README.md

In OHDSI/BigKnn: Large Scale K-Nearest Neighbor Classifier using the Lucene Search Engine

BigKnn

BigKnn is part of HADES.

Introduction

An R package implementing a large scale k-nearest neighbor (KNN) classifier using the Lucene search engine.

Features

• Build KNN classifiers of arbitrary scale (up to millions of rows, millions of features)
• Fast classification performance due to use of highly optimized search engine (Lucene)
• Supports both weighted and unweighted KNN

Examples

covariates <- data.frame(rowIds = c(1,1,1,2,2,3),
                         covariateIds = c(10,11,12,10,11,12),
                         covariateValues = c(1,1,1,1,1,1))

outcomes <- data.frame(rowIds = c(1,2,3),
                       y = c(1,0,0))

dataForPrediction <- Andromeda::andromeda(covariates = covariates, 
                                          outcomes = outcomes)

indexFolder <- "s:/temp/lucene"

buildKnn(outcomes = dataForPrediction$outcomes,
         covariates = dataForPrediction$covariates,
         indexFolder = indexFolder)

prediction <- predictKnn(outcomes = dataForPrediction$outcomes,
                         covariates = dataForPrediction$covariates,
                         indexFolder = indexFolder,
                         k = 10,
                         weighted = TRUE)

Technology

BigKnn is an R package using the Java based Lucene search engine. The data for the KNN is stored in a folder on the local file system.

System Requirements

Running the package requires R with the package rJava installed. Also requires Java 1.8 or higher.

Installation

1. See the instructions here for configuring your R environment, including Java.

2. Use the following commands in R to install the BigKnn package:

r install.packages("remotes") remotes::install_github("ohdsi/BigKnn")

User Documentation

Documentation can be found on the package website.

PDF versions of the documentation are also available: * Package manual: BigKnn manual

Support

• Developer questions/comments/feedback: OHDSI Forum
• We use the GitHub issue tracker for all bugs/issues/enhancements

Contributing

Read here how you can contribute to this package.

License

BigKnn is licensed under Apache License 2.0. Lucene fall under its own Apache License 2.0.

Development

BigKnn is being developed in R Studio and Eclipse

Development status

Stable.

OHDSI/BigKnn documentation built on March 21, 2023, 8:35 a.m.