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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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9-Species Benchmark Set: Data Preprocessing Step?
#333
CCranney
closed
4 months ago
5
Update CHANGELOG.md
#332
melihyilmaz
closed
4 months ago
1
Prepare release v4.2.0
#331
bittremieux
closed
4 months ago
1
Make Casanovo produce Skyline compatible output
#330
wsnoble
opened
4 months ago
0
ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
#329
dadadalizi146
closed
4 months ago
3
Export casanovo to torchscript/onnx
#328
LLautenbacher
opened
4 months ago
1
Don't test on macOS versions with MPS
#327
bittremieux
closed
4 months ago
1
WARNING: Skipped spectra with invalid precursor info
#326
lutfia95
closed
4 months ago
1
Add Casanovo-DB Functionality
#325
VarunAnanth2003
opened
5 months ago
13
More information about the train/val/test split
#324
andradesalazar
closed
5 months ago
2
Automate mzTab validation
#323
wsnoble
closed
1 month ago
8
mzTab validation
#322
wsnoble
closed
3 months ago
0
Add rotary embeddings
#321
wsnoble
opened
5 months ago
0
Implement bidirectional decoding
#320
wsnoble
opened
6 months ago
1
Add contrastive loss term
#319
wsnoble
closed
1 month ago
1
add additional inputs to encoder and decoder
#318
wsnoble
opened
6 months ago
1
Supported file formats documentation
#317
bittremieux
closed
6 months ago
1
Allow csv to handle all newlines
#316
mobiusklein
closed
6 months ago
3
What is the criteria of saving the top k models in Casanovo version 4?
#315
irleader
closed
6 months ago
1
how to train casanovo v4 on huge dataset like massive-kb from scratch?
#314
irleader
closed
6 months ago
3
Save final model
#313
wsnoble
closed
3 months ago
1
No Models Saved, No Validation Loss Reported
#312
grahamdelafield
closed
6 months ago
3
Using HDF5 file as train/val dataset leads to index out of bound error
#311
cfmelend
closed
6 months ago
9
Add FAQ about MGF index tracking
#310
melihyilmaz
closed
6 months ago
3
Question about tracking spectra from MGF files in output
#309
JannikSchneider12
closed
7 months ago
1
Exclude some PTMs for prediction?
#308
JannikSchneider12
closed
7 months ago
2
Version 4 is more accurate but much slower than version 3?
#307
irleader
closed
7 months ago
4
Don't crash when multiple beams have identical peptide scores
#306
bittremieux
closed
7 months ago
1
[v3.5.0 ValueError] in the denovo mode of prediction with pretrained massive-kb model
#305
irleader
closed
7 months ago
1
Add FAQ entry about antibody sequencing
#304
wsnoble
closed
7 months ago
1
Add 9-species model weights link to FAQ
#303
melihyilmaz
closed
7 months ago
1
Casanovo v4.1.0: RuntimeError about NVIDIA driver even CPU mode
#302
progistar
closed
7 months ago
2
Run unit tests on macOS with M1 support
#301
bittremieux
closed
4 months ago
3
Rename max_iters to cosine_schedule_period_iters
#300
bittremieux
closed
7 months ago
2
How to specify custom residues to train Casanovo from scratch?
#298
irleader
closed
7 months ago
1
Prepare for release v4.1.0
#296
bittremieux
closed
7 months ago
1
Add info to log files
#295
wsnoble
closed
2 months ago
0
Add FAQ on how to change the LR scheduler
#294
bittremieux
closed
7 months ago
1
Add learning rate scheduler FAQ
#293
melihyilmaz
closed
7 months ago
1
Add "man pages" for casanovo commands
#292
wsnoble
closed
2 months ago
0
where are the models trained with my own data saved?
#291
DIGEdige
opened
7 months ago
2
Stabilize torch.topk() behavior
#290
melihyilmaz
closed
7 months ago
5
Add non-enzymatic dataset to FAQ
#288
melihyilmaz
closed
7 months ago
1
Retrain for Viruses
#287
lutfia95
closed
8 months ago
2
Ensure --model has to be set when not training from scratch
#286
gdewael
closed
8 months ago
1
Rank of updates array (1) must be greater than or equal to inner-most dimension of indices array (29)
#285
wsnoble
opened
8 months ago
1
KeyError: '$'
#284
patrick-willems
opened
8 months ago
18
Add docs for reproduction of main model training
#283
gdewael
closed
4 months ago
1
devices as a special parameter to check types for
#282
gdewael
closed
8 months ago
5
Allow for flexible GPU selection
#281
gdewael
closed
8 months ago
3
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