├── .gitignore ├── LICENSE ├── README.md ├── bitbirch ├── __init__.py ├── bitbirch.py ├── cluster_analysis.py ├── cluster_control.py ├── plotting_utils.py ├── pruning.py └── refinement.py ├── data ├── BitBIRCH.png ├── chembl_33_np.smi └── image.png ├── development-code ├── bitbirch_dev.py ├── bitbirch_sm_rr_jt.py ├── bitbirch_torch_dev.py └── c_BitBIRCH │ ├── bin │ └── ignore.html │ ├── include │ ├── birch │ │ ├── BFNode.h │ │ ├── BFSubcluster.h │ │ ├── BFTree.h │ │ └── Pair.h │ └── util │ │ ├── Array.h │ │ ├── Instance.h │ │ ├── Integer.h │ │ ├── Smem.h │ │ └── Util.h │ └── src │ ├── birch │ ├── BFNode.c │ ├── BFSubcluster.c │ ├── BFTree.c │ └── Pair.c │ ├── main.c │ └── util │ ├── Array.c │ ├── Instance.c │ ├── Integer.c │ ├── Smem.c │ └── Util.c ├── examples ├── data_splitting │ ├── biogen_logS.csv │ ├── biogen_logS_results.csv │ ├── bitbirch.py │ ├── dataset_splitting.ipynb │ └── lgbm_wrapper.py ├── parallel_birch │ ├── birch_BFs.py │ ├── birch_parallel.py │ ├── chembl_33_np.smi │ ├── parallel_example.ipynb │ ├── sub_final_clustering.sh │ ├── sub_parallel.sh │ └── sub_slurm.sh ├── refinement │ ├── data │ │ ├── BFs reclustering_cluster_metrics.csv │ │ ├── BFs_reclustering_cluster_metrics.csv │ │ ├── diameter_cluster_metrics.csv │ │ ├── diameter_prune_cluster_metrics.csv │ │ ├── diameter_prune_reassign_cluster_metrics.csv │ │ ├── diameter_prune_tolerance_cluster_metrics.csv │ │ ├── diameter_prune_tolerance_reassign_cluster_metrics.csv │ │ └── radius_cluster_metrics.csv │ └── refine_tutorial.ipynb └── simple_birch │ ├── birch_tutorial.ipynb │ ├── data │ ├── diameter_cluster_metrics.csv │ └── refined_cluster_metrics.csv │ └── smiles_assignments.csv └── pyproject.toml /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mqcomplab/bitbirch/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: 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