tidymodels / tidymodels/workflows

address `fit()` slowdown with sparse tibble and formula preprocessor

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Description

Related to #239—just a place to keep notes on the thought process for supporting sparse tibbles with formula preprocessors. In #245, we see:

library(tidymodels)
  
sparse_hotel_rates <- function() {
  # 99.2 sparsity
  hotel_rates <- modeldata::hotel_rates
  
  prefix_colnames <- function(x, prefix) {
    colnames(x) <- paste(colnames(x), prefix, sep = "_")
    x
  }
  
  dummies_country <- hardhat::fct_encode_one_hot(hotel_rates$country)
  dummies_company <- hardhat::fct_encode_one_hot(hotel_rates$company)
  dummies_agent <- hardhat::fct_encode_one_hot(hotel_rates$agent)
  
  res <- cbind(
    hotel_rates["avg_price_per_room"],
    prefix_colnames(dummies_country, "country"),
    prefix_colnames(dummies_company, "company"),
    prefix_colnames(dummies_agent, "agent")
  )
  
  res <- as.matrix(res)
  Matrix::Matrix(res, sparse = TRUE)
}

hotel_data <- sparse_hotel_rates()
hotel_data <- sparsevctrs::coerce_to_sparse_tibble(hotel_data)

spec <- boost_tree() %>%
  set_mode("regression") %>%
  set_engine("xgboost")

form <- avg_price_per_room ~ .
rec <- recipe(form, data = hotel_data)

wflow <- workflow(spec = spec)

system.time({fit(wflow %>% add_recipe(rec), hotel_data)})
#>    user  system elapsed 
#>   0.255   0.014   0.269
system.time({fit(wflow %>% add_formula(form), hotel_data)})
#>    user  system elapsed 
#>   3.847   0.039   3.905

Created on 2024-09-13 with reprex v2.1.1

In the formula preprocessor fit() evaluation, the data type conversions don't actually take a ton of time:

Screenshot 2024-09-13 at 10 16 32 AM

It's just that, with add_formula(), parsnip::xgb_train(x) is a matrix, whereas it's a dgCMatrix when passed with add_recipe(), and xgboost is much slower when data that ought to be sparse is dense.

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by reading related issues #239 and #245, then trace formula preprocessing through fit(), add_formula(), and parsnip::xgb_train(x). Compare the matrix passed by add_formula() with the dgCMatrix passed by add_recipe(); done means formula-based fitting preserves the intended sparse representation without the observed slowdown.

Written by the indexing model from the issue text.

Assessment

Tech stack
r
Domain
machine-learning, performance
Issue type
Bug
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
30/100

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