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Enhanced Protein Generation #10
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- Added protein-specific positional encodings - Implemented structural attention mechanism - Added gradient checkpointing and residual connections - Enhanced sequence validation with structural constraints - Updated MultiHeadAttention implementation - Fixed duplicate layer initialization
- Implemented parallel sequence generation with batch processing - Added advanced sampling strategies (top-k, nucleus, temperature) - Enhanced template-based generation with structural guidance - Added structure prediction feedback loop - Created ProteinTokenizer for text-to-protein conversion - Enhanced sequence validation with structural constraints
- Added real-time structure visualization with py3Dmol - Created ML-driven domain prediction with transformer architecture - Implemented interactive sequence optimization with property prediction - Integrated molecular dynamics with ML-based analysis - Enhanced system with comprehensive protein analysis capabilities
- Added memory_manager.py for efficient memory usage and caching - Created adaptive_processor.py for hardware-specific optimizations - Implemented performance_monitor.py for metrics tracking - Enhanced system with mixed precision training and dynamic optimization - Added comprehensive performance validation capabilities
- Unit tests for optimization components - Integration tests for complete pipeline - Performance benchmarks - Protein structure validation tests - Test fixtures and utilities
- Add main README with project overview - Add architecture documentation - Add advanced features documentation - Add optimization documentation (memory, processing, monitoring) - Add deployment documentation (setup, configuration, monitoring) Documentation provides complete coverage of system components, features, optimization techniques, and deployment procedures.
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Enhanced Protein Generation Implementation
Overview
Enhanced protein generation system with advanced transformer architecture, optimization features, and comprehensive documentation.
Key Features
Implementation Details
Optimization Features
Performance Benchmarks
Documentation
Added comprehensive documentation covering:
Testing
Link to Devin run
https://preview.devin.ai/devin/3be5f4c3b9ba4aa98728802f1f96368a
Future Work
If you have any feedback, you can leave comments in the PR and I'll address them in the app!