 
arXiv:1312.6062v2 fatcat:kfhe7kfnwffiln7ryuxbb5uuru

Neighborhood-Based Stopping Criterion for Contrastive Divergence

Enrique Romero Merino, Ferran Mazzanti Castrillejo, Jordi Delgado Pin
2017 IEEE Transactions on Neural Networks and Learning Systems  
However, not many alternatives to the reconstruction error have been discussed in the literature.  ...  RBMs are often trained using the Contrastive Divergence learning algorithm (CD), an approximation to the gradient of the data log-likelihood.  ...  10 JD: This work was partially supported by SGR2014-890 (MACDA) of the Generalitat de Catalunya and MINECO project APCOM (TIN2014-57226-P)  ... 
doi:10.1109/tnnls.2017.2697455 pmid:28534790 fatcat:eymvbm7bsbbthbdehoxvlri5x4

A Neighbourhood-Based Stopping Criterion for Contrastive Divergence Learning [article]

E. Romero, F. Mazzanti, J. Delgado
2015 arXiv   pre-print
However, not many alternatives to the reconstruction error have been discussed in the literature.  ...  In this manuscript we investigate simple alternatives to the reconstruction error, based on the inclusion of information contained in neighboring states to the training set, as a stopping criterion for  ...  One of the most widely used criteria for stopping is based on the monitorization of the reconstruction error, which is a measure of the capability of the network to produce an output that is consistent  ... 
arXiv:1507.06803v1 fatcat:punnk5zznfaf3jk6us3llblzja

Empirical Analysis of the Divergence of Gibbs Sampling Based Learning Algorithms for Restricted Boltzmann Machines [chapter]

Asja Fischer, Christian Igel
2010 Lecture Notes in Computer Science  
The decrease of the likelihood can not be detected by an increase of the reconstruction error, which has been proposed as a stopping criterion for CD learning.  ...  Taking artificial data sets from the literature we study these divergence effects in more detail.  ...  Acknowledgements We acknowledge support from the German Federal Ministry of Education and Research within the National Network Computational Neuroscience under grant number 01GQ0951.  ... 
doi:10.1007/978-3-642-15825-4_26 fatcat:4gz4hsbfunbudijrjtya2eny3m

Divergent, CoexistingPseudomonas aeruginosaLineages in Chronic Cystic Fibrosis Lung Infections

David Williams, Benjamin Evans, Sam Haldenby, Martin J. Walshaw, Michael A. Brockhurst, Craig Winstanley, Steve Paterson
2015 American Journal of Respiratory and Critical Care Medicine  
An alternative hypothesis is all isolates in a sample forming a single lineage where genetic divergence within the sample is less than to other samples.  ...  The HKY85 nucleotide substitution model was selected for use in Garli with JModelTest2 version 2.1.5 14 according to all available selection criteria.  ...  Figure S1 : LESB58 is an appropriate outgroup for rooting the isolates sampled from the nine patients.  ... 
doi:10.1164/rccm.201409-1646oc pmid:25590983 pmcid:PMC4407486 fatcat:2fkplvg2orgspg4kya4uzqfzeq

Phase retrieval with Bregman divergences and application to audio signal recovery [article]

Pierre-Hugo Vial, Paul Magron, Thomas Oberlin, Cédric Févotte
2021 arXiv   pre-print
Since these divergences are not symmetric with respect to their two input arguments in general, they lead to two different formulations of the problem.  ...  Indeed, the quadratic loss does not properly account for some perceptual properties of audio, and alternative discrepancy measures such as beta-divergences have been preferred in many settings.  ...  Acknowledgments The authors would like to thank the guest editors and the anonymous reviewers for their thorough reading and valuable comments, which helped significantly improving this paper.  ... 
arXiv:2010.00392v2 fatcat:dpmzmik53bfyhfe4nkes762f44

Multi-Resolution Beta-Divergence NMF for Blind Spectral Unmixing [article]

Valentin Leplat, Nicolas Gillis, Cédric Févotte
2021 arXiv   pre-print
Most previous works have focused on the least squares error measure, which is the β-divergence for β = 2.  ...  We show on numerical experiments that the MU are able to obtain high resolutions in both dimensions on two applications: (1) blind unmixing of audio spectrograms: to the best of our knowledge, this is  ...  To compare the accuracy of the solutions W and based on quantitative criteria detailed in subsection IV-A3.  ... 
arXiv:2007.03893v3 fatcat:whbh53miajfa3l6hxk7mk3theq

Chloroplast Genome Evolution in Early Diverged Leptosporangiate Ferns

Hyoung Tae Kim, Myong Gi Chung, Ki-Joong Kim
2014 Molecules and Cells  
In this study, the chloroplast (cp) genome sequences from three early diverged leptosporangiate ferns were completed and analyzed in order to understand the evolution of the genome of the fern lineages  ...  Therefore, our data is in agreement with the view that Osmundales is a distinct early diverged lineage in the leptosporangiate ferns.  ...  Thirty three genes had internal stop codons, and 19 genes had alternative start codons (Table 3) .  ... 
doi:10.14348/molcells.2014.2296 pmid:24823358 pmcid:PMC4044308 fatcat:f3bqv2tfircd3d3ef2wwqefu6q

Evolution of the Vertebrate Cytosolic Malate Dehydrogenase Gene Family: Duplication and Divergence in Actinopterygian Fish

T.J.S. Merritt, J.M. Quattro
2003 Journal of Molecular Evolution  
A general correlation between neural expression and negative charge in isozymes suggests charge represents an adaptation to the neural environment.  ...  Two cytosolic malate dehydrogenase (MDH) isozymes have different spatial expression patterns in certain fishes: one is expressed in all tissues and the second is expressed primarily in the eye and skeletal  ...  The one nonsynonymous substitution involved a chemically conservative alanine-to-serine change (using the criteria of Grantham 1974 ).  ... 
doi:10.1007/s00239-002-2398-x pmid:12612830 fatcat:mll53o2gmzemji2t2sv5z4dxg4

Primate phylogenetic relationships and divergence dates inferred from complete mitochondrial genomes

Luca Pozzi, Jason A. Hodgson, Andrew S. Burrell, Kirstin N. Sterner, Ryan L. Raaum, Todd R. Disotell
2014 Molecular Phylogenetics and Evolution  
In contrast to previous mitogenomic studies, the positions of tarsiers and colugos relative to strepsirrhines and anthropoids are well resolved.  ...  The origins and the divergence times of the most basal lineages within primates have been difficult to resolve mainly due to the incomplete sampling of early fossil taxa.  ...  We also want to thank three anonymous reviewers and the editor for their comments that strongly improve the quality of our study.  ... 
doi:10.1016/j.ympev.2014.02.023 pmid:24583291 pmcid:PMC4059600 fatcat:arsir3saxratjavhxpogna6lu4

Lineage Divergence and Historical Gene Flow in the Chinese Horseshoe Bat (Rhinolophus sinicus)

Xiuguang Mao, Guimei He, Junpeng Zhang, Stephen J. Rossiter, Shuyi Zhang, Dmitry A. Filatov
2013 PLoS ONE  
Closely related taxa living in sympatry provide good opportunities to investigate the origin of barriers to gene flow as well as the extent of reproductive isolation.  ...  To determine the history of lineage divergence and gene flow between these taxa, we applied phylogenetic, demographic and coalescent analyses to multi-locus datasets.  ...  Conceived and designed the experiments: XM SR SZ. Performed the experiments: XM GH. Analyzed the data: XM SR. Contributed reagents/materials/analysis tools: SZ. Wrote the paper: XM SR.  ... 
doi:10.1371/journal.pone.0056786 pmid:23451086 pmcid:PMC3581519 fatcat:52co5in5ffhrfbtcepjk4akrti

Accurate prediction of orthologs in the presence of divergence after duplication [article]

Manuel Lafond, Mona Meghdari Miardan, David Sankoff
2018 bioRxiv   pre-print
However, both types of orthology have applications in important areas such as gene function prediction and phylogenetic reconstruction, motivating the need for methods that can distinguish the two types  ...  This has important consequences on the prediction of orthology relationships, since two orthologous genes separated by divergence after duplication may differ in both sequence and function.  ...  Notably, the well-known "orthologs conjecture" states that orthologs tend to perform similar functions, in contrast with paralogs, which tend to diverge in their functional role.  ... 
doi:10.1101/294405 fatcat:6f7oezawjzbjbdl3esjvirz7f4

Patterns and tempo of PCSK9 pseudogenizations suggest an ancient divergence in mammalian cholesterol homeostasis mechanisms

Barbara van Asch, Luís Filipe Teixeira da Costa
2021 Genetica  
have led to PCSK9 loss in most species.  ...  PCSK9 is an intriguing protease in that it does not act by proteolysis but by preventing LDLR recirculation from endosomes to the plasma membrane.  ...  without contacting the corresponding author of the paper and/or seeking permission from the original provider of the genetic material.  ... 
doi:10.1007/s10709-021-00113-x pmid:33515402 fatcat:jkn5qgozvrdizahksgbawcieei

Divergence times in the termite genus Macrotermes (Isoptera: Termitidae)

R. Brandl, F. Hyodo, M. von Korff-Schmising, K. Maekawa, T. Miura, Y. Takematsu, T. Matsumoto, T. Abe, R. Bagine, M. Kaib
2007 Molecular Phylogenetics and Evolution  
The clades from the Oriental region dated back to the early Tertiary. These estimates of divergence times suggested that Macrotermes invaded Asia during periods with humid climates.  ...  The evolution of fungus-growing termites is supposed to have started in the African rain forests with multiple invasions of semi-arid habitats as well as multiple invasions of the Oriental region.  ...  Acknowledgments We are grateful to the various agencies of the many countries where Macrotermes was sampled to allow us to conduct research in their territories. We thank S. Konate, V.  ... 
doi:10.1016/j.ympev.2007.07.007 pmid:17714956 fatcat:hsppki3rszfkbgyit6p2uo2rgq

Population Genomics in Wild Tomatoes—The Interplay of Divergence and Admixture

Ian Beddows, Aparna Reddy, Thorsten Kloesges, Laura E Rose
2017 Genome Biology and Evolution  
This discovery presents a new opportunity to understand the genomic outcomes of hybridization in plants.  ...  Recombinational speciation is rarely reported, and we discuss the difficulties in identifying it and differentiating between alternative demographic scenarios.  ...  Acknowledgments The authors thank the TGRC for seed and Roger Chetelat for comments, Sandra Knapp for herbarium records, and Hajo Esser for herbarium specimens.  ... 
doi:10.1093/gbe/evx224 pmid:29077853 pmcid:PMC5714242 fatcat:ahmsobhofrepngvuu5ynm3n7ru
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