Batch with different rna length

[giorgiobini]

Hello,

I am wondering if you have any function to pad batches with different size.

Thank you so much in advance!

[sperfu]

Hi there,

Sorry for that, since our framework could deal with sequence with various length, so to avoid out-of-memory issue, we have limited the batch size and set it to a fixed number. Our training model uses batch size of 1 to deal with all the data. So currently we do not support function to pad batches with different sizes.

Thanks.

[sperfu]

Hi,
Regarding to your question on padding batches with different size, I'm afraid we don't have that function. The reason is that different sequence have different length(ranging from 10bp to over a thousand bp). If we pad sequence into the same length, it will inevitably bring useless information, which would deteriorate the performance. So we choose the model batch size 1 with one sequence per input to avoid padding sequence.

Thanks.