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Implemented a new lookup-based TFBIND8 function that retrieves binding scores from a pre-computed dataset. This implements the BoTorch SyntheticTestFunction API and can be used with the genetic algorithm optimizer. Key changes: - Add TFBIND8Lookup class with data loading from variationalsearch GitHub repo - Add unit tests for all class functionality - Add Hydra config for the TFBIND8 benchmark - Update test_functions/__init__.py to expose the new function
- Add TRPBLookup: A 4-residue tryptophan synthase benchmark - Add DHFRLookup: A 9-mer dihydrofolate reductase benchmark - Create synthetic data for both benchmarks with plans to replace with real data - Add comprehensive tests and Hydra configs for both benchmarks - Update __init__.py files to expose the new benchmarks 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <noreply@anthropic.com>
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This PR adds three lookup-based benchmark functions for biological sequence optimization:
All implementations follow a consistent pattern, providing:
These benchmarks will help us compare algorithm performance on biologically-motivated sequence optimization
tasks against Ehrlich functions.