Unsupervised dimensionality reduction for very large datasets: Are we going to the right direction?

2020 ◽  
Vol 196 ◽  
pp. 105777
Author(s):  
Jadson Jose Monteiro Oliveira ◽  
Robson Leonardo Ferreira Cordeiro
Author(s):  
Htay Htay Win ◽  
Aye Thida Myint ◽  
Mi Cho Cho

For years, achievements and discoveries made by researcher are made aware through research papers published in appropriate journals or conferences. Many a time, established s researcher and mainly new user are caught up in the predicament of choosing an appropriate conference to get their work all the time. Every scienti?c conference and journal is inclined towards a particular ?eld of research and there is a extensive group of them for any particular ?eld. Choosing an appropriate venue is needed as it helps in reaching out to the right listener and also to further one’s chance of getting their paper published. In this work, we address the problem of recommending appropriate conferences to the authors to increase their chances of receipt. We present three di?erent approaches for the same involving the use of social network of the authors and the content of the paper in the settings of dimensionality reduction and topic modelling. In all these approaches, we apply Correspondence Analysis (CA) to obtain appropriate relationships between the entities in question, such as conferences and papers. Our models show hopeful results when compared with existing methods such as content-based ?ltering, collaborative ?ltering and hybrid ?ltering.


2001 ◽  
Vol 27 (11) ◽  
pp. 1457-1478 ◽  
Author(s):  
Michael D Beynon ◽  
Tahsin Kurc ◽  
Umit Catalyurek ◽  
Chialin Chang ◽  
Alan Sussman ◽  
...  

2019 ◽  
Vol 35 (19) ◽  
pp. 3608-3616
Author(s):  
Ashley A Superson ◽  
Doug Phelan ◽  
Allyson Dekovich ◽  
Fabia U Battistuzzi

Abstract Motivation The promise of higher phylogenetic stability through increased dataset sizes within tree of life (TOL) reconstructions has not been fulfilled. Among the many possible causes are changes in species composition (taxon sampling) that could influence phylogenetic accuracy of the methods by altering the relative weight of the evolutionary histories of each individual species. This effect would be stronger in clades that are represented by few lineages, which is common in many prokaryote phyla. Indeed, phyla with fewer taxa showed the most discordance among recent TOL studies. We implemented an approach to systematically test how the identity of taxa among a larger dataset and the number of taxa included affected the accuracy of phylogenetic reconstruction. Results Utilizing an empirical dataset within Terrabacteria we found that even within scenarios consisting of the same number of taxa, the species used strongly affected phylogenetic stability. Furthermore, we found that trees with fewer species were more dissimilar to the tree produced from the full dataset. These results hold even when the tree is composed by many phyla and only one of them is being altered. Thus, the effect of taxon sampling in one group does not seem to be buffered by the presence of many other clades, making this issue relevant even to very large datasets. Our results suggest that a systematic evaluation of phylogenetic stability through taxon resampling is advisable even for very large datasets. Availability and implementation https://github.com/BlabOaklandU/PATS.git. Supplementary information Supplementary data are available at Bioinformatics online.


2016 ◽  
Vol 3 (5) ◽  
pp. 160225 ◽  
Author(s):  
Rhodri S. Wilson ◽  
Lei Yang ◽  
Alison Dun ◽  
Annya M. Smyth ◽  
Rory R. Duncan ◽  
...  

Recent advances in optical microscopy have enabled the acquisition of very large datasets from living cells with unprecedented spatial and temporal resolutions. Our ability to process these datasets now plays an essential role in order to understand many biological processes. In this paper, we present an automated particle detection algorithm capable of operating in low signal-to-noise fluorescence microscopy environments and handling large datasets. When combined with our particle linking framework, it can provide hitherto intractable quantitative measurements describing the dynamics of large cohorts of cellular components from organelles to single molecules. We begin with validating the performance of our method on synthetic image data, and then extend the validation to include experiment images with ground truth. Finally, we apply the algorithm to two single-particle-tracking photo-activated localization microscopy biological datasets, acquired from living primary cells with very high temporal rates. Our analysis of the dynamics of very large cohorts of 10 000 s of membrane-associated protein molecules show that they behave as if caged in nanodomains. We show that the robustness and efficiency of our method provides a tool for the examination of single-molecule behaviour with unprecedented spatial detail and high acquisition rates.


Econometrics ◽  
2015 ◽  
Vol 3 (2) ◽  
pp. 317-338 ◽  
Author(s):  
Sandy Burden ◽  
Noel Cressie ◽  
David Steel

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