Model: vgg_A_bn

Accuracy

## [1] "Validation data accuracy: 86.94"

## [1] "Test data accuracy: 86.71"

Accuracy per category

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pred_label precision num_imgs num_correct recall accuracy
cell periphery 0.9478261 1569 1417 0.9031230 0.98160
cytoplasm 0.8565089 1276 1158 0.9075235 0.97504
endosome 0.7693632 689 447 0.6487663 0.96992
er 0.9447514 1755 1539 0.8769231 0.97552
golgi 0.7659574 382 324 0.8481675 0.98744
mitochondrion 0.8892380 1243 1132 0.9106999 0.97984
nuclear periphery 0.9010239 1164 1056 0.9072165 0.98208
nucleolus 0.8593509 1263 1112 0.8804434 0.97336
nucleus 0.9221557 1627 1386 0.8518746 0.97136
peroxisome 0.7043011 164 131 0.7987805 0.99296
spindle pole 0.7108722 781 595 0.7618438 0.96576
vacuole 0.7178808 587 542 0.9233390 0.97936 
## [1] "Mean precision over classes: 0.83"

## [1] "Median precision over classes: 0.86"

## [1] "Mean recall over classes: 0.85"

## [1] "Median recall over classes: 0.88"

## [1] "Mean accuracy over classes: 0.98"

## [1] "Median accuracy over classes: 0.98"

Confusion matrix

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cell periphery cytoplasm endosome er golgi mitochondrion nuclear periphery nucleolus nucleus peroxisome spindle pole vacuole
cell periphery 1417 52 8 43 4 7 8 4 6 0 3 17
cytoplasm 18 1158 15 17 2 8 6 7 7 0 25 13
endosome 2 44 447 5 30 28 9 0 5 14 49 56
er 52 31 12 1539 32 21 21 3 1 6 6 31
golgi 1 2 0 9 324 5 5 11 0 1 12 12
mitochondrion 1 10 4 5 9 1132 9 9 20 12 12 20
nuclear periphery 0 6 4 8 4 11 1056 4 21 4 15 31
nucleolus 0 2 5 0 0 8 4 1112 45 0 77 10
nucleus 2 22 4 1 6 18 12 135 1386 0 21 20
peroxisome 0 0 2 0 3 6 1 1 1 131 18 1
spindle pole 2 25 77 1 1 18 33 1 8 18 595 2
vacuole 0 0 3 1 8 11 8 7 3 0 4 542

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Image-level accuracy

## [1] "Mean accuracy over images: 0.99"

## [1] "Median accuracy over images: 1"
label num_imgs num_correct accuracy
cell periphery 7 7 1.0000000
cytoplasm 108 107 0.9907407
endosome 2 2 1.0000000
er 29 29 1.0000000
golgi 2 2 1.0000000
mitochondrion 45 45 1.0000000
nuclear periphery 5 5 1.0000000
nucleolus 7 7 1.0000000
nucleus 69 67 0.9710145
peroxisome 1 1 1.0000000
spindle pole 2 2 1.0000000
vacuole 5 5 1.0000000

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

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

## [1] "Median accuracy over images: 1"
label num_imgs num_correct accuracy
cell periphery 7 7 1
cytoplasm 66 66 1
endosome 2 2 1
er 27 27 1
golgi 2 2 1
mitochondrion 42 42 1
nuclear periphery 5 5 1
nucleolus 7 7 1
nucleus 57 57 1
peroxisome 1 1 1
spindle pole 2 2 1
vacuole 4 4 1

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: 18"

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## [1] "True class: spindle pole, predicted as: endosome, count: 77"

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## [1] "True class: nucleus, predicted as: nucleolus, count: 135"

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## [1] "True class: endosome, predicted as: vacuole, count: 56"

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## [1] "True class: endosome, predicted as: spindle pole, count: 49"

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