[Breaking] Set output margin to True for custom objective. (#5564)

* Set output margin to True for custom objective in Python and R.

* Add a demo for writing multi-class custom objective function.

* Run tests on selected demos.

R-package/R/utils.R

@@ -145,7 +145,7 @@ xgb.iter.update <- function(booster_handle, dtrain, iter, obj = NULL) {
   if (is.null(obj)) {
     .Call(XGBoosterUpdateOneIter_R, booster_handle, as.integer(iter), dtrain)
   } else {
-    pred <- predict(booster_handle, dtrain, training = TRUE)
+    pred <- predict(booster_handle, dtrain, outputmargin = TRUE, training = TRUE)
     gpair <- obj(pred, dtrain)
     .Call(XGBoosterBoostOneIter_R, booster_handle, dtrain, gpair$grad, gpair$hess)
   }

R-package/tests/testthat/test_custom_objective.R

@@ -58,3 +58,20 @@ test_that("custom objective using DMatrix attr works", {
   bst <- xgb.train(param, dtrain, num_round, watchlist)
   expect_equal(class(bst), "xgb.Booster")
 })
+
+test_that("custom objective with multi-class works", {
+  data = as.matrix(iris[, -5])
+  label =  as.numeric(iris$Species) - 1
+  dtrain <- xgb.DMatrix(data = data, label = label)
+  nclasses <- 3
+
+  fake_softprob <- function(preds, dtrain) {
+    expect_true(all(matrix(preds) == 0.5))
+    grad <- rnorm(dim(as.matrix(preds))[1])
+    expect_equal(dim(data)[1] * nclasses, dim(as.matrix(preds))[1])
+    hess <- rnorm(dim(as.matrix(preds))[1])
+    return (list(grad = grad, hess = hess))
+  }
+  param$objective = fake_softprob
+  bst <- xgb.train(param, dtrain, 1, num_class=nclasses)
+})

demo/guide-python/README.md

@@ -3,6 +3,7 @@ XGBoost Python Feature Walkthrough
 * [Basic walkthrough of wrappers](basic_walkthrough.py)
 * [Customize loss function, and evaluation metric](custom_objective.py)
 * [Re-implement RMSLE as customized metric and objective](custom_rmsle.py)
+* [Re-Implement `multi:softmax` objective as customized objective](custom_softmax.py)
 * [Boosting from existing prediction](boost_from_prediction.py)
 * [Predicting using first n trees](predict_first_ntree.py)
 * [Generalized Linear Model](generalized_linear_model.py)

demo/guide-python/basic_walkthrough.py

@@ -1,16 +1,22 @@
-#!/usr/bin/python
+#!/usr/bin/env python
 import numpy as np
 import scipy.sparse
 import pickle
 import xgboost as xgb
+import os
 
-### simple example
+# Make sure the demo knows where to load the data.
+CURRENT_DIR = os.path.dirname(os.path.abspath(__file__))
+XGBOOST_ROOT_DIR = os.path.dirname(os.path.dirname(CURRENT_DIR))
+DEMO_DIR = os.path.join(XGBOOST_ROOT_DIR, 'demo')
+
+# simple example
 # load file from text file, also binary buffer generated by xgboost
-dtrain = xgb.DMatrix('../data/agaricus.txt.train')
-dtest = xgb.DMatrix('../data/agaricus.txt.test')
+dtrain = xgb.DMatrix(os.path.join(DEMO_DIR, 'data', 'agaricus.txt.train'))
+dtest = xgb.DMatrix(os.path.join(DEMO_DIR, 'data', 'agaricus.txt.test'))
 
 # specify parameters via map, definition are same as c++ version
-param = {'max_depth':2, 'eta':1, 'silent':1, 'objective':'binary:logistic'}
+param = {'max_depth': 2, 'eta': 1, 'objective': 'binary:logistic'}
 
 # specify validations set to watch performance
 watchlist = [(dtest, 'eval'), (dtrain, 'train')]
@@ -20,12 +26,14 @@ bst = xgb.train(param, dtrain, num_round, watchlist)
 # this is prediction
 preds = bst.predict(dtest)
 labels = dtest.get_label()
-print('error=%f' % (sum(1 for i in range(len(preds)) if int(preds[i] > 0.5) != labels[i]) / float(len(preds))))
+print('error=%f' %
+      (sum(1 for i in range(len(preds)) if int(preds[i] > 0.5) != labels[i]) /
+       float(len(preds))))
 bst.save_model('0001.model')
 # dump model
 bst.dump_model('dump.raw.txt')
 # dump model with feature map
-bst.dump_model('dump.nice.txt', '../data/featmap.txt')
+bst.dump_model('dump.nice.txt', os.path.join(DEMO_DIR, 'data/featmap.txt'))
 
 # save dmatrix into binary buffer
 dtest.save_binary('dtest.buffer')
@@ -50,14 +58,18 @@ assert np.sum(np.abs(preds3 - preds)) == 0
 # build dmatrix from scipy.sparse
 print('start running example of build DMatrix from scipy.sparse CSR Matrix')
 labels = []
-row = []; col = []; dat = []
+row = []
+col = []
+dat = []
 i = 0
-for l in open('../data/agaricus.txt.train'):
+for l in open(os.path.join(DEMO_DIR, 'data', 'agaricus.txt.train')):
     arr = l.split()
     labels.append(int(arr[0]))
     for it in arr[1:]:
-        k,v = it.split(':')
-        row.append(i); col.append(int(k)); dat.append(float(v))
+        k, v = it.split(':')
+        row.append(i)
+        col.append(int(k))
+        dat.append(float(v))
     i += 1
 csr = scipy.sparse.csr_matrix((dat, (row, col)))
 dtrain = xgb.DMatrix(csr, label=labels)
@@ -72,8 +84,8 @@ watchlist = [(dtest, 'eval'), (dtrain, 'train')]
 bst = xgb.train(param, dtrain, num_round, watchlist)
 
 print('start running example of build DMatrix from numpy array')
-# NOTE: npymat is numpy array, we will convert it into scipy.sparse.csr_matrix in internal implementation
-# then convert to DMatrix
+# NOTE: npymat is numpy array, we will convert it into scipy.sparse.csr_matrix
+# in internal implementation then convert to DMatrix
 npymat = csr.todense()
 dtrain = xgb.DMatrix(npymat, label=labels)
 watchlist = [(dtest, 'eval'), (dtrain, 'train')]

demo/guide-python/custom_rmsle.py

@@ -15,6 +15,7 @@ import numpy as np
 import xgboost as xgb
 from typing import Tuple, Dict, List
 from time import time
+import argparse
 import matplotlib
 from matplotlib import pyplot as plt
 
@@ -150,12 +151,7 @@ def py_rmsle(dtrain: xgb.DMatrix, dtest: xgb.DMatrix) -> Dict:
     return results
 
 
-if __name__ == '__main__':
-    dtrain, dtest = generate_data()
-    rmse_evals = native_rmse(dtrain, dtest)
-    rmsle_evals = native_rmsle(dtrain, dtest)
-    py_rmsle_evals = py_rmsle(dtrain, dtest)
-
+def plot_history(rmse_evals, rmsle_evals, py_rmsle_evals):
     fig, axs = plt.subplots(3, 1)
     ax0: matplotlib.axes.Axes = axs[0]
     ax1: matplotlib.axes.Axes = axs[1]
@@ -177,3 +173,25 @@ if __name__ == '__main__':
 
     plt.show()
     plt.close()
+
+
+def main(args):
+    dtrain, dtest = generate_data()
+    rmse_evals = native_rmse(dtrain, dtest)
+    rmsle_evals = native_rmsle(dtrain, dtest)
+    py_rmsle_evals = py_rmsle(dtrain, dtest)
+
+    if args.plot != 0:
+        plot_history(rmse_evals, rmsle_evals, py_rmsle_evals)
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(
+        description='Arguments for custom RMSLE objective function demo.')
+    parser.add_argument(
+        '--plot',
+        type=int,
+        default=1,
+        help='Set to 0 to disable plotting the evaluation history.')
+    args = parser.parse_args()
+    main(args)

demo/guide-python/custom_softmax.py

@@ -0,0 +1,148 @@
+'''Demo for creating customized multi-class objective function.  This demo is
+only applicable after (excluding) XGBoost 1.0.0, as before this version XGBoost
+returns transformed prediction for multi-class objective function.  More
+details in comments.
+
+'''
+
+import numpy as np
+import xgboost as xgb
+from matplotlib import pyplot as plt
+import argparse
+
+np.random.seed(1994)
+
+kRows = 100
+kCols = 10
+kClasses = 4                    # number of classes
+
+kRounds = 10                    # number of boosting rounds.
+
+# Generate some random data for demo.
+X = np.random.randn(kRows, kCols)
+y = np.random.randint(0, 4, size=kRows)
+
+m = xgb.DMatrix(X, y)
+
+
+def softmax(x):
+    '''Softmax function with x as input vector.'''
+    e = np.exp(x)
+    return e / np.sum(e)
+
+
+def softprob_obj(predt: np.ndarray, data: xgb.DMatrix):
+    '''Loss function.  Computing the gradient and approximated hessian (diagonal).
+    Reimplements the `multi:softprob` inside XGBoost.
+
+    '''
+    labels = data.get_label()
+    if data.get_weight().size == 0:
+        # Use 1 as weight if we don't have custom weight.
+        weights = np.ones((kRows, 1), dtype=float)
+    else:
+        weights = data.get_weight()
+
+    # The prediction is of shape (rows, classes), each element in a row
+    # represents a raw prediction (leaf weight, hasn't gone through softmax
+    # yet).  In XGBoost 1.0.0, the prediction is transformed by a softmax
+    # function, fixed in later versions.
+    assert predt.shape == (kRows, kClasses)
+
+    grad = np.zeros((kRows, kClasses), dtype=float)
+    hess = np.zeros((kRows, kClasses), dtype=float)
+
+    eps = 1e-6
+
+    # compute the gradient and hessian, slow iterations in Python, only
+    # suitable for demo.  Also the one in native XGBoost core is more robust to
+    # numeric overflow as we don't do anything to mitigate the `exp` in
+    # `softmax` here.
+    for r in range(predt.shape[0]):
+        target = labels[r]
+        p = softmax(predt[r, :])
+        for c in range(predt.shape[1]):
+            assert target >= 0 or target <= kClasses
+            g = p[c] - 1.0 if c == target else p[c]
+            g = g * weights[r]
+            h = max((2.0 * p[c] * (1.0 - p[c]) * weights[r]).item(), eps)
+            grad[r, c] = g
+            hess[r, c] = h
+
+    # Right now (XGBoost 1.0.0), reshaping is necessary
+    grad = grad.reshape((kRows * kClasses, 1))
+    hess = hess.reshape((kRows * kClasses, 1))
+    return grad, hess
+
+
+def predict(booster, X):
+    '''A customized prediction function that converts raw prediction to
+    target class.
+
+    '''
+    # Output margin means we want to obtain the raw prediction obtained from
+    # tree leaf weight.
+    predt = booster.predict(X, output_margin=True)
+    out = np.zeros(kRows)
+    for r in range(predt.shape[0]):
+        # the class with maximum prob (not strictly prob as it haven't gone
+        # through softmax yet so it doesn't sum to 1, but result is the same
+        # for argmax).
+        i = np.argmax(predt[r])
+        out[r] = i
+    return out
+
+
+def plot_history(custom_results, native_results):
+    fig, axs = plt.subplots(2, 1)
+    ax0 = axs[0]
+    ax1 = axs[1]
+
+    x = np.arange(0, kRounds, 1)
+    ax0.plot(x, custom_results['train']['merror'], label='Custom objective')
+    ax0.legend()
+    ax1.plot(x, native_results['train']['merror'], label='multi:softmax')
+    ax1.legend()
+
+    plt.show()
+
+
+def main(args):
+    custom_results = {}
+    # Use our custom objective function
+    booster_custom = xgb.train({'num_class': kClasses},
+                               m,
+                               num_boost_round=kRounds,
+                               obj=softprob_obj,
+                               evals_result=custom_results,
+                               evals=[(m, 'train')])
+
+    predt_custom = predict(booster_custom, m)
+
+    native_results = {}
+    # Use the same objective function defined in XGBoost.
+    booster_native = xgb.train({'num_class': kClasses},
+                               m,
+                               num_boost_round=kRounds,
+                               evals_result=native_results,
+                               evals=[(m, 'train')])
+    predt_native = booster_native.predict(m)
+
+    # We are reimplementing the loss function in XGBoost, so it should
+    # be the same for normal cases.
+    assert np.all(predt_custom == predt_native)
+
+    if args.plot != 0:
+        plot_history(custom_results, native_results)
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(
+        description='Arguments for custom softmax objective function demo.')
+    parser.add_argument(
+        '--plot',
+        type=int,
+        default=1,
+        help='Set to 0 to disable plotting the evaluation history.')
+    args = parser.parse_args()
+    main(args)

doc/tutorials/custom_metric_obj.rst

@@ -14,7 +14,7 @@ concepts should be readily applicable to other language bindings.
    * The customized functions defined here are only applicable to single node training.
      Distributed environment requires syncing with ``xgboost.rabit``, the interface is
      subject to change hence beyond the scope of this tutorial.
-   * We also plan to re-design the interface for multi-classes objective in the future.
+   * We also plan to improve the interface for multi-classes objective in the future.
 
 In the following sections, we will provide a step by step walk through of implementing
 ``Squared Log Error(SLE)`` objective function:
@@ -136,3 +136,12 @@ Notice that the parameter ``disable_default_eval_metric`` is used to suppress th
 in XGBoost.
 
 For fully reproducible source code and comparison plots, see `custom_rmsle.py <https://github.com/dmlc/xgboost/tree/master/demo/guide-python/custom_rmsle.py>`_.
+
+
+******************************
+Multi-class objective function
+******************************
+
+A similiar demo for multi-class objective funtion is also available, see
+`demo/guide-python/custom_softmax.py <https://github.com/dmlc/xgboost/tree/master/demo/guide-python/custom_rmsle.py>`_
+for details.

python-package/xgboost/core.py

@@ -1367,7 +1367,7 @@ class Booster(object):
                                                     ctypes.c_int(iteration),
                                                     dtrain.handle))
         else:
-            pred = self.predict(dtrain, training=True)
+            pred = self.predict(dtrain, output_margin=True, training=True)
             grad, hess = fobj(pred, dtrain)
             self.boost(dtrain, grad, hess)
 

src/gbm/gbtree.cc

@@ -295,6 +295,9 @@ void GBTree::BoostNewTrees(HostDeviceVector<GradientPair>* gpair,
     }
   }
   // update the trees
+  CHECK_EQ(gpair->Size(), p_fmat->Info().num_row_)
+      << "Mismatching size between number of rows from input data and size of "
+         "gradient vector.";
   for (auto& up : updaters_) {
     up->Update(gpair, p_fmat, new_trees);
   }

tests/python/test_demos.py

@@ -0,0 +1,32 @@
+import os
+import subprocess
+import sys
+import pytest
+
+
+CURRENT_DIR = os.path.dirname(__file__)
+ROOT_DIR = os.path.dirname(os.path.dirname(CURRENT_DIR))
+DEMO_DIR = os.path.join(ROOT_DIR, 'demo', 'guide-python')
+
+
+def test_basic_walkthrough():
+    script = os.path.join(DEMO_DIR, 'basic_walkthrough.py')
+    cmd = ['python', script]
+    subprocess.check_call(cmd)
+    os.remove('dump.nice.txt')
+    os.remove('dump.raw.txt')
+
+
+def test_custom_multiclass_objective():
+    script = os.path.join(DEMO_DIR, 'custom_softmax.py')
+    cmd = ['python', script, '--plot=0']
+    subprocess.check_call(cmd)
+
+
+def test_custom_rmsle_objective():
+    major, minor = sys.version_info[:2]
+    if minor < 6:
+        pytest.skip('Skipping RMLSE test due to Python version being too low.')
+    script = os.path.join(DEMO_DIR, 'custom_rmsle.py')
+    cmd = ['python', script, '--plot=0']
+    subprocess.check_call(cmd)