From e32588f4e3e3e68db46da22236d90b46a46921db Mon Sep 17 00:00:00 2001 From: Melih Yilmaz <32707537+melihyilmaz@users.noreply.github.com> Date: Fri, 23 Feb 2024 11:05:00 -0800 Subject: [PATCH 1/3] Add model weights link --- docs/faq.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/docs/faq.md b/docs/faq.md index 8a46feb8..59f6631e 100644 --- a/docs/faq.md +++ b/docs/faq.md @@ -145,6 +145,10 @@ You can use any of the scheduler classes available in [`torch.optim.lr_scheduler ## Miscellaneous +**Where can I find Casanovo model weights trained on the nine-species benchmark?** + +You can find the Casanovo weights from 9-species benchmark training [here](https://doi.org/10.5281/zenodo.10694984) on Zenodo, each set of weights are trained and validated on 8 species using the default configurations, with the remaining species held out for testing. You can use these weights with Casanovo v4.x.x. + **How can I generate a precision–coverage curve?** You can evaluate a trained Casanovo model compared to ground-truth peptide labels using a precision–coverage curve. From d73bf122791d29830fc907288131a8fc7823192d Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Fri, 23 Feb 2024 19:12:33 +0000 Subject: [PATCH 2/3] Generate new screengrabs with rich-codex --- docs/images/help.svg | 164 ++++++++++++++++++++++++++++++++++++++++--- 1 file changed, 153 insertions(+), 11 deletions(-) diff --git a/docs/images/help.svg b/docs/images/help.svg index baf2e237..42180a3f 100644 --- a/docs/images/help.svg +++ b/docs/images/help.svg @@ -1,4 +1,4 @@ - + - - + + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - + - - $ casanovo --help + + $ casanovo --help + +Usage:casanovo [OPTIONS] COMMAND [ARGS]...                                     + + ┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓  + ┃                                  Casanovo                                  ┃  + ┗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛  + Casanovo de novo sequences peptides from tandem mass spectra using a            + Transformer model. Casanovo currently supports mzML, mzXML, and MGF files for   + de novo sequencing and annotated MGF files, such as those from MassIVE-KB, for  + training new models.                                                            + + Links:                                                                          + + • Documentation: https://casanovo.readthedocs.io + • Official code repository: https://github.com/Noble-Lab/casanovo + + If you use Casanovo in your work, please cite:                                  + + • Yilmaz, M., Fondrie, W. E., Bittremieux, W., Oh, S. & Noble, W. S. De novo   +mass spectrometry peptide sequencing with a transformer model. Proceedings   +of the 39th International Conference on Machine Learning - ICML '22 (2022)   +doi:10.1101/2022.02.07.479481.                                               + +╭─ Options ────────────────────────────────────────────────────────────────────╮ +│--help-h    Show this message and exit.                                    │ +╰──────────────────────────────────────────────────────────────────────────────╯ +╭─ Commands ───────────────────────────────────────────────────────────────────╮ +│configure Generate a Casanovo configuration file to customize.              │ +│evaluate  Evaluate de novo peptide sequencing performance.                  │ +│sequence  De novo sequence peptides from tandem mass spectra.               │ +│train     Train a Casanovo model on your own data.                          │ +│version   Get the Casanovo version information                              │ +╰──────────────────────────────────────────────────────────────────────────────╯ + From 36b0c7f387ab24fbc675a85359d7ca7a3ed5c547 Mon Sep 17 00:00:00 2001 From: Wout Bittremieux Date: Fri, 23 Feb 2024 21:09:28 +0100 Subject: [PATCH 3/3] Clarify that these weights should only be used for benchmarking --- docs/faq.md | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/docs/faq.md b/docs/faq.md index 59f6631e..c37fc901 100644 --- a/docs/faq.md +++ b/docs/faq.md @@ -147,7 +147,10 @@ You can use any of the scheduler classes available in [`torch.optim.lr_scheduler **Where can I find Casanovo model weights trained on the nine-species benchmark?** -You can find the Casanovo weights from 9-species benchmark training [here](https://doi.org/10.5281/zenodo.10694984) on Zenodo, each set of weights are trained and validated on 8 species using the default configurations, with the remaining species held out for testing. You can use these weights with Casanovo v4.x.x. +You can find the Casanovo weights corresponding to the nine-species benchmark [on Zenodo](https://doi.org/10.5281/zenodo.10694984), compatible with Casanovo v4.x.x. +These weights correspond to training and validation on eight species using the default configurations, with the remaining species held out for testing, as indicated by the file names. +Note that these weights are only intended for evaluation purposes on this specific benchmark dataset. +For general-purpose usage of Casanovo, use its [default weights](https://casanovo.readthedocs.io/en/latest/getting_started.html#download-model-weights) instead, as these will give significantly improved performance. **How can I generate a precision–coverage curve?**