Closed mattvan83 closed 4 years ago
I don't see an error msg here - post the very end of the output also?
also, for n=100 samples, you don't need 250 repetitions. 50 should be fine.
for debugging purposes, just run it with 10 reps, and see if it finishes?
The problem is that nothing comes after what what I outputed. All repetitions have run but the program seems to be blocked thereafter.
that's very weird - I will try look into this over the weekend
Hi Matthieu,
I ran neuropredict with your 1D feature sets on my laptop with the latest version (from #51), and it completed fine - see below.. Obviously there most things are different here (model, version etc), but I don't think 1D features are the problem. Try random forests model with only 10 reps?
(base) $ 17:37:15 SQuark-3 Sources >> neuropredict -m meta_data.csv -d mask_WMpet_av45_early.ero1.* -n 10 -c 1
neuropredict version 0.6.dev3+21.gee9da15.dirty for Classification
Positive class inferred for AUC calculation: DIS
Requested features for analysis:
get_data_matrix from /Users/Reddy/Downloads/Sources/mask_WMpet_av45_early.ero1.25mm.csv
get_data_matrix from /Users/Reddy/Downloads/Sources/mask_WMpet_av45_early.ero1.5mm.csv
Data import is done.
Requested processing for the following subgroups:
CN,DIS
--------------------------------------------------------------------------------
Processing subgroup : CN,DIS (1/1)
--------------------------------------------------------------------------------
CN_DIS:
101 samples, 2 modalities, dims: [1, 1]
Identifiers: 0, 1
Attributes:
Classes n=2, sizes CN: 71, DIS: 30
Ignoring imputation strategy chosen, as no missing data were found!
CURRENT EXPERIMENT:
--------------------------------------------------
Training percentage : 0.5
Number of CV repetitions : 10
Number of processors : 1
Dim reduction method : variancethreshold
Dim reduction size : tenth
Predictive model chosen : randomforestclassifier
Grid search level : light
Estimated chance accuracy : 0.500
Saving results to:
/Users/Reddy/Downloads/Sources/neuropredict_results/CN_DIS
CV run 0 dataset 0 : accuracy_score 0.667 balanced_accuracy_score 0.529
CV run 0 dataset 1 : accuracy_score 0.627 balanced_accuracy_score 0.529
CV run 1 dataset 0 : accuracy_score 0.784 balanced_accuracy_score 0.690
CV run 1 dataset 1 : accuracy_score 0.725 balanced_accuracy_score 0.630
CV run 2 dataset 0 : accuracy_score 0.529 balanced_accuracy_score 0.670
CV run 2 dataset 1 : accuracy_score 0.549 balanced_accuracy_score 0.682
CV run 3 dataset 0 : accuracy_score 0.725 balanced_accuracy_score 0.669
CV run 3 dataset 1 : accuracy_score 0.667 balanced_accuracy_score 0.647
CV run 4 dataset 0 : accuracy_score 0.765 balanced_accuracy_score 0.682
CV run 4 dataset 1 : accuracy_score 0.745 balanced_accuracy_score 0.691
CV run 5 dataset 0 : accuracy_score 0.706 balanced_accuracy_score 0.603
CV run 5 dataset 1 : accuracy_score 0.686 balanced_accuracy_score 0.548
CV run 6 dataset 0 : accuracy_score 0.725 balanced_accuracy_score 0.619
CV run 6 dataset 1 : accuracy_score 0.647 balanced_accuracy_score 0.625
CV run 7 dataset 0 : accuracy_score 0.725 balanced_accuracy_score 0.678
CV run 7 dataset 1 : accuracy_score 0.784 balanced_accuracy_score 0.718
CV run 8 dataset 0 : accuracy_score 0.706 balanced_accuracy_score 0.575
CV run 8 dataset 1 : accuracy_score 0.686 balanced_accuracy_score 0.562
CV run 9 dataset 0 : accuracy_score 0.725 balanced_accuracy_score 0.691
CV run 9 dataset 1 : accuracy_score 0.706 balanced_accuracy_score 0.676
Results saved to /Users/Reddy/Downloads/Sources/neuropredict_results/CN_DIS/results_neuropredict.pkl
Error in removing temp dir - remove it yourself:
{} /Users/Reddy/Downloads/Sources/neuropredict_results/CN_DIS/temp_dump
Metrics : accuracy_score, balanced_accuracy_score, area_under_roc
# runs : 20, # datasets : 2
accuracy_score
0 : median 0.7255 SD 0.0662
1 : median 0.6863 SD 0.0625
balanced_accuracy_score
0 : median 0.6695 SD 0.0532
1 : median 0.6388 SD 0.0618
area_under_roc
0 : median 0.7272 SD 0.0510
1 : median 0.6954 SD 0.0715
Results have been saved to
/Users/Reddy/Downloads/Sources/neuropredict_results/CN_DIS/results_neuropredict.pkl
All done.
Also, using the latest stable release from pypi 0.5.2 also works (after the fix for get_data_matrix()
).. I'd say something in your setup isn't right.
(base) $ 18:20:58 SQuark-3 Sources >> neuropredict -m meta_data.csv -d mask_WMpet_av45_early.ero1.* -n 10 -c 1
Positive class inferred for AUC calculation: CN
Running neuropredict 0.5.2
Requested features for analysis:
get_data_matrix from /Users/Reddy/Downloads/Sources/mask_WMpet_av45_early.ero1.25mm.csv
get_data_matrix from /Users/Reddy/Downloads/Sources/mask_WMpet_av45_early.ero1.5mm.csv
Ignoring imputation strategy chosen, as no missing data were found!
Data import is done.
Requested processing for the following subgroups:
DIS,CN
--------------------------------------------------------------------------------
Processing subgroup : DIS,CN (1/1)
--------------------------------------------------------------------------------
Training percentage : 0.5
Number of CV repetitions : 10
Classifier chosen : randomforestclassifier
Feature selection chosen : variancethreshold
Level of grid search : light
Number of processors : 1
Saving the results to
/Users/Reddy/Downloads/Sources/neuropredict_results/CN_DIS
-------------------------
All datasets contain:
101 samples, 2 classes, 1 features
Class CN : 71 samples
Class DIS : 30 samples
-------------------------
Estimated chance accuracy : 0.500
Different classes in the training set are stratified to match the smallest class!
CV trial 0 feature 0 mask_WMpet_av45_early.ero1.25mm : balanced accuracy: 0.7369 weighted AUC: 0.7542
CV trial 0 feature 1 mask_WMpet_av45_early.ero1.5mm : balanced accuracy: 0.7458 weighted AUC: 0.8024
CV trial 1 feature 0 mask_WMpet_av45_early.ero1.25mm : balanced accuracy: 0.7702 weighted AUC: 0.8173
CV trial 1 feature 1 mask_WMpet_av45_early.ero1.5mm : balanced accuracy: 0.7768 weighted AUC: 0.7911
CV trial 2 feature 0 mask_WMpet_av45_early.ero1.25mm : balanced accuracy: 0.7702 weighted AUC: 0.7601
CV trial 2 feature 1 mask_WMpet_av45_early.ero1.5mm : balanced accuracy: 0.6256 weighted AUC: 0.6708
CV trial 3 feature 0 mask_WMpet_av45_early.ero1.25mm : balanced accuracy: 0.7304 weighted AUC: 0.7423
CV trial 3 feature 1 mask_WMpet_av45_early.ero1.5mm : balanced accuracy: 0.6815 weighted AUC: 0.7631
CV trial 4 feature 0 mask_WMpet_av45_early.ero1.25mm : balanced accuracy: 0.7637 weighted AUC: 0.7274
CV trial 4 feature 1 mask_WMpet_av45_early.ero1.5mm : balanced accuracy: 0.5190 weighted AUC: 0.5958
CV trial 5 feature 0 mask_WMpet_av45_early.ero1.25mm : balanced accuracy: 0.7637 weighted AUC: 0.8030
CV trial 5 feature 1 mask_WMpet_av45_early.ero1.5mm : balanced accuracy: 0.7458 weighted AUC: 0.7815
CV trial 6 feature 0 mask_WMpet_av45_early.ero1.25mm : balanced accuracy: 0.7256 weighted AUC: 0.7357
CV trial 6 feature 1 mask_WMpet_av45_early.ero1.5mm : balanced accuracy: 0.7167 weighted AUC: 0.6839
CV trial 7 feature 0 mask_WMpet_av45_early.ero1.25mm : balanced accuracy: 0.6750 weighted AUC: 0.6756
CV trial 7 feature 1 mask_WMpet_av45_early.ero1.5mm : balanced accuracy: 0.6262 weighted AUC: 0.5863
CV trial 8 feature 0 mask_WMpet_av45_early.ero1.25mm : balanced accuracy: 0.6905 weighted AUC: 0.6500
CV trial 8 feature 1 mask_WMpet_av45_early.ero1.5mm : balanced accuracy: 0.6435 weighted AUC: 0.6685
CV trial 9 feature 0 mask_WMpet_av45_early.ero1.25mm : balanced accuracy: 0.6637 weighted AUC: 0.6869
CV trial 9 feature 1 mask_WMpet_av45_early.ero1.5mm : balanced accuracy: 0.6548 weighted AUC: 0.6827
The most frequently selected parameter values are:
For feature set 0 : mask_WMpet_av45_early.ero1.25mm
random_forest_clf__criterion : gini
random_forest_clf__max_features : sqrt
random_forest_clf__min_samples_leaf : 1
random_forest_clf__n_estimators : 50
For feature set 1 : mask_WMpet_av45_early.ero1.5mm
random_forest_clf__criterion : gini
random_forest_clf__max_features : sqrt
random_forest_clf__min_samples_leaf : 1
random_forest_clf__n_estimators : 50
Exporting accuracy distribution .. Done.
Exporting confusion matrices .. Done.
Exporting misclassfiication rates .. Done.
Exporting feature importance values .. Done.
Exporting subject-wise misclf frequencies .. Done.
Median performance summary:
feature 0 mask_WMpet_av45_early.ero1.25mm : balanced accuracy 0.73 AUC 0.74
feature 1 mask_WMpet_av45_early.ero1.5mm : balanced accuracy 0.67 AUC 0.68
Saving the visualizations to
/Users/Reddy/Downloads/Sources/neuropredict_results
reopen if you still find it as an issue.
Hello,
I have problems when using multiple 1-D features with the following command:
The CV trial were well launched for the first subgroup CN,MCI for both 1-D features but it seemed that at the end of CV trials the process got stuck at this stage:
If I launch the previous command line with only one 1-D feature as follows, everything is going well:
Do you have any idea?
Best,
Matthieu
Sources.zip