Random-Exemplar Similarity

Generated by scripts/run_isolation_similarity.py.

This is an isolation-style similarity experiment, not sklearn's anomaly-detection IsolationForest. Each trial samples exemplar witnesses and feature columns, assigns every witness to the nearest sampled exemplar, and turns repeated co-assignment into a distance matrix.

Outputs

outputs/tables/isolation_random_exemplar__athanasius_epistles_data_bin_csv__distance_matrix.csv
outputs/tables/isolation_random_exemplar__athanasius_epistles_data_bin_csv__similarity_matrix.csv
outputs/figures/athanasius_epistles_data_bin_csv_isolation_dendrogram.png
outputs/figures/athanasius_epistles_data_bin_csv_isolation_distance_vs_ultrametric.png
outputs/tables/isolation_random_exemplar__athanasius_epistles_data_multistate_csv__distance_matrix.csv
outputs/tables/isolation_random_exemplar__athanasius_epistles_data_multistate_csv__similarity_matrix.csv
outputs/figures/athanasius_epistles_data_multistate_csv_isolation_dendrogram.png
outputs/figures/athanasius_epistles_data_multistate_csv_isolation_distance_vs_ultrametric.png
outputs/tables/isolation_similarity_summary.csv
outputs/tables/isolation_clade_separation.csv
paper/tables/isolation_similarity_summary.tex

Summary

dataset	trials	exemplar_count	feature_fraction	mean_distance	ultrametricity_score	mae_to_cophenetic_ultrametric	rmse_to_cophenetic_ultrametric	spearman_vs_hamming	mean_clade_similarity_separation
athanasius_epistles_data_bin_csv	500	3	0.5	0.646879	0.0136364	0.0673156	0.0952269	0.961923	0.413188
athanasius_epistles_data_multistate_csv	500	3	0.5	0.61197	0.0227273	0.0565714	0.0790267	0.939394	0.463517

Clade Separation

dataset	node_id	node_members	node_size	within_similarity	cross_similarity	similarity_separation	support_fraction
athanasius_epistles_data_bin_csv	N2	F G	2	0.908	0.2307	0.6773	1
athanasius_epistles_data_bin_csv	N4	M223 M2423	2	0.862	0.2648	0.5972	1
athanasius_epistles_data_bin_csv	N5	D F G	3	0.682667	0.226593	0.456074	0.833333
athanasius_epistles_data_bin_csv	N3	M1739 U1	2	0.74	0.3584	0.3816	1
athanasius_epistles_data_bin_csv	N1	B C	2	0.732	0.3775	0.3545	1
athanasius_epistles_data_bin_csv	N6	A B C M1739 P46 U1	6	0.509733	0.278056	0.231678	0.833333
athanasius_epistles_data_bin_csv	N7	A Ath B C M1739 M223 M2423 P46 U1	9	0.420556	0.226593	0.193963	0.833333
athanasius_epistles_data_multistate_csv	N2	F G	2	0.976	0.2273	0.7487	1
athanasius_epistles_data_multistate_csv	N4	M223 M2423	2	0.944	0.3298	0.6142	1
athanasius_epistles_data_multistate_csv	N5	D F G	3	0.777333	0.203111	0.574222	0.833333
athanasius_epistles_data_multistate_csv	N3	M1739 U1	2	0.784	0.407	0.377	1
athanasius_epistles_data_multistate_csv	N6	A B C M1739 P46 U1	6	0.612	0.287667	0.324333	0.833333
athanasius_epistles_data_multistate_csv	N1	B C	2	0.746	0.431	0.315	1
athanasius_epistles_data_multistate_csv	N7	A Ath B C M1739 M223 M2423 P46 U1	9	0.494278	0.203111	0.291167	0.833333