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Table 2 SOM-VN improved precision and recall over CAGT and magnitude-based models

From: Self-organizing maps with variable neighborhoods facilitate learning of chromatin accessibility signal shapes associated with regulatory elements

Sample Method Promoter Enhancer Weak
Precision Recall Precision Recall Precision Recall
A549 CAGT 0.14 0.53 0.24 0.10 0.77 0.58
Magnitude 0.15 1.00 N/A N/A 0.05 0.00
SOM-VN 0.19 0.86 0.29 0.05 0.90 0.67
GM12878 CAGT N/Aa N/A N/A N/A 0.76 1.00
Magnitude N/A N/A N/A N/A 0.82 1.00
SOM-VN 0.60 0.50 N/A N/A 0.82 0.97
B-Cell (L) CAGT N/A N/A 0.12 0.18 0.81 0.76
Magnitude 0.07 0.94 0.60 0.15 0.05 0.00
SOM-VN 0.63 0.13 0.25 0.28 0.83 0.88
B-Cell (H) CAGT N/A N/A 0.27 1.00 0.22 0.00
Magnitude 0.06 0.99 0.11 0.00 0.14 0.00
SOM-VN 0.58 0.36 0.43 0.88 0.93 0.72
Brain (L) Magnitude N/A N/A N/A N/A 0.84 1.00
SOM-VN N/A N/A N/A N/A 0.83 1.00
Brain (H) Magnitude 0.12 1.00 N/A N/A N/A N/A
SOM-VN 0.50 0.33 0.37 0.32 0.81 0.89
H1 (L) CAGT 0.05 0.71 N/A N/A 0.64 0.10
Magnitude 0.09 1.00 N/A N/A 0.05 0.00
SOM-VN 0.22 0.80 N/A N/A 0.89 0.86
H1 (H) CAGT N/A N/A N/A N/A 0.68 1.00
Magnitude N/A N/A N/A N/A 0.78 1.00
SOM-VN 0.57 0.57 N/A N/A 0.76 0.96
Heart (L) CAGT N/A N/A 0.42 0.05 0.76 0.99
Magnitude N/A N/A 0.14 0.00 0.76 1.00
SOM-VN 0.73 0.04 0.45 0.45 0.84 0.92
Heart (H) CAGT N/A N/A 0.36 0.94 0.78 0.20
Magnitude N/A N/A 0.02 0.00 0.72 1.00
SOM-VN 0.25 0.01 0.43 0.96 0.96 0.52
HeLa (L) CAGT N/A N/A N/A N/A 0.74 1.00
Magnitude N/A N/A N/A N/A 0.78 1.00
SOM-VN 0.41 0.66 0.30 0.00 0.84 0.92
HeLa (H) CAGT 0.25 0.12 N/A N/A 0.65 0.94
Magnitude N/A N/A N/A N/A 0.76 1.00
SOM-VN 0.32 0.73 0.35 0.04 0.81 0.76
Stomach (L) CAGT N/A N/A N/A N/A 0.69 1.00
Magnitude N/A N/A 0.05 0.00 0.74 1.00
SOM-VN 0.60 0.22 0.41 0.11 0.77 0.97
Stomach (H) CAGT 0.22 0.14 0.30 0.80 0.65 0.18
Magnitude 0.14 0.00 N/A N/A 0.70 1.00
SOM-VN 0.61 0.31 0.38 0.88 0.91 0.62
  1. aN/A values indicate that no shapes were learned for the corresponding RE in the corresponding sample