Model: random-forest

Accuracy

## [1] "Validation data accuracy: 75.42"

## [1] "Test data accuracy: 75"

Accuracy per category

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pred_label precision num_imgs num_correct recall accuracy
cell periphery 0.8421818 1569 1158 0.7380497 0.94976
cytoplasm 0.7351940 1276 1080 0.8463950 0.95320
endosome 0.5388430 689 326 0.4731495 0.94864
er 0.8077396 1755 1315 0.7492877 0.93976
golgi 0.6945107 382 291 0.7617801 0.98248
mitochondrion 0.6627827 1243 967 0.7779566 0.93856
nuclear periphery 0.7811994 1164 964 0.8281787 0.96240
nucleolus 0.8927973 1263 1066 0.8440222 0.97400
nucleus 0.8620470 1627 1356 0.8334358 0.96096
peroxisome 0.4420290 164 61 0.3719512 0.98560
spindle pole 0.5845539 781 439 0.5620999 0.94768
vacuole 0.5374046 587 352 0.5996593 0.95696 
## [1] "Mean precision over classes: 0.7"

## [1] "Median precision over classes: 0.71"

## [1] "Mean recall over classes: 0.7"

## [1] "Median recall over classes: 0.76"

## [1] "Mean accuracy over classes: 0.96"

## [1] "Median accuracy over classes: 0.96"

Confusion matrix

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cell periphery cytoplasm endosome er golgi mitochondrion nuclear periphery nucleolus nucleus peroxisome spindle pole vacuole
cell periphery 1158 127 6 112 81 42 7 1 11 0 1 23
cytoplasm 32 1080 9 82 5 23 3 0 10 0 4 28
endosome 15 44 326 13 7 156 15 0 6 11 75 21
er 158 128 26 1315 21 23 14 0 2 0 0 68
golgi 3 3 0 29 291 18 1 6 0 0 0 31
mitochondrion 3 9 42 14 7 967 75 14 35 17 24 36
nuclear periphery 2 3 2 31 2 20 964 2 83 2 4 49
nucleolus 0 5 2 2 0 23 7 1066 43 2 101 12
nucleus 4 23 13 10 2 27 41 101 1356 1 17 32
peroxisome 0 0 1 0 0 19 1 0 0 61 82 0
spindle pole 0 42 168 3 0 72 1 0 9 44 439 3
vacuole 0 5 10 17 3 69 105 4 18 0 4 352

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Image-level accuracy

## [1] "Mean accuracy over images: 0.95"

## [1] "Median accuracy over images: 1"
label num_imgs num_correct accuracy
cell periphery 7 6 0.8571429
cytoplasm 108 105 0.9722222
endosome 2 1 0.5000000
er 29 27 0.9310345
golgi 2 2 1.0000000
mitochondrion 45 45 1.0000000
nuclear periphery 5 5 1.0000000
nucleolus 7 6 0.8571429
nucleus 69 66 0.9565217
peroxisome 1 0 0.0000000
spindle pole 2 2 1.0000000
vacuole 5 4 0.8000000

Image-level accuracy (at least 10 sub-images)

## [1] "Mean accuracy over images: 0.96"

## [1] "Median accuracy over images: 1"
label num_imgs num_correct accuracy
cell periphery 7 6 0.8571429
cytoplasm 66 64 0.9696970
endosome 2 1 0.5000000
er 27 26 0.9629630
golgi 2 2 1.0000000
mitochondrion 42 42 1.0000000
nuclear periphery 5 5 1.0000000
nucleolus 7 6 0.8571429
nucleus 57 56 0.9824561
peroxisome 1 0 0.0000000
spindle pole 2 2 1.0000000
vacuole 4 4 1.0000000

Misclassifications - false negatives

## [1] "cell periphery"

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## [1] "cytoplasm"

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## [1] "endosome"

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## [1] "er"

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## [1] "golgi"

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## [1] "mitochondrion"

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## [1] "nuclear periphery"

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## [1] "nucleolus"

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## [1] "nucleus"

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## [1] "peroxisome"

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## [1] "spindle pole"

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## [1] "vacuole"

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Misclassifications - false positives

## [1] "cell periphery"

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## [1] "cytoplasm"

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## [1] "endosome"

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## [1] "er"

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## [1] "golgi"

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## [1] "mitochondrion"

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## [1] "nuclear periphery"

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## [1] "nucleolus"

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## [1] "nucleus"

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## [1] "peroxisome"

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## [1] "spindle pole"

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## [1] "vacuole"

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Common mistakes (top 5)

## [1] "True class: peroxisome, predicted as: spindle pole, count: 82"

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## [1] "True class: endosome, predicted as: mitochondrion, count: 156"

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## [1] "True class: spindle pole, predicted as: endosome, count: 168"

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## [1] "True class: vacuole, predicted as: nuclear periphery, count: 105"

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## [1] "True class: vacuole, predicted as: mitochondrion, count: 69"

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