User: arronar
arronar • 150
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Posts by arronar
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... I see... Sorry for letting this misconception. ...
written 6 months ago by
arronar • 150
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... What kind of inspection? Are you looking for graphs with a specific number of expanded nodes or anything different? ...
written 6 months ago by
arronar • 150
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... > One way of approaching the problem of finding a threshold
> automatically could be to find the edges that if removed would
> disconnect the graph (they are called bridges and I think there's an
> algorithm for finding them).
Isn't what the fourth paragraph is talking about? Also based ...
written 6 months ago by
arronar • 150
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... I don't think that the 4th paragraph is referring to thresholding the adjacency matrix. As I understood they propose to apply the threshold to the edge relevance scores. I have already implemented the k-walk algorithm and the results I got are in the form of the dataframe described in the OP. So now ...
written 6 months ago by
arronar • 150
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... Thank you for your answer but it confused me a little bit. Why did you choose as initial nodes the A,B and C? For some reason, you chose the induced network to be constructed by those nodes. As I understood from the literature,the induced graph should be the result of the whole process. Why choose o ...
written 6 months ago by
arronar • 150
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... Hi.
Given a matrix that describes the edges' and their weights of a connected graph (see below) I want to extract a subgraph based on a threshold value **x** for the edges' weights. In literature, I read that one can search for the **maximal x**, such that the induced subgraph is connected. Since ...
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... I'm keeping the ones with accuracy >65% and then the best one of them. I'm doing CV 50 times because I realized that each time, models have different accuracy. E.g the first could have 34% accuracy while the second 72%. If I don't use CV will the algorithm keep the best one? ...
written 10 months ago by
arronar • 150
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... Hi.
I'm trying to apply, random forest algorithm onto microarray results in order to get a list with the most significant predictors. So far I was executing the following pipeline.
buildForest <- function (RF.data, storeDir)
{
acc = numeric()
for(i in 1:50){
...
written 10 months ago by
arronar • 150
• updated
10 months ago by
Jean-Karim Heriche ♦ 17k
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... Oh. my god. row.names are in lowercase while the gene-sets in uppercase. That is the cause of the problem. ...
written 10 months ago by
arronar • 150
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... `> GSC.C2.msigdb` returns :
First 50 (out of 4738) gene set names:
[1] "KEGG_GLYCOLYSIS..." "KEGG_CITRATE_CY..." "KEGG_PENTOSE_PH..." "KEGG_PENTOSE_AN..." "KEGG_FRUCTOSE_A..."
[6] "KEGG_GALACTOSE_..." "KEGG_ASCORBATE_..." "KEGG_FATTY_ACID..." "KEGG_STEROID_BI..." "KEGG_PRIMARY_BI.. ...
written 10 months ago by
arronar • 150
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