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Fiora is an in silico fragmentation algorithm for small compounds and produces simulated tandem mass spectra (MS/MS). The framework uses a graph neural network as the core module and edge prediction to identify likely bond cleavages and fragment ion intensities.

License: MIT License

Jupyter Notebook 97.69% Python 2.31%
bioinformatics gnn-model metabolomics tandem-ms

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fiora's Issues

Fiora not running

Hi, I'm receiving errors while trying to run the Fiora code on my laptop (MacBook M1 Pro). I have all of the files in the same directory.

Below is a screenshot + copied text of the error:

Screen Shot 2024-07-01 at 10 34 46 PM

(base) andrewkim@Andrews-MacBook-Pro-3656 share % fiora-predict -i examples/example_input.csv -o examples/expected_output.txt --model share/v0.0.1_merged_depth6_Jan24+CCS+RT.pt --rt --ccs --annotation

Running fiora prediction with the following parameters: Namespace(input='examples/example_input.csv', output='examples/expected_output.txt', model='share/v0.0.1_merged_depth6_Jan24+CCS+RT.pt', dev='cpu', rt=True, ccs=True, annotation=True)

Warning: Failed loading the model share/v0.0.1_merged_depth6_Jan24+CCS+RT.pt. Fallback: Loading the model from state dictionary.
Error: Failed loading from state dict.

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