"""Partition samples in the construction of a tree. This module contains the algorithms for moving sample indices to the left and right child node given a split determined by the splitting algorithm in `_splitter.pyx`. Partitioning is done in a way that is efficient for both dense data, and sparse data stored in a Compressed Sparse Column (CSC) format. """ # Authors: The scikit-learn developers # SPDX-License-Identifier: BSD-3-Clause from cython cimport final from libc.math cimport isnan, log2 from libc.stdlib cimport qsort from libc.string cimport memcpy import numpy as np from scipy.sparse import issparse # Constant to switch between algorithm non zero value extract algorithm # in SparsePartitioner cdef float32_t EXTRACT_NNZ_SWITCH = 0.1 # Allow for 32 bit float comparisons cdef float32_t INFINITY_32t = np.inf @final cdef class DensePartitioner: """Partitioner specialized for dense data. Note that this partitioner is agnostic to the splitting strategy (best vs. random). """ def __init__( self, const float32_t[:, :] X, intp_t[::1] samples, float32_t[::1] feature_values, const uint8_t[::1] missing_values_in_feature_mask, ): self.X = X self.samples = samples self.feature_values = feature_values self.missing_values_in_feature_mask = missing_values_in_feature_mask cdef inline void init_node_split(self, intp_t start, intp_t end) noexcept nogil: """Initialize splitter at the beginning of node_split.""" self.start = start self.end = end self.n_missing = 0 cdef inline void sort_samples_and_feature_values( self, intp_t current_feature ) noexcept nogil: """Simultaneously sort based on the feature_values. Missing values are stored at the end of feature_values. The number of missing values observed in feature_values is stored in self.n_missing. """ cdef: intp_t i, current_end float32_t[::1] feature_values = self.feature_values const float32_t[:, :] X = self.X intp_t[::1] samples = self.samples intp_t n_missing = 0 const uint8_t[::1] missing_values_in_feature_mask = self.missing_values_in_feature_mask # Sort samples along that feature; by copying the values into an array and # sorting the array in a manner which utilizes the cache more effectively. if missing_values_in_feature_mask is not None and missing_values_in_feature_mask[current_feature]: i, current_end = self.start, self.end - 1 # Missing values are placed at the end and do not participate in the sorting. while i <= current_end: # Finds the right-most value that is not missing so that # it can be swapped with missing values at its left. if isnan(X[samples[current_end], current_feature]): n_missing += 1 current_end -= 1 continue # X[samples[current_end], current_feature] is a non-missing value if isnan(X[samples[i], current_feature]): samples[i], samples[current_end] = samples[current_end], samples[i] n_missing += 1 current_end -= 1 feature_values[i] = X[samples[i], current_feature] i += 1 else: # When there are no missing values, we only need to copy the data into # feature_values for i in range(self.start, self.end): feature_values[i] = X[samples[i], current_feature] sort(&feature_values[self.start], &samples[self.start], self.end - self.start - n_missing) self.n_missing = n_missing cdef inline void find_min_max( self, intp_t current_feature, float32_t* min_feature_value_out, float32_t* max_feature_value_out, ) noexcept nogil: """Find the minimum and maximum value for current_feature. Missing values are stored at the end of feature_values. The number of missing values observed in feature_values is stored in self.n_missing. """ cdef: intp_t p, current_end float32_t current_feature_value const float32_t[:, :] X = self.X intp_t[::1] samples = self.samples float32_t min_feature_value = INFINITY_32t float32_t max_feature_value = -INFINITY_32t float32_t[::1] feature_values = self.feature_values intp_t n_missing = 0 const uint8_t[::1] missing_values_in_feature_mask = self.missing_values_in_feature_mask # We are copying the values into an array and finding min/max of the array in # a manner which utilizes the cache more effectively. We need to also count # the number of missing-values there are. if missing_values_in_feature_mask is not None and missing_values_in_feature_mask[current_feature]: p, current_end = self.start, self.end - 1 # Missing values are placed at the end and do not participate in the # min/max calculation. while p <= current_end: # Finds the right-most value that is not missing so that # it can be swapped with missing values towards its left. if isnan(X[samples[current_end], current_feature]): n_missing += 1 current_end -= 1 continue # X[samples[current_end], current_feature] is a non-missing value if isnan(X[samples[p], current_feature]): samples[p], samples[current_end] = samples[current_end], samples[p] n_missing += 1 current_end -= 1 current_feature_value = X[samples[p], current_feature] feature_values[p] = current_feature_value if current_feature_value < min_feature_value: min_feature_value = current_feature_value elif current_feature_value > max_feature_value: max_feature_value = current_feature_value p += 1 else: min_feature_value = X[samples[self.start], current_feature] max_feature_value = min_feature_value feature_values[self.start] = min_feature_value for p in range(self.start + 1, self.end): current_feature_value = X[samples[p], current_feature] feature_values[p] = current_feature_value if current_feature_value < min_feature_value: min_feature_value = current_feature_value elif current_feature_value > max_feature_value: max_feature_value = current_feature_value min_feature_value_out[0] = min_feature_value max_feature_value_out[0] = max_feature_value self.n_missing = n_missing cdef inline void next_p(self, intp_t* p_prev, intp_t* p) noexcept nogil: """Compute the next p_prev and p for iterating over feature values. The missing values are not included when iterating through the feature values. """ cdef: float32_t[::1] feature_values = self.feature_values intp_t end_non_missing = self.end - self.n_missing while ( p[0] + 1 < end_non_missing and feature_values[p[0] + 1] <= feature_values[p[0]] + FEATURE_THRESHOLD ): p[0] += 1 p_prev[0] = p[0] # By adding 1, we have # (feature_values[p] >= end) or (feature_values[p] > feature_values[p - 1]) p[0] += 1 cdef inline intp_t partition_samples( self, float64_t current_threshold ) noexcept nogil: """Partition samples for feature_values at the current_threshold.""" cdef: intp_t p = self.start intp_t partition_end = self.end - self.n_missing intp_t[::1] samples = self.samples float32_t[::1] feature_values = self.feature_values while p < partition_end: if feature_values[p] <= current_threshold: p += 1 else: partition_end -= 1 feature_values[p], feature_values[partition_end] = ( feature_values[partition_end], feature_values[p] ) samples[p], samples[partition_end] = samples[partition_end], samples[p] return partition_end cdef inline void partition_samples_final( self, intp_t best_pos, float64_t best_threshold, intp_t best_feature, intp_t best_n_missing, ) noexcept nogil: """Partition samples for X at the best_threshold and best_feature. If missing values are present, this method partitions `samples` so that the `best_n_missing` missing values' indices are in the right-most end of `samples`, that is `samples[end_non_missing:end]`. """ cdef: # Local invariance: start <= p <= partition_end <= end intp_t start = self.start intp_t p = start intp_t end = self.end - 1 intp_t partition_end = end - best_n_missing intp_t[::1] samples = self.samples const float32_t[:, :] X = self.X float32_t current_value if best_n_missing != 0: # Move samples with missing values to the end while partitioning the # non-missing samples while p < partition_end: # Keep samples with missing values at the end if isnan(X[samples[end], best_feature]): end -= 1 continue # Swap sample with missing values with the sample at the end current_value = X[samples[p], best_feature] if isnan(current_value): samples[p], samples[end] = samples[end], samples[p] end -= 1 # The swapped sample at the end is always a non-missing value, so # we can continue the algorithm without checking for missingness. current_value = X[samples[p], best_feature] # Partition the non-missing samples if current_value <= best_threshold: p += 1 else: samples[p], samples[partition_end] = samples[partition_end], samples[p] partition_end -= 1 else: # Partitioning routine when there are no missing values while p < partition_end: if X[samples[p], best_feature] <= best_threshold: p += 1 else: samples[p], samples[partition_end] = samples[partition_end], samples[p] partition_end -= 1 @final cdef class SparsePartitioner: """Partitioner specialized for sparse CSC data. Note that this partitioner is agnostic to the splitting strategy (best vs. random). """ def __init__( self, object X, intp_t[::1] samples, intp_t n_samples, float32_t[::1] feature_values, const uint8_t[::1] missing_values_in_feature_mask, ): if not (issparse(X) and X.format == "csc"): raise ValueError("X should be in csc format") self.samples = samples self.feature_values = feature_values # Initialize X cdef intp_t n_total_samples = X.shape[0] self.X_data = X.data self.X_indices = X.indices self.X_indptr = X.indptr self.n_total_samples = n_total_samples # Initialize auxiliary array used to perform split self.index_to_samples = np.full(n_total_samples, fill_value=-1, dtype=np.intp) self.sorted_samples = np.empty(n_samples, dtype=np.intp) cdef intp_t p for p in range(n_samples): self.index_to_samples[samples[p]] = p self.missing_values_in_feature_mask = missing_values_in_feature_mask cdef inline void init_node_split(self, intp_t start, intp_t end) noexcept nogil: """Initialize splitter at the beginning of node_split.""" self.start = start self.end = end self.is_samples_sorted = 0 self.n_missing = 0 cdef inline void sort_samples_and_feature_values( self, intp_t current_feature ) noexcept nogil: """Simultaneously sort based on the feature_values.""" cdef: float32_t[::1] feature_values = self.feature_values intp_t[::1] index_to_samples = self.index_to_samples intp_t[::1] samples = self.samples self.extract_nnz(current_feature) # Sort the positive and negative parts of `feature_values` sort(&feature_values[self.start], &samples[self.start], self.end_negative - self.start) if self.start_positive < self.end: sort( &feature_values[self.start_positive], &samples[self.start_positive], self.end - self.start_positive ) # Update index_to_samples to take into account the sort for p in range(self.start, self.end_negative): index_to_samples[samples[p]] = p for p in range(self.start_positive, self.end): index_to_samples[samples[p]] = p # Add one or two zeros in feature_values, if there is any if self.end_negative < self.start_positive: self.start_positive -= 1 feature_values[self.start_positive] = 0. if self.end_negative != self.start_positive: feature_values[self.end_negative] = 0. self.end_negative += 1 # XXX: When sparse supports missing values, this should be set to the # number of missing values for current_feature self.n_missing = 0 cdef inline void find_min_max( self, intp_t current_feature, float32_t* min_feature_value_out, float32_t* max_feature_value_out, ) noexcept nogil: """Find the minimum and maximum value for current_feature.""" cdef: intp_t p float32_t current_feature_value, min_feature_value, max_feature_value float32_t[::1] feature_values = self.feature_values self.extract_nnz(current_feature) if self.end_negative != self.start_positive: # There is a zero min_feature_value = 0 max_feature_value = 0 else: min_feature_value = feature_values[self.start] max_feature_value = min_feature_value # Find min, max in feature_values[start:end_negative] for p in range(self.start, self.end_negative): current_feature_value = feature_values[p] if current_feature_value < min_feature_value: min_feature_value = current_feature_value elif current_feature_value > max_feature_value: max_feature_value = current_feature_value # Update min, max given feature_values[start_positive:end] for p in range(self.start_positive, self.end): current_feature_value = feature_values[p] if current_feature_value < min_feature_value: min_feature_value = current_feature_value elif current_feature_value > max_feature_value: max_feature_value = current_feature_value min_feature_value_out[0] = min_feature_value max_feature_value_out[0] = max_feature_value cdef inline void next_p(self, intp_t* p_prev, intp_t* p) noexcept nogil: """Compute the next p_prev and p for iterating over feature values.""" cdef: intp_t p_next float32_t[::1] feature_values = self.feature_values if p[0] + 1 != self.end_negative: p_next = p[0] + 1 else: p_next = self.start_positive while (p_next < self.end and feature_values[p_next] <= feature_values[p[0]] + FEATURE_THRESHOLD): p[0] = p_next if p[0] + 1 != self.end_negative: p_next = p[0] + 1 else: p_next = self.start_positive p_prev[0] = p[0] p[0] = p_next cdef inline intp_t partition_samples( self, float64_t current_threshold ) noexcept nogil: """Partition samples for feature_values at the current_threshold.""" return self._partition(current_threshold, self.start_positive) cdef inline void partition_samples_final( self, intp_t best_pos, float64_t best_threshold, intp_t best_feature, intp_t n_missing, ) noexcept nogil: """Partition samples for X at the best_threshold and best_feature.""" self.extract_nnz(best_feature) self._partition(best_threshold, best_pos) cdef inline intp_t _partition(self, float64_t threshold, intp_t zero_pos) noexcept nogil: """Partition samples[start:end] based on threshold.""" cdef: intp_t p, partition_end intp_t[::1] index_to_samples = self.index_to_samples float32_t[::1] feature_values = self.feature_values intp_t[::1] samples = self.samples if threshold < 0.: p = self.start partition_end = self.end_negative elif threshold > 0.: p = self.start_positive partition_end = self.end else: # Data are already split return zero_pos while p < partition_end: if feature_values[p] <= threshold: p += 1 else: partition_end -= 1 feature_values[p], feature_values[partition_end] = ( feature_values[partition_end], feature_values[p] ) sparse_swap(index_to_samples, samples, p, partition_end) return partition_end cdef inline void extract_nnz(self, intp_t feature) noexcept nogil: """Extract and partition values for a given feature. The extracted values are partitioned between negative values feature_values[start:end_negative[0]] and positive values feature_values[start_positive[0]:end]. The samples and index_to_samples are modified according to this partition. The extraction corresponds to the intersection between the arrays X_indices[indptr_start:indptr_end] and samples[start:end]. This is done efficiently using either an index_to_samples based approach or binary search based approach. Parameters ---------- feature : intp_t, Index of the feature we want to extract non zero value. """ cdef intp_t[::1] samples = self.samples cdef float32_t[::1] feature_values = self.feature_values cdef intp_t indptr_start = self.X_indptr[feature], cdef intp_t indptr_end = self.X_indptr[feature + 1] cdef intp_t n_indices = (indptr_end - indptr_start) cdef intp_t n_samples = self.end - self.start cdef intp_t[::1] index_to_samples = self.index_to_samples cdef intp_t[::1] sorted_samples = self.sorted_samples cdef const int32_t[::1] X_indices = self.X_indices cdef const float32_t[::1] X_data = self.X_data # Use binary search if n_samples * log(n_indices) < # n_indices and index_to_samples approach otherwise. # O(n_samples * log(n_indices)) is the running time of binary # search and O(n_indices) is the running time of index_to_samples # approach. if ((1 - self.is_samples_sorted) * n_samples * log2(n_samples) + n_samples * log2(n_indices) < EXTRACT_NNZ_SWITCH * n_indices): extract_nnz_binary_search(X_indices, X_data, indptr_start, indptr_end, samples, self.start, self.end, index_to_samples, feature_values, &self.end_negative, &self.start_positive, sorted_samples, &self.is_samples_sorted) # Using an index to samples technique to extract non zero values # index_to_samples is a mapping from X_indices to samples else: extract_nnz_index_to_samples(X_indices, X_data, indptr_start, indptr_end, samples, self.start, self.end, index_to_samples, feature_values, &self.end_negative, &self.start_positive) cdef int compare_SIZE_t(const void* a, const void* b) noexcept nogil: """Comparison function for sort. This must return an `int` as it is used by stdlib's qsort, which expects an `int` return value. """ return ((a)[0] - (b)[0]) cdef inline void binary_search(const int32_t[::1] sorted_array, int32_t start, int32_t end, intp_t value, intp_t* index, int32_t* new_start) noexcept nogil: """Return the index of value in the sorted array. If not found, return -1. new_start is the last pivot + 1 """ cdef int32_t pivot index[0] = -1 while start < end: pivot = start + (end - start) / 2 if sorted_array[pivot] == value: index[0] = pivot start = pivot + 1 break if sorted_array[pivot] < value: start = pivot + 1 else: end = pivot new_start[0] = start cdef inline void extract_nnz_index_to_samples(const int32_t[::1] X_indices, const float32_t[::1] X_data, int32_t indptr_start, int32_t indptr_end, intp_t[::1] samples, intp_t start, intp_t end, intp_t[::1] index_to_samples, float32_t[::1] feature_values, intp_t* end_negative, intp_t* start_positive) noexcept nogil: """Extract and partition values for a feature using index_to_samples. Complexity is O(indptr_end - indptr_start). """ cdef int32_t k cdef intp_t index cdef intp_t end_negative_ = start cdef intp_t start_positive_ = end for k in range(indptr_start, indptr_end): if start <= index_to_samples[X_indices[k]] < end: if X_data[k] > 0: start_positive_ -= 1 feature_values[start_positive_] = X_data[k] index = index_to_samples[X_indices[k]] sparse_swap(index_to_samples, samples, index, start_positive_) elif X_data[k] < 0: feature_values[end_negative_] = X_data[k] index = index_to_samples[X_indices[k]] sparse_swap(index_to_samples, samples, index, end_negative_) end_negative_ += 1 # Returned values end_negative[0] = end_negative_ start_positive[0] = start_positive_ cdef inline void extract_nnz_binary_search(const int32_t[::1] X_indices, const float32_t[::1] X_data, int32_t indptr_start, int32_t indptr_end, intp_t[::1] samples, intp_t start, intp_t end, intp_t[::1] index_to_samples, float32_t[::1] feature_values, intp_t* end_negative, intp_t* start_positive, intp_t[::1] sorted_samples, bint* is_samples_sorted) noexcept nogil: """Extract and partition values for a given feature using binary search. If n_samples = end - start and n_indices = indptr_end - indptr_start, the complexity is O((1 - is_samples_sorted[0]) * n_samples * log(n_samples) + n_samples * log(n_indices)). """ cdef intp_t n_samples if not is_samples_sorted[0]: n_samples = end - start memcpy(&sorted_samples[start], &samples[start], n_samples * sizeof(intp_t)) qsort(&sorted_samples[start], n_samples, sizeof(intp_t), compare_SIZE_t) is_samples_sorted[0] = 1 while (indptr_start < indptr_end and sorted_samples[start] > X_indices[indptr_start]): indptr_start += 1 while (indptr_start < indptr_end and sorted_samples[end - 1] < X_indices[indptr_end - 1]): indptr_end -= 1 cdef intp_t p = start cdef intp_t index cdef intp_t k cdef intp_t end_negative_ = start cdef intp_t start_positive_ = end while (p < end and indptr_start < indptr_end): # Find index of sorted_samples[p] in X_indices binary_search(X_indices, indptr_start, indptr_end, sorted_samples[p], &k, &indptr_start) if k != -1: # If k != -1, we have found a non zero value if X_data[k] > 0: start_positive_ -= 1 feature_values[start_positive_] = X_data[k] index = index_to_samples[X_indices[k]] sparse_swap(index_to_samples, samples, index, start_positive_) elif X_data[k] < 0: feature_values[end_negative_] = X_data[k] index = index_to_samples[X_indices[k]] sparse_swap(index_to_samples, samples, index, end_negative_) end_negative_ += 1 p += 1 # Returned values end_negative[0] = end_negative_ start_positive[0] = start_positive_ cdef inline void sparse_swap(intp_t[::1] index_to_samples, intp_t[::1] samples, intp_t pos_1, intp_t pos_2) noexcept nogil: """Swap sample pos_1 and pos_2 preserving sparse invariant.""" samples[pos_1], samples[pos_2] = samples[pos_2], samples[pos_1] index_to_samples[samples[pos_1]] = pos_1 index_to_samples[samples[pos_2]] = pos_2 cdef inline void shift_missing_values_to_left_if_required( SplitRecord* best, intp_t[::1] samples, intp_t end, ) noexcept nogil: """Shift missing value sample indices to the left of the split if required. Note: this should always be called at the very end because it will move samples around, thereby affecting the criterion. This affects the computation of the children impurity, which affects the computation of the next node. """ cdef intp_t i, p, current_end # The partitioner partitions the data such that the missing values are in # samples[-n_missing:] for the criterion to consume. If the missing values # are going to the right node, then the missing values are already in the # correct position. If the missing values go left, then we move the missing # values to samples[best.pos:best.pos+n_missing] and update `best.pos`. if best.n_missing > 0 and best.missing_go_to_left: for p in range(best.n_missing): i = best.pos + p current_end = end - 1 - p samples[i], samples[current_end] = samples[current_end], samples[i] best.pos += best.n_missing def _py_sort(float32_t[::1] feature_values, intp_t[::1] samples, intp_t n): """Used for testing sort.""" sort(&feature_values[0], &samples[0], n) # Sort n-element arrays pointed to by feature_values and samples, simultaneously, # by the values in feature_values. Algorithm: Introsort (Musser, SP&E, 1997). cdef inline void sort(float32_t* feature_values, intp_t* samples, intp_t n) noexcept nogil: if n == 0: return cdef intp_t maxd = 2 * log2(n) introsort(feature_values, samples, n, maxd) cdef inline void swap(float32_t* feature_values, intp_t* samples, intp_t i, intp_t j) noexcept nogil: # Helper for sort feature_values[i], feature_values[j] = feature_values[j], feature_values[i] samples[i], samples[j] = samples[j], samples[i] cdef inline float32_t median3(float32_t* feature_values, intp_t n) noexcept nogil: # Median of three pivot selection, after Bentley and McIlroy (1993). # Engineering a sort function. SP&E. Requires 8/3 comparisons on average. cdef float32_t a = feature_values[0], b = feature_values[n / 2], c = feature_values[n - 1] if a < b: if b < c: return b elif a < c: return c else: return a elif b < c: if a < c: return a else: return c else: return b # Introsort with median of 3 pivot selection and 3-way partition function # (robust to repeated elements, e.g. lots of zero features). cdef void introsort(float32_t* feature_values, intp_t *samples, intp_t n, intp_t maxd) noexcept nogil: cdef float32_t pivot cdef intp_t i, l, r while n > 1: if maxd <= 0: # max depth limit exceeded ("gone quadratic") heapsort(feature_values, samples, n) return maxd -= 1 pivot = median3(feature_values, n) # Three-way partition. i = l = 0 r = n while i < r: if feature_values[i] < pivot: swap(feature_values, samples, i, l) i += 1 l += 1 elif feature_values[i] > pivot: r -= 1 swap(feature_values, samples, i, r) else: i += 1 introsort(feature_values, samples, l, maxd) feature_values += r samples += r n -= r cdef inline void sift_down(float32_t* feature_values, intp_t* samples, intp_t start, intp_t end) noexcept nogil: # Restore heap order in feature_values[start:end] by moving the max element to start. cdef intp_t child, maxind, root root = start while True: child = root * 2 + 1 # find max of root, left child, right child maxind = root if child < end and feature_values[maxind] < feature_values[child]: maxind = child if child + 1 < end and feature_values[maxind] < feature_values[child + 1]: maxind = child + 1 if maxind == root: break else: swap(feature_values, samples, root, maxind) root = maxind cdef void heapsort(float32_t* feature_values, intp_t* samples, intp_t n) noexcept nogil: cdef intp_t start, end # heapify start = (n - 2) / 2 end = n while True: sift_down(feature_values, samples, start, end) if start == 0: break start -= 1 # sort by shrinking the heap, putting the max element immediately after it end = n - 1 while end > 0: swap(feature_values, samples, 0, end) sift_down(feature_values, samples, 0, end) end = end - 1