immuneml - v3.0.0a4

Alpha release - Experimental features: generative models, clustering, dimensionality reduction - Integrated LIgO for simulation (LigoSim instruction) - Internally rely on bionumpy for data storage - Major documentation updates with focus on new developers (new docs for integrating new components, minor updates to MLMethod and DatasetEncoder interfaces, scripts for automatically testing new components) - Added functionalities for analysing antigen-binding associated motifs

- Python
Published by LonnekeScheffer almost 2 years ago

immuneml - v2.2.5

What's Changed

• some new reports
• bug fixes in importers, encoders, and data model
• CompAIRR helper updates

- Python
Published by pavlovicmilena over 2 years ago

immuneml - v2.2.4

What's new

• update and reorganize requirements
• documentation updates

- Python
Published by pavlovicmilena almost 3 years ago

immuneml - v2.2.3

What's Changed

• Make CompAIRR encoder more RAM efficient
• Bugfix element generator make subset
• Speed up CompAIRRSequenceAbundance encoder
• Caching speed improvement MatchedSequences/MatchedReceptors
• Bugfix: consider positive_class when making binary mapping
• Support custom import of Olga columns
• Set up LOOCV for sequence datasets
• Add manual splitting for sequence and receptor datasets
• Label mapping bugfixes

Full Changelog: https://github.com/uio-bmi/immuneML/compare/v2.2.2...v2.2.3

- Python
Published by pavlovicmilena about 3 years ago

immuneml - v2.2.2

What's Changed

• minor updates related to versions of dependencies

Full Changelog: https://github.com/uio-bmi/immuneML/compare/v2.2.1...v2.2.2

- Python
Published by pavlovicmilena almost 4 years ago

immuneml - v2.2.1

What's Changed

• updated documentation
• minor bug fixes in ROC curve reports
• minor bug fixes in class mappings

Full Changelog: https://github.com/uio-bmi/immuneML/compare/v2.2.0...v2.2.1

- Python
Published by pavlovicmilena almost 4 years ago

immuneml - v2.2.0

What's Changed

• Windows-specific bug fixes
• Kmer abundance encoder
• Bug fixes: CompAIRRSequenceAbundance encoder memory, other minor fixes

Full Changelog: https://github.com/uio-bmi/immuneML/compare/v2.1.2...v2.2.0

- Python
Published by pavlovicmilena almost 4 years ago

immuneml - v2.1.2

What's Changed

• added support for sequence dataset in word2vec encoder
• updated reference encoders with different summarizing strategies
• minor bug fixes

Full Changelog: https://github.com/uio-bmi/immuneML/compare/v2.1.1...v2.1.2

- Python
Published by pavlovicmilena about 4 years ago

immuneml - v2.1.1

Minor updates:

• add keep_fraction option to FeatureComparison report
• fix optimization metric in sklearn
• copy reports to HTML output for ExploratoryAnalysis instruction
• fix encodings based on nucleotide sequences
• make the standard dataset name in Galaxy Tools "dataset"
• try to fix dependency issues (minor updates added to FAQ)

- Python
Published by pavlovicmilena about 4 years ago

immuneml - v2.1.0

Major change: integrate immuneML with CompAIRR (https://github.com/uio-bmi/compairr):

• add CompAIRRSequenceAbundance and CompAIRRDistance encoder,
• update docker to include CompAIRR,
• minor bug fixes.

- Python
Published by pavlovicmilena over 4 years ago

immuneml - v2.0.6

Minor updates:

• moved Metric.py from the environment package to the ml_metrics package
• updated YAML load(..) calls without specified Loader to safe_load(..) instead
• bugfix: removed caching from scikit-learn models
• updated cache location for multiple processes

- Python
Published by pavlovicmilena over 4 years ago

immuneml - v2.0.5

Minor bug fixes and usability improvements:

• added checks for encoder-ML compatibility when parsing
• added Moristia-Horn distance metric and improved HTML output for DistanceEncoder
• added LabelHelper for parsing labels
• added label checks before starting ComparisonData matrix computation
• removed sequence_weight requirement from FullSequenceImplanting YAML (it was not used)
• improved docs

- Python
Published by pavlovicmilena over 4 years ago

immuneml - v2.0.4

Minor bugfix: updated SequenceMetadata object to convert 'nan' for RegionType to None (manifested before as an error on loading existing ImmuneML-formatted dataset from disk).

- Python
Published by pavlovicmilena over 4 years ago

immuneml - v2.0.3

• standardized import/export metadata for repertoire datasets to always have field "identifier" instead of mixing it with "repertoire_identifier"

- Python
Published by pavlovicmilena over 4 years ago

immuneml - v2.0.2

• integrate with Zenodo to make the code citable

- Python
Published by pavlovicmilena over 4 years ago

immuneml - v2.0.1

Updates in v2.0.1 include minor bug fixes:

• fix path handling and serialization for ImmuneML format
• fix exported metadata for datasets with implanted signals
• minor updates related to Galaxy API

- Python
Published by pavlovicmilena over 4 years ago

immuneml - v2.0.0

Updates in version 2:

• datasets are now stored using binary numpy and YAML files and do not rely on pickle anymore;
• Pickle import and export is replaced with ImmuneML import and export where datasets are represented as YAML files, while the content (repertoire data, receptors, sequences) are stored in numpy files;
• 'storeencodeddata' option is removed from instructions; to store the encoded data, use DesignMatrixExporter report.

The package is also available at: https://pypi.org/project/immuneML/2.0.0/

- Python
Published by pavlovicmilena over 4 years ago