mdanb

Edge attributes for BIO dataset

1

In the paper, you describe the BIO dataset as having 7 edge attributes corresponding to different interactions (coexpression, neighborhood etc...). However, when I stepped through the code, I noticed that...

Is desc applicable to bulk RNA seq?

Using GNNExplainer on my own data

4

This was previously asked but has not been addressed. Is it possible currently to run the GNNExplainer on our own data and models? If so, is it possible to get...

I'm using the following code to get a heatmap. I tried two different methods, specified in the comments in the code. The only difference between the two is that in...

Are you aware of tools that work with your model to explain its predictions?

Final layer choice to use concat instead of pooling

1

I noticed that in your implementation, you choose to concatenate node embeddings in the end before doing classification (in the logistic layer) instead of using pooling. Was wondering if you...

In your paper, you have the following diagram, which seems to suggest that ID regularization is done prior to the last layer of the decoder.  However,...

Does SAUCIE not require any normalization at all of the data (e.g TMM/RPKM/TPM etc…)? It just takes raw counts?

Applying BERMUDA to bulk RNA seq

1

I have a relatively large bulk RNA seq dataset (~ 1300 samples, from ~70 experiments) that I'd like to correct for significant batch effects. Is it valid/possible to apply BERMUDA...

Is it possible to provide the PPI network example you mention in your paper?