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sknnr

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⚠️ WARNING: sknnr is in active development! ⚠️

What is sknnr?

sknnr is a package for running k-nearest neighbor (kNN) imputation1 methods using estimators that are fully compatible with scikit-learn. Notably, common methods such as most similar neighbor (MSN, Moeur & Stage 1995), gradient nearest neighbor (GNN, Ohmann & Gregory, 2002), and random forest nearest neighbors2 (RFNN, Crookston & Finley, 2008) are included in this package.

Features

Why the Name "sknnr"?

sknnr is an acronym of its main three components:

  1. "s" is for scikit-learn. All estimators in this package derive from the sklearn.BaseEstimator class and comply with the requirements associated with developing custom estimators.
  2. "knn" is for k-nearest neighbors. All estimators use the k >= 1 samples that are nearest in feature space to create their prediction. Each estimator in this package defines that feature space in a different way which often leads to different neighbors chosen for the prediction.
  3. "r" is for regression. Estimators in this package are run in regression mode. For nearest neighbor imputation, this is simply an (optionally-weighted) average of its k neighbors. When k is set to 1, this effectively behaves as in classification mode. All estimators support multi-output prediction so that multiple features can be predicted with the same estimator.

Quick-Start

  1. Follow the installation guide.
  2. Import any sknnr estimator, like MSNRegressor, as a drop-in replacement for a scikit-learn regressor. 
    from sknnr import MSNRegressor

est = MSNRegressor()
  3. Load a custom dataset like SWO Ecoplot (or bring your own). 
    from sknnr.datasets import load_swo_ecoplot

X, y = load_swo_ecoplot(return_X_y=True, as_frame=True)
  4. Train, predict, and score as usual. 
    from sklearn.model_selection import train_test_split

X_train, X_test, y_train, y_test = train_test_split(X, y)

est = est.fit(X_train, y_train)
est.score(X_test, y_test)
  5. Check out the additional features like independent scoring, dataframe indexing, and dimensionality reduction. 
    # Evaluate the model using the second-nearest neighbor in the test set
print(est.fit(X, y).independent_score_)

# Get the dataframe index of the nearest neighbor to each plot
print(est.kneighbors(return_dataframe_index=True, return_distance=False))

# Apply dimensionality reduction using CCorA ordination
MSNRegressor(n_components=3).fit(X_train, y_train)

History and Inspiration

sknnr was heavily inspired by (and endeavors to implement functionality of) the yaImpute package for R (Crookston & Finley 2008). As Crookston and Finley (2008) note in their abstract,

Although nearest neighbor imputation is used in a host of disciplines, the methods implemented in the yaImpute package are tailored to imputation-based forest attribute estimation and mapping ... [there is] a growing interest in nearest neighbor imputation methods for spatially explicit forest inventory, and a need within this research community for software that facilitates comparison among different nearest neighbor search algorithms and subsequent imputation techniques.

Indeed, many regional (e.g. LEMMA) and national (e.g. BIGMAP, TreeMap) projects use nearest-neighbor methods to estimate and map forest attributes across time and space.

To that end, sknnr ports and expands the functionality present in yaImpute into a Python package that helps facilitate intercomparison between k-nearest neighbor methods (and other built-in estimators from scikit-learn) using an API which is familiar to scikit-learn users.

Acknowledgements

Thanks to Andrew Hudak (USDA Forest Service Rocky Mountain Research Station) for the inclusion of the Moscow Mountain / St. Joes dataset (Hudak 2010), and the USDA Forest Service Region 6 Ecology Team for the inclusion of the SWO Ecoplot dataset (Atzet et al., 1996). Development of this package was funded by:

  • an appointment to the United States Forest Service (USFS) Research Participation Program administered by the Oak Ridge Institute for Science and Education (ORISE) through an interagency agreement between the U.S. Department of Energy (DOE) and the U.S. Department of Agriculture (USDA).
  • a joint venture agreement between USFS Pacific Northwest Research Station and Oregon State University (agreement 19-JV-11261959-064).
  • a cost-reimbursable agreement between USFS Region 6 and Oregon State University (agreeement 21-CR-11062756-046).

References

  • Atzet, T, DE White, LA McCrimmon, PA Martinez, PR Fong, and VD Randall. 1996. Field guide to the forested plant associations of southwestern Oregon. USDA Forest Service. Pacific Northwest Region, Technical Paper R6-NR-ECOL-TP-17-96.
  • Crookston, NL, Finley, AO. 2008. yaImpute: An R package for kNN imputation. Journal of Statistical Software, 23(10), 16.
  • Hudak, A.T. 2010. Field plot measures and predictive maps for "Nearest neighbor imputation of species-level, plot-scale forest structure attributes from LiDAR data". Fort Collins, CO: U.S. Department of Agriculture, Forest Service, Rocky Mountain Research Station. https://www.fs.usda.gov/rds/archive/Catalog/RDS-2010-0012.
  • Moeur M, Stage AR. 1995. Most Similar Neighbor: An Improved Sampling Inference Procedure for Natural Resources Planning. Forest Science, 41(2), 337–359.
  • Ohmann JL, Gregory MJ. 2002. Predictive Mapping of Forest Composition and Structure with Direct Gradient Analysis and Nearest Neighbor Imputation in Coastal Oregon, USA. Canadian Journal of Forest Research, 32, 725–741.

  1. In a mapping context, kNN imputation refers to predicting feature values for a target from its k-nearest neighbors, and should not be confused with the usual scikit-learn usage as a pre-filling strategy for missing input data, e.g. KNNImputer. ↩

  2. In development! ↩

  3. All estimators and parameters with equivalent functionality in yaImpute are tested to 3 decimal places against the R package. ↩