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Application of Breiman's Random Forest to Modeling Structure-Activity Relationships of Pharmaceutical Molecules [chapter]

Vladimir Svetnik, Andy Liaw, Christopher Tong, Ting Wang
<span title="">2004</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;
Leo Breiman's Random Forest ensemble learning procedure is applied to the problem of Quantitative Structure-Activity Relationship (QSAR) modeling for pharmaceutical molecules.  ...  This entails using a quantitative description of a compound's molecular structure to predict that compound's biological activity as measured in an in vitro assay.  ...  This problem is an example of Quantitative Structure-Activity Relationship (QSAR) modeling [Eki00,Haw01].  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-540-25966-4_33">doi:10.1007/978-3-540-25966-4_33</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/rbzukbezzbfctivz2byxhp3sx4">fatcat:rbzukbezzbfctivz2byxhp3sx4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190225202607/http://pdfs.semanticscholar.org/73e0/b40b19e485292903d246a9af17e17426913f.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/73/e0/73e0b40b19e485292903d246a9af17e17426913f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-540-25966-4_33"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Data Mining Classification Methods Applied In Drug Design

Mária Stachová, Lukáš Sobíšek
<span title="2012-08-21">2012</span> <i title="Zenodo"> Zenodo </i> &nbsp;
Those models were applied to predict the biological activity of molecules, potential new drug candidates.  ...  For this purpose logistic regression, Bayesian logistic regression and random forest models were built using R software. TheBayesian logistic regression in Latent GOLD software was created as well.  ...  We thank Andrej Boháč for providing us the training set of molecules and we also thank Marek Skoršepa for scoring our selected molecules.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.1329401">doi:10.5281/zenodo.1329401</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fyhlrybebbddpd3jy6rlq5rozm">fatcat:fyhlrybebbddpd3jy6rlq5rozm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201228191744/https://zenodo.org/record/1329402/files/963.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/e2/05/e2059ddb7389cf09523135807bb8a69214576c9e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.1329401"> <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>

Comparative Study of Classification Algorithms Using Molecular Descriptors in Toxicological DataBases [chapter]

Max Pereira, Vítor Santos Costa, Rui Camacho, Nuno A. Fonseca, Carlos Simões, Rui M. M. Brito
<span title="">2009</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;
Despite the accumulated knowledge by pharmaceutical companies that continually improve the process of finding new drugs, a myriad of factors affect the activity of putative candidate molecules in vivo  ...  Typically, it starts by screening databases of small organic molecules for chemical structures with potential of binding to a target receptor and prioritizing the most promising ones.  ...  We used Breiman's"random forests" as a popular methods that benefits from some of the understandability of trees and has been shown to achieve quite good accuracies.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-642-03223-3_11">doi:10.1007/978-3-642-03223-3_11</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ca6duj4zqjcdngw7bta6ag2kxy">fatcat:ca6duj4zqjcdngw7bta6ag2kxy</a> </span>
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Small Random Forest Models for Effective Chemogenomic Active Learning

Christin Rakers, Daniel Reker, J.B. Brown
<span title="">2017</span> <i title="Division of Chemical Information and Computer Sciences"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/na7s6vrtjvdyzhomacc44iqmiy" style="color: black;">Journal of Computer Aided Chemistry</a> </i> &nbsp;
Prediction models were actively trained based on random forest classification using 500 decision trees per experiment.  ...  In a new direction for chemogenomic active learning, we address the question of how forest size influences model evolution and performance.  ...  (to J.B.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2751/jcac.18.124">doi:10.2751/jcac.18.124</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/z4onn42nh5ahnay7232yfswwo4">fatcat:z4onn42nh5ahnay7232yfswwo4</a> </span>
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Random forests for verbal autopsy analysis: multisite validation study using clinical diagnostic gold standards

Abraham D Flaxman, Alireza Vahdatpour, Sean Green, Spencer L James, Christopher JL Murray
<span title="2011-08-04">2011</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/fojkordzabcylidoghjut5yuq4" style="color: black;">Population Health Metrics</a> </i> &nbsp;
Methods: The Random Forest (RF) Method from machine learning (ML) was adapted to predict cause of death by training random forests to distinguish between each pair of causes, and then combining the results  ...  We also compared the quality of RF to PCVA for all of these metrics. We performed this analysis separately for adult, child, and neonatal VAs.  ...  Examples of using ML techniques in various domains include gene selection and classification of microarray data [6] , modeling structural activity of pharmaceutical molecules [7] , and protein interaction  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1478-7954-9-29">doi:10.1186/1478-7954-9-29</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21816105">pmid:21816105</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3160922/">pmcid:PMC3160922</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vo4j3bvsxrcizm5kqb5jdqt73e">fatcat:vo4j3bvsxrcizm5kqb5jdqt73e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170810065954/https://profiles.uonbi.ac.ke/odundo_paul/files/random_forests_for_verbal_autopsy_analysis_population_health_metrics_0811.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/a9/efa9cc6f43a0c00f4f947cb9927c4f7b5f16c1dd.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1478-7954-9-29"> <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/PMC3160922" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Machine Learning-based Virtual Screening and Its Applications to Alzheimer's Drug Discovery: A Review

Kristy A Carpenter, Xudong Huang
<span title="2018-06-07">2018</span> <i title="Bentham Science"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/xtiwjcbzsbd35jtqmz56mrpmb4" style="color: black;">Current pharmaceutical design</a> </i> &nbsp;
Machines (SVM), Random Forests (RF), and Artificial Neural Networks (ANN).  ...  After training the model, it is validated and, if sufficiently accurate, used on previously unseen databases to screen for novel compounds with desired drug target binding activity.  ...  ACKNOWLEDGEMENTS This work was partially funded by a NIH grant R01AG056614 (to XH). The authors would like to thank the MIT externship program for allowing KAC to be a student intern at MGH.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2174/1381612824666180607124038">doi:10.2174/1381612824666180607124038</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29879881">pmid:29879881</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6327115/">pmcid:PMC6327115</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/kvowpmifvjhpblsqbgkquamwmi">fatcat:kvowpmifvjhpblsqbgkquamwmi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200513132853/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC6327115&amp;blobtype=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/fd/2f/fd2fa2b57511069e05573be448cd93af256656e2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2174/1381612824666180607124038"> <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/PMC6327115" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Building blocks for automated elucidation of metabolites: Machine learning methods for NMR prediction

Stefan Kuhn, Bjorn Egert, Steffen Neumann, Christoph Steinbeck
<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;
Random forest, J48 decision tree and support vector machines achieved similar overall errors.  ...  Computer-Assisted Structure Elucidation (CASE) of biological metabolites will be an important tool to leverage this lack of knowledge.  ...  Thanks to all NMRShiftDB contributors for their contributions of data to NMR-ShiftDB.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-9-400">doi:10.1186/1471-2105-9-400</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18817546">pmid:18817546</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2605476/">pmcid:PMC2605476</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/r7koygbn2bccfmpqmbatkkdimu">fatcat:r7koygbn2bccfmpqmbatkkdimu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170830084803/https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-9-400?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/c6/14/c61450ab3ce2474def6ed3f92f2824cb82f9633f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-9-400"> <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/PMC2605476" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Innovativeness, Work Flexibility, and Place Characteristics: A Spatial Econometric and Machine Learning Approach

Mehmet Güney Celbiş, Pui-Hang Wong, Karima Kourtit, Peter Nijkamp
<span title="2021-12-03">2021</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/oglosmy3gbhuzobyjit4qalakq" style="color: black;">Sustainability</a> </i> &nbsp;
In particular, through a spatial econometric model, we identified an optimum level for weekly work time of about 36 h, which is supported by our findings from tree-based ensemble models.  ...  Our study confirms that individual freedom in the work place, flexible work hours, job security, living in suburban areas, low stress, private business activity, and the ability to take free time off work  ...  Application of Breiman’s Random Forest to modeling structure-activity relationships of pharmaceutical molecules.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/su132313426">doi:10.3390/su132313426</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/l3st2dvsjnftjecat3thwndmbi">fatcat:l3st2dvsjnftjecat3thwndmbi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20211208170737/https://mdpi-res.com/d_attachment/sustainability/sustainability-13-13426/article_deploy/sustainability-13-13426-v2.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/3e/28/3e28740398c00919990af0245f04db5db98d3092.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/su132313426"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> mdpi.com </button> </a>

Automatic feature subset selection for decision tree-based ensemble methods in the prediction of bioactivity

Dong-Sheng Cao, Qing-Song Xu, Yi-Zeng Liang, Xian Chen, Hong-Dong Li
<span title="">2010</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/rmiisgaqtnemzkay2alvut2g5q" style="color: black;">Chemometrics and Intelligent Laboratory Systems</a> </i> &nbsp;
In the structure-activity relationship (SAR) study, a learning algorithm is usually faced with the problem of selecting a compact subset of descriptors related to the property of interest, while ignoring  ...  Six real SAR datasets related to different categorical bioactivities of compounds are used to evaluate the proposed method.  ...  Acknowledgements We also would like to thank the reviewers for their useful discussions, comments and suggestions throughout this entire work.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.chemolab.2010.06.008">doi:10.1016/j.chemolab.2010.06.008</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/pijj6hcn2rfyfgf5ajtjszexmm">fatcat:pijj6hcn2rfyfgf5ajtjszexmm</a> </span>
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Similarity based classification studies for prediction of ABCB1 (P-glycoprotein) substrates and non-substrates

Rita Schwaha
<span title="">2013</span> <span class="release-stage">unpublished</span>
To further explore the concept of shape similarity the parameters derived from the program ROCS of Openeye via shape overlay between two molecules were also used as descriptors.  ...  The first three reference sets are based on Tudor Oprea's chemography idea of satellite structures on the fringes of the chemical space.  ...  similar activity profiles is as old as the idea of quantitative structure activity relationships itself.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.25365/thesis.29514">doi:10.25365/thesis.29514</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/cxqw6gxmu5entlg2audf75355e">fatcat:cxqw6gxmu5entlg2audf75355e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200221000838/http://othes.univie.ac.at/29514/1/2013-05-25_9815835.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/9b/92/9b92e5e617aa2fcda4c7d8e78177922193a40767.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.25365/thesis.29514"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>