InstaNovo v1.2.2

What's Changed

• Use correct version for gh-action-pypi-publish action by @BioGeek in #127

Full Changelog: 1.2.1...1.2.2

InstaNovo v1.2.1

What's Changed

• Update to v1.2.1 and fix CI by @BioGeek in #125
• Docs job in CI should ignore upstream skipped jobs by @BioGeek in #126

Full Changelog: 1.2.0...1.2.1

InstaNovo v1.2.0

• Added multi-gpu support for training and prediction
• Switched from Lightning to Accelerate
• Significant improvements (over 10x on GPU) to beam search and knapsack beam search
• Minor improvements with the v1.2.0 transformer model: instanovo-v1.2.0.ckpt
• Added support for negative masses in knapsack
• Various other fixes and improvements

InstaNovo v1.1.4

What's Changed

• build(deps): bump astral-sh/setup-uv from 5 to 6 by @dependabot in #100
• fix: diffusion sampling and checkpoint download by @rcatzel in #111
• chore: bump version number to v.1.1.4 by @rcatzel in #112

Full Changelog: 1.1.3...1.1.4

InstaNovo v1.1.3

What's Changed

• chore: bump version number to v1.1.2 by @BioGeek in #104
• docs: add InstaNovo-P notebook by @BioGeek in #105
• InstaNovo v1.1.3 by @rcatzel in #109

Notes

• Update codebase to use new diffusion checkpoint, instanovoplus-v1.1.0
• Update diffusion predict script with refinement configuration options, and multiple prediction sampling for improved performance
  • refine_all: If True, all predictions will be refined
  • refine_threshold: Only predictions with a confidence score less than this will be refined
  • n_preds: Number of diffusion predictions to sample per spectrum
• Include updated model performance benchmarking in README.md
• Added option to specify valid_path as a DictConfig, where keys represent the validation group and values represent the validation path.
  • Eg. "acpt": "/path/to/acpt/*-valid-*.parquet"
  • This will add an "acpt" group in the validation metrics
• Added add_source_file_column option to SpectrumDataFrame, which adds the path to the original input file as a column "source_file"
• Added add_spectrum_id option to SpectrumDataFrame, which adds unique index values to the input file as a column "spectrum_id"
• Updated s3 utils to use a class instead of individual functions
  • Added functionality to wrap write methods and optionally specify an s3 path which will get automatically uploaded
  • Added functionality to automatically download files to a temporary directory when converting s3 paths
• Allow --output-path to remain unspecified in evaluation mode for:
  • Transformer model
  • Diffusion model when not in refinement mode

New Checkpoints

• Trained a new InstaNovo+ v1.1.0 checkpoint on the Extended Massive-KB dataset - instanovoplus-v1.1.0.ckpt. To be used standalone, or in conjunction with instanovo-v1.1.0.ckpt for best results.

Full Changelog: 1.1.2...1.1.3

InstaNovo v1.1.2: InstaNovo-P v1.0.0 checkpoint

What's Changed

This release includes the checkpoint for our de novo sequencing model for phosphoproteomics InstaNovo-P v1.0.0!

• docs: re-enable building docs by @BioGeek in #85
• Fix docs by @BioGeek in #88
• Auto detect device by @rcatzel in #91
• Notebook comparing InstaNovo v0.1 versus InstaNovo v1.1 by @BioGeek in #95
• docs: add coverage badge by @BioGeek in #89
• instanovo-phospho-v1.0.0 by @jesperdlau in #103

New Contributors

• @jesperdlau made their first contribution in #103

Full Changelog: 1.1.1...1.1.2

InstaNovo v1.1.1

What's Changed

Code updates for publication release

• fix: add sample data by @BioGeek in #81
• docs: update readme for publication by @KevinEloff @BioGeek @rcatzel in #82
• fix: add diffusion device option, set automatically on load by @KevinEloff in #83
• fix: use separate diffusion sdf instance, minor release bump by @rcatzel in #84

Full Changelog: 1.1.0...1.1.1

InstaNovo v1.1.0

What's Changed

• Updated to use Typer @BioGeek
  • Typer includes options to predict with InstaNovo and refine with InstaNovo+ in one command
• Updated dependency management to use UV @BioGeek
• Re-added updated diffusion code @rcatzel
  • A preliminary checkpoint has been added
• Adds support for UNIMOD ProForma format in the residue class (backwards compatible with original format)
• Adds automatic UNIMOD conversion of old model checkpoints during loading by default
• Adds support for specifying a list of globs for SpectrumDataFrame
• Removed (+25.98) N-terminal modification from training, and added to suppressed list by default
• Fixed bug where tempdir would not be initialised if all input data is in .parquet format, causing a crash when performing a preshuffle.
• Updated predict script to always calculate delta_mass_ppm even in de novo mode.
• Updated README.md
  • Added usage for UV and Typer
  • Added link to Acknowledgements
  • Added Natively Supported Modifications table with unimod ID
  • Added Output description table
  • Updated Using your own datasets table to remove the modified_sequence column

New checkpoints

• Trained a new checkpoint with corrected cysteine modification and added MassiveKB data: instanovo-v1.1.0
• Preliminary InstaNovo+ checkpoint trained on the same data: instanovoplus-v1.1.0-alpha

Notes:

• A bug with Implicit Cysteine modification has been corrected in the AC-PT. This bug affects the previous instanovo_extended.ckpt checkpoint from the 1.0.0 release. This bug caused significant performance issues on downstream datasets.
• The diffusion checkpoint is an alpha release with an updated checkpoint coming soon.

InstaNovo v1.0.1

What's Changed

• build(deps): bump pypa/gh-action-pypi-publish from 1.4.2 to 1.10.3 by @dependabot in #55

• build(deps): bump actions/setup-python from 4 to 5 by @dependabot in #42

• Update starter notebook, add charge check, fix sdpa by @KevinEloff in #61

• build(deps): bump pypa/gh-action-pypi-publish from 1.10.3 to 1.11.0 by @dependabot in #64

• fix: ZeroDivisionError when predicting on small sample file by @BioGeek in #68

• V1.0.1 release by @BioGeek in #69

• fix: Resolve "AttributeError: 'SpectrumDataFrame' object has no attribute 'df'"

• feat: update notebooks to v1.0.0

• feat: Automatic model download and improve residues
  Co-Authored-By: Kevin Eloff k.eloff@instadeep.com

• feat: update tests for v1.0.1 release
  Co-Authored-By: Rachel Catzel r.catzel@instadeep.com

• feat: update packages

New Contributors

• @dependabot made their first contribution in #55

Full Changelog: 1.0.0...1.0.1

InstaNovo 1.0.0

Improved code utility and data validation

• Check labels match precursor
• Check for data leakage
• Verify residue vocabulary
• Added better residue support
  • Fine-tuning trainer automatically updates model weights with new sizes
• Added Flash attention, torch.compile(), AMP (fp16)
• Added improved fast greedy search
• Improved test coverage

Added Spectrum Data Handler

• Supports lazy loading with asynchronous prefetching
• Filtering and sampling performed non-destructively (by updating the row filter)
• Two-fold shuffling strategy for training ensures optimal load times

Extended model checkpoint released. Trained on 32M spectra with additional PTMs:

• AC-PT
• Additional PRIDE dataset
• Additional phosphorylation dataset