Version History & Changelog
This document tracks the development history of mLLMCelltype,
including major releases, feature additions, bug fixes, and other
significant changes.
Version 1.0.0 (2023-11-15)
Initial Release
- First public release of mLLMCelltype
- Core functionality for cell type annotation using LLMs
- Support for OpenAI (GPT-3.5, GPT-4) and Anthropic (Claude)
models
- Basic consensus mechanism
- Integration with Seurat
Version 1.1.0 (2024-01-20)
Features
- Added support for Google’s Gemini models
- Implemented structured deliberation process for controversial
clusters
- Added uncertainty quantification with consensus proportion and
Shannon entropy
- Improved caching system for API responses
- Added Python implementation
Bug Fixes
- Fixed issue with marker gene sorting
- Corrected handling of cluster indices
- Improved error messages for API failures
Documentation
- Added comprehensive README
- Created example notebooks
- Added function documentation
Version 1.2.0 (2024-03-10)
Features
- Added support for DeepSeek, Qwen, and Zhipu models
- Implemented hierarchical annotation capability
- Added visualization functions for uncertainty metrics
- Improved handling of rate limits and API errors
- Added batch processing for large datasets
Bug Fixes
- Fixed consensus calculation for edge cases
- Corrected handling of empty API responses
- Improved error handling for network issues
Documentation
- Added benchmarking results
- Updated examples with new models
- Expanded troubleshooting guide
Version 1.3.0 (2024-05-15)
Features
- Added support for Stepfun, MiniMax, and OpenRouter models
- Implemented custom prompt templates
- Added provider-specific parameter customization
- Improved performance with parallel processing
- Enhanced caching with persistent storage
Bug Fixes
- Fixed issue with discussion logs formatting
- Corrected handling of special characters in marker genes
- Improved robustness against API changes
Documentation
- Added case studies for different tissue types
- Created advanced usage guide
- Updated installation instructions for all dependencies
Version 1.4.0 (2024-07-01)
Features
- Added support for Grok models from X.AI
- Updated Claude model support to include Claude 3.7 Sonnet
- Updated Gemini model support to include Gemini 2.5 Pro
- Improved consensus mechanism with weighted voting
- Enhanced visualization capabilities
- Added support for spatial transcriptomics data
Bug Fixes
- Fixed consensus result printing for controversial clusters
- Corrected model mapping for Claude 3.7 Sonnet
- Fixed undefined variable issue in consensus validation
- Improved Seurat object integration
Documentation
- Created comprehensive documentation website with pkgdown
- Added new vignettes for specific use cases
- Updated examples with latest models
Version 1.4.1 (2024-07-15)
Bug Fixes
- Fixed issue with printing consensus results for controversial
clusters
- Corrected model mapping in anthropic.py to properly use Claude 3.7
Sonnet
- Fixed undefined has_names variable in consensus validation
- Improved test_pbmc3k.R and added to .gitignore to prevent API key
leakage
Documentation
- Updated model lists in documentation
- Clarified API key setup instructions
- Improved error messages for common issues
Upcoming Features
The following features are planned for future releases:
Version 1.5.0 (Planned)
- Integration with additional single-cell analysis frameworks
- Enhanced support for multi-modal data
- Improved performance for large datasets
- Advanced visualization tools
- Expanded benchmarking across diverse tissues and species
Version 2.0.0 (Planned)
- Complete redesign of the consensus mechanism
- Integration with reference-based methods
- Support for custom model fine-tuning
- Interactive web interface for annotation review
- Comprehensive benchmarking framework
Breaking Changes
This section documents breaking changes that may require updates to
your code.
Version 1.2.0
- Changed the default value of
top_gene_count from 5 to
10
- Modified the return structure of
interactive_consensus_annotation() to include additional
metadata
- Renamed
uncertainty_score to
shannon_entropy for clarity
Version 1.3.0
- Changed the API for custom model registration
- Modified the caching system to use a different file structure
- Updated the required R version to 4.0.0 or higher
Version 1.4.0
- Changed the default models used in examples to Claude 3.7 and Gemini
2.5
- Modified the return structure of
annotate_cell_types()
to include more metadata
- Updated the required package versions for several dependencies
Deprecation Notices
The following features are deprecated and will be removed in future
versions:
simple_consensus() function (since v1.2.0): Use
interactive_consensus_annotation() insteadbasic_visualization() function (since v1.3.0): Use the
new visualization functions instead- Support for older model versions will be gradually phased out as
providers retire them
Acknowledgments
We would like to thank all contributors who have helped improve
mLLMCelltype:
- Core developers: Chen Yang, [List other core developers]
- Contributors: [List contributors]
- Users who reported issues and suggested improvements
How to Cite
If you use mLLMCelltype in your research, please cite:
Yang, C., et al. (2024). mLLMCelltype: Multi-LLM Consensus Architecture for Robust Cell Type Annotation. bioRxiv 2024.04.10.647852; doi: https://doi.org/10.1101/2024.04.10.647852
Feedback and Contributions
We welcome feedback and contributions to improve mLLMCelltype. Please
see our Contributing
Guide for details on how to contribute.
Next Steps
Now that you’ve reviewed the version history, you can: