isotree 0.1.0
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- checksums.yaml +7 -0
- data/CHANGELOG.md +3 -0
- data/LICENSE.txt +25 -0
- data/README.md +111 -0
- data/ext/isotree/ext.cpp +178 -0
- data/ext/isotree/extconf.rb +21 -0
- data/lib/isotree.rb +9 -0
- data/lib/isotree/isolation_forest.rb +94 -0
- data/lib/isotree/version.rb +3 -0
- data/vendor/isotree/LICENSE +25 -0
- data/vendor/isotree/README.md +167 -0
- data/vendor/isotree/src/Makevars +4 -0
- data/vendor/isotree/src/RcppExports.cpp +267 -0
- data/vendor/isotree/src/Rwrapper.cpp +762 -0
- data/vendor/isotree/src/crit.cpp +912 -0
- data/vendor/isotree/src/dealloc.cpp +66 -0
- data/vendor/isotree/src/dist.cpp +749 -0
- data/vendor/isotree/src/extended.cpp +790 -0
- data/vendor/isotree/src/fit_model.cpp +1068 -0
- data/vendor/isotree/src/helpers_iforest.cpp +309 -0
- data/vendor/isotree/src/impute.cpp +1205 -0
- data/vendor/isotree/src/isoforest.cpp +771 -0
- data/vendor/isotree/src/isotree.hpp +929 -0
- data/vendor/isotree/src/merge_models.cpp +116 -0
- data/vendor/isotree/src/mult.cpp +607 -0
- data/vendor/isotree/src/predict.cpp +849 -0
- data/vendor/isotree/src/serialize.cpp +262 -0
- data/vendor/isotree/src/utils.cpp +1574 -0
- metadata +154 -0
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/* Isolation forests and variations thereof, with adjustments for incorporation
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* of categorical variables and missing values.
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* Writen for C++11 standard and aimed at being used in R and Python.
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*
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* This library is based on the following works:
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* [1] Liu, Fei Tony, Kai Ming Ting, and Zhi-Hua Zhou.
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* "Isolation forest."
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* 2008 Eighth IEEE International Conference on Data Mining. IEEE, 2008.
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* [2] Liu, Fei Tony, Kai Ming Ting, and Zhi-Hua Zhou.
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* "Isolation-based anomaly detection."
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* ACM Transactions on Knowledge Discovery from Data (TKDD) 6.1 (2012): 3.
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* [3] Hariri, Sahand, Matias Carrasco Kind, and Robert J. Brunner.
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* "Extended Isolation Forest."
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* arXiv preprint arXiv:1811.02141 (2018).
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* [4] Liu, Fei Tony, Kai Ming Ting, and Zhi-Hua Zhou.
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* "On detecting clustered anomalies using SCiForest."
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* Joint European Conference on Machine Learning and Knowledge Discovery in Databases. Springer, Berlin, Heidelberg, 2010.
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* [5] https://sourceforge.net/projects/iforest/
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* [6] https://math.stackexchange.com/questions/3388518/expected-number-of-paths-required-to-separate-elements-in-a-binary-tree
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* [7] Quinlan, J. Ross. C4. 5: programs for machine learning. Elsevier, 2014.
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* [8] Cortes, David. "Distance approximation using Isolation Forests." arXiv preprint arXiv:1910.12362 (2019).
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* [9] Cortes, David. "Imputing missing values with unsupervised random trees." arXiv preprint arXiv:1911.06646 (2019).
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*
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* BSD 2-Clause License
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* Copyright (c) 2019, David Cortes
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* All rights reserved.
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are met:
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* * Redistributions of source code must retain the above copyright notice, this
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* list of conditions and the following disclaimer.
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* * Redistributions in binary form must reproduce the above copyright notice,
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* this list of conditions and the following disclaimer in the documentation
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* and/or other materials provided with the distribution.
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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* DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
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* FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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* DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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* SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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* CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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* OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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* OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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*/
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#include "isotree.hpp"
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#define pw1(x) ((x))
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#define pw2(x) ((x) * (x))
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#define pw3(x) ((x) * (x) * (x))
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#define pw4(x) ((x) * (x) * (x) * (x))
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double calc_kurtosis(size_t ix_arr[], size_t st, size_t end, double x[], MissingAction missing_action)
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{
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long double m = 0;
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long double M2 = 0, M3 = 0, M4 = 0;
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long double delta, delta_s, delta_div;
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long double diff, n;
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if (missing_action == Fail)
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{
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for (size_t row = st; row <= end; row++)
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{
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n = (long double)(row - st + 1);
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delta = x[ix_arr[row]] - m;
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delta_div = delta / n;
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delta_s = delta_div * delta_div;
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diff = delta * (delta_div * (long double)(row - st));
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m += delta_div;
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M4 += diff * delta_s * (n * n - 3 * n + 3) + 6 * delta_s * M2 - 4 * delta_div * M3;
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M3 += diff * delta_div * (n - 2) - 3 * delta_div * M2;
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M2 += diff;
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}
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return ( M4 / M2 ) * ( (long double)(end - st + 1) / M2 );
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}
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else
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{
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size_t cnt = 0;
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for (size_t row = st; row <= end; row++)
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{
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if (!is_na_or_inf(x[ix_arr[row]]))
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{
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cnt++;
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n = (long double) cnt;
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delta = x[ix_arr[row]] - m;
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delta_div = delta / n;
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delta_s = delta_div * delta_div;
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diff = delta * (delta_div * (long double)(cnt - 1));
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m += delta_div;
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M4 += diff * delta_s * (n * n - 3 * n + 3) + 6 * delta_s * M2 - 4 * delta_div * M3;
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M3 += diff * delta_div * (n - 2) - 3 * delta_div * M2;
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M2 += diff;
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}
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}
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return ( M4 / M2 ) * ( (long double)cnt / M2 );
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}
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}
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double calc_kurtosis(size_t ix_arr[], size_t st, size_t end, size_t col_num,
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double Xc[], sparse_ix Xc_ind[], sparse_ix Xc_indptr[],
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MissingAction missing_action)
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{
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/* ix_arr must be already sorted beforehand */
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if (Xc_indptr[col_num] == Xc_indptr[col_num + 1])
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return 0;
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long double s1 = 0;
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long double s2 = 0;
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long double s3 = 0;
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long double s4 = 0;
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size_t cnt = end - st + 1;
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if (cnt <= 1) return 0;
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size_t st_col = Xc_indptr[col_num];
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size_t end_col = Xc_indptr[col_num + 1] - 1;
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size_t curr_pos = st_col;
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size_t ind_end_col = Xc_ind[end_col];
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size_t *ptr_st = std::lower_bound(ix_arr + st, ix_arr + end + 1, Xc_ind[st_col]);
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if (missing_action != Fail)
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{
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for (size_t *row = ptr_st;
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row != ix_arr + end + 1 && curr_pos != end_col + 1 && ind_end_col >= *row;
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)
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{
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if (Xc_ind[curr_pos] == *row)
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{
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if (is_na_or_inf(Xc[curr_pos]))
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{
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cnt--;
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}
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else
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{
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s1 += pw1(Xc[curr_pos]);
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s2 += pw2(Xc[curr_pos]);
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s3 += pw3(Xc[curr_pos]);
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s4 += pw4(Xc[curr_pos]);
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}
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if (row == ix_arr + end || curr_pos == end_col) break;
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curr_pos = std::lower_bound(Xc_ind + curr_pos + 1, Xc_ind + end_col + 1, *(++row)) - Xc_ind;
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}
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else
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{
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if (Xc_ind[curr_pos] > *row)
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row = std::lower_bound(row + 1, ix_arr + end + 1, Xc_ind[curr_pos]);
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else
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curr_pos = std::lower_bound(Xc_ind + curr_pos + 1, Xc_ind + end_col + 1, *row) - Xc_ind;
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}
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}
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}
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else
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{
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for (size_t *row = ptr_st;
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row != ix_arr + end + 1 && curr_pos != end_col + 1 && ind_end_col >= *row;
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)
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{
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if (Xc_ind[curr_pos] == *row)
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{
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s1 += pw1(Xc[curr_pos]);
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s2 += pw2(Xc[curr_pos]);
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s3 += pw3(Xc[curr_pos]);
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s4 += pw4(Xc[curr_pos]);
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if (row == ix_arr + end || curr_pos == end_col) break;
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curr_pos = std::lower_bound(Xc_ind + curr_pos + 1, Xc_ind + end_col + 1, *(++row)) - Xc_ind;
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}
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else
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{
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if (Xc_ind[curr_pos] > *row)
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row = std::lower_bound(row + 1, ix_arr + end + 1, Xc_ind[curr_pos]);
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else
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curr_pos = std::lower_bound(Xc_ind + curr_pos + 1, Xc_ind + end_col + 1, *row) - Xc_ind;
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}
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}
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}
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if (cnt <= 1 || s2 == 0 || s2 == pw2(s1)) return 0;
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long double cnt_l = (long double) cnt;
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long double sn = s1 / cnt_l;
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long double v = s2 / cnt_l - pw2(sn);
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if (v <= 0) return 0;
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return (s4 - 4 * s3 * sn + 6 * s2 * pw2(sn) - 4 * s1 * pw3(sn) + cnt_l * pw4(sn)) / (cnt_l * pw2(v));
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}
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double calc_kurtosis(size_t ix_arr[], size_t st, size_t end, int x[], int ncat, size_t buffer_cnt[], double buffer_prob[],
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MissingAction missing_action, CategSplit cat_split_type, RNG_engine &rnd_generator)
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{
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/* This calculation proceeds as follows:
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- If splitting by subsets, it will assign a random weight ~Unif(0,1) to
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each category, and approximate kurtosis by sampling from such distribution
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with the same probabilities as given by the current counts.
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- If splitting by isolating one category, will binarize at each categorical level,
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assume the values are zero or one, and output the average assuming each categorical
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level has equal probability of being picked.
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(Note that both are misleading heuristics, but might be better than random)
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*/
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size_t cnt = end - st + 1;
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std::fill(buffer_cnt, buffer_cnt + ncat + 1, (size_t)0);
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double sum_kurt = 0;
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if (missing_action == Fail)
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{
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for (size_t row = st; row <= end; row++)
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buffer_cnt[x[ix_arr[row]]]++;
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}
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else
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{
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for (size_t row = st; row <= end; row++)
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{
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if (x[ix_arr[row]] >= 0)
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buffer_cnt[x[ix_arr[row]]]++;
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else
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buffer_cnt[ncat]++;
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}
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}
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cnt -= buffer_cnt[ncat];
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if (cnt <= 1) return 0;
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long double cnt_l = (long double) cnt;
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for (int cat = 0; cat < ncat; cat++)
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buffer_prob[cat] = buffer_cnt[cat] / cnt_l;
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switch(cat_split_type)
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{
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case SubSet:
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{
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long double temp_v;
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long double s1, s2, s3, s4;
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long double coef;
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std::uniform_real_distribution<double> runif(0, 1);
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size_t ntry = 50;
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for (size_t iternum = 0; iternum < 50; iternum++)
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{
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s1 = 0; s2 = 0; s3 = 0; s4 = 0;
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for (int cat = 0; cat < ncat; cat++)
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{
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coef = runif(rnd_generator);
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s1 += buffer_prob[cat] * pw1(coef);
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s2 += buffer_prob[cat] * pw2(coef);
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s3 += buffer_prob[cat] * pw3(coef);
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s4 += buffer_prob[cat] * pw4(coef);
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}
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temp_v = s2 - pw2(s1);
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if (temp_v <= 0)
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ntry--;
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else
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sum_kurt += (s4 - 4 * s3 * pw1(s1) + 6 * s2 * pw2(s1) - 4 * s1 * pw3(s1) + pw4(s1)) / pw2(temp_v);
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}
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if (!ntry)
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return 0;
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else
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return sum_kurt / (long double)ntry;
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}
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case SingleCateg:
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{
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double p;
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int ncat_present = ncat;
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for (int cat = 0; cat < ncat; cat++)
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{
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p = buffer_prob[cat];
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if (p == 0)
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ncat_present--;
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else
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sum_kurt += (p - 4 * p * pw1(p) + 6 * p * pw2(p) - 4 * p * pw3(p) + pw4(p)) / pw2(p - pw2(p));
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}
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if (ncat_present <= 1)
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return 0;
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else
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return sum_kurt / (double) ncat_present;
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}
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}
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return -1; /* this will never be reached, but CRAN complains otherwise */
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}
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double expected_sd_cat(double p[], size_t n, size_t pos[])
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{
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if (n <= 1) return 0;
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long double cum_var = -square(p[pos[0]]) / 3.0 - p[pos[0]] * p[pos[1]] / 2.0 + p[pos[0]] / 3.0 - square(p[pos[1]]) / 3.0 + p[pos[1]] / 3.0;
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for (size_t cat1 = 2; cat1 < n; cat1++)
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{
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cum_var += p[pos[cat1]] / 3.0 - square(p[pos[cat1]]) / 3.0;
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for (size_t cat2 = 0; cat2 < cat1; cat2++)
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cum_var -= p[pos[cat1]] * p[pos[cat2]] / 2.0;
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}
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return sqrt(fmax(cum_var, 1e-8));
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}
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double expected_sd_cat(size_t counts[], double p[], size_t n, size_t pos[])
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{
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if (n <= 1) return 0;
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size_t tot = std::accumulate(pos, pos + n, (size_t)0, [&counts](size_t tot, const size_t ix){return tot + counts[ix];});
|
312
|
+
long double cnt_div = (long double) tot;
|
313
|
+
for (size_t cat = 0; cat < n; cat++)
|
314
|
+
p[pos[cat]] = (long double)counts[pos[cat]] / cnt_div;
|
315
|
+
|
316
|
+
return expected_sd_cat(p, n, pos);
|
317
|
+
}
|
318
|
+
|
319
|
+
double expected_sd_cat_single(size_t counts[], double p[], size_t n, size_t pos[], size_t cat_exclude, size_t cnt)
|
320
|
+
{
|
321
|
+
if (cat_exclude == 0)
|
322
|
+
return expected_sd_cat(counts, p, n-1, pos + 1);
|
323
|
+
|
324
|
+
else if (cat_exclude == (n-1))
|
325
|
+
return expected_sd_cat(counts, p, n-1, pos);
|
326
|
+
|
327
|
+
size_t ix_exclude = pos[cat_exclude];
|
328
|
+
|
329
|
+
long double cnt_div = (long double) (cnt - counts[ix_exclude]);
|
330
|
+
for (size_t cat = 0; cat < n; cat++)
|
331
|
+
p[pos[cat]] = (long double)counts[pos[cat]] / cnt_div;
|
332
|
+
|
333
|
+
double cum_var;
|
334
|
+
if (cat_exclude != 1)
|
335
|
+
cum_var = -square(p[pos[0]]) / 3.0 - p[pos[0]] * p[pos[1]] / 2.0 + p[pos[0]] / 3.0 - square(p[pos[1]]) / 3.0 + p[pos[1]] / 3.0;
|
336
|
+
else
|
337
|
+
cum_var = -square(p[pos[0]]) / 3.0 - p[pos[0]] * p[pos[2]] / 2.0 + p[pos[0]] / 3.0 - square(p[pos[2]]) / 3.0 + p[pos[2]] / 3.0;
|
338
|
+
for (size_t cat1 = (cat_exclude == 1)? 3 : 2; cat1 < n; cat1++)
|
339
|
+
{
|
340
|
+
if (pos[cat1] == ix_exclude) continue;
|
341
|
+
cum_var += p[pos[cat1]] / 3.0 - square(p[pos[cat1]]) / 3.0;
|
342
|
+
for (size_t cat2 = 0; cat2 < cat1; cat2++)
|
343
|
+
{
|
344
|
+
if (pos[cat2] == ix_exclude) continue;
|
345
|
+
cum_var -= p[pos[cat1]] * p[pos[cat2]] / 2.0;
|
346
|
+
}
|
347
|
+
|
348
|
+
}
|
349
|
+
return sqrt(fmax(cum_var, 1e-8));
|
350
|
+
}
|
351
|
+
|
352
|
+
double numeric_gain(size_t cnt_left, size_t cnt_right,
|
353
|
+
long double sum_left, long double sum_right,
|
354
|
+
long double sum_sq_left, long double sum_sq_right,
|
355
|
+
double sd_full, long double cnt)
|
356
|
+
{
|
357
|
+
long double residual =
|
358
|
+
(long double) cnt_left * calc_sd_raw_l(cnt_left, sum_left, sum_sq_left) +
|
359
|
+
(long double) cnt_right * calc_sd_raw_l(cnt_right, sum_right, sum_sq_right);
|
360
|
+
return 1 - residual / (cnt * sd_full);
|
361
|
+
}
|
362
|
+
|
363
|
+
double numeric_gain_no_div(size_t cnt_left, size_t cnt_right,
|
364
|
+
long double sum_left, long double sum_right,
|
365
|
+
long double sum_sq_left, long double sum_sq_right,
|
366
|
+
double sd_full, long double cnt)
|
367
|
+
{
|
368
|
+
long double residual =
|
369
|
+
(long double) cnt_left * calc_sd_raw_l(cnt_left, sum_left, sum_sq_left) +
|
370
|
+
(long double) cnt_right * calc_sd_raw_l(cnt_right, sum_right, sum_sq_right);
|
371
|
+
return sd_full - residual / cnt;
|
372
|
+
}
|
373
|
+
|
374
|
+
double categ_gain(size_t cnt_left, size_t cnt_right,
|
375
|
+
long double s_left, long double s_right,
|
376
|
+
long double base_info, long double cnt)
|
377
|
+
{
|
378
|
+
return (
|
379
|
+
base_info -
|
380
|
+
(((cnt_left <= 1)? 0 : ((long double)cnt_left * logl((long double)cnt_left))) - s_left) -
|
381
|
+
(((cnt_right <= 1)? 0 : ((long double)cnt_right * logl((long double)cnt_right))) - s_right)
|
382
|
+
) / cnt;
|
383
|
+
}
|
384
|
+
|
385
|
+
|
386
|
+
#define avg_between(a, b) (((a) + (b)) / 2)
|
387
|
+
#define sd_gain(sd, sd_left, sd_right) (1.0 - ((sd_left) + (sd_right)) / (2.0 * (sd)))
|
388
|
+
|
389
|
+
/* for split-criterion in hyperplanes (see below for version aimed at single-variable splits) */
|
390
|
+
double eval_guided_crit(double *restrict x, size_t n, GainCriterion criterion, double min_gain,
|
391
|
+
double &split_point, double &xmin, double &xmax)
|
392
|
+
{
|
393
|
+
/* Note: the input 'x' is supposed to be a linear combination of standardized variables, so
|
394
|
+
all numbers are assumed to be small and in the same scale */
|
395
|
+
|
396
|
+
/* here it's assumed the 'x' vector matches exactly with 'ix_arr' + 'st' */
|
397
|
+
if (n == 2)
|
398
|
+
{
|
399
|
+
split_point = avg_between(x[0], x[1]);
|
400
|
+
return 0;
|
401
|
+
}
|
402
|
+
|
403
|
+
/* sort in ascending order */
|
404
|
+
std::sort(x, x + n);
|
405
|
+
if (x[0] == x[n-1]) return -HUGE_VAL;
|
406
|
+
xmin = x[0]; xmax = x[n-1];
|
407
|
+
|
408
|
+
/* compute sum - sum_sq - sd in one pass */
|
409
|
+
long double sum = 0;
|
410
|
+
long double sum_sq = 0;
|
411
|
+
double sd_full;
|
412
|
+
for (size_t row = 0; row < n; row++)
|
413
|
+
{
|
414
|
+
sum += x[row];
|
415
|
+
sum_sq += square(x[row]);
|
416
|
+
}
|
417
|
+
sd_full = calc_sd_raw(n, sum, sum_sq);
|
418
|
+
|
419
|
+
/* try splits by moving observations one at a time from right to left */
|
420
|
+
long double sum_left = 0;
|
421
|
+
long double sum_sq_left = 0;
|
422
|
+
long double sum_right = sum;
|
423
|
+
long double sum_sq_right = sum_sq;
|
424
|
+
double this_gain = -HUGE_VAL;
|
425
|
+
double best_gain = -HUGE_VAL;
|
426
|
+
|
427
|
+
switch(criterion)
|
428
|
+
{
|
429
|
+
case Averaged:
|
430
|
+
{
|
431
|
+
for (size_t row = 0; row < n-1; row++)
|
432
|
+
{
|
433
|
+
sum_left += x[row];
|
434
|
+
sum_sq_left += square(x[row]);
|
435
|
+
sum_right -= x[row];
|
436
|
+
sum_sq_right -= square(x[row]);
|
437
|
+
|
438
|
+
if (x[row] == x[row + 1]) continue;
|
439
|
+
|
440
|
+
this_gain = sd_gain(sd_full,
|
441
|
+
calc_sd_raw(row + 1, sum_left, sum_sq_left),
|
442
|
+
calc_sd_raw(n - row - 1, sum_right, sum_sq_right)
|
443
|
+
);
|
444
|
+
if (this_gain > min_gain && this_gain > best_gain)
|
445
|
+
{
|
446
|
+
best_gain = this_gain;
|
447
|
+
split_point = avg_between(x[row], x[row + 1]);
|
448
|
+
}
|
449
|
+
}
|
450
|
+
break;
|
451
|
+
}
|
452
|
+
|
453
|
+
case Pooled:
|
454
|
+
{
|
455
|
+
long double cnt = (long double) n;
|
456
|
+
for (size_t row = 0; row < n-1; row++)
|
457
|
+
{
|
458
|
+
sum_left += x[row];
|
459
|
+
sum_sq_left += square(x[row]);
|
460
|
+
sum_right -= x[row];
|
461
|
+
sum_sq_right -= square(x[row]);
|
462
|
+
|
463
|
+
if (x[row] == x[row + 1]) continue;
|
464
|
+
|
465
|
+
this_gain = numeric_gain(row + 1, n - row - 1,
|
466
|
+
sum_left, sum_right,
|
467
|
+
sum_sq_left, sum_sq_right,
|
468
|
+
sd_full, cnt
|
469
|
+
);
|
470
|
+
|
471
|
+
if (this_gain > min_gain && this_gain > best_gain)
|
472
|
+
{
|
473
|
+
best_gain = this_gain;
|
474
|
+
split_point = avg_between(x[row], x[row + 1]);
|
475
|
+
}
|
476
|
+
}
|
477
|
+
break;
|
478
|
+
}
|
479
|
+
}
|
480
|
+
|
481
|
+
if (best_gain <= -HUGE_VAL && this_gain <= min_gain && this_gain > -HUGE_VAL)
|
482
|
+
return 0;
|
483
|
+
else
|
484
|
+
return best_gain;
|
485
|
+
}
|
486
|
+
|
487
|
+
/* for split-criterion in single-variable splits */
|
488
|
+
#define std_val(x, m, sd) ( ((x) - (m)) / (sd) )
|
489
|
+
double eval_guided_crit(size_t *restrict ix_arr, size_t st, size_t end, double *restrict x,
|
490
|
+
size_t &split_ix, double &split_point, double &xmin, double &xmax,
|
491
|
+
GainCriterion criterion, double min_gain, MissingAction missing_action)
|
492
|
+
{
|
493
|
+
/* move NAs to the front if there's any, exclude them from calculations */
|
494
|
+
if (missing_action != Fail)
|
495
|
+
st = move_NAs_to_front(ix_arr, st, end, x);
|
496
|
+
|
497
|
+
if (st >= end) return -HUGE_VAL;
|
498
|
+
else if (st == (end-1))
|
499
|
+
{
|
500
|
+
split_point = avg_between(x[ix_arr[st]], x[ix_arr[end]]);
|
501
|
+
split_ix = st;
|
502
|
+
return 0;
|
503
|
+
}
|
504
|
+
|
505
|
+
/* sort in ascending order */
|
506
|
+
std::sort(ix_arr + st, ix_arr + end + 1, [&x](const size_t a, const size_t b){return x[a] < x[b];});
|
507
|
+
if (x[ix_arr[st]] == x[ix_arr[end]]) return -HUGE_VAL;
|
508
|
+
xmin = x[ix_arr[st]]; xmax = x[ix_arr[end]];
|
509
|
+
|
510
|
+
/* Note: these variables are not standardized beforehand, so a single-pass gain
|
511
|
+
calculation for both branches would suffer from numerical instability and perhaps give
|
512
|
+
negative standard deviations if the sample size is large or the values have different
|
513
|
+
orders of magnitude */
|
514
|
+
|
515
|
+
/* first get mean and sd */
|
516
|
+
double x_mean, x_sd;
|
517
|
+
calc_mean_and_sd(ix_arr, st, end, x,
|
518
|
+
Fail, x_sd, x_mean);
|
519
|
+
|
520
|
+
/* compute sum - sum_sq - sd in one pass, on the standardized values */
|
521
|
+
double zval;
|
522
|
+
long double sum = 0;
|
523
|
+
long double sum_sq = 0;
|
524
|
+
double sd_full;
|
525
|
+
for (size_t row = st; row <= end; row++)
|
526
|
+
{
|
527
|
+
zval = std_val(x[ix_arr[row]], x_mean, x_sd);
|
528
|
+
sum += zval;
|
529
|
+
sum_sq += square(zval);
|
530
|
+
}
|
531
|
+
sd_full = calc_sd_raw(end - st + 1, sum, sum_sq);
|
532
|
+
|
533
|
+
/* try splits by moving observations one at a time from right to left */
|
534
|
+
long double sum_left = 0;
|
535
|
+
long double sum_sq_left = 0;
|
536
|
+
long double sum_right = sum;
|
537
|
+
long double sum_sq_right = sum_sq;
|
538
|
+
double this_gain = -HUGE_VAL;
|
539
|
+
double best_gain = -HUGE_VAL;
|
540
|
+
|
541
|
+
switch(criterion)
|
542
|
+
{
|
543
|
+
case Averaged:
|
544
|
+
{
|
545
|
+
for (size_t row = st; row < end; row++)
|
546
|
+
{
|
547
|
+
zval = std_val(x[ix_arr[row]], x_mean, x_sd);
|
548
|
+
sum_left += zval;
|
549
|
+
sum_sq_left += square(zval);
|
550
|
+
sum_right -= zval;
|
551
|
+
sum_sq_right -= square(zval);
|
552
|
+
|
553
|
+
if (x[ix_arr[row]] == x[ix_arr[row + 1]]) continue;
|
554
|
+
|
555
|
+
this_gain = sd_gain(sd_full,
|
556
|
+
calc_sd_raw(row - st + 1, sum_left, sum_sq_left),
|
557
|
+
calc_sd_raw(end - row, sum_right, sum_sq_right)
|
558
|
+
);
|
559
|
+
if (this_gain > min_gain && this_gain > best_gain)
|
560
|
+
{
|
561
|
+
best_gain = this_gain;
|
562
|
+
split_point = avg_between(x[ix_arr[row]], x[ix_arr[row + 1]]);
|
563
|
+
split_ix = row;
|
564
|
+
}
|
565
|
+
}
|
566
|
+
break;
|
567
|
+
}
|
568
|
+
|
569
|
+
case Pooled:
|
570
|
+
{
|
571
|
+
long double cnt = (long double)(end - st + 1);
|
572
|
+
for (size_t row = st; row < end; row++)
|
573
|
+
{
|
574
|
+
zval = std_val(x[ix_arr[row]], x_mean, x_sd);
|
575
|
+
sum_left += zval;
|
576
|
+
sum_sq_left += square(zval);
|
577
|
+
sum_right -= zval;
|
578
|
+
sum_sq_right -= square(zval);
|
579
|
+
|
580
|
+
if (x[ix_arr[row]] == x[ix_arr[row + 1]]) continue;
|
581
|
+
|
582
|
+
this_gain = numeric_gain_no_div(row - st + 1, end - row,
|
583
|
+
sum_left, sum_right,
|
584
|
+
sum_sq_left, sum_sq_right,
|
585
|
+
sd_full, cnt
|
586
|
+
);
|
587
|
+
|
588
|
+
if (this_gain > min_gain && this_gain > best_gain)
|
589
|
+
{
|
590
|
+
best_gain = this_gain;
|
591
|
+
split_point = avg_between(x[ix_arr[row]], x[ix_arr[row + 1]]);
|
592
|
+
split_ix = row;
|
593
|
+
}
|
594
|
+
}
|
595
|
+
break;
|
596
|
+
}
|
597
|
+
}
|
598
|
+
|
599
|
+
if (best_gain <= -HUGE_VAL && this_gain <= min_gain && this_gain > -HUGE_VAL)
|
600
|
+
return 0;
|
601
|
+
else
|
602
|
+
return best_gain;
|
603
|
+
}
|
604
|
+
|
605
|
+
double eval_guided_crit(size_t ix_arr[], size_t st, size_t end,
|
606
|
+
size_t col_num, double Xc[], sparse_ix Xc_ind[], sparse_ix Xc_indptr[],
|
607
|
+
double buffer_arr[], size_t buffer_pos[],
|
608
|
+
double &split_point, double &xmin, double &xmax,
|
609
|
+
GainCriterion criterion, double min_gain, MissingAction missing_action)
|
610
|
+
{
|
611
|
+
todense(ix_arr, st, end,
|
612
|
+
col_num, Xc, Xc_ind, Xc_indptr,
|
613
|
+
buffer_arr);
|
614
|
+
std::iota(buffer_pos, buffer_pos + (end - st + 1), (size_t)0);
|
615
|
+
size_t temp;
|
616
|
+
return eval_guided_crit(buffer_pos, 0, end - st, buffer_arr, temp, split_point,
|
617
|
+
xmin, xmax, criterion, min_gain, missing_action);
|
618
|
+
}
|
619
|
+
|
620
|
+
/* How this works:
|
621
|
+
- For Averaged criterion, will take the expected standard deviation that would be gotten with the category counts
|
622
|
+
if each category got assigned a real number at random ~ Unif(0,1) and the data were thus converted to
|
623
|
+
numerical. In such case, the best split (highest sd gain) is always putting the second-highest count in one
|
624
|
+
branch, so there is no point in doing a full search over other permutations. In order to get more reasonable
|
625
|
+
splits, when using the option to split by subsets of categories, it will sort the counts and evaluate only
|
626
|
+
splits in which the categories are grouped in sorted order - in such cases it tends to pick either the
|
627
|
+
smallest or the largest category to assign to one branch, but sometimes picks groups too.
|
628
|
+
- For Pooled criterion, will take shannon entropy, which tends to make a more even split. In the case of splitting
|
629
|
+
by a single category, it always puts the largest category in a separate branch. In the case of subsets,
|
630
|
+
it can either evaluate possible splits over all permutations (not feasible if there are too many categories),
|
631
|
+
or look up for splits in sorted order just like for Averaged criterion.
|
632
|
+
Splitting by averaged Gini gain (like with Averaged) also selects always the second-largest category to put in one branch,
|
633
|
+
while splitting by weighted Gini (like with Pooled) usually selects the largest category to put in one branch. The
|
634
|
+
Gini gain is not easily comparable to that of numerical columns, so it's not offered as an option here.
|
635
|
+
*/
|
636
|
+
/* https://math.stackexchange.com/questions/3343384/expected-variance-and-kurtosis-from-pmf-in-which-possible-discrete-values-are-dr */
|
637
|
+
double eval_guided_crit(size_t *restrict ix_arr, size_t st, size_t end, int *restrict x, int ncat,
|
638
|
+
size_t *restrict buffer_cnt, size_t *restrict buffer_pos, double *restrict buffer_prob,
|
639
|
+
int &chosen_cat, char *restrict split_categ, char *restrict buffer_split,
|
640
|
+
GainCriterion criterion, double min_gain, bool all_perm, MissingAction missing_action, CategSplit cat_split_type)
|
641
|
+
{
|
642
|
+
/* move NAs to the front if there's any, exclude them from calculations */
|
643
|
+
if (missing_action != Fail)
|
644
|
+
st = move_NAs_to_front(ix_arr, st, end, x);
|
645
|
+
|
646
|
+
if (st >= end) return -HUGE_VAL;
|
647
|
+
|
648
|
+
/* count categories */
|
649
|
+
memset(buffer_cnt, 0, sizeof(size_t) * ncat);
|
650
|
+
for (size_t row = st; row <= end; row++)
|
651
|
+
buffer_cnt[x[ix_arr[row]]]++;
|
652
|
+
|
653
|
+
double this_gain = -HUGE_VAL;
|
654
|
+
double best_gain = -HUGE_VAL;
|
655
|
+
std::iota(buffer_pos, buffer_pos + ncat, (size_t)0);
|
656
|
+
size_t st_pos = 0;
|
657
|
+
|
658
|
+
switch(cat_split_type)
|
659
|
+
{
|
660
|
+
case SingleCateg:
|
661
|
+
{
|
662
|
+
size_t cnt = end - st + 1;
|
663
|
+
size_t ncat_present = 0;
|
664
|
+
|
665
|
+
switch(criterion)
|
666
|
+
{
|
667
|
+
case Averaged:
|
668
|
+
{
|
669
|
+
/* move zero-counts to the beginning */
|
670
|
+
size_t temp;
|
671
|
+
for (int cat = 0; cat < ncat; cat++)
|
672
|
+
{
|
673
|
+
if (buffer_cnt[cat])
|
674
|
+
{
|
675
|
+
ncat_present++;
|
676
|
+
buffer_prob[cat] = (long double) buffer_cnt[cat] / (long double) cnt;
|
677
|
+
}
|
678
|
+
|
679
|
+
else
|
680
|
+
{
|
681
|
+
temp = buffer_pos[st_pos];
|
682
|
+
buffer_pos[st_pos] = buffer_pos[cat];
|
683
|
+
buffer_pos[cat] = temp;
|
684
|
+
st_pos++;
|
685
|
+
}
|
686
|
+
}
|
687
|
+
|
688
|
+
if (ncat_present <= 1) return -HUGE_VAL;
|
689
|
+
|
690
|
+
double sd_full = expected_sd_cat(buffer_prob, ncat_present, buffer_pos + st_pos);
|
691
|
+
|
692
|
+
/* try isolating each category one at a time */
|
693
|
+
for (size_t pos = st_pos; (int)pos < ncat; pos++)
|
694
|
+
{
|
695
|
+
this_gain = sd_gain(sd_full,
|
696
|
+
0.0,
|
697
|
+
expected_sd_cat_single(buffer_cnt, buffer_prob, ncat_present, buffer_pos + st_pos, pos - st_pos, cnt)
|
698
|
+
);
|
699
|
+
if (this_gain > min_gain && this_gain > best_gain)
|
700
|
+
{
|
701
|
+
best_gain = this_gain;
|
702
|
+
chosen_cat = buffer_pos[pos];
|
703
|
+
}
|
704
|
+
}
|
705
|
+
break;
|
706
|
+
}
|
707
|
+
|
708
|
+
case Pooled:
|
709
|
+
{
|
710
|
+
/* here it will always pick the largest one */
|
711
|
+
size_t ncat_present = 0;
|
712
|
+
size_t cnt_max = 0;
|
713
|
+
for (int cat = 0; cat < ncat; cat++)
|
714
|
+
{
|
715
|
+
if (buffer_cnt[cat])
|
716
|
+
{
|
717
|
+
ncat_present++;
|
718
|
+
if (cnt_max < buffer_cnt[cat])
|
719
|
+
{
|
720
|
+
cnt_max = buffer_cnt[cat];
|
721
|
+
chosen_cat = cat;
|
722
|
+
}
|
723
|
+
}
|
724
|
+
}
|
725
|
+
|
726
|
+
if (ncat_present <= 1) return -HUGE_VAL;
|
727
|
+
|
728
|
+
long double cnt_left = (long double)((end - st + 1) - cnt_max);
|
729
|
+
this_gain = (
|
730
|
+
(long double)cnt * logl((long double)cnt)
|
731
|
+
- cnt_left * logl(cnt_left)
|
732
|
+
- (long double)cnt_max * logl((long double)cnt_max)
|
733
|
+
) / cnt;
|
734
|
+
best_gain = (this_gain > min_gain)? this_gain : best_gain;
|
735
|
+
break;
|
736
|
+
}
|
737
|
+
}
|
738
|
+
break;
|
739
|
+
}
|
740
|
+
|
741
|
+
case SubSet:
|
742
|
+
{
|
743
|
+
/* sort by counts */
|
744
|
+
std::sort(buffer_pos, buffer_pos + ncat, [&buffer_cnt](const size_t a, const size_t b){return buffer_cnt[a] < buffer_cnt[b];});
|
745
|
+
|
746
|
+
/* set split as: (1):left (0):right (-1):not_present */
|
747
|
+
memset(buffer_split, 0, ncat * sizeof(char));
|
748
|
+
|
749
|
+
long double cnt = (long double)(end - st + 1);
|
750
|
+
|
751
|
+
switch(criterion)
|
752
|
+
{
|
753
|
+
case Averaged:
|
754
|
+
{
|
755
|
+
/* determine first non-zero and convert to probabilities */
|
756
|
+
double sd_full;
|
757
|
+
for (int cat = 0; cat < ncat; cat++)
|
758
|
+
{
|
759
|
+
if (buffer_cnt[buffer_pos[cat]])
|
760
|
+
{
|
761
|
+
buffer_prob[buffer_pos[cat]] = (long double)buffer_cnt[buffer_pos[cat]] / cnt;
|
762
|
+
}
|
763
|
+
|
764
|
+
else
|
765
|
+
{
|
766
|
+
buffer_split[buffer_pos[cat]] = -1;
|
767
|
+
st_pos++;
|
768
|
+
}
|
769
|
+
}
|
770
|
+
|
771
|
+
if ((int)st_pos >= (ncat-1)) return -HUGE_VAL;
|
772
|
+
|
773
|
+
/* calculate full SD assuming they take values randomly ~Unif(0, 1) */
|
774
|
+
size_t ncat_present = (size_t)ncat - st_pos;
|
775
|
+
sd_full = expected_sd_cat(buffer_prob, ncat_present, buffer_pos + st_pos);
|
776
|
+
if (ncat_present >= log2ceil(SIZE_MAX)) all_perm = false;
|
777
|
+
|
778
|
+
/* move categories one at a time */
|
779
|
+
for (size_t pos = st_pos; pos < ((size_t)ncat - st_pos - 1); pos++)
|
780
|
+
{
|
781
|
+
buffer_split[buffer_pos[pos]] = 1;
|
782
|
+
this_gain = sd_gain(sd_full,
|
783
|
+
expected_sd_cat(buffer_cnt, buffer_prob, pos - st_pos + 1, buffer_pos + st_pos),
|
784
|
+
expected_sd_cat(buffer_cnt, buffer_prob, (size_t)ncat - pos - 1, buffer_pos + pos + 1)
|
785
|
+
);
|
786
|
+
if (this_gain > min_gain && this_gain > best_gain)
|
787
|
+
{
|
788
|
+
best_gain = this_gain;
|
789
|
+
memcpy(split_categ, buffer_split, ncat * sizeof(char));
|
790
|
+
}
|
791
|
+
}
|
792
|
+
|
793
|
+
break;
|
794
|
+
}
|
795
|
+
|
796
|
+
case Pooled:
|
797
|
+
{
|
798
|
+
long double s = 0;
|
799
|
+
|
800
|
+
/* determine first non-zero and get base info */
|
801
|
+
for (int cat = 0; cat < ncat; cat++)
|
802
|
+
{
|
803
|
+
if (buffer_cnt[buffer_pos[cat]])
|
804
|
+
{
|
805
|
+
s += (buffer_cnt[buffer_pos[cat]] <= 1)?
|
806
|
+
0 : ((long double) buffer_cnt[buffer_pos[cat]] * logl((long double)buffer_cnt[buffer_pos[cat]]));
|
807
|
+
}
|
808
|
+
|
809
|
+
else
|
810
|
+
{
|
811
|
+
buffer_split[buffer_pos[cat]] = -1;
|
812
|
+
st_pos++;
|
813
|
+
}
|
814
|
+
}
|
815
|
+
|
816
|
+
if ((int)st_pos >= (ncat-1)) return -HUGE_VAL;
|
817
|
+
|
818
|
+
/* calculate base info */
|
819
|
+
long double base_info = cnt * logl(cnt) - s;
|
820
|
+
|
821
|
+
if (all_perm)
|
822
|
+
{
|
823
|
+
size_t cnt_left, cnt_right;
|
824
|
+
double s_left, s_right;
|
825
|
+
size_t ncat_present = (size_t)ncat - st_pos;
|
826
|
+
size_t ncomb = pow2(ncat_present) - 1;
|
827
|
+
size_t best_combin;
|
828
|
+
|
829
|
+
for (size_t combin = 1; combin < ncomb; combin++)
|
830
|
+
{
|
831
|
+
cnt_left = 0; cnt_right = 0;
|
832
|
+
s_left = 0; s_right = 0;
|
833
|
+
for (size_t pos = st_pos; (int)pos < ncat; pos++)
|
834
|
+
{
|
835
|
+
if (extract_bit(combin, pos))
|
836
|
+
{
|
837
|
+
cnt_left += buffer_cnt[buffer_pos[pos]];
|
838
|
+
s_left += (buffer_cnt[buffer_pos[pos]] <= 1)?
|
839
|
+
0 : ((long double) buffer_cnt[buffer_pos[pos]]
|
840
|
+
* logl((long double) buffer_cnt[buffer_pos[pos]]));
|
841
|
+
}
|
842
|
+
|
843
|
+
else
|
844
|
+
{
|
845
|
+
cnt_right += buffer_cnt[buffer_pos[pos]];
|
846
|
+
s_right += (buffer_cnt[buffer_pos[pos]] <= 1)?
|
847
|
+
0 : ((long double) buffer_cnt[buffer_pos[pos]]
|
848
|
+
* logl((long double) buffer_cnt[buffer_pos[pos]]));
|
849
|
+
}
|
850
|
+
}
|
851
|
+
|
852
|
+
this_gain = categ_gain(cnt_left, cnt_right,
|
853
|
+
s_left, s_right,
|
854
|
+
base_info, cnt);
|
855
|
+
|
856
|
+
if (this_gain > min_gain && this_gain > best_gain)
|
857
|
+
{
|
858
|
+
best_gain = this_gain;
|
859
|
+
best_combin = combin;
|
860
|
+
}
|
861
|
+
|
862
|
+
}
|
863
|
+
|
864
|
+
if (best_gain > min_gain)
|
865
|
+
for (size_t pos = 0; pos < ncat_present; pos++)
|
866
|
+
split_categ[buffer_pos[st_pos + pos]] = extract_bit(best_combin, pos);
|
867
|
+
|
868
|
+
}
|
869
|
+
|
870
|
+
else
|
871
|
+
{
|
872
|
+
/* try moving the categories one at a time */
|
873
|
+
size_t cnt_left = 0;
|
874
|
+
size_t cnt_right = end - st + 1;
|
875
|
+
double s_left = 0;
|
876
|
+
double s_right = s;
|
877
|
+
|
878
|
+
for (size_t pos = st_pos; pos < (ncat - st_pos - 1); pos++)
|
879
|
+
{
|
880
|
+
buffer_split[buffer_pos[pos]] = 1;
|
881
|
+
s_left += (buffer_cnt[buffer_pos[pos]] <= 1)?
|
882
|
+
0 : ((long double)buffer_cnt[buffer_pos[pos]] * logl((long double)buffer_cnt[buffer_pos[pos]]));
|
883
|
+
s_right -= (buffer_cnt[buffer_pos[pos]] <= 1)?
|
884
|
+
0 : ((long double)buffer_cnt[buffer_pos[pos]] * logl((long double)buffer_cnt[buffer_pos[pos]]));
|
885
|
+
cnt_left += buffer_cnt[buffer_pos[pos]];
|
886
|
+
cnt_right -= buffer_cnt[buffer_pos[pos]];
|
887
|
+
|
888
|
+
this_gain = categ_gain(cnt_left, cnt_right,
|
889
|
+
s_left, s_right,
|
890
|
+
base_info, cnt);
|
891
|
+
|
892
|
+
if (this_gain > min_gain && this_gain > best_gain)
|
893
|
+
{
|
894
|
+
best_gain = this_gain;
|
895
|
+
memcpy(split_categ, buffer_split, ncat * sizeof(char));
|
896
|
+
}
|
897
|
+
}
|
898
|
+
}
|
899
|
+
|
900
|
+
break;
|
901
|
+
}
|
902
|
+
}
|
903
|
+
}
|
904
|
+
}
|
905
|
+
|
906
|
+
if (st == (end-1)) return 0;
|
907
|
+
|
908
|
+
if (best_gain <= -HUGE_VAL && this_gain <= min_gain && this_gain > -HUGE_VAL)
|
909
|
+
return 0;
|
910
|
+
else
|
911
|
+
return best_gain;
|
912
|
+
}
|