- Jul 2018
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breast-cancer-research.biomedcentral.com breast-cancer-research.biomedcentral.com
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cluster
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survival
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limma
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- Jun 2018
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www.nature.com www.nature.com
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PA (Ingenuity Systems; www.ingenuity.com)
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topGO
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WGCNA package
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Firehose (https://con-fluence.broadinstitute.org/display/GDAC/Home)
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TheCancer Genome Atlas’ (TCGA)
Tags
Annotators
URL
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- Apr 2018
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arxiv.org arxiv.org
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The architecture and the network weights are trained and opti-mized using a score-based approach
scores are derived via MMD and the gaussian kernel which is differentiable. So the loss function on our neural networks actually changes.
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Eis set to theuniform distribution on[0;1],U[0;1]
Seems like they use the uniform distribution for error terms.
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nterventions
interventions = freeze one variable and get join distribution from the rest.
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MaximumMean Discrepancy (MMD)
MMD is given as the distance metric between \(P\) and \(\hat{P}\). MMD requires a feature mapping and uses gaussian kernel here.
Here is a post on MMD: stats.stackexchange MMD
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Theideal score, to be minimized, is the distance between the jointdistributionPassociated with the ground truth FCM, andthe joint distributionbPdefined by the estimated(^G;^f;E)
Score for these models given by the distance between the true joint distribution P and \(\hat{P}\). But what is distance?
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compact suppor
A function has compact support if it is zero outside of a compact set. A subset of Euclidean space is called compact if it is closed and bounded.
Basically we're saying there are functions f_i for deriving variable X_i from their parents.
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causal Markov
all d-separations imply conditional independences in the observational distribution.
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causal sufficiency
causal sufficiency = no unobserved confounders.
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skeleton
skeleton is the undirected version of a directed graph.
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Causal generative neural networks - Use neural networks to as factors in functional causal model.
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- Mar 2018
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watermark.silverchair.com watermark.silverchair.com
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The ontologies used to annotate histopathology findings (ie, theanatomy ontology and histopathology ontology) were storedcentrally within the eTOX project using a tool calledOntoBrowser
annotations require ontologies. ontobrowser may be a good place to look.
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A massive curation effort took place to mapall verbatim terms used in reports to preferred terms from theontologies
demonstrates a need for a curation platform.
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- Jun 2015
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Local file Local file
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linkage analysis
Analysis of genetic ancestry to determine likely regions of genetic disease etiology
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- May 2015
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Local file Local file
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paper motivates the idea of michael's acceptor specific similarity map.
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