oluwadarelab / hic-gnn Goto Github PK

Hi,

I'm very interested in your tool.
But I work on the plants and wonder if this tool can work on the plants. Or do I need to train this tool with plant data?

Best,
Han

Hello Dr.Van:
I am a university student, being major in clinical medicine, from SZU in CN.
Firstly, I appreciate your work, bringing such an amazing job to the world. HiC-GNN brings me to a new aspect to understand What GNN can do, and how to improve my work, in which I intend to use GCNN to solve a bioproblem.
Secondly, Some confuse met while Reading Paper:
1. If redundancy nodes in the procedure--Binning Proceduing affects the Feature embedding(or representation) using LINE. (Or Ask Although the adjance node the be the node duplication. why redundancy nodes didn't not affect the embedding?)
2. How to deal with the different result of redundancy nodes predicted by the model? Make average?
3. Is 'Generalization' proceduing the work that minimize the ||oA-b||F and the target parameter is the Model? (Actually I didn't understand what T means.)

Thanks for your Time!!!

Hello, @OluwadareLab

I am interested in applying HiC-GNN to our HiC data.

Could you explain more about the requirement of input files to HiC-GNN_main.py? Does the input matrix need normalization or not?
If I extract input matrix of contact map from .hic files generated by Juicer using juicer_tools dump, should I use "juicer_tools dump observed NONE xxxxxxxx.hic ..." (without normalization)? Or I need choose a normalization method from "VC/VC_SQRT/KR"

Thanks so much for your helps!

Hi there,

I was trying to run the HiC-GNN_main.py in my server and I got this error message:

(jiale) msbb@msbb-System-Product-Name:~/jiale/tools/HiC-GNN$ python HiC-GNN_main.py
Traceback (most recent call last):
  File "/home/msbb/jiale/tools/HiC-GNN/HiC-GNN_main.py", line 2, in <module>
    from ge import LINE
ImportError: cannot import name 'LINE' from 'ge' (/home/msbb/anaconda3/envs/jiale/lib/python3.12/site-packages/ge/__init__.py)

Do you have any ideas about what should I do now?

Best
Jiale

Hi,

thanks for this tool!
Could you please list the requirements that I need to install? I installed so far numpy and ge, but I'm getting an error because of the line from ge import LINE:

$ python3 HiC-GNN_main.py
Traceback (most recent call last):
  File "/scratch/gnn/HiC-GNN/HiC-GNN_main.py", line 2, in <module>
    from ge import LINE
ImportError: cannot import name 'LINE' from 'ge' (/scratch/gnn/conda_gnn/lib/python3.11/site-packages/ge/__init__.py)

Also, what other modules do I need to install?