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exchanger: Bayesian Entity Resolution with Exchangeable Random Partition Priors

Overview

This R package implements the Bayesian entity resolution model described in (Marchant, Rubinstein, and Steorts 2023). The model assumes records are generated from a latent population of entities via a distortion process. Entity resolution is performed by inferring the latent linkage structure using a Markov chain Monte Carlo algorithm.

Features

  • Supports user-defined attribute distance functions for modeling the distortion process.
  • Supports missing values.
  • Implements the Ewens-Pitman (EP) family of exchangeable clustering priors (Pitman 2006), with support for hyperpriors on the EP parameters. This includes the Ewens partition (related to the Dirichlet process), Pitman-Yor partition (related to the Pitman-Yor process) and Generalized Coupon partition (related to finite mixture models).
  • Inference is implemented in C++ using partially-collapsed Gibbs sampling (Dyk and Park 2008). Several computational tricks are used to improve scalability.

Installation

exchanger is not currently available on CRAN. The latest development version can be installed from source using devtools as follows:

library(devtools)
install_github("cleanzr/exchanger")

Example

We demonstrate how to perform entity resolution using the RLdata500 test data set included with the package. RLdata500 contains 500 synthetic personal records, 50 of which are duplicates with randomly-generated errors. In the code block, below we load the package and examine the first few rows of RLdata500.

library(exchanger)
library(comparator)     # provides string comparison functions
library(clevr)          # provides functions for supervised evaluation
head(RLdata500)
#>   fname_c1 fname_c2 lname_c1 lname_c2   by bm bd
#> 1  CARSTEN     <NA>    MEIER     <NA> 1949  7 22
#> 2     GERD     <NA>    BAUER     <NA> 1968  7 27
#> 3   ROBERT     <NA> HARTMANN     <NA> 1930  4 30
#> 4   STEFAN     <NA>    WOLFF     <NA> 1957  9  2
#> 5     RALF     <NA>  KRUEGER     <NA> 1966  1 13
#> 6  JUERGEN     <NA>   FRANKE     <NA> 1929  7  4

Next we specify the model parameters for the entity attributes. For simplicity, we use a uniform prior for the distortion probability associated with each attribute.

unif_prior <- BetaRV(1, 1)

We model the distortion for the name attributes (fname_c1 and lname_c1) using Levenshtein (edit) distance. The transform_dist_fn applies a threshold at a distance of 3, so that any pair of names y, x with an edit distance strictly greater than 3 are assumed to be “infinitely” apart. This improves computational efficiency, as the inference algorithm exploits the fact that x can never be a distortion of y if their distance is strictly greater than 3. For the date attributes (by, bm and bd) we assume a constant distance function, which means all values in the domain are equally likely a priori as a distorted alternative. The CategoricalAttribute constructor provides a shortcut for an attribute with a constant distance function.

attr_params <- list(
  fname_c1 = Attribute(transform_dist_fn(Levenshtein(), threshold=3), 
                         distort_prob_prior = unif_prior),
  lname_c1 = Attribute(transform_dist_fn(Levenshtein(), threshold=3), 
                         distort_prob_prior = unif_prior),
  by = CategoricalAttribute(distort_prob_prior = unif_prior),
  bm = CategoricalAttribute(distort_prob_prior = unif_prior),
  bd = CategoricalAttribute(distort_prob_prior = unif_prior)
)

Finally we specify the prior over the linkage structure (clustering). Here we use a Pitman-Yor random partition for the prior, with hyperpriors on the concentration and discount parameters.

clust_prior <- PitmanYorRP(alpha = GammaRV(1, 1), d = BetaRV(1, 1))

All that remains is to initialize the model and run inference. For demonstration purposes, we only generate 100 posterior samples of the linkage structure.

model <- exchanger(RLdata500, attr_params, clust_prior)
result <- run_inference(model, n_samples=100, thin_interval=10, burnin_interval=1000)

We can obtain a point estimate of the most likely linkage structure using the shared most probable maximal matching sets method (Steorts, Hall, and Fienberg 2016).

pred_clust <- smp_clusters(result)

Then we evaluate with respect to the true matching.

n_records <- nrow(RLdata500)
true_pairs <- membership_to_pairs(identity.RLdata500)
pred_pairs <- clusters_to_pairs(pred_clust)
measures <- eval_report_pairs(true_pairs, pred_pairs, num_pairs=n_records*(n_records-1)/2)
print(measures)
#> $precision
#> [1] 0.98
#> 
#> $recall
#> [1] 0.98
#> 
#> $specificity
#> [1] 0.999992
#> 
#> $sensitivity
#> [1] 0.98
#> 
#> $f1score
#> [1] 0.98
#> 
#> $accuracy
#> [1] 0.999984
#> 
#> $balanced_accuracy
#> [1] 0.989996

License

GPL-3

References

Dyk, David A. van, and Taeyoung Park. 2008. “Partially Collapsed Gibbs Samplers.” Journal of the American Statistical Association 103 (482): 790–96. https://doi.org/10.1198/016214508000000409.

Marchant, Neil G., Benjamin I. P. Rubinstein, and Rebecca C. Steorts. 2023. “Bayesian Graphical Entity Resolution using Exchangeable Random Partition Priors.” Journal of Survey Statistics and Methodology, January. https://doi.org/10.1093/jssam/smac030.

Pitman, Jim. 2006. “Exchangeable Random Partitions.” In Combinatorial Stochastic Processes: Ecole d’Eté de Probabilités de Saint-Flour XXXII – 2002, edited by Jean Picard, 37–53. Berlin, Heidelberg: Springer Berlin Heidelberg. https://doi.org/10.1007/3-540-34266-4_3.

Steorts, Rebecca C., Rob Hall, and Stephen E. Fienberg. 2016. “A Bayesian Approach to Graphical Record Linkage and Deduplication.” Journal of the American Statistical Association 111 (516): 1660–72. https://doi.org/10.1080/01621459.2015.1105807.