vflow 0.1.1

A framework for doing stability analysis with PCS.

A library for making stability analysis simple, following the veridical data-science framework.

Why use vflow?

Using vflow's simple wrappers easily enables many best practices for data science, and makes writing pipelines easy.

Stability	Computation	Reproducibility
Replace a single function (e.g. preprocessing) with a set of functions and easily assess the stability of downstream results	Automatic parallelization and caching throughout the pipeline	Automatic experiment tracking and saving

Here we show a simple example of an entire data-science pipeline with several perturbations (e.g. different data subsamples, models, and metrics) written simply using vflow.

import sklearn
from sklearn.metrics import accuracy_score, balanced_accuracy_score
from vflow import init_args, Vset

# initialize data
X, y = sklearn.datasets.make_classification()
X_train, X_test, y_train, y_test = init_args(
    sklearn.model_selection.train_test_split(X, y),
    names=['X_train', 'X_test', 'y_train', 'y_test']  # optionally name the args
)

# subsample data
subsampling_funcs = [
    sklearn.utils.resample for _ in range(3)
]
subsampling_set = Vset(name='subsampling',
                       modules=subsampling_funcs,
                       output_matching=True)
X_trains, y_trains = subsampling_set(X_train, y_train)

# fit models
models = [
    sklearn.linear_model.LogisticRegression(),
    sklearn.tree.DecisionTreeClassifier()
]
modeling_set = Vset(name='modeling',
                    modules=models,
                    module_keys=["LR", "DT"])
modeling_set.fit(X_trains, y_trains)
preds_test = modeling_set.predict(X_test)

# get metrics
binary_metrics_set = Vset(name='binary_metrics',
                          modules=[accuracy_score, balanced_accuracy_score],
                          module_keys=["Acc", "Bal_Acc"])
binary_metrics = binary_metrics_set.evaluate(preds_test, y_test)

Once we've written this pipeline, we can easily measure the stability of metrics (e.g. "Accuracy") to our choice of subsampling or model.

Documentation

See the docs for reference on the API

Notebook examples (Note that some of these require more dependencies than just those required for vflow - to install all, use the notebooks dependencies in the setup.py file)

Synthetic classification

Enhancer genomics

fMRI voxel prediction

Fashion mnist classification

Clinical decision rule vetting

Installation

Install with pip install vflow (see here for help). For dev version (unstable), clone the repo and run python setup.py develop from the repo directory.

References

• interface: easily build on scikit-learn and dvc (data version control)
• computation: integration with ray and caching with joblib
• tracking: mlflow
• pull requests very welcome! (see contributing.md)