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A grammar-based distance metric enables fast and accurate clustering of large sets of 16S sequences

David J Russell, Samuel F Way, Andrew K Benson, Khalid Sayood
<span title="2010-12-17">2010</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
We propose a sequence clustering algorithm and compare the partition quality and execution time of the proposed algorithm with those of a popular existing algorithm.  ...  The proposed clustering algorithm uses a grammar-based distance metric to determine partitioning for a set of biological sequences.  ...  Acknowledgements We would like to thank the National Institutes of Health (NIH) for partial funding of this work and Nina Murray for her careful critique of the paper.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-11-601">doi:10.1186/1471-2105-11-601</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21167044">pmid:21167044</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3022630/">pmcid:PMC3022630</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/r42i322w45hyjgaurxw3zpy7km">fatcat:r42i322w45hyjgaurxw3zpy7km</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190501052923/https://digitalcommons.unl.edu/cgi/viewcontent.cgi?referer=&amp;httpsredir=1&amp;article=1189&amp;context=electricalengineeringfacpub" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/b7/94/b794d9986ecda2f6ff66200454f33a0ea362e05a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-11-601"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3022630" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

FROM BIOLOGY TO EDUCATION: SCORING AND CLUSTERING MULTILINGUAL TEXT SEQUENCES AND OTHER SEQUENTIAL TASKS

Jana Z. Sukkarieh, Matthias von Davier, Kentaro Yamamoto
<span title="">2012</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/jf5pdoipu5gyfag6ffep34ce3e" style="color: black;">ETS Research Report Series</a> </i> &nbsp;
We also thank Mike Wagner for explaining the semantics of the attributes in the log files and answering our questions and both Mike and Ramin Hemat for extracting the required data in the log files for  ...  This solution not only facilitates automatic scoring but plays an important role in clustering students' responses; consequently, it has a nontrivial impact on the refinement of the items and/or their  ...  Selecting a tolerance for Dissimilarity. Figure 9 . 9 Response clustering.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/j.2333-8504.2012.tb02307.x">doi:10.1002/j.2333-8504.2012.tb02307.x</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ajhtpqyhp5abpelwhwk3i2xzzm">fatcat:ajhtpqyhp5abpelwhwk3i2xzzm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170813010604/https://www.ets.org/Media/Research/pdf/RR-12-25.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/5d/21/5d219aaa66f2cedec3594922fd092e8af95f7891.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/j.2333-8504.2012.tb02307.x"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a>

Criteria for polynomial-time (conceptual) clustering

Leonard Pitt, Robert E. Reinke
<span title="">1988</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/h4nnd7sxwzcwhetu5qkjbcdh6u" style="color: black;">Machine Learning</a> </i> &nbsp;
Research in cluster analysis has resulted in a large number of algorithms and similarity measurements for clustering scientific data.  ...  solvable by a simple and widely used clustering technique, the agglomerative-hierarchical algorithm.  ...  Acknowledgements We are grateful to the referee for two thorough reviews and for simplifying the proof of Theorem 1 while extending its scope. L.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/bf00116830">doi:10.1007/bf00116830</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/yq6srn2aevejvhvuyr6bzn45em">fatcat:yq6srn2aevejvhvuyr6bzn45em</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180727221050/https://link.springer.com/content/pdf/10.1023%2FA%3A1022825229661.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/5a/bb/5abb88836e5634164698c917a36556b571be8214.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/bf00116830"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Simultaneous Separation And Segmentation In Layered Music

Prem Seetharaman, Bryan Pardo
<span title="2016-08-07">2016</span> <i title="Zenodo"> Zenodo </i> &nbsp;
SDR SIR SAR Separation quality measure Methods for comparison For separation, we compare our approach to a separation method in [25] .  ...  We evaluate the algorithm based on separation quality, as well as segmentation accuracy.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.1417986">doi:10.5281/zenodo.1417986</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/kdkm2wm2vjgufgis5ab7urgg5a">fatcat:kdkm2wm2vjgufgis5ab7urgg5a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201225150452/https://zenodo.org/record/1417987/files/SeetharamanP16.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/64/41/6441844b02b778ceaf5d17f9e28c185926f74d2d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.1417986"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> zenodo.org </button> </a>

Efficient Selection of Unique and Popular Oligos for Large EST Databases [chapter]

Jie Zheng, Timothy J. Close, Tao Jiang, Stefano Lonardi
<span title="">2003</span> <i title="Springer Berlin Heidelberg"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2w3awgokqne6te4nvlofavy5a4" style="color: black;">Lecture Notes in Computer Science</a> </i> &nbsp;
Each of the algorithms takes only a couple of hours (on a 1.2 GHz CPU, 1 GB RAM machine) to run on a dataset 28 Mbases of barley ESTs from the HarvEST database.  ...  We present simulation results on synthetic data and a preliminary analysis of the barley EST database.  ...  The authors would like to thank Steve Wanamaker for producing the sequence assemblies and unigene datasets that were used in this work.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/3-540-44888-8_28">doi:10.1007/3-540-44888-8_28</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jee3jfxv4bfctcsbva53q52beq">fatcat:jee3jfxv4bfctcsbva53q52beq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170829154151/http://www.cs.ucr.edu/~stelo/papers/cpm03.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/be/8e/be8e712ea06d72730ff3a449711e42b0898ba5b9.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/3-540-44888-8_28"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Efficient selection of unique and popular oligos for large EST databases

J. Zheng, T. J. Close, T. Jiang, S. Lonardi
<span title="2004-04-01">2004</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a> </i> &nbsp;
Each of the algorithms takes only a couple of hours (on a 1.2 GHz CPU, 1 GB RAM machine) to run on a dataset 28 Mbases of barley ESTs from the HarvEST database.  ...  We present simulation results on synthetic data and a preliminary analysis of the barley EST database.  ...  The authors would like to thank Steve Wanamaker for producing the sequence assemblies and unigene datasets that were used in this work.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/bth210">doi:10.1093/bioinformatics/bth210</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/15059835">pmid:15059835</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/mkxvgk7tfbbjrhgg4x45r54c74">fatcat:mkxvgk7tfbbjrhgg4x45r54c74</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170829154151/http://www.cs.ucr.edu/~stelo/papers/cpm03.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/be/8e/be8e712ea06d72730ff3a449711e42b0898ba5b9.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/bth210"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

A distance measure between plant architectures

Pascal Ferraro, Christophe Godin
<span title="">2000</span> <i title="EDP Sciences"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wuinenwsbbdshheyn7pwuiwzbe" style="color: black;">Annals of Forest Science</a> </i> &nbsp;
The core of the method relies on an adaptation of an algorithm for comparing rooted tree graphs, recently proposed by Zhang in theoretical computer science.  ...  Using this algorithm a distance between two plants is defined as the cost of transforming one into the other (using basic "edit operations").  ...  Then, for each matrix, a classical clustering method [15] was applied to automatically separate the set of 10 pines into two clusters.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1051/forest:2000134">doi:10.1051/forest:2000134</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/sxuoyanapvew3bkwxrcfanlm5i">fatcat:sxuoyanapvew3bkwxrcfanlm5i</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20110523201324/http://hal.archives-ouvertes.fr/docs/00/30/66/21/PDF/view.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ef/69/ef6918116df649cbaafa84bbb36e2235ed78e96c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1051/forest:2000134"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Automating Network Protocol Identification [chapter]

Ryan Goss, Geoff Nitschke
<span title="2014-08-07">2014</span> <i title="Auerbach Publications"> Case Studies in Intelligent Computing </i> &nbsp;
This score measured how tightly grouped the members of each cluster are and was thus a measure of the success of the clustering process.  ...  For the DBSCAN method, a data set of 1421 data points with 11 dimensions (discriminators) was recorded. The DBSCAN method evaluates each data point only once for each run of the algorithm.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1201/b17333-7">doi:10.1201/b17333-7</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5dkakuylyjehppwl6dxgvxdj74">fatcat:5dkakuylyjehppwl6dxgvxdj74</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170921222039/http://pubs.cs.uct.ac.za/archive/00000975/01/Ch6_-_Automating_Network.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/49/79/4979de3c464a682934647a23d65cf114ee814681.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1201/b17333-7"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Alignment-free sequence comparison: benefits, applications, and tools

Andrzej Zielezinski, Susana Vinga, Jonas Almeida, Wojciech M. Karlowski
<span title="2017-10-03">2017</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6bzsiicmhvczjnsm7jbog7ysaa" style="color: black;">Genome Biology</a> </i> &nbsp;
The strength of these methods makes them particularly useful for next-generation sequencing data processing and analysis.  ...  We address these questions and provide a guide to the currently available alignment-free sequence analysis tools.  ...  However, Kolmogorov did not address the method to find the shortest description of a given string of characters.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13059-017-1319-7">doi:10.1186/s13059-017-1319-7</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28974235">pmid:28974235</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5627421/">pmcid:PMC5627421</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5s7yd22l7bbmpljqc7fj4cbifm">fatcat:5s7yd22l7bbmpljqc7fj4cbifm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180424063529/https://genomebiology.biomedcentral.com/track/pdf/10.1186/s13059-017-1319-7" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/5e/3b/5e3bc176613e72dac2c9665263873032e6a9bee0.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13059-017-1319-7"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5627421" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

A General Framework for Density Based Time Series Clustering Exploiting a Novel Admissible Pruning Strategy [article]

Nurjahan Begum, Liudmila Ulanova, Hoang Anh Dau, Jun Wang, Eamonn Keogh
<span title="2016-12-02">2016</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
For datasets where even this level of speedup is inadequate, we show that we can use a simple heuristic to order the unavoidable calculations in a most-useful-first ordering, thus casting the clustering  ...  This pruning strategy is admissible and gives us provably identical results to the brute force algorithm, but is at least an order of magnitude faster.  ...  (a) and (b) , there is a very wide range of choices for the values of dc, which leads to high-quality clustering.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1612.00637v1">arXiv:1612.00637v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/saz7gkro2nccnopm6aevj6m5ye">fatcat:saz7gkro2nccnopm6aevj6m5ye</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200930191645/https://arxiv.org/ftp/arxiv/papers/1612/1612.00637.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/60/e0/60e065dbb795cc0d76ec187116eb87d1f42b5485.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1612.00637v1" title="arxiv.org access"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> arxiv.org </button> </a>

A SNP Genotyping Array for Hexaploid Oat

Nicholas A. Tinker, Shiaoman Chao, Gerard R. Lazo, Rebekah E. Oliver, Yung-Fen Huang, Jesse A. Poland, Eric N. Jellen, Peter J. Maughan, Andrzej Kilian, Eric W. Jackson
<span title="">2014</span> <i title="Crop Science Society of America"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2beftrmbpbhajielvgjvw76hu4" style="color: black;">The Plant Genome</a> </i> &nbsp;
We also evaluate a new cluster-based method of calling SNPs.  ...  In addition, we report an annotation of the SNPs and the loci that they represent, we share lessons learned during the assay development, and we evaluate a new cluster-based method for calling SNP genotypes  ...  Acknowledgements We are grateful to numerous collaborators who provided useful discussion and contributed germplasm for use in developing this assay. These include:  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3835/plantgenome2014.03.0010">doi:10.3835/plantgenome2014.03.0010</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/mfzftbs32racfjnft6fzgrjlfi">fatcat:mfzftbs32racfjnft6fzgrjlfi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170808153517/https://www.crops.org/files/publications/tpg/first-look/tpg-2014-03-0010.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/65/90/6590970748c292e1583c4e529d9fb4f9af8404cf.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3835/plantgenome2014.03.0010"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a>

Improving quality and performance of schema matching in large scale

Fabien Duchateau, Zohra Bellahsene, Mathieu Roche
<span title="2008-10-31">2008</span> <i title="Lavoisier"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/quh3djrbmrd7pnzo2z2z6e5cpa" style="color: black;">Ingénierie des Systèmes d&#39;Information</a> </i> &nbsp;
In this article, we present the BMatch approach to efficiently match a large number of schemas. The quality aspect is based on the combination of terminological and contextual methods.  ...  Finally, experiments with real sets of schemas show that our approach is scalable and outperforms the most referenced matching tools both in quality of matches and performance time. RÉSUMÉ.  ...  Matching quality We present three metrics to evaluate the quality of our matching tool, namely precision, recall and F-measure, that we use to compare BMatch results with those of COMA++ and Similarity  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3166/isi.13.5.59-82">doi:10.3166/isi.13.5.59-82</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/hwli4c6l6zem5kqubnzra3w6bi">fatcat:hwli4c6l6zem5kqubnzra3w6bi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170813061000/http://liris.cnrs.fr/~fduchate/docs/papers/duchateau-isi08.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/92/5d/925dc4e8ac30d3f9256ab729c0e70afd1c50e6e2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3166/isi.13.5.59-82"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Survey of Clustering Algorithms

R. Xu, D. WunschII
<span title="">2005</span> <i title="Institute of Electrical and Electronics Engineers (IEEE)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/22mhkeaq5zdqlmtti5oidj26fi" style="color: black;">IEEE Transactions on Neural Networks</a> </i> &nbsp;
We survey clustering algorithms for data sets appearing in statistics, computer science, and machine learning, and illustrate their applications in some benchmark data sets, the traveling salesman problem  ...  Several tightly related topics, proximity measure, and cluster validation, are also discussed.  ...  ACKNOWLEDGMENT The authors would like to thank the Eisen Laboratory in Stanford University for use of their CLUSTER and TreeView software and Whitehead Institute/MIT Center for Genome Research for use  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/tnn.2005.845141">doi:10.1109/tnn.2005.845141</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/15940994">pmid:15940994</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/v5xnatqzlrhbhkm47w75jnepde">fatcat:v5xnatqzlrhbhkm47w75jnepde</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170809133609/http://www.nsu.ru/xmlui/bitstream/handle/nsu/4031/Survey_Of_Clustering_Algorithms.pdf?sequence=1" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/fe/9c/fe9cc3780abc853148fd674afabf56ea73c78ebd.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/tnn.2005.845141"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> ieee.com </button> </a>

Algorithms for Similarity Relation Learning from High Dimensional Data [chapter]

Andrzej Janusz
<span title="">2014</span> <i title="Springer Berlin Heidelberg"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2w3awgokqne6te4nvlofavy5a4" style="color: black;">Lecture Notes in Computer Science</a> </i> &nbsp;
In a more general setting, this type of quality assessment can be used to measure quality in a semantic clustering task [70] and motivates the semi-supervised clustering algorithms [4] .  ...  The second reason for using the similarity in the clustering task is related to the problem of evaluation of a clustering quality.  ...  For this reason, the quality of the models employed in the experiments was evaluated using the balanced accuracy (BAC) measure.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-642-54756-0_7">doi:10.1007/978-3-642-54756-0_7</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/yhgu7zhirjbdvgdbubbdo7hckq">fatcat:yhgu7zhirjbdvgdbubbdo7hckq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190228170608/http://pdfs.semanticscholar.org/95ab/610be21e5dedd29ce2790ec4f395ae3500a7.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/95/ab/95ab610be21e5dedd29ce2790ec4f395ae3500a7.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-642-54756-0_7"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Clustering of high throughput gene expression data

Harun Pirim, Burak Ekşioğlu, Andy D. Perkins, Çetin Yüceer
<span title="">2012</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/zfqmu5yfvjbg3f4h6f7a5j3jr4" style="color: black;">Computers &amp; Operations Research</a> </i> &nbsp;
However, this paper presents a review of the current clustering algorithms designed especially for analyzing gene expression data.  ...  Clustering is one of the methods used to gain insight into biological processes, particularly at the genomics level. Clearly, clustering can be used in many areas of biological data analysis.  ...  Knowing or predicting the number of clusters correctly for a flat clustering algorithm affects the quality of the clusters.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.cor.2012.03.008">doi:10.1016/j.cor.2012.03.008</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23144527">pmid:23144527</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3491664/">pmcid:PMC3491664</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zfc3l22vmvfvlphpqmoox5ka54">fatcat:zfc3l22vmvfvlphpqmoox5ka54</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190221213403/http://pdfs.semanticscholar.org/33fa/e16f7a656594580dba8f6b803577f16e581a.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/33/fa/33fae16f7a656594580dba8f6b803577f16e581a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.cor.2012.03.008"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3491664" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>
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