Thursday, December 1, 2022
HomeArtificial Intelligenceweighted quantile summaries, energy iteration clustering, spark_write_rds(), and extra

weighted quantile summaries, energy iteration clustering, spark_write_rds(), and extra

Sparklyr 1.6 is now obtainable on CRAN!

To put in sparklyr 1.6 from CRAN, run

On this weblog put up, we will spotlight the next options and enhancements from sparklyr 1.6:

Weighted quantile summaries

Apache Spark is well-known for supporting approximate algorithms that commerce off marginal quantities of accuracy for higher pace and parallelism. Such algorithms are notably useful for performing preliminary knowledge explorations at scale, as they allow customers to shortly question sure estimated statistics inside a predefined error margin, whereas avoiding the excessive value of tangible computations. One instance is the Greenwald-Khanna algorithm for on-line computation of quantile summaries, as described in Greenwald and Khanna (2001). This algorithm was initially designed for environment friendly (epsilon)– approximation of quantiles inside a big dataset with out the notion of knowledge factors carrying completely different weights, and the unweighted model of it has been applied as approxQuantile() since Spark 2.0. Nevertheless, the identical algorithm will be generalized to deal with weighted inputs, and as sparklyr consumer @Zhuk66 talked about in this difficulty, a weighted model of this algorithm makes for a helpful sparklyr characteristic.

To correctly clarify what weighted-quantile means, we should make clear what the load of every knowledge level signifies. For instance, if we have now a sequence of observations ((1, 1, 1, 1, 0, 2, -1, -1)), and wish to approximate the median of all knowledge factors, then we have now the next two choices:

  • Both run the unweighted model of approxQuantile() in Spark to scan by means of all 8 knowledge factors

  • Or alternatively, “compress” the info into 4 tuples of (worth, weight): ((1, 0.5), (0, 0.125), (2, 0.125), (-1, 0.25)), the place the second part of every tuple represents how usually a worth happens relative to the remainder of the noticed values, after which discover the median by scanning by means of the 4 tuples utilizing the weighted model of the Greenwald-Khanna algorithm

We are able to additionally run by means of a contrived instance involving the usual regular distribution as an example the facility of weighted quantile estimation in sparklyr 1.6. Suppose we can’t merely run qnorm() in R to guage the quantile operate of the usual regular distribution at (p = 0.25) and (p = 0.75), how can we get some obscure concept in regards to the 1st and third quantiles of this distribution? A method is to pattern a lot of knowledge factors from this distribution, after which apply the Greenwald-Khanna algorithm to our unweighted samples, as proven under:


sc <- spark_connect(grasp = "native")

num_samples <- 1e6
samples <- knowledge.body(x = rnorm(num_samples))

samples_sdf <- copy_to(sc, samples, title = random_string())

samples_sdf %>%
    column = "x",
    chances = c(0.25, 0.75),
    relative.error = 0.01
  ) %>%
##        25%        75%
## -0.6629242  0.6874939

Discover that as a result of we’re working with an approximate algorithm, and have specified relative.error = 0.01, the estimated worth of (-0.6629242) from above might be wherever between the twenty fourth and the twenty sixth percentile of all samples. Actually, it falls within the (25.36896)-th percentile:

## [1] 0.2536896

Now how can we make use of weighted quantile estimation from sparklyr 1.6 to acquire comparable outcomes? Easy! We are able to pattern a lot of (x) values uniformly randomly from ((-infty, infty)) (or alternatively, simply choose a lot of values evenly spaced between ((-M, M)) the place (M) is roughly (infty)), and assign every (x) worth a weight of (displaystyle frac{1}{sqrt{2 pi}}e^{-frac{x^2}{2}}), the usual regular distribution’s likelihood density at (x). Lastly, we run the weighted model of sdf_quantile() from sparklyr 1.6, as proven under:


sc <- spark_connect(grasp = "native")

num_samples <- 1e6
M <- 1000
samples <- tibble::tibble(
  x = M * seq(-num_samples / 2 + 1, num_samples / 2) / num_samples,
  weight = dnorm(x)

samples_sdf <- copy_to(sc, samples, title = random_string())

samples_sdf %>%
    column = "x",
    weight.column = "weight",
    chances = c(0.25, 0.75),
    relative.error = 0.01
  ) %>%
##    25%    75%
## -0.696  0.662

Voilà! The estimates usually are not too far off from the twenty fifth and seventy fifth percentiles (in relation to our abovementioned most permissible error of (0.01)):

## [1] 0.2432144
## [1] 0.7460144

Energy iteration clustering

Energy iteration clustering (PIC), a easy and scalable graph clustering methodology introduced in Lin and Cohen (2010), first finds a low-dimensional embedding of a dataset, utilizing truncated energy iteration on a normalized pairwise-similarity matrix of all knowledge factors, after which makes use of this embedding because the “cluster indicator,” an intermediate illustration of the dataset that results in quick convergence when used as enter to k-means clustering. This course of could be very effectively illustrated in determine 1 of Lin and Cohen (2010) (reproduced under)

by which the leftmost picture is the visualization of a dataset consisting of three circles, with factors coloured in crimson, inexperienced, and blue indicating clustering outcomes, and the next pictures present the facility iteration course of progressively reworking the unique set of factors into what seems to be three disjoint line segments, an intermediate illustration that may be quickly separated into 3 clusters utilizing k-means clustering with (okay = 3).

In sparklyr 1.6, ml_power_iteration() was applied to make the PIC performance in Spark accessible from R. It expects as enter a 3-column Spark dataframe that represents a pairwise-similarity matrix of all knowledge factors. Two of the columns on this dataframe ought to comprise 0-based row and column indices, and the third column ought to maintain the corresponding similarity measure. Within the instance under, we are going to see a dataset consisting of two circles being simply separated into two clusters by ml_power_iteration(), with the Gaussian kernel getting used because the similarity measure between any 2 factors:

gen_similarity_matrix <- operate() {
  # Guassian similarity measure
  guassian_similarity <- operate(pt1, pt2) {
    exp(-sum((pt2 - pt1) ^ 2) / 2)
  # generate evenly distributed factors on a circle centered on the origin
  gen_circle <- operate(radius, num_pts) {
    seq(0, num_pts - 1) %>%
        operate(idx) {
          theta <- 2 * pi * idx / num_pts
          radius * c(x = cos(theta), y = sin(theta))
  # generate factors on each circles
  pts <- rbind(
    gen_circle(radius = 1, num_pts = 80),
    gen_circle(radius = 4, num_pts = 80)
  # populate the pairwise similarity matrix (saved as a 3-column dataframe)
  similarity_matrix <- knowledge.body()
  for (i in seq(2, nrow(pts)))
    similarity_matrix <- similarity_matrix %>%
      rbind(seq(i - 1L) %>%
        purrr::map_dfr(~ listing(
          src = i - 1L, dst = .x - 1L,
          similarity = guassian_similarity(pts[i,], pts[.x,])



sc <- spark_connect(grasp = "native")
sdf <- copy_to(sc, gen_similarity_matrix())
clusters <- ml_power_iteration(
  sdf, okay = 2, max_iter = 10, init_mode = "diploma",
  src_col = "src", dst_col = "dst", weight_col = "similarity"

clusters %>% print(n = 160)
## # A tibble: 160 x 2
##        id cluster
##     <dbl>   <int>
##   1     0       1
##   2     1       1
##   3     2       1
##   4     3       1
##   5     4       1
##   ...
##   157   156       0
##   158   157       0
##   159   158       0
##   160   159       0

The output reveals factors from the 2 circles being assigned to separate clusters, as anticipated, after solely a small variety of PIC iterations.

spark_write_rds() + collect_from_rds()

spark_write_rds() and collect_from_rds() are applied as a much less memory- consuming different to accumulate(). In contrast to accumulate(), which retrieves all components of a Spark dataframe by means of the Spark driver node, therefore doubtlessly inflicting slowness or out-of-memory failures when accumulating giant quantities of knowledge, spark_write_rds(), when used at the side of collect_from_rds(), can retrieve all partitions of a Spark dataframe instantly from Spark staff, slightly than by means of the Spark driver node. First, spark_write_rds() will distribute the duties of serializing Spark dataframe partitions in RDS model 2 format amongst Spark staff. Spark staff can then course of a number of partitions in parallel, every dealing with one partition at a time and persisting the RDS output on to disk, slightly than sending dataframe partitions to the Spark driver node. Lastly, the RDS outputs will be re-assembled to R dataframes utilizing collect_from_rds().

Proven under is an instance of spark_write_rds() + collect_from_rds() utilization, the place RDS outputs are first saved to HDFS, then downloaded to the native filesystem with hadoop fs -get, and eventually, post-processed with collect_from_rds():


num_partitions <- 10L
sc <- spark_connect(grasp = "yarn", spark_home = "/usr/lib/spark")
flights_sdf <- copy_to(sc, flights, repartition = num_partitions)

# Spark staff serialize all partition in RDS format in parallel and write RDS
# outputs to HDFS
  dest_uri = "hdfs://<namenode>:8020/flights-part-{partitionId}.rds"

# Run `hadoop fs -get` to obtain RDS information from HDFS to native file system
for (partition in seq(num_partitions) - 1)
    c("fs", "-get", sprintf("hdfs://<namenode>:8020/flights-part-%d.rds", partition))

# Publish-process RDS outputs
partitions <- seq(num_partitions) - 1 %>%
  lapply(operate(partition) collect_from_rds(sprintf("flights-part-%d.rds", partition)))

# Optionally, name `rbind()` to mix knowledge from all partitions right into a single R dataframe
flights_df <-, partitions)

Just like different latest sparklyr releases, sparklyr 1.6 comes with plenty of dplyr-related enhancements, equivalent to

  • Help for the place() predicate inside choose() and summarize(throughout(...)) operations on Spark dataframes
  • Addition of if_all() and if_any() features
  • Full compatibility with dbplyr 2.0 backend API

choose(the place(...)) and summarize(throughout(the place(...)))

The dplyr the place(...) assemble is beneficial for making use of a variety or aggregation operate to a number of columns that fulfill some boolean predicate. For instance,

returns all numeric columns from the iris dataset, and

computes the typical of every numeric column.

In sparklyr 1.6, each forms of operations will be utilized to Spark dataframes, e.g.,

if_all() and if_any()

if_all() and if_any() are two comfort features from dplyr 1.0.4 (see right here for extra particulars) that successfully mix the outcomes of making use of a boolean predicate to a tidy choice of columns utilizing the logical and/or operators.

Ranging from sparklyr 1.6, if_all() and if_any() can be utilized to Spark dataframes, .e.g.,

Compatibility with dbplyr 2.0 backend API

Sparklyr 1.6 is totally suitable with the newer dbplyr 2.0 backend API (by implementing all interface adjustments really helpful in right here), whereas nonetheless sustaining backward compatibility with the earlier version of dbplyr API, in order that sparklyr customers won’t be compelled to modify to any explicit model of dbplyr.

This ought to be a principally non-user-visible change as of now. Actually, the one discernible conduct change would be the following code


[1] 2

if sparklyr is working with dbplyr 2.0+, and

[1] 1

if in any other case.


In chronological order, we wish to thank the next contributors for making sparklyr 1.6 superior:

We might additionally like to offer a giant shout-out to the fantastic open-source group behind sparklyr, with out whom we’d not have benefitted from quite a few sparklyr-related bug reviews and have recommendations.

Lastly, the writer of this weblog put up additionally very a lot appreciates the extremely beneficial editorial recommendations from @skeydan.

For those who want to study extra about sparklyr, we suggest trying out,, and in addition some earlier sparklyr launch posts equivalent to sparklyr 1.5 and sparklyr 1.4.

That’s all. Thanks for studying!

Greenwald, Michael, and Sanjeev Khanna. 2001. “Area-Environment friendly On-line Computation of Quantile Summaries.” SIGMOD Rec. 30 (2): 58–66.

Lin, Frank, and William Cohen. 2010. “Energy Iteration Clustering.” In, 655–62.



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