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Directed acyclic graph kernels for structural RNA analysis

Kengo Sato, Toutai Mituyama, Kiyoshi Asai, Yasubumi Sakakibara
<span title="">2008</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
Results: We have developed a new technique based on directed acyclic graphs (DAGs) derived from base-pairing probability matrices of RNA sequences that significantly increases the computation speed of  ...  Conclusion: Stem kernels can be utilized as a reliable similarity measure of structural RNAs, and can be used in various kernel-based applications.  ...  Acknowledgements This work was supported in part by a grant from "Functional RNA Project" funded by the New Energy and Industrial Technology Development Organization (NEDO) of Japan, and was also supported  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-9-318">doi:10.1186/1471-2105-9-318</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18647390">pmid:18647390</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2515856/">pmcid:PMC2515856</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/d6zjro22q5aevmtoauqczq27uu">fatcat:d6zjro22q5aevmtoauqczq27uu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170830113643/https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-9-318?site=http://bmcbioinformatics.biomedcentral.com" 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/dd/fa/ddfa10664bc1f8fd40bf558bf7ea640c8dde27c4.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-9-318"> <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/PMC2515856" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Graph Classification [chapter]

Koji Tsuda, Hiroto Saigo
<span title="">2010</span> <i title="Springer US"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/z6l23qz6lbahndyc65abg7sqju" style="color: black;">Managing and Mining Graph Data</a> </i> &nbsp;
In particular, we focus on two representative methods, graph kernels and graph boosting, and we present other methods in relation to the two methods.  ...  In drug discovery applications, for example, a graph and its target value correspond to a chemical compound and its chemical activity.  ...  Acyclic Graphs. Let us first consider the case of acyclic graphs. In an acyclic graph, if there is a directed path from vertex 1 to 2 , then there is no directed path from vertex 2 to 1 .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-1-4419-6045-0_11">doi:10.1007/978-1-4419-6045-0_11</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/series/ads/TsudaS10.html">dblp:series/ads/TsudaS10</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7qyefise4fb2dbo7lpkymhgufq">fatcat:7qyefise4fb2dbo7lpkymhgufq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190303104934/http://pdfs.semanticscholar.org/b430/6178fb343b4c6e66e64d101606b04f4b5a22.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/b4/30/b4306178fb343b4c6e66e64d101606b04f4b5a22.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-1-4419-6045-0_11"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Kernel approaches for genic interaction extraction

S. Kim, J. Yoon, J. Yang
<span title="2007-11-14">2007</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;
For this purpose, we view the dependency structure of a sentence as a graph, which allows the system to deal with an essential one from the complex syntactic structure by finding the shortest path between  ...  We suggest four kernels: predicate, walk, dependency and hybrid kernels to adequately encapsulate information required for a relation prediction based on the sentential structures involved in two entities  ...  Thus, we allow edges of the Directed Acyclic Graph (DAG) to be traversed in any direction when finding the path, so for each original dependent-head edge labeled with an 'UP' direction, we add the corresponding  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btm544">doi:10.1093/bioinformatics/btm544</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18003645">pmid:18003645</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/p56wbgkrajbpbnq2fxzhdf7yle">fatcat:p56wbgkrajbpbnq2fxzhdf7yle</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170810095000/http://mllab.sogang.ac.kr/publications/bioinformatics-2008-vol24-no1-pp118-126.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/e6/a7/e6a7695ad378a24c8574a89e6020cc06c34a3d1a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btm544"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

Predicting activities without computing descriptors: graph machines for QSAR§

A. Goulon, T. Picot, A. Duprat, G. Dreyfus
<span title="">2007</span> <i title="Informa UK Limited"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/7ukqzi3azffcjjyhjno5nksl2e" style="color: black;">SAR and QSAR in environmental research (Print)</a> </i> &nbsp;
For each example of the data set, a mathematical function (graph machine) is built, whose structure reflects the structure of the molecule under consideration; it is the combination of identical parameterized  ...  In that approach, which is similar in spirit to recursive networks, molecules are considered as structured data, represented as graphs.  ...  Acyclic graphs For each acyclic graph G i of G, a function g i ! n ! !  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1080/10629360601054313">doi:10.1080/10629360601054313</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/17365965">pmid:17365965</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/53gdkwazrvexvdmryckpgpzhkm">fatcat:53gdkwazrvexvdmryckpgpzhkm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20061125034243/http://www.neurones.espci.fr/Articles_PS/SAR%26QSAR.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/3a/93/3a9364c6037a3b8f9a7531cf88a7324cb2d48687.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1080/10629360601054313"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> tandfonline.com </button> </a>

An Introduction to Recursive Neural Networks and Kernel Methods for Cheminformatics

Alessio Micheli, Alessandro Sperduti, Antonina Starita
<span title="2007-05-01">2007</span> <i title="Bentham Science Publishers Ltd."> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/xtiwjcbzsbd35jtqmz56mrpmb4" style="color: black;">Current pharmaceutical design</a> </i> &nbsp;
The aim of this paper is to introduce the reader to new developments in Neural Networks and Kernel Machines concerning the treatment of structured domains.  ...  Specifically, we discuss the research on these relatively new models to introduce a novel and more general approach to QSPR/QSAR analysis.  ...  Section 4), directed acyclic graphs and directed positional acyclic graphs (DPAG), directed cyclic graphs, undirected graphs (see Fig. (3) ).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2174/138161207780765981">doi:10.2174/138161207780765981</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/17504168">pmid:17504168</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/melxr62d6fhl5p23ki6faztitm">fatcat:melxr62d6fhl5p23ki6faztitm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20080222001716/http://www.math.unipd.it/~sperduti/PAPERI/micheli-sperduti-starita2.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/7d/11/7d119dc0690f9cd554b272fbb412a4e57cffb9d7.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2174/138161207780765981"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

A Survey of Graph Mining Techniques for Biological Datasets [chapter]

S. Parthasarathy, S. Tatikonda, D. Ucar
<span title="">2010</span> <i title="Springer US"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/z6l23qz6lbahndyc65abg7sqju" style="color: black;">Managing and Mining Graph Data</a> </i> &nbsp;
We conclude this article with a discussion of the key results and identify some interesting directions for future research.  ...  Examples abound ranging from the analysis of protein interaction networks to the analysis of phylogenetic data.  ...  , genetics, chemical structure analysis, and Glycan structure analysis.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-1-4419-6045-0_18">doi:10.1007/978-1-4419-6045-0_18</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/series/ads/ParthasarathyTU10.html">dblp:series/ads/ParthasarathyTU10</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/aeu53r3dbzd67d5whkjypv64uq">fatcat:aeu53r3dbzd67d5whkjypv64uq</a> </span>
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Sequencing Platform Modeling and Analysis

Li-Xuan Qin, Yen-Tsung Huang
<span title="">2015</span> <i title="SAGE Publications"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/arhjbkogknfc5m4fvcz76b7r6m" style="color: black;">Cancer Informatics</a> </i> &nbsp;
Their method represented the causal structure by directed acyclic graphs and constructed genespecific network modules to constitute a gene and its corresponding regulators; the method then correlated each  ...  . • RNA Expression Level: Identification of molecular signatures is an important aspect of the analysis of RNA expression data.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4137/cin.s24698">doi:10.4137/cin.s24698</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25780336">pmid:25780336</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4348078/">pmcid:PMC4348078</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5c7byvxfcne5np5htrixmcnvhm">fatcat:5c7byvxfcne5np5htrixmcnvhm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180720144035/http://insights.sagepub.com/redirect_file.php?fileId=6296&amp;filename=4697-CIN-Introductory-Editorial:-Sequencing-Platform-Modeling-and-Analysis.pdf&amp;fileType=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/c6/3a/c63a482f14331597451e8a7b5bb235f53332fa89.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4137/cin.s24698"> <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> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4348078" 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 novel Bayesian network inference algorithm for integrative analysis of heterogeneous deep sequencing data

Yi Liu, Nan Qiao, Shanshan Zhu, Ming Su, Na Sun, Jerome Boyd-Kirkup, Jing-Dong J Han
<span title="2013-01-15">2013</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/dtytuhrzcbdsbixdngpw3dnxfy" style="color: black;">Cell Research</a> </i> &nbsp;
To relax the acyclic constraint, we developed a post-BN learning graph search method, which successfully recovered some known interactions otherwise missed (Supplementary information, Methods S1, Notes  ...  two other ways to define the kernel for tag distributions.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/cr.2013.8">doi:10.1038/cr.2013.8</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23318583">pmid:23318583</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3587713/">pmcid:PMC3587713</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2foetppfe5g5pfib3arplqaiaa">fatcat:2foetppfe5g5pfib3arplqaiaa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170809080354/http://www.picb.ac.cn/hanlab/paper/yiliu.CR.2013.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/3a/0c/3a0c377a0181732a3dcfd1bd49665bff957f3f62.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/cr.2013.8"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3587713" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

On the Complexity of Sequence to Graph Alignment [article]

Chirag Jain, Haowen Zhang, Yu Gao, Srinivas Aluru
<span title="2019-01-17">2019</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
models for alphabets of size ≥ 2.  ...  In this paper, we study sequence to graph alignment problems under Hamming and edit distance models, and linear and affine gap penalty functions, for multiple variants of the problem that allow changes  ...  However, formulating the sequence to graph alignment problem as a dynamic programming recursion, while easy for directed acyclic graphs through the use of topological ordering, is difficult for general  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/522912">doi:10.1101/522912</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2avas7kkonbibmgjmjysko6aiq">fatcat:2avas7kkonbibmgjmjysko6aiq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190501145917/https://www.biorxiv.org/content/biorxiv/early/2019/01/17/522912.full.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/8c/d6/8cd6dfc1436d20ffad57e72f541cadf14d3bdc20.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/522912"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Revealing post-transcriptional microRNA–mRNA regulations in Alzheimer's disease through ensemble graphs

Rubén Armañanzas
<span title="">2018</span> <i title="Springer Nature America, Inc"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4srzxifvfrdlhjhg3dimznkp7m" style="color: black;">BMC Genomics</a> </i> &nbsp;
We present here a novel method for the network analysis of messenger RNA post-translational regulation by microRNA molecules.  ...  Furthermore, additional network structures suggest previously unreported regulations in the state of the art of Alzheimer's research.  ...  In order to build a directed acyclic graph for the network classifier, the following iterative procedure was followed: i) in an empty graph add all the nodes connected by the first t number of edges in  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12864-018-5025-y">doi:10.1186/s12864-018-5025-y</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jknhm6hjpncxtlg55hctu2et5a">fatcat:jknhm6hjpncxtlg55hctu2et5a</a> </span>
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Inferring Disease-Associated Piwi-Interacting RNAs via Graph Attention Networks [article]

Kai Zheng, Zhu-Hong You, lei wang, Leon Wong, Zhan-Heng Chen, Han-Jing Jiang
<span title="2020-01-09">2020</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
In particular, we introduced the attention-based Graph Neural Networks to the field of bio-association prediction for the first time, and proposed an abstract network topology suitable for small samples  ...  However, in the real world, the network of interactions between molecules is enormously intricate and noisy, which poses a problem for efficient graph mining.  ...  ACKNOWLEDGEMENTS We thank anonymous reviewers for very valuable suggestions.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.01.08.898155">doi:10.1101/2020.01.08.898155</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/q7vs3qbimfgvpljcpmimabusiy">fatcat:q7vs3qbimfgvpljcpmimabusiy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200324103915/https://www.biorxiv.org/content/biorxiv/early/2020/01/09/2020.01.08.898155.full.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/19/c9/19c91568828c59f45695b9bd09be0098a0c92ede.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.01.08.898155"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Page 2489 of Mathematical Reviews Vol. , Issue 95d [page]

<span title="">1995</span> <i title="American Mathematical Society"> <a target="_blank" rel="noopener" href="https://archive.org/details/pub_mathematical-reviews" style="color: black;">Mathematical Reviews </a> </i> &nbsp;
The kernel of that representation is a minimal directed acyclic graph (DAG) containing all suboptimal alignments.  ...  This paper provides a computational underpinning for such iterative noise filtration in alignment graphs.  ... 
<span class="external-identifiers"> </span>
<a target="_blank" rel="noopener" href="https://archive.org/details/sim_mathematical-reviews_1995-04_95d/page/2489" title="read fulltext microfilm" 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> Archive [Microfilm] <div class="menu fulltext-thumbnail"> <img src="https://archive.org/serve/sim_mathematical-reviews_1995-04_95d/__ia_thumb.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a>

Gradient-based optimization of hyperparameters for base-pairing profile local alignment kernels

Kengo Sato, Yutaka Saito, Yasubumi Sakakibara
<span title="">2009</span> <i title="Universal Academy Press Inc"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/jf2bmhtlzjh4zjrkh3rivxd2sq" style="color: black;">Genome Informatics Series</a> </i> &nbsp;
We have recently proposed novel kernel functions, called base-pairing profile local alignment (BPLA) kernels for discrimination and detection of functional RNA sequences using SVMs.  ...  We employ STRAL's scoring function which takes into account sequence similarities as well as upstream and downstream base-pairing probabilities, which enables us to model secondary structures of RNA sequences  ...  We thank our colleagues BPLA Kernels 137 from the RNA Informatics Team at the Computational Biology Research Center (CBRC) for fruitful discussions.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20180268">pmid:20180268</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6mnro4t5djcb7c4gqpgudjz3pa">fatcat:6mnro4t5djcb7c4gqpgudjz3pa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20160703043234/http://www.jsbi.org/pdfs/journal1/GIW09/GIW09012.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/54/b1/54b1abae8dae0a156071c110accd884819de1ad7.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a>

miTarget: microRNA target gene prediction using a support vector machine

Sung-Kyu Kim, Jin-Wu Nam, Je-Keun Rhee, Wha-Jin Lee, Byoung-Tak Zhang
<span title="2006-09-18">2006</span> <i title="Springer (Biomed Central Ltd.)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
It uses a radial basis function kernel as a similarity measure for SVM features, categorized by structural, thermodynamic, and position-based features.  ...  MicroRNAs (miRNAs) are small noncoding RNAs, which play significant roles as posttranscriptional regulators.  ...  DAG, directed acyclic graph. (page number not for citation purposes)  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-7-411">doi:10.1186/1471-2105-7-411</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/16978421">pmid:16978421</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC1594580/">pmcid:PMC1594580</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fbk34qt5frfrdkeygwltpxfqvy">fatcat:fbk34qt5frfrdkeygwltpxfqvy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190427001640/https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-7-411" 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/b5/e3/b5e3290f314c964e64a99addd876288b74d32ede.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-7-411"> <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/PMC1594580" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The Image Segmentation Based On K-Means With MAP

Bhavana R Maale
<span title="2020-07-25">2020</span> <i title="The World Academy of Research in Science and Engineering"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/aib7mcm6ancujcehv2hnowlqi4" style="color: black;">International Journal of Networks and Systems</a> </i> &nbsp;
So the future work can be the development of a Maximum Posterior (MAP) estimation for graph generation that optimizes the graph structure jointly with label inference.  ...  problem has proven non-trivial, however, and it involves the object of multi-class image partition tasks that are difficult due to the high similarity of objects from various groups and irregularly found structures  ...  Extension of this forward-backward algorithm, known as the propagation of beliefs, resulted in exact solutions for two major types of Directed Acyclic Graphs (DAG): Trees and Ploy.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.30534/ijns/2020/01942020">doi:10.30534/ijns/2020/01942020</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/kzwjazkigjcfbivj5owffkwdeq">fatcat:kzwjazkigjcfbivj5owffkwdeq</a> </span>
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