epac

Embarrassingly Parallel Array Computing: EPAC is a machine learning workflow builder.

Given a database:

    from sklearn import datasets
    X, y = datasets.make_classification(n_samples=12,
                                        n_features=10,
                                        n_informative=2,
                                        random_state=1)

• You can build a big machine workflow:

    Permutation (Perm) + Cross-validation (CV) of SVM(linear) and SVM(rbf)
    ----------------------------------------------------------------------
             Perms          Perm (Splitter)
        /     |       \
       0      1       2     Samples
              |
              CV            CV (Splitter)
          /   |   \
         0    1    2        Folds
              |
           Methods          Methods (Splitter)
       /           \
    SVM(linear)  SVM(rbf)   Classifiers (Estimator)

using very simple codes:

    from sklearn.svm import SVC
    from epac import Perms, CV, Methods
    perms_cv_svm = Perms(CV(
                     Methods(*[SVC(kernel="linear"), SVC(kernel="rbf")]),
                     n_folds=3),
                     n_perms=3)
    perms_cv_svm.run(X=X, y=y) # Top-down process: computing recognition rates, etc.
    perms_cv_svm.reduce() # Bottom-up process: computing p-values, etc.

Then you can get results like:

ResultSet(
[{'key': SVC(kernel=linear), 'y/test/score_f1': [ 0.5  0.5], 'y/test/score_recall_mean/pval': [ 0.5], 'y/test/score_recall/pval': [ 0.5  0.5], 'y/test/score_accuracy/pval': [ 0.5], 'y/test/score_f1/pval': [ 0.5  0.5], 'y/test/score_precision/pval': [ 0.5  0.5], 'y/test/score_precision': [ 0.5  0.5], 'y/test/score_recall': [ 0.5  0.5], 'y/test/score_accuracy': 0.5, 'y/test/score_recall_mean': 0.5},
 {'key': SVC(kernel=rbf), 'y/test/score_f1': [ 0.5  0.5], 'y/test/score_recall_mean/pval': [ 1.], 'y/test/score_recall/pval': [ 0.  1.], 'y/test/score_accuracy/pval': [ 1.], 'y/test/score_f1/pval': [ 1.  1.], 'y/test/score_precision/pval': [ 1.  1.], 'y/test/score_precision': [ 0.5  0.5], 'y/test/score_recall': [ 0.5  0.5], 'y/test/score_accuracy': 0.5, 'y/test/score_recall_mean': 0.5}])

• Run epac tree in parallel on local multi-core machine or even on DRM system using soma-workflow.

    from epac import LocalEngine
    local_engine = LocalEngine(tree_root=perms_cv_svm, num_processes=2)
    perms_cv_svm = local_engine.run(X=X, y=y)
    perms_cv_svm.reduce()

• Design your own machine learning algorithm as a plug-in node in epac tree.

    ## 1) Design your classifier
    ## =========================
    class MySVC:
        def __init__(self, C=1.0):
            self.C = C
        def transform(self, X, y):
            from sklearn.svm import SVC 
            svc = SVC(C=self.C)
            svc.fit(X, y)
            # "transform" should return a dictionary
            return {"y/pred": svc.predict(X), "y": y}

    ## 2) Design your reducer for recall rates
    ## ===========================================
    from epac.map_reduce.reducers import Reducer  
    class MyReducer(Reducer):
        def reduce(self, result):
            from sklearn.metrics import precision_recall_fscore_support 
            pred_list = []
            # iterate all the results of each classifier
            # then you can design you own reducer!
            for res in result:
                precision, recall, f1_score, support = \
                        precision_recall_fscore_support(res['y'], res['y/pred'])
                pred_list.append({res['key']: recall})
            return pred_list

    ## 3) Build a tree, and then compute results 
    ## =========================================
    from epac import Methods 
    my_svc1 = MySVC(C=1.0)
    my_svc2 = MySVC(C=2.0)
    two_svc = Methods(my_svc1, my_svc2)
    two_svc.reducer = MyReducer()
    #           Methods
    #          /      \
    # MySVC(C=1.0)  MySVC(C=2.0) 
    # top-down process to call transform
    two_svc.run(X=X, y=y)
    # buttom-up process to compute scores
    two_svc.reduce()

You can get results: [{'MySVC(C=1.0)': array([ 1., 1.])}, {'MySVC(C=2.0)': array([ 1., 1.])}]

Important links

Installation http://neurospin.github.io/pylearn-epac/installation.html

Tutorials http://neurospin.github.io/pylearn-epac/tutorials.html

Documentation http://neurospin.github.io/pylearn-epac

Presentation Embarrassingly Parallel Array Computing