Multiomics-Analytics-Group/abaco: ABaCO 0.1.1

Summary

This release includes updates to the source code and documentation for a better understanding of the model's implementation. It specifically adds comprehensive notebooks for computational performance benchmarking and multi-study correction analysis.

📄 New Notebooks

• Performance Benchmarking and Fine-tuning example: Added docs/tutorial/report-performance.ipynb.
  • Example using a simulated dataset on fine-tuning the loss weights with a small subset of the training data.
  • Provides detailed evaluation of wall-clock running times and peak GPU memory usage.
• Multi-studies Case: Added docs/tutorial/demo-parkinson.ipynb.
  • Demonstrates model performance on a composite of 9 studies dataset (merging multiple test cases).
  • Validates the preservation of biological signals without adding biases in high-heterogeneity settings.
• Inflammatory Bowel Disease Case Study: Added docs/tutorial/tutorial-ibd.ipynb.
  • Added the implementation of the Inflammatory Bowel Disease (IBD) case study as a tutorial notebook.
  • Dealing with outlier training runs for analysis of problematic taxonomic groups.

🛠 Source Changes

• Fixed a bug that wasn't allowing the use of the VMM prior configuration at metaABaCo().