Merge readme #13
Merged
Merge readme #13
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
We made a significant rework on PARM and now introduce **version 0.1.0**. Key changes include transitioning from individual model weight files to a directory-based approach for managing model folds (now each PARM model is trained five times/folds), adding support for batch processing, and introducing new parameters like `filter_size` and `type_loss` for user-trained models. ### Updates to Model Loading and Management: * Replaced the `model_weights` parameter with `model_directory` in `PARM_mutagenesis` and `PARM_predict` functions to dynamically load all model folds from a specified directory. These two functions now take the average of all folds to output the predictions and the mutagenesis matrix. * Integrated support for the `filter_size` parameter in `load_PARM` and related functions, allowing customization of convolutional filter sizes. ### Improvements to `PARM_predict`: * Introduced `n_seqs_per_batch` and `store_sequence` parameters in `PARM_predict` to enable batch processing and control output verbosity. Predictions are now averaged across all folds for each sequence. * Enhanced the `get_prediction` function to support batch predictions. ### Code Quality and Consistency: * Standardized parameter formatting and fixed minor inconsistencies in function signatures and docstrings. * Improved error messages for better debugging, such as mismatched model prefixes and invalid motif scanning types. ### Minor Fixes: * Corrected string formatting in logging statements and ensured consistent use of single quotes.
Improve support for user-trained PARM models
add training data
Update README.md to use an env, remove Anaconda
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
No description provided.