e8a6597957
* [R] fix predict contributions for data with no colnames * [R] add a render parameter for xgb.plot.multi.trees; fixes #2628 * [R] update Rd's * [R] remove unnecessary dep-package from R cmake install * silence type warnings; readability * [R] silence complaint about incomplete line at the end * [R] initial version of xgb.plot.shap() * [R] more work on xgb.plot.shap * [R] enforce black font in xgb.plot.tree; fixes #2640 * [R] if feature names are available, check in predict that they are the same; fixes #2857 * [R] cran check and lint fixes * remove tabs * [R] add references; a test for plot.shap
149 lines
6.1 KiB
R
149 lines
6.1 KiB
R
#' Project all trees on one tree and plot it
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#'
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#' Visualization of the ensemble of trees as a single collective unit.
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#'
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#' @param model produced by the \code{xgb.train} function.
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#' @param feature_names names of each feature as a \code{character} vector.
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#' @param features_keep number of features to keep in each position of the multi trees.
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#' @param plot_width width in pixels of the graph to produce
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#' @param plot_height height in pixels of the graph to produce
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#' @param render a logical flag for whether the graph should be rendered (see Value).
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#' @param ... currently not used
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#'
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#' @details
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#'
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#' This function tries to capture the complexity of a gradient boosted tree model
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#' in a cohesive way by compressing an ensemble of trees into a single tree-graph representation.
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#' The goal is to improve the interpretability of a model generally seen as black box.
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#'
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#' Note: this function is applicable to tree booster-based models only.
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#'
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#' It takes advantage of the fact that the shape of a binary tree is only defined by
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#' its depth (therefore, in a boosting model, all trees have similar shape).
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#'
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#' Moreover, the trees tend to reuse the same features.
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#'
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#' The function projects each tree onto one, and keeps for each position the
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#' \code{features_keep} first features (based on the Gain per feature measure).
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#'
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#' This function is inspired by this blog post:
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#' \url{https://wellecks.wordpress.com/2015/02/21/peering-into-the-black-box-visualizing-lambdamart/}
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#'
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#' @return
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#'
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#' When \code{render = TRUE}:
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#' returns a rendered graph object which is an \code{htmlwidget} of class \code{grViz}.
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#' Similar to ggplot objects, it needs to be printed to see it when not running from command line.
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#'
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#' When \code{render = FALSE}:
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#' silently returns a graph object which is of DiagrammeR's class \code{dgr_graph}.
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#' This could be useful if one wants to modify some of the graph attributes
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#' before rendering the graph with \code{\link[DiagrammeR]{render_graph}}.
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#'
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#' @examples
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#'
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#' data(agaricus.train, package='xgboost')
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#'
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#' bst <- xgboost(data = agaricus.train$data, label = agaricus.train$label, max_depth = 15,
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#' eta = 1, nthread = 2, nrounds = 30, objective = "binary:logistic",
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#' min_child_weight = 50, verbose = 0)
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#'
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#' p <- xgb.plot.multi.trees(model = bst, features_keep = 3)
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#' print(p)
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#'
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#' \dontrun{
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#' # Below is an example of how to save this plot to a file.
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#' # Note that for `export_graph` to work, the DiagrammeRsvg and rsvg packages must also be installed.
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#' library(DiagrammeR)
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#' gr <- xgb.plot.multi.trees(model=bst, features_keep = 3, render=FALSE)
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#' export_graph(gr, 'tree.pdf', width=1500, height=600)
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#' }
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#'
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#' @export
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xgb.plot.multi.trees <- function(model, feature_names = NULL, features_keep = 5, plot_width = NULL, plot_height = NULL,
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render = TRUE, ...){
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check.deprecation(...)
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tree.matrix <- xgb.model.dt.tree(feature_names = feature_names, model = model)
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# first number of the path represents the tree, then the following numbers are related to the path to follow
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# root init
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root.nodes <- tree.matrix[stri_detect_regex(ID, "\\d+-0"), ID]
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tree.matrix[ID %in% root.nodes, abs.node.position := root.nodes]
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precedent.nodes <- root.nodes
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while(tree.matrix[,sum(is.na(abs.node.position))] > 0) {
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yes.row.nodes <- tree.matrix[abs.node.position %in% precedent.nodes & !is.na(Yes)]
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no.row.nodes <- tree.matrix[abs.node.position %in% precedent.nodes & !is.na(No)]
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yes.nodes.abs.pos <- yes.row.nodes[, abs.node.position] %>% paste0("_0")
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no.nodes.abs.pos <- no.row.nodes[, abs.node.position] %>% paste0("_1")
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tree.matrix[ID %in% yes.row.nodes[, Yes], abs.node.position := yes.nodes.abs.pos]
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tree.matrix[ID %in% no.row.nodes[, No], abs.node.position := no.nodes.abs.pos]
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precedent.nodes <- c(yes.nodes.abs.pos, no.nodes.abs.pos)
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}
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tree.matrix[!is.na(Yes), Yes := paste0(abs.node.position, "_0")]
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tree.matrix[!is.na(No), No := paste0(abs.node.position, "_1")]
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remove.tree <- . %>% stri_replace_first_regex(pattern = "^\\d+-", replacement = "")
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tree.matrix[,`:=`(abs.node.position = remove.tree(abs.node.position),
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Yes = remove.tree(Yes),
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No = remove.tree(No))]
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nodes.dt <- tree.matrix[
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, .(Quality = sum(Quality))
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, by = .(abs.node.position, Feature)
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][, .(Text = paste0(Feature[1:min(length(Feature), features_keep)],
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" (",
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format(Quality[1:min(length(Quality), features_keep)], digits=5),
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")") %>%
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paste0(collapse = "\n"))
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, by = abs.node.position]
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edges.dt <- tree.matrix[Feature != "Leaf", .(abs.node.position, Yes)] %>%
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list(tree.matrix[Feature != "Leaf",.(abs.node.position, No)]) %>%
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rbindlist() %>%
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setnames(c("From", "To")) %>%
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.[, .N, .(From, To)] %>%
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.[, N:=NULL]
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nodes <- DiagrammeR::create_node_df(
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n = nrow(nodes.dt),
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label = nodes.dt[,Text]
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)
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edges <- DiagrammeR::create_edge_df(
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from = match(edges.dt[,From], nodes.dt[,abs.node.position]),
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to = match(edges.dt[,To], nodes.dt[,abs.node.position]),
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rel = "leading_to")
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graph <- DiagrammeR::create_graph(
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nodes_df = nodes,
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edges_df = edges,
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attr_theme = NULL
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) %>%
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DiagrammeR::add_global_graph_attrs(
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attr_type = "graph",
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attr = c("layout", "rankdir"),
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value = c("dot", "LR")
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) %>%
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DiagrammeR::add_global_graph_attrs(
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attr_type = "node",
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attr = c("color", "fillcolor", "style", "shape", "fontname"),
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value = c("DimGray", "beige", "filled", "rectangle", "Helvetica")
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) %>%
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DiagrammeR::add_global_graph_attrs(
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attr_type = "edge",
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attr = c("color", "arrowsize", "arrowhead", "fontname"),
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value = c("DimGray", "1.5", "vee", "Helvetica"))
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if (!render) return(invisible(graph))
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DiagrammeR::render_graph(graph, width = plot_width, height = plot_height)
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}
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globalVariables(c(".N", "N", "From", "To", "Text", "Feature", "no.nodes.abs.pos",
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"ID", "Yes", "No", "Tree", "yes.nodes.abs.pos", "abs.node.position"))
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