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Noble-Lab
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casanovo
De Novo Mass Spectrometry Peptide Sequencing with a Transformer Model
https://casanovo.readthedocs.io
Apache License 2.0
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Use geometric mean to calculate peptide score
#280
bittremieux
closed
7 months ago
1
Non-enzymatic weights file for latest version
#279
patrick-willems
closed
8 months ago
4
How to train Casanovo
#278
wsnoble
closed
8 months ago
3
Download non-enzyme data; apply to top-down data
#277
wsnoble
closed
8 months ago
1
Update `output` command-line description
#276
bittremieux
closed
2 weeks ago
6
Remove `train_from_scratch` config option
#275
bittremieux
closed
8 months ago
1
Update Actions versions
#274
bittremieux
closed
8 months ago
1
Prepare release v4.0
#273
bittremieux
closed
9 months ago
1
Casanovo does not check for repeated m/z values in spectra
#272
cfmelend
opened
9 months ago
2
Casanovo's 'sequence' mode crashes when n_beams=10
#271
cfmelend
closed
7 months ago
4
Minor fix to label smoothing
#270
melihyilmaz
closed
9 months ago
1
Optimize beam search
#269
bittremieux
opened
10 months ago
3
Check for invalid/missin config entries
#268
bittremieux
closed
9 months ago
1
fine-tune the massivekb-pretrained model with additional modifications
#267
irleader
closed
10 months ago
1
Restart
#266
cfmelend
closed
8 months ago
0
Fix spectra skipping and add min_n_peaks option
#265
melihyilmaz
opened
10 months ago
0
Add min_peaks config option
#264
wsnoble
opened
10 months ago
1
Remove train_from_scratch
#263
wsnoble
closed
8 months ago
1
Add label smoothing to learning rate scheduler branch
#262
melihyilmaz
closed
11 months ago
0
Label smoothing in training
#261
melihyilmaz
closed
9 months ago
1
MacOS error: Rank of updates array (1) must be greater than or equal to inner-most dimension of indices array (29)
#260
wsnoble
closed
7 months ago
1
TPU warnings when running on Colab
#259
bittremieux
closed
3 months ago
3
Remove gradient calculation during inference
#258
melihyilmaz
closed
11 months ago
1
Issue error for unrecognized/missing config file entry
#257
ishagokhale
closed
10 months ago
1
Document how to check that the GPU is used
#256
bittremieux
closed
11 months ago
1
Issue error for unrecognized/missing entries in user's config file issue #236
#255
ishagokhale
closed
11 months ago
0
resolves issue #238: remove custom_encoder option
#254
ishagokhale
closed
11 months ago
1
Correctly report AA precision and recall during validation
#253
bittremieux
closed
11 months ago
1
Bug in evaluation script during training
#252
KevinEloff
closed
11 months ago
1
Slow speed making Casanovo impractical for most shotgun data.
#251
mhoopmann
closed
11 months ago
6
Removed custom_encoder option
#250
ishagokhale
closed
11 months ago
1
Add option to change learning rate scheduler
#249
justin-a-sanders
closed
7 months ago
7
enzymatic digestion by enzymes other than trypsin
#248
MengTingHe2023
closed
1 year ago
2
Add the option to turn off the precursor m/z filter entirely
#247
melihyilmaz
opened
1 year ago
1
Use config options and auto-downloaded weights
#246
melihyilmaz
closed
9 months ago
6
precursor_mass_tol is being ignored
#245
wsnoble
closed
9 months ago
1
Add more detailed logging to assist user debugging
#244
justin-a-sanders
closed
2 months ago
7
RuntimeError: No GPUs available.
#243
hxxhust163
closed
11 months ago
1
Make the learning rate scheduler more flexible
#242
wsnoble
closed
7 months ago
9
fix documentation of --output
#241
wsnoble
closed
2 weeks ago
8
Casanovo makes no predictions when n_beams = 1
#240
justin-a-sanders
closed
1 year ago
2
Enzyme main
#239
cfmelend
closed
7 months ago
1
Remove custom_encoder from the config file
#238
wsnoble
closed
11 months ago
0
Redo the config file
#237
wsnoble
closed
1 year ago
0
Issue an error for unrecognized config file entries
#236
wsnoble
closed
9 months ago
1
Upgrade depthcharge to v0.2.3
#235
bittremieux
closed
1 year ago
1
Added shuffling to trainset dataloaders, no shuffle by default for ot…
#234
cfmelend
closed
1 year ago
1
Prepare for release 3.5
#233
bittremieux
closed
1 year ago
1
Terminal mods predicted mid-peptide
#232
wsnoble
closed
7 months ago
3
Add lines to force gradient calculation.
#231
VarunAnanth2003
closed
1 year ago
1
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