Model: DeepYeast

Accuracy

DeepYeast accuracy on validation data was 0.869, and on test data 0.867.

Accuracy per category

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Class Precision Number of cell images Correct calls Recall Accuracy
cell periphery 0.948 1569 1417 0.903 0.982
cytoplasm 0.857 1276 1158 0.908 0.975
endosome 0.769 689 447 0.649 0.970
er 0.945 1755 1539 0.877 0.976
golgi 0.766 382 324 0.848 0.987
mitochondrion 0.889 1243 1132 0.911 0.980
nuclear periphery 0.901 1164 1056 0.907 0.982
nucleolus 0.859 1263 1112 0.880 0.973
nucleus 0.922 1627 1386 0.852 0.971
peroxisome 0.704 164 131 0.799 0.993
spindle pole 0.711 781 595 0.762 0.966
vacuole 0.718 587 542 0.923 0.979

Across classes, the mean and median precision were 0.83 and 0.86 respectively, recall 0.85 and 0.88, and accuracy 0.98 and 0.98.

Confusion matrix

Each element \(M_{ij}\) in the confusion matrix \(M\) shows the number of observations from class \(i\) which were predicted as class \(j\). The confusion matrix in the figure below has been normalized by class support size (each row has been divided by the number of elements in that class).

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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

To see misclassification patterns more clearly, the diagonal of the confusion matrix has been excluded in the following figure.

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Protein classification accuracy

Across proteins, the mean and median accuracy were 0.989 and 1.000, respectively.

Class Number of proteins Correct calls Accuracy
cell periphery 7 7 1.000
cytoplasm 108 107 0.991
endosome 2 2 1.000
er 29 29 1.000
golgi 2 2 1.000
mitochondrion 45 45 1.000
nuclear periphery 5 5 1.000
nucleolus 7 7 1.000
nucleus 69 67 0.971
peroxisome 1 1 1.000
spindle pole 2 2 1.000
vacuole 5 5 1.000

Protein classification accuracy (at least 10 cell images)

Across proteins with at least 10 cell images, the mean and median accuracy were 1.000 and 1.000, respectively.

Class Number of proteins Correct calls 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

Original and scaled cell images, respectively.

## [1] "cell periphery, false negative rate: 0.097"

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## [1] "cytoplasm, false negative rate: 0.092"

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## [1] "endosome, false negative rate: 0.351"

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## [1] "er, false negative rate: 0.123"

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## [1] "golgi, false negative rate: 0.152"

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## [1] "mitochondrion, false negative rate: 0.089"

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## [1] "nuclear periphery, false negative rate: 0.093"

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## [1] "nucleolus, false negative rate: 0.12"

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## [1] "nucleus, false negative rate: 0.148"

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## [1] "peroxisome, false negative rate: 0.201"

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## [1] "spindle pole, false negative rate: 0.238"

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## [1] "vacuole, false negative rate: 0.077"

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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 (total images 164), predicted as: spindle pole, count: 18 (11.0% error)"

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## [1] "True class: spindle pole (total images 781), predicted as: endosome, count: 77 (9.9% error)"

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## [1] "True class: nucleus (total images 1627), predicted as: nucleolus, count: 135 (8.3% error)"

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## [1] "True class: endosome (total images 689), predicted as: vacuole, count: 56 (8.1% error)"

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## [1] "True class: endosome (total images 689), predicted as: spindle pole, count: 49 (7.1% error)"

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