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camillemoyer icyfermion kevinmcdonnell6 afoxcow sdiebolt cguetot hearthewind kdbanapindi mantourobot ningzhibin rxnataliezhang changzhijiang liangzhendong123 wesley-wt ftimes guigc

deepnovov2's Issues

Pretrained Weights available?

Hi, I am hoping to use the pretrained DeepNovo model (V1) to generate feature embeddings for my data to benchmark. Is a pretrained model available to download? Alternatively, did you train your model from scratch or did you port the weights from the author's tensorflow github?

documentation

Hi Rui,

Thanks for the work.
Is there a detailed documentation I could refer to?

denovo_search denovo_input_feature_file

Hi,

If I want to make predictions for a new mgf file, do I have to leave an empty cell for the 'seq' column in its feature file?

I noted that the headers of the feature files are defined as follow;
"spec_group_id","m/z","z","rt_mean","seq","scans","profile","feature area"

On the other hand, do you have any setting recommendations (deepnovo_config.py) for data coming from a QExactive-HF?

best,

Carlos

best model at epoch None step None

Hi there again,

I am trying to create an small model. However I got this message


2021-02-11 09:06:40,625 [INFO] __main__: training mode
2021-02-11 09:06:40,626 [INFO] data_reader: input spectrum file: /home/cguetot/projects/epigg/deepnovo/species/models/A3/input_files/spectrum.mgf
2021-02-11 09:06:40,626 [INFO] data_reader: input feature file: /home/cguetot/projects/epigg/deepnovo/species/models/A3/input_files/feature.train.csv
2021-02-11 09:06:40,626 [INFO] data_reader: build spectrum location from scratch
2021-02-11 09:06:43,778 [INFO] data_reader: read 4737 features, 0 skipped by mass, 0 skipped by unknown modification, 0 skipped by length
2021-02-11 09:06:43,778 [INFO] train_func: 148 steps per epoch
2021-02-11 09:06:43,778 [INFO] data_reader: input spectrum file: /home/cguetot/projects/epigg/deepnovo/species/models/A3/input_files/spectrum.mgf
2021-02-11 09:06:43,778 [INFO] data_reader: input feature file: /home/cguetot/projects/epigg/deepnovo/species/models/A3/input_files/feature.valid.csv
2021-02-11 09:06:43,778 [INFO] data_reader: read cached spectrum locations
2021-02-11 09:06:43,785 [INFO] data_reader: read 876 features, 0 skipped by mass, 0 skipped by unknown modification, 0 skipped by length
2021-02-11 09:06:43,811 [INFO] train_func: initialize a set of new parameters
2021-02-11 09:24:43,300 [INFO] train_func: best model at epoch None step None

when I try with more data everything seems to be ok.

  • What is the error?
  • What can I do to fix it?
    best,

Carlos

peptide_score and predicted_score_max

Dears,
is there a description on how these two scores (peptide_score and predicted_score_max) are calculated, what is the scale, what to they represent?

Bests,
-A

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