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idptools / parrot

Python package for protein sequence-based bidirectional recurrent neural network. Generalizable to a variety of protein bioinformatic applications.
MIT License
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Stats not exported by default #9

Closed BroderCodes closed 2 years ago

BroderCodes commented 2 years ago

For me, the perfomance_stats.txt file is not generated by default.

alexholehouse commented 2 years ago

Hello Dr. Schmidt!

Do you have a minimum command example (maybe with some toy data) where this doesn't work? I ask because I feel like on my system it does generate so want to figure out where this goes the wrong @degriffith do you have time to take a look at this?

degriffith commented 2 years ago

I am also not able to reproduce this issue, what version of PARROT are you using @BroderCodes ?

alexholehouse commented 2 years ago

Ohhh I wonder if this is a Windows vs. macOS/Linux issue?

BroderCodes commented 2 years ago

I've been using PARROT v1.5 on Ubuntu 20.04.4 LTS. Below info from terminal (with anonymized user name and file paths):

Input: (parrot) @.***:~/path/to/data$ parrot-train TrainingSet.tsv Model -d residues -c 6 -e 200 --stop auto --include-figs

Output: warning in stationary: failed to import cython module: falling back to numpy warning in coregionalize: failed to import cython module: falling back to numpy warning in choleskies: failed to import cython module: falling back to numpy Warning: Stop condition is set to 'auto' and num_epochs > 10. Network training may take a long time.

PARROT with user-specified parameters

Validation set loss per epoch: Epoch 0 Loss 54.1416 Epoch 5 Loss 25.6067 ...

On Mon, Jun 6, 2022 at 9:59 PM Alex Holehouse @.***> wrote:

Hello Dr. Schmidt!

Do you have a minimum command example (maybe with some toy data) where this doesn't work? I ask because I feel like on my system it does generate so want to figure out where this goes the wrong @degriffith https://github.com/degriffith do you have time to take a look at this?

— Reply to this email directly, view it on GitHub https://github.com/idptools/parrot/issues/9#issuecomment-1148196439, or unsubscribe https://github.com/notifications/unsubscribe-auth/AS7PIIQ2KWNOSTUGF6AHB4LVN3JJLANCNFSM5XZ2SBPA . You are receiving this because you authored the thread.Message ID: @.***>

alexholehouse commented 2 years ago

FWIW it only generates perfomance_stats.txt after training is fully complete (i.e. finishes and generates figures etc). I doubt this is the issue but just wanted to throw this out there!

degriffith commented 2 years ago

Ah I see, so the performance stats file functionality wasn't added until v1.6.0, and right now the current version is v1.6.2! If you update idptools-parrot using pip this should hopefully fix the issue. Let us know if for some reason it doesn't, or if updating causes any clashes with installed package versions.

BroderCodes commented 2 years ago

Yeah, it was the version difference.