Ecosyste.ms: Issues

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GitHub / Noble-Lab/casanovo issues and pull requests

#399 - Experimental vs Calculated MZ Bug Fix

Pull Request - State: closed - Opened by Lilferrit 5 days ago - 2 comments

#398 - Number of spectra in mgf do not match number of results in mztab

Issue - State: closed - Opened by Heisenburger2020 13 days ago - 3 comments
Labels: question

#396 - Embedding function

Issue - State: closed - Opened by XiaojieGan 22 days ago - 2 comments
Labels: question

#395 - PeptideDecoder

Issue - State: closed - Opened by XiaojieGan 22 days ago - 5 comments
Labels: question

#394 - m/z and intensity embedding

Issue - State: closed - Opened by XiaojieGan 27 days ago - 3 comments
Labels: question

#393 - Missing Training Data for Vigna mungo Species in MASSIVE FTP

Issue - State: closed - Opened by tangz7725 28 days ago - 3 comments
Labels: documentation

#392 - Switched to Geometric Mean for Peptide Level Scores

Pull Request - State: closed - Opened by Lilferrit about 1 month ago - 1 comment

#391 - Casanovo Nextflow Workflow Documentation

Pull Request - State: closed - Opened by Lilferrit about 1 month ago - 1 comment

#390 - Read the Docs Update to Reflect New Command Line Functionality

Pull Request - State: closed - Opened by Lilferrit about 1 month ago - 1 comment

#389 - Document nextflow workflow

Issue - State: closed - Opened by wsnoble about 1 month ago
Labels: documentation

#388 - Remove pylance depthcharge incompatibility work around.

Issue - State: open - Opened by Lilferrit about 1 month ago
Labels: enhancement

#387 - Remove depthcharge MGF prefix bug workaround

Issue - State: open - Opened by Lilferrit about 2 months ago - 1 comment
Labels: enhancement

#386 - Use full file path in the `MztabWriter` run map instead of just the file name.

Issue - State: open - Opened by Lilferrit about 2 months ago - 1 comment
Labels: bug, enhancement

#385 - Update pytorch lightning requirement

Pull Request - State: closed - Opened by justin-a-sanders about 2 months ago - 1 comment

#384 - Update docs with model weights

Pull Request - State: closed - Opened by melihyilmaz 2 months ago - 1 comment
Labels: documentation

#383 - WARNING: Skipped 56750 spectra with invalid precursor info - results in error

Issue - State: closed - Opened by mriffle 2 months ago - 2 comments
Labels: bug

#382 - Use `lightning.pytorch.loggers.TensorBoardLogger` for tensorboard logging.

Issue - State: open - Opened by Lilferrit 2 months ago
Labels: enhancement

#381 - Switch to geometric mean for peptide scores

Issue - State: closed - Opened by wsnoble 2 months ago
Labels: enhancement

#380 - Eval metrics and circular import bug fix.

Pull Request - State: closed - Opened by Lilferrit 2 months ago - 4 comments

#379 - Intermittent circular import error

Issue - State: closed - Opened by Lilferrit 2 months ago
Labels: bug

#378 - `log_metrics` skipped spectra incorrect behavior

Issue - State: closed - Opened by Lilferrit 2 months ago
Labels: bug

#377 - ReadTheDocs needs to be updated with new functionalities

Issue - State: closed - Opened by bittremieux 2 months ago
Labels: documentation

#376 - Log optimizer and training metrics to CSV file

Pull Request - State: closed - Opened by Lilferrit 2 months ago - 2 comments

#375 - Implement early stopping / validation patience interval.

Issue - State: open - Opened by Lilferrit 2 months ago - 1 comment
Labels: enhancement

#374 - Tensorboard io

Pull Request - State: closed - Opened by Lilferrit 2 months ago - 3 comments

#373 - Write TensorBoard summary to output directory.

Issue - State: closed - Opened by Lilferrit 2 months ago - 2 comments
Labels: enhancement

#372 - File IO command line options revision

Pull Request - State: closed - Opened by Lilferrit 3 months ago - 1 comment

#370 - Eliminate the `model_save_folder_path` config option

Issue - State: closed - Opened by Lilferrit 3 months ago
Labels: enhancement

#369 - Flexible format for scan titles

Pull Request - State: open - Opened by bittremieux 3 months ago

#368 - PSM Data Class

Pull Request - State: closed - Opened by Lilferrit 3 months ago - 1 comment

#367 - Some questions when I tried to train a new casanovo model from scratch...

Issue - State: closed - Opened by dadadalizi146 3 months ago - 7 comments
Labels: question

#366 - Make "psms" tuple used for output a named tuple

Issue - State: closed - Opened by VarunAnanth2003 3 months ago - 1 comment
Labels: enhancement

#365 - Save best model

Pull Request - State: closed - Opened by Lilferrit 3 months ago - 1 comment

#364 - Upgrade Codecove to v4

Pull Request - State: closed - Opened by Lilferrit 4 months ago - 1 comment

#363 - Codecov Github Actions job fails in MacOS container.

Issue - State: closed - Opened by Lilferrit 4 months ago
Labels: bug

#362 - MzTab Validation

Pull Request - State: closed - Opened by Lilferrit 4 months ago - 5 comments

#361 - Update paper reference

Pull Request - State: closed - Opened by bittremieux 4 months ago

#360 - Bug report template

Pull Request - State: closed - Opened by bittremieux 4 months ago - 3 comments

#359 - Eliminate evaluate Command

Pull Request - State: closed - Opened by Lilferrit 4 months ago - 7 comments

#358 - RuntimeError: CUDA error: the launch timed out and was terminated

Issue - State: closed - Opened by mriffle 4 months ago - 3 comments

#357 - End of run report logging error fix

Pull Request - State: closed - Opened by Lilferrit 4 months ago - 2 comments

#355 - Eliminate the eval command

Issue - State: closed - Opened by wsnoble 4 months ago - 4 comments
Labels: enhancement

#354 - ValueError upon unexpected scan title format

Issue - State: open - Opened by MNTsnowman 5 months ago - 7 comments
Labels: bug

#353 - PyTorch (GPU) not working on Win 11 box

Issue - State: closed - Opened by tomvaiuw 5 months ago - 4 comments
Labels: help wanted

#352 - Full implementation of Casanovo-DB

Pull Request - State: closed - Opened by VarunAnanth2003 5 months ago - 1 comment
Labels: enhancement

#351 - Designate a filename for the "best" model

Issue - State: closed - Opened by wsnoble 5 months ago - 11 comments
Labels: enhancement

#350 - Migration to depthcharge v0.4.8

Pull Request - State: open - Opened by andradesalazar 5 months ago - 10 comments

#349 - Download weight file from URL

Pull Request - State: closed - Opened by Lilferrit 5 months ago - 5 comments

#348 - Fix documentation of --output and updated output settings.

Pull Request - State: closed - Opened by Lilferrit 5 months ago - 2 comments

#347 - Make Casanovo model compatible with torch.compile

Issue - State: open - Opened by Lilferrit 5 months ago
Labels: enhancement

#346 - Add mzTab validator to github actions

Issue - State: closed - Opened by wsnoble 5 months ago - 1 comment

#345 - Use Fourier embeddings

Issue - State: open - Opened by wsnoble 5 months ago
Labels: enhancement

#344 - Restrict NumPy to pre-2.0

Pull Request - State: closed - Opened by bittremieux 5 months ago - 1 comment

#343 - Enhanced Sequencing Run Logging

Pull Request - State: closed - Opened by Lilferrit 5 months ago - 11 comments

#342 - CLI documentation page generation

Pull Request - State: closed - Opened by Lilferrit 5 months ago - 1 comment

#341 - mzTab validation fix

Pull Request - State: closed - Opened by Lilferrit 5 months ago - 1 comment

#340 - 313 save final model

Pull Request - State: closed - Opened by Lilferrit 5 months ago - 8 comments

#339 - Numpy release 2.0.0 breaks depthcharge dependency

Issue - State: closed - Opened by Lilferrit 5 months ago - 2 comments
Labels: bug

#338 - Is there a way to know which spectras are ITMS instead of FTMS?

Issue - State: closed - Opened by Heisenburger2020 5 months ago - 3 comments
Labels: question

#337 - Migrating PeptideMass, PeptideDecoder, and PeptideEncoder from depthcharge v0.2.3 to casanovo

Issue - State: open - Opened by CCranney 6 months ago - 3 comments
Labels: question

#334 - Compatible 9-species data reference

Pull Request - State: closed - Opened by bittremieux 6 months ago - 1 comment

#333 - 9-Species Benchmark Set: Data Preprocessing Step?

Issue - State: closed - Opened by CCranney 6 months ago - 5 comments
Labels: question

#332 - Update CHANGELOG.md

Pull Request - State: closed - Opened by melihyilmaz 6 months ago - 1 comment

#331 - Prepare release v4.2.0

Pull Request - State: closed - Opened by bittremieux 6 months ago - 1 comment

#330 - Make Casanovo produce Skyline compatible output

Issue - State: open - Opened by wsnoble 6 months ago
Labels: enhancement

#328 - Export casanovo to torchscript/onnx

Issue - State: open - Opened by LLautenbacher 6 months ago - 1 comment
Labels: enhancement

#327 - Don't test on macOS versions with MPS

Pull Request - State: closed - Opened by bittremieux 7 months ago - 1 comment

#326 - WARNING: Skipped spectra with invalid precursor info

Issue - State: closed - Opened by lutfia95 7 months ago - 1 comment
Labels: question

#325 - Add Casanovo-DB Functionality

Pull Request - State: open - Opened by VarunAnanth2003 7 months ago - 13 comments
Labels: enhancement

#324 - More information about the train/val/test split

Issue - State: closed - Opened by andradesalazar 7 months ago - 2 comments
Labels: question

#323 - Automate mzTab validation

Issue - State: closed - Opened by wsnoble 7 months ago - 8 comments
Labels: enhancement

#322 - mzTab validation

Issue - State: closed - Opened by wsnoble 7 months ago
Labels: bug, good first issue

#321 - Add rotary embeddings

Issue - State: open - Opened by wsnoble 7 months ago
Labels: enhancement

#320 - Implement bidirectional decoding

Issue - State: open - Opened by wsnoble 8 months ago - 1 comment
Labels: enhancement

#319 - Add contrastive loss term

Issue - State: closed - Opened by wsnoble 8 months ago - 1 comment
Labels: enhancement

#318 - add additional inputs to encoder and decoder

Issue - State: open - Opened by wsnoble 8 months ago - 1 comment
Labels: enhancement

#317 - Supported file formats documentation

Pull Request - State: closed - Opened by bittremieux 8 months ago - 1 comment

#316 - Allow csv to handle all newlines

Pull Request - State: closed - Opened by mobiusklein 8 months ago - 3 comments

#315 - What is the criteria of saving the top k models in Casanovo version 4?

Issue - State: closed - Opened by irleader 8 months ago - 1 comment
Labels: question

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

Issue - State: closed - Opened by irleader 8 months ago - 3 comments
Labels: question

#313 - Save final model

Issue - State: closed - Opened by wsnoble 8 months ago - 1 comment
Labels: enhancement, good first issue

#312 - No Models Saved, No Validation Loss Reported

Issue - State: closed - Opened by grahamdelafield 8 months ago - 3 comments
Labels: question

#311 - Using HDF5 file as train/val dataset leads to index out of bound error

Issue - State: closed - Opened by cfmelend 9 months ago - 9 comments
Labels: bug

#310 - Add FAQ about MGF index tracking

Pull Request - State: closed - Opened by melihyilmaz 9 months ago - 3 comments

#309 - Question about tracking spectra from MGF files in output

Issue - State: closed - Opened by JannikSchneider12 9 months ago - 1 comment
Labels: question

#308 - Exclude some PTMs for prediction?

Issue - State: closed - Opened by JannikSchneider12 9 months ago - 2 comments
Labels: question

#307 - Version 4 is more accurate but much slower than version 3?

Issue - State: closed - Opened by irleader 9 months ago - 4 comments
Labels: question

#306 - Don't crash when multiple beams have identical peptide scores

Pull Request - State: closed - Opened by bittremieux 9 months ago - 1 comment

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

Issue - State: closed - Opened by irleader 9 months ago - 1 comment
Labels: bug

#304 - Add FAQ entry about antibody sequencing

Pull Request - State: closed - Opened by wsnoble 9 months ago - 1 comment
Labels: documentation

#303 - Add 9-species model weights link to FAQ

Pull Request - State: closed - Opened by melihyilmaz 9 months ago - 1 comment

#302 - Casanovo v4.1.0: RuntimeError about NVIDIA driver even CPU mode

Issue - State: closed - Opened by progistar 9 months ago - 2 comments
Labels: enhancement

#301 - Run unit tests on macOS with M1 support

Pull Request - State: closed - Opened by bittremieux 9 months ago - 3 comments

#300 - Rename max_iters to cosine_schedule_period_iters

Pull Request - State: closed - Opened by bittremieux 9 months ago - 2 comments

#298 - How to specify custom residues to train Casanovo from scratch?

Issue - State: closed - Opened by irleader 9 months ago - 1 comment
Labels: question

#296 - Prepare for release v4.1.0

Pull Request - State: closed - Opened by bittremieux 9 months ago - 1 comment

#295 - Add info to log files

Issue - State: closed - Opened by wsnoble 9 months ago
Labels: enhancement