Input-Output Dimension

[ekokrek]

Hello,

I tried to predict high resolution matrix using the processed file that you share.

My assumptions were:

• This file contains raw low resolution matrix (downsampling ratio: 1/16)
• It is the downsampled version of GM12878 primary or replicate intrachromosomal contacts.

I placed the above file into the specified directory. Then choosing the 1/16 model parameters, I ran the following code.

python data_predict.py -lr 40kb -ckpt save/deephic_raw_16.pth -c GM12878

The chromosome I am interested in is 12. The size of this chromosome is 133851895 bases; so when it is binned at 10kb, one should have 13,386 bins. However, the predicted chromosome 12 matrix has dimensions of 13,398 x 13,398. When I checked the input file, I've seen that 'sizes' key in the dictionary holds this same value of 13398 for chromosome 12. That discrepancy occurs in other chromosomes too.

So the question is: How are these shapes/sizes are calculated?

Thanks in advance!