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I attempted to reproduce your results on the bpRNA dataset by following the instructions in the README file.
However I got results that are different than the published ones.
# My Results
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Hello,
I am wondering if the training datasets used in the publication (RNAStralign, TR0, and fine-tuning dataset for bpRNA-new) are available? I was able to find the evaluation datasets from Googl…
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1. As a next step for this project, Marc should try to retrain the MXfold2 PyTorch models to see if the retrained model can reproduce the performance using the same neural network architecture and par…
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Hi Dear developer,
I got an error when procesing training data with TR0 data provided by MXfold2
$ python process_data_newdataset.py TR0
Traceback (most recent call last):
File "process_data_n…
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Sorry for the delays!
[scores.zip](https://github.com/kad-ecoli/rna3db/files/5469708/scores.zip)
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I have tested e2efold on a set of 361 PDB chains, where secondary structures for RNAs shorter than 600 nucleotides are predicted by ``e2efold_productive/e2efold_productive_short.py``, while those lon…
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Hi, first of all, thank you very much for publishing this code!
I have a question about the fine tuned secondary structure prediction.
The predict_ss_rna.py script demonstrates how to use the fine t…
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[1] As we discussed today, it is not correct to combine all three subsets of SPOT-RNA PDB dataset into one single set. Instead, you should train on the training set (TR1), validate hyperparameters (e.…
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thank your great job, I want to know what datasets you used for RNA-FM-ResNet_bpRNA.pth and RNA-FM-ResNet_RNAStralign.pth respectively. I guess you use the TR0 training set to obtain RNA-FM-ResNet_bpR…
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Hello. From the source code, I think the original dataset you use as the input for process_data_newdataset.py is different from that used in e2efold with ct format(https://drive.google.com/open?id=19…