genomenlp - v2.8.5

• Fix a bug where passing a config to train did not override output URL
• Raise a warning when local and remote sources clash
• Fix a bug where automated download does not work for cross validation

- Jupyter Notebook
Published by tyronechen almost 3 years ago

genomenlp - v2.8.2

• Enable fit_powerlaw to pull models from wandb directly.

- Jupyter Notebook
Published by tyronechen almost 3 years ago

genomenlp - v2.8.1

• Enable pooling of different token files
• Update documentation for associated scripts

- Jupyter Notebook
Published by tyronechen almost 3 years ago

genomenlp - v2.8.0

• Can now compare empirical token distributions across runs

- Jupyter Notebook
Published by tyronechen almost 3 years ago

genomenlp - v2.7.2

• Fix a bug where casing and sequence splitting did not occur correctly during tokenisation

- Jupyter Notebook
Published by tyronechen almost 3 years ago

genomenlp - v2.7.1

• Fix a bug where tokenise_bio did not load dependencies correctly
• Add sequence breaking functionality to tokenise_bio -b for splitting long seqs that may cause memory issues (eg chr1)
• Add sequence casing functionality to tokenise_bio -c for changing data input during tokeniser training to upper or lower case

- Jupyter Notebook
Published by tyronechen almost 3 years ago

genomenlp - v2.6.3

• Can now sweep on a subset of data by using the --partition_percent option

- Jupyter Notebook
Published by tyronechen almost 3 years ago

genomenlp - v2.5.0

• Fix a bug where train was not functioning correctly (class label encodings)

- Jupyter Notebook
Published by tyronechen almost 3 years ago

genomenlp - v2.4.4

• Fix a bug where csv files were truncated if the input sequence is too long
• Fix a bug where embeddings were not generated correctly in create_embedding_bio_sp.py

- Jupyter Notebook
Published by tyronechen almost 3 years ago

genomenlp - v2.4.3

• Add support for reverse complementing some non-standard nucleotides
• Fix bug in k-merisation process where a non-existing tokeniser file was parsed

- Jupyter Notebook
Published by tyronechen almost 3 years ago

genomenlp - v2.4.2

• Fix a bug where the default output directory for fit_powerlaw was set incorrectly

- Jupyter Notebook
Published by tyronechen about 3 years ago

genomenlp - v2.4.1

• Resolve local API with Hf API clash for cross validation correctly
• Change the metrics flag to be the same through all steps to avoid confusion

- Jupyter Notebook
Published by tyronechen about 3 years ago

genomenlp - v2.2.0

• Resolve local API with Hf API clash for cross validation
• Fix a bug where class labels were encoded wrongly in cross validation

- Jupyter Notebook
Published by tyronechen about 3 years ago

genomenlp - v2.1.4

• Point zenodo citations to always go to latest release
• Update citation function output after scripts accordingly

- Jupyter Notebook
Published by tyronechen about 3 years ago

genomenlp - v2.1.2

• Add automatic labelling (filenames) for kmerise_bio
• Also output citations on successful script exit

- Jupyter Notebook
Published by tyronechen about 3 years ago

genomenlp - v2.1.0

• Added html to pdf conversion utility for visualising classification weights

- Jupyter Notebook
Published by tyronechen about 3 years ago

genomenlp - genomenlp

• Updated dependencies for conda installation (no code change)

- Jupyter Notebook
Published by tyronechen about 3 years ago

genomenlp - genomenlp

• Added interpretability for deep learning classifier
• Reverse complement now works on RNA
• Fixed evaluation failing when attention weights are exported
• Fixed a number of dependency issues during building

- Jupyter Notebook
Published by tyronechen about 3 years ago

genomenlp - First release with no major bugs

- Jupyter Notebook
Published by tyronechen over 3 years ago

genomenlp - First release

- Jupyter Notebook
Published by tyronechen over 3 years ago