changed the defaults for nnd algorithm and other changes

ncn-foreigners · May 7, 2024 · d9790fc · d9790fc
1 parent 041fccf
commit d9790fc
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Showing 16 changed files with 54 additions and 42 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -25,6 +25,7 @@ Imports:
   rnndescent,
   igraph,
   data.table,
+  RcppAlgos,
   methods
 Suggests: 
     tinytest,

diff --git a/NAMESPACE b/NAMESPACE
@@ -6,6 +6,7 @@ export(controls_ann)
 export(controls_txt)
 export(pair_ann)
 import(data.table)
+importFrom(RcppAlgos,comboGeneral)
 importFrom(RcppAnnoy,AnnoyAngular)
 importFrom(RcppAnnoy,AnnoyEuclidean)
 importFrom(RcppAnnoy,AnnoyHamming)
@@ -31,6 +32,5 @@ importFrom(text2vec,create_vocabulary)
 importFrom(text2vec,itoken)
 importFrom(text2vec,itoken_parallel)
 importFrom(text2vec,vocab_vectorizer)
-importFrom(utils,combn)
 importFrom(utils,setTxtProgressBar)
 importFrom(utils,txtProgressBar)
diff --git a/R/blocking.R b/R/blocking.R
@@ -9,7 +9,7 @@
 #' @importFrom igraph graph_from_data_frame
 #' @importFrom igraph make_clusters
 #' @importFrom igraph compare
-#' @importFrom utils combn
+#' @importFrom RcppAlgos comboGeneral
 #'
 #'
 #' @title Block records based on text data.
@@ -41,6 +41,7 @@
 #' \itemize{
 #' \item{\code{result} -- \code{data.table} with indices (rows) of x, y, block and distance between points}
 #' \item{\code{method} -- name of the ANN algorithm used,}
+#' \item{\code{deduplication} -- information whether deduplication was applied,}
 #' \item{\code{metrics} -- metrics for quality assessment, if \code{true_blocks} is provided,}
 #' \item{\code{colnames} -- variable names (colnames) used for search,}
 #' \item{\code{graph} -- \code{igraph} class object.}
@@ -96,12 +97,11 @@ blocking <- function(x,
               is.character(x) | is.matrix(x) | inherits(x, "Matrix"))
 
   ## assuming rows (for nnd)
-  stopifnot("Minimum 3 cases required for x" = NROW(x) > 2)
-
-  if (!is.null(y)) {
-    stopifnot("Minimum 3 cases required for y" = NROW(y) > 2)
-  }
-
+  # stopifnot("Minimum 3 cases required for x" = NROW(x) > 2)
+  #
+  # if (!is.null(y)) {
+  #   stopifnot("Minimum 3 cases required for y" = NROW(y) > 2)
+  # }
 
   if (!is.null(ann_write)) {
     stopifnot("Path provided in the `ann_write` is incorrect" = file.exists(ann_write) )
@@ -314,11 +314,10 @@ blocking <- function(x,
 
     }
 
-    #consider using RcppAlgos::comboGeneral(nrow(pairs_to_eval_long), 2,  nThreads=n_threads)
-    candidate_pairs <- utils::combn(nrow(pairs_to_eval_long), 2)
+    candidate_pairs <- RcppAlgos::comboGeneral(nrow(pairs_to_eval_long), 2,  nThreads=n_threads)
 
-    same_block <- pairs_to_eval_long$block_id[candidate_pairs[1, ]] == pairs_to_eval_long$block_id[candidate_pairs[2, ]]
-    same_truth <- pairs_to_eval_long$true_id[candidate_pairs[1, ]] == pairs_to_eval_long$true_id[candidate_pairs[2, ]]
+    same_block <- pairs_to_eval_long$block_id[candidate_pairs[, 1]] == pairs_to_eval_long$block_id[candidate_pairs[,2]]
+    same_truth <- pairs_to_eval_long$true_id[candidate_pairs[,1]] == pairs_to_eval_long$true_id[candidate_pairs[,2]]
 
     confusion <- table(same_block, same_truth)
 
@@ -343,6 +342,7 @@ blocking <- function(x,
       method = ann,
       deduplication = deduplication,
       metrics = if (is.null(true_blocks)) NULL else eval_metrics,
+      confusion = if (is.null(true_blocks)) NULL else confusion,
       colnames = colnames_xy,
       graph = if (graph) {
         igraph::graph_from_data_frame(x_df[, c("x", "y")], directed = F)

diff --git a/R/controls.R b/R/controls.R
@@ -20,7 +20,7 @@ controls_ann <- function(
     sparse = FALSE,
     k_search = 30,
     nnd = list(k_build = 30,
-               use_alt_metric = TRUE,
+               use_alt_metric = FALSE,
                init = "tree",
                n_trees = NULL,
                leaf_size = NULL,

diff --git a/R/method_nnd.R b/R/method_nnd.R
@@ -54,19 +54,19 @@ method_nnd <- function(x,
   ## query k dependent on the study
   ## there is a problem when dataset is small
 
-  if (deduplication == T) {
-    k_nnd_query <- k
-  } else if (nrow(x) < 10) {
-    k_nnd_query <- k
-  } else if (nrow(x) < control$k_search) {
-    k_nnd_query <- nrow(x)
-  } else {
-    k_nnd_query <- control$k_search
-  }
+#   if (deduplication == T) {
+#     k_nnd_query <- k
+#   } else if (nrow(x) < 10) {
+#     k_nnd_query <- k
+#   } else if (nrow(x) < control$k_search) {
+#     k_nnd_query <- nrow(x)
+#   } else {
+#     k_nnd_query <- control$k_search
+#   }
 
   l_1nn <- rnndescent::rnnd_query(index = l_ind,
                                   query = y,
-                                  k = k_nnd_query,
+                                  k = if (nrow(x) < control$k_search) nrow(x) else control$k_search,
                                   epsilon = 0.1,
                                   max_search_fraction = 1,
                                   init = NULL,

diff --git a/R/methods.R b/R/methods.R
@@ -21,7 +21,7 @@ print.blocking <- function(x,...) {
     cat("========================================================\n")
     cat("Evaluation metrics (standard):\n" )
     metrics <- as.numeric(sprintf("%.4f", x$metrics*100))
-    names(metrics)  <- names(result2$metrics)
+    names(metrics)  <- names(x$metrics)
     print(metrics)
 
   }

diff --git a/README.md b/README.md
@@ -131,11 +131,11 @@ Table with blocking results contains:
 blocking_result$result
 #>        x     y block       dist
 #>    <int> <int> <num>      <num>
-#> 1:     1     2     1 0.10000005
-#> 2:     1     3     1 0.14188367
-#> 3:     1     4     1 0.28286284
-#> 4:     5     6     2 0.08333336
-#> 5:     5     7     2 0.13397458
+#> 1:     1     2     1 0.10000002
+#> 2:     2     3     1 0.14188367
+#> 3:     2     4     1 0.28286284
+#> 4:     5     6     2 0.08333331
+#> 5:     5     7     2 0.13397455
 #> 6:     5     8     2 0.27831215
 ```
 
@@ -148,17 +148,19 @@ pair_ann(x = df_example, on = "txt") |>
   score_simple("score", on = "txt") |>
   select_threshold("threshold", score = "score", threshold = 0.55) |>
   link(selection = "threshold")
-#>   Total number of pairs: 6 pairs
+#>   Total number of pairs: 8 pairs
 #> 
 #> Key: <.y>
 #>       .y    .x       txt.x           txt.y
 #>    <int> <int>      <char>          <char>
 #> 1:     2     1 jankowalski     kowalskijan
 #> 2:     3     1 jankowalski    kowalskimjan
-#> 3:     4     1 jankowalski        kowaljan
-#> 4:     6     5 montypython     pythonmonty
-#> 5:     7     5 montypython cyrkmontypython
-#> 6:     8     5 montypython           monty
+#> 3:     3     2 kowalskijan    kowalskimjan
+#> 4:     4     1 jankowalski        kowaljan
+#> 5:     4     2 kowalskijan        kowaljan
+#> 6:     6     5 montypython     pythonmonty
+#> 7:     7     5 montypython cyrkmontypython
+#> 8:     8     5 montypython           monty
 ```
 
 Linking records using the same function where `df_base` is the

diff --git a/inst/tinytest/test_annoy.R b/inst/tinytest/test_annoy.R
@@ -24,6 +24,7 @@ expect_equal(
     method = "annoy",
     deduplication = FALSE,
     metrics = NULL,
+    confusion = NULL,
     colnames = c("al", "an", "ho", "ij", "ja", "ki", "ko", "ls", "mo",
                  "nt", "ow", "py", "sk", "ty", "wa", "yp", "yt", "on", "th"),
     graph = NULL),
@@ -50,6 +51,7 @@ expect_equal(
     method = "annoy",
     deduplication = FALSE,
     metrics = NULL,
+    confusion = NULL,
     colnames = c("al", "an", "ho", "ij", "ja", "ki", "ko", "ls", "mo", "ow",
                  "py", "sk", "ty", "wa", "yp", "yt", "nt", "on", "th"),
     graph = NULL),

diff --git a/inst/tinytest/test_blocking.R b/inst/tinytest/test_blocking.R
@@ -53,7 +53,7 @@ expect_equal(
 
 expect_equal(
   blocking(x = df_base$txt, y = df_example$txt, ann = "lsh")$result$block,
-  c(rep(2,3),rep(1,4), 3)
+  c(rep(2,3),rep(1,4),3)
 )
 
 expect_silent(

diff --git a/inst/tinytest/test_hnsw.R b/inst/tinytest/test_hnsw.R
@@ -25,6 +25,7 @@ expect_equal(
     method = "hnsw",
     deduplication = FALSE,
     metrics = NULL,
+    confusion = NULL,
     colnames = c("al", "an", "ho", "ij", "ja", "ki", "ko", "ls", "mo", "ow",
                  "py", "sk", "ty", "wa", "yp", "yt", "nt", "on", "th"),
     graph = NULL),
@@ -56,6 +57,7 @@ expect_equal(
     method = "hnsw",
     deduplication = FALSE,
     metrics = NULL,
+    confusion = NULL,
     colnames = c("al", "an", "ho", "ij", "ja", "ki", "ko", "ls", "mo", "nt",
                  "ow", "py", "sk", "ty", "wa", "yp", "yt", "on", "th"),
     graph = NULL),

diff --git a/inst/tinytest/test_mlpack.R b/inst/tinytest/test_mlpack.R
@@ -14,6 +14,7 @@ expect_equal(
     method = "lsh",
     deduplication = FALSE,
     metrics = NULL,
+    confusion = NULL,
     colnames = c("al", "an", "ho", "ij", "ja", "ki", "ko", "ls", "mo", "ow",
                  "py", "sk", "ty", "wa", "yp", "yt", "nt", "on", "th"),
     graph = NULL),
@@ -34,6 +35,7 @@ expect_equal(
     method = "kd",
     deduplication = FALSE,
     metrics = NULL,
+    confusion = NULL,
     colnames =c("al", "an", "ho", "ij", "ja", "ki", "ko", "ls", "mo", "ow",
                 "py", "sk", "ty", "wa", "yp", "yt", "nt", "on", "th"),
     graph = NULL),
@@ -67,6 +69,7 @@ expect_equal(
     method = "lsh",
     deduplication = FALSE,
     metrics = NULL,
+    confusion = NULL,
     colnames = c("al", "an", "ho", "ij", "ja", "ki", "ko", "ls", "mo", "nt", "ow",
                  "py", "sk", "ty", "wa", "yp", "yt", "on", "th"),
     graph = NULL),
@@ -88,6 +91,7 @@ expect_equal(
     method = "kd",
     deduplication = FALSE,
     metrics = NULL,
+    confusion = NULL,
     colnames = c("al", "an", "ho", "ij", "ja", "ki", "ko", "ls", "mo", "nt", "ow",
                  "py", "sk", "ty", "wa", "yp", "yt", "on", "th"),
     graph = NULL),

diff --git a/inst/tinytest/test_reclin2.R b/inst/tinytest/test_reclin2.R
@@ -6,7 +6,7 @@ expect_silent(
 
 expect_equal(
   dim(pair_ann(x = df_example, on = "txt")),
-  c(6, 3)
+  c(8, 3)
 )
 
 expect_equal(

diff --git a/inst/tinytest/test_true_blocks.R b/inst/tinytest/test_true_blocks.R
diff --git a/man/blocking.Rd b/man/blocking.Rd
diff --git a/man/controls_ann.Rd b/man/controls_ann.Rd
diff --git a/vignettes/v2-reclin.Rmd b/vignettes/v2-reclin.Rmd
@@ -101,7 +101,7 @@ The goal of this exercise is to link units from the CIS dataset to the CENSUS da
 
 ```{r}
 set.seed(2024)
-result1 <- blocking(x = census$txt, y = cis$txt, verbose = 1)
+result1 <- blocking(x = census$txt, y = cis$txt, verbose = 1, n_threads = 8)
 ```
 
 Distribution of distances for each pair.
@@ -140,7 +140,7 @@ So in our example we have `r nrow(matches)` pairs.
 ```{r}
 set.seed(2024)
 result2 <- blocking(x = census$txt, y = cis$txt, verbose = 1,
-                    true_blocks = matches[, .(x, y, block)], n_threads = 4)
+                    true_blocks = matches[, .(x, y, block)], n_threads = 8)
 ```
 
 Let's see how our approach handled this problem.
@@ -149,7 +149,7 @@ Let's see how our approach handled this problem.
 result2
 ```
 
-It seems that the default parameters of the NND method result in an FNR of `r sprintf("%.2f",result2$metrics["fnr"]*100)`%, which is quite large. We can see if increasing the number of `k` (and thus `max_candidates`) as suggested in the [Nearest Neighbor Descent
+It seems that the default parameters of the NND method result in an FNR of `r sprintf("%.2f",result2$metrics["fnr"]*100)`%. We can see if increasing the number of `k` (and thus `max_candidates`) as suggested in the [Nearest Neighbor Descent
 ](https://jlmelville.github.io/rnndescent/articles/nearest-neighbor-descent.html) vignette will help. 
 
 
@@ -159,7 +159,7 @@ ann_control_pars <- controls_ann()
 ann_control_pars$k_search <- 60
 
 result3 <- blocking(x = census$txt, y = cis$txt, verbose = 1, 
-                    true_blocks = matches[, .(x, y, block)], n_threads = 4, 
+                    true_blocks = matches[, .(x, y, block)], n_threads = 8, 
                     control_ann = ann_control_pars)
 ```
 
@@ -173,7 +173,7 @@ Finally, compare the NND and HNSW algorithm for this example.
 
 ```{r}
 result4 <- blocking(x = census$txt, y = cis$txt, verbose = 1, 
-                    true_blocks = matches[, .(x, y, block)], n_threads = 4, 
+                    true_blocks = matches[, .(x, y, block)], n_threads = 8, 
                     ann = "hnsw", seed = 2024)
 ```