Noble-Lab/casanovo

Issues

• Eliminate the `model_save_folder_path` config option

  #370 opened 3 months ago by Lilferrit
  0

• Add contrastive loss term

  #319 opened 4 months ago by wsnoble
  1

• Some questions when I tried to train a new casanovo model from scratch...

  #367 opened 4 months ago by dadadalizi146
  7

• The speed of the inference is very slow when using a model that I've trained myself from scratch.

  #371 opened 4 months ago by dadadalizi146
  2

• Make "psms" tuple used for output a named tuple

  #366 opened 4 months ago by VarunAnanth2003
  1

• ValueError upon unexpected scan title format

  #354 opened 5 months ago by MNTsnowman
  7

• Eliminate the eval command

  #355 opened 4 months ago by wsnoble
  4

• Designate a filename for the "best" model

  #351 opened 4 months ago by wsnoble
  11

• KeyError: '$'

  #284 opened 10 months ago by patrick-willems
  18

• Automate mzTab validation

  #323 opened 4 months ago by wsnoble
  8

• Rank of updates array (1) must be greater than or equal to inner-most dimension of indices array (29)

  #285 opened 10 months ago by wsnoble
  1

• Migrating PeptideMass, PeptideDecoder, and PeptideEncoder from depthcharge v0.2.3 to casanovo

  #337 opened 7 months ago by CCranney
  3

• Codecov Github Actions job fails in MacOS container.

  #363 opened 4 months ago by Lilferrit
  0

• RuntimeError: CUDA error: the launch timed out and was terminated

  #358 opened 5 months ago by mriffle
  3

• Greater than or equal to character ≥ causes logging error in end of run report.

  #356 opened 5 months ago by Lilferrit
  0

• PyTorch (GPU) not working on Win 11 box

  #353 opened 5 months ago by tomvaiuw
  4

• Add info to log files

  #295 opened 5 months ago by wsnoble
  0

• Add "man pages" for casanovo commands

  #292 opened 5 months ago by wsnoble
  0

• Save final model

  #313 opened 5 months ago by wsnoble
  1

• where are the models trained with my own data saved?

  #291 opened 10 months ago by DIGEdige
  2

• Implement bidirectional decoding

  #320 opened 9 months ago by wsnoble
  1

• Make Casanovo model compatible with torch.compile

  #347 opened 6 months ago by Lilferrit
  0

• mzTab validation

  #322 opened 6 months ago by wsnoble
  0

• Add mzTab validator to github actions

  #346 opened 6 months ago by wsnoble
  1

• Numpy release 2.0.0 breaks depthcharge dependency

  #339 opened 6 months ago by Lilferrit
  2

• Use Fourier embeddings

  #345 opened 6 months ago by wsnoble
  0

• Is there a way to know which spectras are ITMS instead of FTMS?

  #338 opened 6 months ago by Heisenburger2020
  3

• 9-Species Benchmark Set: Data Preprocessing Step?

  #333 opened 7 months ago by CCranney
  5

• Using HDF5 file as train/val dataset leads to index out of bound error

  #311 opened 9 months ago by cfmelend
  9

• Add docs for reproduction of main model training

  #283 opened 7 months ago by gdewael
  1

• ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()

  #329 opened 7 months ago by dadadalizi146
  3

• Export casanovo to torchscript/onnx

  #328 opened 7 months ago by LLautenbacher
  1

• Make Casanovo produce Skyline compatible output

  #330 opened 7 months ago by wsnoble
  0

• WARNING: Skipped spectra with invalid precursor info

  #326 opened 7 months ago by lutfia95
  1

• More information about the train/val/test split

  #324 opened 8 months ago by andradesalazar
  2

• Add rotary embeddings

  #321 opened 8 months ago by wsnoble
  0

• add additional inputs to encoder and decoder

  #318 opened 9 months ago by wsnoble
  1

• What is the criteria of saving the top k models in Casanovo version 4?

  #315 opened 9 months ago by irleader
  1

• how to train casanovo v4 on huge dataset like massive-kb from scratch?

  #314 opened 9 months ago by irleader
  3

• No Models Saved, No Validation Loss Reported

  #312 opened 9 months ago by grahamdelafield
  3

• Version 4 is more accurate but much slower than version 3?

  #307 opened 9 months ago by irleader
  4

• Question about tracking spectra from MGF files in output

  #309 opened 9 months ago by JannikSchneider12
  1

• Exclude some PTMs for prediction?

  #308 opened 9 months ago by JannikSchneider12
  2

• [v3.5.0 ValueError] in the denovo mode of prediction with pretrained massive-kb model

  #305 opened 10 months ago by irleader
  1

• Casanovo v4.1.0: RuntimeError about NVIDIA driver even CPU mode

  #302 opened 10 months ago by progistar
  2

• How to specify custom residues to train Casanovo from scratch?

  #298 opened 10 months ago by irleader
  1

• Retrain for Viruses

  #287 opened 10 months ago by lutfia95
  2

• Allow for flexible GPU selection

  #281 opened a year ago by gdewael
  3

• Non-enzymatic weights file for latest version

  #279 opened a year ago by patrick-willems
  4

• How to train Casanovo

  #278 opened a year ago by wsnoble
  3