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SCNS: a graphical tool for reconstructing executable regulatory networks from single-cell genomic data

Steven Woodhouse, Nir Piterman, Christoph M. Wintersteiger, Berthold Göttgens, Jasmin Fisher
<span title="2018-05-25">2018</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/xua5vbjwszdirewaoqnikiu5zm" style="color: black;">BMC Systems Biology</a> </i> &nbsp;
In order to take advantage of this data, however, there is a need for general-purpose, user-friendly and efficient computational tools that can be readily used by biologists who do not have specialist  ...  Pseudotime-network-inference requires a-priori information about the topology of the network, which is inferred via partial correlation.  ...  Comparison to (partial) correlation networks We compared the network constructed by SCNS to the networks inferred via correlation and partial correlation, which are the standard approaches for inferring  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12918-018-0581-y">doi:10.1186/s12918-018-0581-y</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29801503">pmid:29801503</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5970485/">pmcid:PMC5970485</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/eyqjpteukngujdzcnnqjlaeiuu">fatcat:eyqjpteukngujdzcnnqjlaeiuu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180721013437/https://bmcsystbiol.biomedcentral.com/track/pdf/10.1186/s12918-018-0581-y" 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/10/b9/10b9017710cc38e8dd1707427eb63359ff9cb84f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12918-018-0581-y"> <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/PMC5970485" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Inference of Boolean Networks Using Sensitivity Regularization

Wenbin Liu, Harri Lähdesmäki, Edward R. Dougherty, Ilya Shmulevich
<span title="">2008</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/gm2h5mhstjf3tmwayeiyvkxxve" style="color: black;">EURASIP Journal on Bioinformatics and Systems Biology</a> </i> &nbsp;
Using Boolean networks, for which there are well-defined notions of ordered, critical, and chaotic dynamical regimes as well as well-studied inference procedures, we analyze the expected inference error  ...  We demonstrate that taking criticality into account via a penalty term in the inference procedure improves the accuracy of prediction both in terms of state transitions and network wiring, particularly  ...  Hence, for each selected variable set, we estimate the error of the corresponding Boolean function via the .632 bootstrap [46, 47] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1155/2008/780541">doi:10.1155/2008/780541</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18604289">pmid:18604289</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3171400/">pmcid:PMC3171400</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qbr3pkhrobhnxbahk7mv6vkkx4">fatcat:qbr3pkhrobhnxbahk7mv6vkkx4</a> </span>
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Computing Minimal Boolean Models of Gene Regulatory Networks [article]

Guy Karlebach, Peter N Robinson
<span title="2021-05-23">2021</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Methods: We present a novel methodology for integrating experimental data and performing a search for the optimal consistent structure via optimization of a linear objective function under a set of linear  ...  Properties of the inferred network show the importance of a general approach.  ...  Furthermore, the inferred logic was diverse and showed that constraints on the logic functions should be avoided.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2021.05.22.445266">doi:10.1101/2021.05.22.445266</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/42zgb5qyzrcsbkbnosbq3wkzs4">fatcat:42zgb5qyzrcsbkbnosbq3wkzs4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210716194509/https://www.biorxiv.org/content/biorxiv/early/2021/06/05/2021.05.22.445266.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/43/23/4323d9e49ad06450334e85f8dd5b8e403e48e395.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2021.05.22.445266"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

A Novel Algorithm for the Maximal Fit Problem in Boolean Networks [article]

Guy Karlebach
<span title="2016-06-20">2016</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
A GRN links the expression levels of a set of genes via regulatory controls that gene products exert on one another.  ...  In this paper we introduce a novel algorithm for this problem that makes use of sampling in order to handle large datasets.  ...  If the noise is not correlated with a specific regulation function, then as datasets become large, inferring individual network states is more difficult than inferring the types of regulatory interactions  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1505.07335v3">arXiv:1505.07335v3</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/iqobmljjmneqfknlcueuwyhsyy">fatcat:iqobmljjmneqfknlcueuwyhsyy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200929225137/https://arxiv.org/ftp/arxiv/papers/1505/1505.07335.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/5c/89/5c89f8fa0d2c42057bfd26f170fab6d799e6759c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1505.07335v3" 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 Survey of Computational Approaches to Reconstruct and Partition Biological Networks [chapter]

Lipi Acharya, Thair Judeh, Dongxiao Zhu
<span title="2012-06-21">2012</span> <i title="John Wiley &amp; Sons, Inc."> Statistical and Machine Learning Approaches for Network Analysis </i> &nbsp;
By assigning multiple Boolean functions to a node, the risk associated with an inaccurate inference of a single Boolean function from gene expression data is greatly reduced.  ...  For a directed acyclic graph, the edges of a directed k-clique always point from a node with a higher order to a node with a lower order.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/9781118346990.ch1">doi:10.1002/9781118346990.ch1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/nxykyfoherf6fpzfpwo5acyy6a">fatcat:nxykyfoherf6fpzfpwo5acyy6a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170705113639/http://www.cs.wayne.edu/dzhu/networkSurvey.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/70/4e/704e243953edd0ae18f0e0c7533425c0055697ee.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/9781118346990.ch1"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a>

Estimation of Gene Regulatory Networks

Matthew N McCall
<span title="">2013</span> <i title="Postdoc Journal"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/3xl55sfkcjgexa3vusbbouriku" style="color: black;">Postdoc Journal</a> </i> &nbsp;
A plethora of algorithms have been developed to infer network structure from experimental data.  ...  Complex gene regulatory networks, not individual genes, control cellular function. Genes and gene products act together to determine cellular phenotypes.  ...  The fundamental Boolean network inference problem is finding transition functions that explain the observed data.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27595119">pmid:27595119</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5010161/">pmcid:PMC5010161</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ikybbiruo5frbimjcbw5wihizq">fatcat:ikybbiruo5frbimjcbw5wihizq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200208100701/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC5010161&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/73/62/7362517234a7d3adde824c4a633809b3b27d6ccb.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5010161" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Estimation of Gene Regulatory Networks

Matthew N McCall
<span title="2013-01-21">2013</span> <i title="Postdoc Journal"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/3xl55sfkcjgexa3vusbbouriku" style="color: black;">Postdoc Journal</a> </i> &nbsp;
The fundamental Boolean network inference problem is finding transition functions that explain the observed data.  ...  Network Inference Many network inference algorithms function by scoring potential models and selecting models with a better score.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.14304/surya.jpr.v1n1.7">doi:10.14304/surya.jpr.v1n1.7</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/scq7ikrkjjddxctjm77ayq7dhq">fatcat:scq7ikrkjjddxctjm77ayq7dhq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170809124211/http://www.postdocjournal.com/file_journal/550_25693926.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/4b/b1/4bb17ac9a9da025aa8ce4592900d826e39b39298.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.14304/surya.jpr.v1n1.7"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Optimally designing games for behavioural research

A. N. Rafferty, M. Zaharia, T. L. Griffiths
<span title="2014-05-07">2014</span> <i title="The Royal Society"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/pgnawoixszagldk2tfhndhrgzu" style="color: black;">Proceedings of the Royal Society A</a> </i> &nbsp;
For these applications, it is often important to make inferences about the knowledge and cognitive processes of players based on their behaviour.  ...  In this framework, we use Markov decision processes to model players' actions within a game, and then make inferences about the parameters of a cognitive model from these actions.  ...  One of the goals of inferring the participants' reward functions was to determine whether using the inferred functions would lead to a correlation between expected and actual information gain.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1098/rspa.2013.0828">doi:10.1098/rspa.2013.0828</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25002821">pmid:25002821</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4032552/">pmcid:PMC4032552</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/cf2xcvfjnzhlzmw3r74zs677ci">fatcat:cf2xcvfjnzhlzmw3r74zs677ci</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170705162845/http://rspa.royalsocietypublishing.org/content/royprsa/470/2167/20130828.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/ea/3e/ea3ec1bd41a3000376ffb5cde979552d1b967ee4.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1098/rspa.2013.0828"> <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/PMC4032552" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Local cause of coherence in Boolean networks [article]

Chikoo Oosawa, Kazuhiro Takemoto, Shogo Matsumoto, Michael A. Savageau
<span title="2006-11-26">2006</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
With a large number of output connections from a hub, the effects of Boolean function on the hub are more prominent.  ...  functions for the nodes.  ...  In particular, the tendency can be seen in higher ranked hubs in both styles I and II, demonstrating that the transmission characteristic functions are useful tools to infer network dynamics.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/nlin/0611049v1">arXiv:nlin/0611049v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5sal3pqhhvglvkjqbjxlmok7j4">fatcat:5sal3pqhhvglvkjqbjxlmok7j4</a> </span>
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Deriving pairwise transfer entropy from network structure and motifs [article]

Leonardo Novelli, Fatihcan M. Atay, Jürgen Jost, Joseph T. Lizier
<span title="2019-11-07">2019</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Moreover, similar empirical results on random Boolean networks suggest that the dependence of the transfer entropy on the in-degree extends to nonlinear dynamics.  ...  As such, the effect of the clustered motifs has implications for computing the directed functional connectivity via the pairwise TE: the directed functional connectivity is better able to infer links within  ...  Now, consider the higher order cases.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1911.02931v1">arXiv:1911.02931v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/lenhastdyfhqnb3n62mp45emqe">fatcat:lenhastdyfhqnb3n62mp45emqe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200905060831/https://arxiv.org/pdf/1911.02931v1.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/db/92dbec0e9a417c0fe7d0f30b9825c2c2bbe7bb86.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1911.02931v1" 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>

Stability of Signaling Pathways during Aging—A Boolean Network Approach

Julian Schwab, Lea Siegle, Silke Kühlwein, Michael Kühl, Hans Kestler
<span title="2017-12-18">2017</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/j5h4zct24vcofi5scx6ttoapnq" style="color: black;">Biology</a> </i> &nbsp;
Boolean networks can be inferred from time-series of gene expression data.  ...  Boolean networks as models of biological pathways allow for simulation of signaling behavior.  ...  These algorithms are based on correlation [52] and Fourier transformation [53] . An algorithm to infer Boolean functions from binarized time-series data was given by Lähdismäki et al. [22] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/biology6040046">doi:10.3390/biology6040046</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29258225">pmid:29258225</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5745451/">pmcid:PMC5745451</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/novik66yibgi3bwweldlvp4dzy">fatcat:novik66yibgi3bwweldlvp4dzy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190228121953/http://pdfs.semanticscholar.org/91d9/cce1d65cd8eb2e0b86c74418ea9de321e1d2.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/91/d9/91d9cce1d65cd8eb2e0b86c74418ea9de321e1d2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/biology6040046"> <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> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5745451" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Deriving pairwise transfer entropy from network structure and motifs

Leonardo Novelli, Fatihcan M. Atay, Jürgen Jost, Joseph T. Lizier
<span title="2020-04-29">2020</span> <i title="The Royal Society"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/pgnawoixszagldk2tfhndhrgzu" style="color: black;">Proceedings of the Royal Society A</a> </i> &nbsp;
Moreover, similar empirical results on random Boolean networks suggest that the dependence of the TE on the in-degree extends to nonlinear dynamics.  ...  As such, the effect of the clustered motifs has implications for computing the directed functional connectivity via the pairwise TE: the directed functional connectivity is better able to infer links within  ...  Now, consider the higher-order cases.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1098/rspa.2019.0779">doi:10.1098/rspa.2019.0779</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32398937">pmid:32398937</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7209155/">pmcid:PMC7209155</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6a4uniwwnbbcrgrjpobtzci3g4">fatcat:6a4uniwwnbbcrgrjpobtzci3g4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210716211039/http://repository.bilkent.edu.tr/bitstream/handle/11693/75737/Deriving_pairwise_transfer_entropy_from_network_structure_and_motifs.pdf;jsessionid=10F8F1F3119C9322BAEB5C2B93B37339?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/d4/8a/d48afb2600d1cce94f2d66593a4af317108956da.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1098/rspa.2019.0779"> <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/PMC7209155" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Computational methods for discovering gene networks from expression data

W.-P. Lee, W.-S. Tzou
<span title="2009-01-01">2009</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/op7ztx4fhvairowgqifu7dnvsi" style="color: black;">Briefings in Bioinformatics</a> </i> &nbsp;
We review different kinds of computational methods biologists use to infer networks of varying levels of accuracy and complexity.  ...  The primary concern of biologists is how to translate the inferred network into hypotheses that can be tested with real-life experiments.  ...  [76] introduced a second-order coefficient, in which first-order correlation coefficients are used as descriptors for comparing two doublets (yielding a quadruplet).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bib/bbp028">doi:10.1093/bib/bbp028</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19505889">pmid:19505889</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/l4z4t4pyyjdtdbhotfpenacp3a">fatcat:l4z4t4pyyjdtdbhotfpenacp3a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190303181732/http://pdfs.semanticscholar.org/b162/fd3d4fb398f3b6417783c5cb430708a79c3b.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/b1/62/b162fd3d4fb398f3b6417783c5cb430708a79c3b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bib/bbp028"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

MaskedNet: The First Hardware Inference Engine Aiming Power Side-Channel Protection [article]

Anuj Dubey, Rosario Cammarota, Aydin Aysu
<span title="2019-12-02">2019</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
First, it shows DPA attacks during inference to extract the secret model parameters such as weights and biases of a neural network.  ...  The resulting design uses novel masked components such as masked adder trees for fully-connected layers and masked Rectifier Linear Units for activation functions.  ...  Our implementation is designed to be first-order secure but can likewise be extended for higher order attacks.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1910.13063v3">arXiv:1910.13063v3</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/iand6q5qb5g2lpgtbsh6bnlmfy">fatcat:iand6q5qb5g2lpgtbsh6bnlmfy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200829151252/https://arxiv.org/pdf/1910.13063v3.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/68/54/6854c4c8dfca1de802f2662db62deb7ba2bc10b2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1910.13063v3" 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>

Detection of Node Failure Localization in Communication Networks

Nidhi Shekhawat, Shanil Panchamia, Ushasukhanya S
<span title="2018-07-20">2018</span> <i title="Science Publishing Corporation"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/piy2nrvrjrfcfoz5nmre6zwa4i" style="color: black;">International Journal of Engineering &amp; Technology</a> </i> &nbsp;
Here both the methods in 1) and 2) can be transformed into the functions of a per-node property, which can be computed resourcefully based on the above satisfactory/compulsory conditions.  ...  Range Tomography efforts to unite the higher resolution of Analogue tomography with the expediency of Boolean tomography.  ...  The paper offered an algorithm that solves this problem precisely under weaker hypothesis than those mandatory by Boolean Inference and more demanding network circumstances (sparse topologies, link correlations  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.14419/ijet.v7i3.12.17778">doi:10.14419/ijet.v7i3.12.17778</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/kdmlfo6ejnculez7hcol5lm4q4">fatcat:kdmlfo6ejnculez7hcol5lm4q4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200215022819/https://www.sciencepubco.com/index.php/ijet/article/download/17778/7866" 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/6f/15/6f15d12f1c30c0b74e29f0ee4341bd19d16b41e4.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.14419/ijet.v7i3.12.17778"> <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>
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