Branch Marker Analysis
Generated by scripts/run_branch_marker_analysis.py.
A branch marker is a feature-state whose witness set matches, or nearly matches, a consensus clade. This is a diagnostic for shared derived readings, not a proof that the branch is historically clean.
Outputs
outputs/tables/branch_marker_scores.csvoutputs/tables/branch_marker_best.csvoutputs/tables/branch_marker_leave_one_out.csvoutputs/tables/branch_marker_leave_one_out_summary.csvpaper/tables/branch_marker_best.texpaper/tables/branch_marker_leave_one_out.tex
Best Full-Data Markers
| dataset | node_id | node_members | node_size | node_support_fraction | feature | state | state_witnesses | state_size | tp | fp | fn | tn | precision | recall | specificity | f1 | jaccard | accuracy | mcc | fisher_p | perfect_marker |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| athanasius_epistles_data_bin_csv | N1 | B C | 2 | 1 | 1Cor.9.16.2 | 1 | B C D F G | 5 | 2 | 3 | 0 | 7 | 0.4 | 1 | 0.7 | 0.571429 | 0.4 | 0.75 | 0.52915 | 0.151515 | 0 |
| athanasius_epistles_data_bin_csv | N1 | B C | 2 | 1 | Phil.2.5.1 | 0 | A Ath B C U1 | 5 | 2 | 3 | 0 | 7 | 0.4 | 1 | 0.7 | 0.571429 | 0.4 | 0.75 | 0.52915 | 0.151515 | 0 |
| athanasius_epistles_data_bin_csv | N1 | B C | 2 | 1 | Eph.3.19.2 | 1 | B P46 | 2 | 1 | 1 | 1 | 9 | 0.5 | 0.5 | 0.9 | 0.5 | 0.333333 | 0.833333 | 0.4 | 0.318182 | 0 |
| athanasius_epistles_data_bin_csv | N2 | F G | 2 | 1 | Rom.8.22.2 | 1 | F G | 2 | 2 | 0 | 0 | 10 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 0.0151515 | 1 |
| athanasius_epistles_data_bin_csv | N2 | F G | 2 | 1 | Phil.2.6.1 | 1 | F G P46 | 3 | 2 | 1 | 0 | 9 | 0.666667 | 1 | 0.9 | 0.8 | 0.666667 | 0.916667 | 0.774597 | 0.0454545 | 0 |
| athanasius_epistles_data_bin_csv | N2 | F G | 2 | 1 | Rom.15.19.1.b2 | 1 | D F G | 3 | 2 | 1 | 0 | 9 | 0.666667 | 1 | 0.9 | 0.8 | 0.666667 | 0.916667 | 0.774597 | 0.0454545 | 0 |
| athanasius_epistles_data_bin_csv | N3 | M1739 U1 | 2 | 1 | Col.1.16.2 | 1 | M1739 P46 U1 | 3 | 2 | 1 | 0 | 9 | 0.666667 | 1 | 0.9 | 0.8 | 0.666667 | 0.916667 | 0.774597 | 0.0454545 | 0 |
| athanasius_epistles_data_bin_csv | N3 | M1739 U1 | 2 | 1 | Eph.3.18.1 | 1 | A M1739 M223 M2423 U1 | 5 | 2 | 3 | 0 | 7 | 0.4 | 1 | 0.7 | 0.571429 | 0.4 | 0.75 | 0.52915 | 0.151515 | 0 |
| athanasius_epistles_data_bin_csv | N3 | M1739 U1 | 2 | 1 | Phil.2.9.1 | 1 | A C M1739 P46 U1 | 5 | 2 | 3 | 0 | 7 | 0.4 | 1 | 0.7 | 0.571429 | 0.4 | 0.75 | 0.52915 | 0.151515 | 0 |
| athanasius_epistles_data_bin_csv | N4 | M223 M2423 | 2 | 1 | 1Cor.9.16.1 | 1 | M223 M2423 | 2 | 2 | 0 | 0 | 10 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 0.0151515 | 1 |
| athanasius_epistles_data_bin_csv | N4 | M223 M2423 | 2 | 1 | 1Cor.15.47.1.b2 | 1 | A M223 M2423 | 3 | 2 | 1 | 0 | 9 | 0.666667 | 1 | 0.9 | 0.8 | 0.666667 | 0.916667 | 0.774597 | 0.0454545 | 0 |
| athanasius_epistles_data_bin_csv | N4 | M223 M2423 | 2 | 1 | Phil.2.5.2 | 0 | Ath M223 M2423 | 3 | 2 | 1 | 0 | 9 | 0.666667 | 1 | 0.9 | 0.8 | 0.666667 | 0.916667 | 0.774597 | 0.0454545 | 0 |
| athanasius_epistles_data_bin_csv | N5 | D F G | 3 | 0.833333 | Rom.15.19.1.b2 | 1 | D F G | 3 | 3 | 0 | 0 | 9 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 0.00454545 | 1 |
| athanasius_epistles_data_bin_csv | N5 | D F G | 3 | 0.833333 | 1Cor.11.2.2.b2 | 1 | C D F G | 4 | 3 | 1 | 0 | 8 | 0.75 | 1 | 0.888889 | 0.857143 | 0.75 | 0.916667 | 0.816497 | 0.0181818 | 0 |
| athanasius_epistles_data_bin_csv | N5 | D F G | 3 | 0.833333 | Rom.15.19.1.b1 | 0 | Ath D F G | 4 | 3 | 1 | 0 | 8 | 0.75 | 1 | 0.888889 | 0.857143 | 0.75 | 0.916667 | 0.816497 | 0.0181818 | 0 |
| athanasius_epistles_data_bin_csv | N6 | A B C M1739 P46 U1 | 6 | 0.833333 | 1Cor.11.2.1 | 0 | A Ath B C M1739 P46 U1 | 7 | 6 | 1 | 0 | 5 | 0.857143 | 1 | 0.833333 | 0.923077 | 0.857143 | 0.916667 | 0.845154 | 0.00757576 | 0 |
| athanasius_epistles_data_bin_csv | N6 | A B C M1739 P46 U1 | 6 | 0.833333 | Phil.2.9.1 | 1 | A C M1739 P46 U1 | 5 | 5 | 0 | 1 | 6 | 1 | 0.833333 | 1 | 0.909091 | 0.833333 | 0.916667 | 0.845154 | 0.00757576 | 0 |
| athanasius_epistles_data_bin_csv | N6 | A B C M1739 P46 U1 | 6 | 0.833333 | 1Cor.4.6.3.b1 | 1 | A B C D M1739 M223 P46 U1 | 8 | 6 | 2 | 0 | 4 | 0.75 | 1 | 0.666667 | 0.857143 | 0.75 | 0.833333 | 0.707107 | 0.030303 | 0 |
| athanasius_epistles_data_bin_csv | N7 | A Ath B C M1739 M223 M2423 P46 U1 | 9 | 0.833333 | Rom.15.19.1.b2 | 0 | A Ath B C M1739 M223 M2423 P46 U1 | 9 | 9 | 0 | 0 | 3 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 0.00454545 | 1 |
| athanasius_epistles_data_bin_csv | N7 | A Ath B C M1739 M223 M2423 P46 U1 | 9 | 0.833333 | Rom.8.22.2 | 0 | A Ath B C D M1739 M223 M2423 P46 U1 | 10 | 9 | 1 | 0 | 2 | 0.9 | 1 | 0.666667 | 0.947368 | 0.9 | 0.916667 | 0.774597 | 0.0454545 | 0 |
| athanasius_epistles_data_bin_csv | N7 | A Ath B C M1739 M223 M2423 P46 U1 | 9 | 0.833333 | 1Cor.11.2.2.b2 | 0 | A Ath B M1739 M223 M2423 P46 U1 | 8 | 8 | 0 | 1 | 3 | 1 | 0.888889 | 1 | 0.941176 | 0.888889 | 0.916667 | 0.816497 | 0.0181818 | 0 |
| athanasius_epistles_data_multistate_csv | N1 | B C | 2 | 1 | 1Cor.11.2.3 | 4 | C | 1 | 1 | 0 | 1 | 10 | 1 | 0.5 | 1 | 0.666667 | 0.5 | 0.916667 | 0.6742 | 0.166667 | 0 |
| athanasius_epistles_data_multistate_csv | N1 | B C | 2 | 1 | 1Cor.15.55.1 | 2 | B C M1739 P46 U1 | 5 | 2 | 3 | 0 | 7 | 0.4 | 1 | 0.7 | 0.571429 | 0.4 | 0.75 | 0.52915 | 0.151515 | 0 |
| athanasius_epistles_data_multistate_csv | N1 | B C | 2 | 1 | 1Cor.9.16.2 | 2 | B C D F G | 5 | 2 | 3 | 0 | 7 | 0.4 | 1 | 0.7 | 0.571429 | 0.4 | 0.75 | 0.52915 | 0.151515 | 0 |
| athanasius_epistles_data_multistate_csv | N2 | F G | 2 | 1 | 1Cor.4.6.3 | 5 | F G | 2 | 2 | 0 | 0 | 10 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 0.0151515 | 1 |
| athanasius_epistles_data_multistate_csv | N2 | F G | 2 | 1 | 1Cor15.54.1 | 5 | F G | 2 | 2 | 0 | 0 | 10 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 0.0151515 | 1 |
| athanasius_epistles_data_multistate_csv | N2 | F G | 2 | 1 | Rom.8.22.2 | 2 | F G | 2 | 2 | 0 | 0 | 10 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 0.0151515 | 1 |
| athanasius_epistles_data_multistate_csv | N3 | M1739 U1 | 2 | 1 | Col.1.16.2 | 2 | M1739 P46 U1 | 3 | 2 | 1 | 0 | 9 | 0.666667 | 1 | 0.9 | 0.8 | 0.666667 | 0.916667 | 0.774597 | 0.0454545 | 0 |
| athanasius_epistles_data_multistate_csv | N3 | M1739 U1 | 2 | 1 | 1Cor15.54.1 | 2 | U1 | 1 | 1 | 0 | 1 | 10 | 1 | 0.5 | 1 | 0.666667 | 0.5 | 0.916667 | 0.6742 | 0.166667 | 0 |
| athanasius_epistles_data_multistate_csv | N3 | M1739 U1 | 2 | 1 | 1Cor.15.55.1 | 2 | B C M1739 P46 U1 | 5 | 2 | 3 | 0 | 7 | 0.4 | 1 | 0.7 | 0.571429 | 0.4 | 0.75 | 0.52915 | 0.151515 | 0 |
Leave-One-Out Summary
| dataset | node_id | folds | member_folds | top_marker_accuracy | top_marker_member_accuracy | top_marker_nonmember_accuracy | folds_with_perfect_train_marker | mean_perfect_train_marker_count | perfect_marker_vote_accuracy | mean_perfect_marker_correct_fraction |
|---|---|---|---|---|---|---|---|---|---|---|
| athanasius_epistles_data_bin_csv | N1 | 12 | 2 | 0.333333 | 0.5 | 0.3 | 0 | 0 | nan | nan |
| athanasius_epistles_data_bin_csv | N2 | 12 | 2 | 1 | 1 | 1 | 12 | 1.16667 | 0.833333 | 0.916667 |
| athanasius_epistles_data_bin_csv | N3 | 12 | 2 | 0.916667 | 1 | 0.9 | 1 | 0.0833333 | 0 | 0 |
| athanasius_epistles_data_bin_csv | N4 | 12 | 2 | 0.916667 | 0.5 | 1 | 12 | 1.25 | 0.833333 | 0.875 |
| athanasius_epistles_data_bin_csv | N5 | 12 | 3 | 0.916667 | 0.666667 | 1 | 12 | 1.25 | 0.833333 | 0.875 |
| athanasius_epistles_data_bin_csv | N6 | 12 | 6 | 0.5 | 0.666667 | 0.333333 | 2 | 0.166667 | 0 | 0 |
| athanasius_epistles_data_bin_csv | N7 | 12 | 9 | 0.916667 | 1 | 0.666667 | 12 | 1.25 | 0.916667 | 0.875 |
| athanasius_epistles_data_multistate_csv | N1 | 12 | 2 | 0.833333 | 0 | 1 | 1 | 0.0833333 | 0 | 0 |
| athanasius_epistles_data_multistate_csv | N2 | 12 | 2 | 1 | 1 | 1 | 12 | 4.75 | 0.916667 | 0.892593 |
| athanasius_epistles_data_multistate_csv | N3 | 12 | 2 | 0.833333 | 0.5 | 0.9 | 2 | 0.166667 | 0 | 0 |
| athanasius_epistles_data_multistate_csv | N4 | 12 | 2 | 0.833333 | 0 | 1 | 12 | 1.58333 | 0.666667 | 0.763889 |
| athanasius_epistles_data_multistate_csv | N5 | 12 | 3 | 0.916667 | 0.666667 | 1 | 12 | 5.41667 | 1 | 0.949074 |
| athanasius_epistles_data_multistate_csv | N6 | 12 | 6 | 1 | 1 | 1 | 12 | 1.33333 | 0.916667 | 0.833333 |
| athanasius_epistles_data_multistate_csv | N7 | 12 | 9 | 0.833333 | 0.888889 | 0.666667 | 12 | 1.25 | 0.833333 | 0.902778 |