isotree 0.2.2 → 0.3.0
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- checksums.yaml +4 -4
- data/CHANGELOG.md +8 -1
- data/LICENSE.txt +2 -2
- data/README.md +32 -14
- data/ext/isotree/ext.cpp +144 -31
- data/ext/isotree/extconf.rb +7 -7
- data/lib/isotree/isolation_forest.rb +110 -30
- data/lib/isotree/version.rb +1 -1
- data/vendor/isotree/LICENSE +1 -1
- data/vendor/isotree/README.md +165 -27
- data/vendor/isotree/include/isotree.hpp +2111 -0
- data/vendor/isotree/include/isotree_oop.hpp +394 -0
- data/vendor/isotree/inst/COPYRIGHTS +62 -0
- data/vendor/isotree/src/RcppExports.cpp +525 -52
- data/vendor/isotree/src/Rwrapper.cpp +1931 -268
- data/vendor/isotree/src/c_interface.cpp +953 -0
- data/vendor/isotree/src/crit.hpp +4232 -0
- data/vendor/isotree/src/dist.hpp +1886 -0
- data/vendor/isotree/src/exp_depth_table.hpp +134 -0
- data/vendor/isotree/src/extended.hpp +1444 -0
- data/vendor/isotree/src/external_facing_generic.hpp +399 -0
- data/vendor/isotree/src/fit_model.hpp +2401 -0
- data/vendor/isotree/src/{dealloc.cpp → headers_joined.hpp} +38 -22
- data/vendor/isotree/src/helpers_iforest.hpp +813 -0
- data/vendor/isotree/src/{impute.cpp → impute.hpp} +353 -122
- data/vendor/isotree/src/indexer.cpp +515 -0
- data/vendor/isotree/src/instantiate_template_headers.cpp +118 -0
- data/vendor/isotree/src/instantiate_template_headers.hpp +240 -0
- data/vendor/isotree/src/isoforest.hpp +1659 -0
- data/vendor/isotree/src/isotree.hpp +1804 -392
- data/vendor/isotree/src/isotree_exportable.hpp +99 -0
- data/vendor/isotree/src/merge_models.cpp +159 -16
- data/vendor/isotree/src/mult.hpp +1321 -0
- data/vendor/isotree/src/oop_interface.cpp +842 -0
- data/vendor/isotree/src/oop_interface.hpp +278 -0
- data/vendor/isotree/src/other_helpers.hpp +219 -0
- data/vendor/isotree/src/predict.hpp +1932 -0
- data/vendor/isotree/src/python_helpers.hpp +134 -0
- data/vendor/isotree/src/ref_indexer.hpp +154 -0
- data/vendor/isotree/src/robinmap/LICENSE +21 -0
- data/vendor/isotree/src/robinmap/README.md +483 -0
- data/vendor/isotree/src/robinmap/include/tsl/robin_growth_policy.h +406 -0
- data/vendor/isotree/src/robinmap/include/tsl/robin_hash.h +1620 -0
- data/vendor/isotree/src/robinmap/include/tsl/robin_map.h +807 -0
- data/vendor/isotree/src/robinmap/include/tsl/robin_set.h +660 -0
- data/vendor/isotree/src/serialize.cpp +4300 -139
- data/vendor/isotree/src/sql.cpp +141 -59
- data/vendor/isotree/src/subset_models.cpp +174 -0
- data/vendor/isotree/src/utils.hpp +3808 -0
- data/vendor/isotree/src/xoshiro.hpp +467 -0
- data/vendor/isotree/src/ziggurat.hpp +405 -0
- metadata +38 -104
- data/vendor/cereal/LICENSE +0 -24
- data/vendor/cereal/README.md +0 -85
- data/vendor/cereal/include/cereal/access.hpp +0 -351
- data/vendor/cereal/include/cereal/archives/adapters.hpp +0 -163
- data/vendor/cereal/include/cereal/archives/binary.hpp +0 -169
- data/vendor/cereal/include/cereal/archives/json.hpp +0 -1019
- data/vendor/cereal/include/cereal/archives/portable_binary.hpp +0 -334
- data/vendor/cereal/include/cereal/archives/xml.hpp +0 -956
- data/vendor/cereal/include/cereal/cereal.hpp +0 -1089
- data/vendor/cereal/include/cereal/details/helpers.hpp +0 -422
- data/vendor/cereal/include/cereal/details/polymorphic_impl.hpp +0 -796
- data/vendor/cereal/include/cereal/details/polymorphic_impl_fwd.hpp +0 -65
- data/vendor/cereal/include/cereal/details/static_object.hpp +0 -127
- data/vendor/cereal/include/cereal/details/traits.hpp +0 -1411
- data/vendor/cereal/include/cereal/details/util.hpp +0 -84
- data/vendor/cereal/include/cereal/external/base64.hpp +0 -134
- data/vendor/cereal/include/cereal/external/rapidjson/allocators.h +0 -284
- data/vendor/cereal/include/cereal/external/rapidjson/cursorstreamwrapper.h +0 -78
- data/vendor/cereal/include/cereal/external/rapidjson/document.h +0 -2652
- data/vendor/cereal/include/cereal/external/rapidjson/encodedstream.h +0 -299
- data/vendor/cereal/include/cereal/external/rapidjson/encodings.h +0 -716
- data/vendor/cereal/include/cereal/external/rapidjson/error/en.h +0 -74
- data/vendor/cereal/include/cereal/external/rapidjson/error/error.h +0 -161
- data/vendor/cereal/include/cereal/external/rapidjson/filereadstream.h +0 -99
- data/vendor/cereal/include/cereal/external/rapidjson/filewritestream.h +0 -104
- data/vendor/cereal/include/cereal/external/rapidjson/fwd.h +0 -151
- data/vendor/cereal/include/cereal/external/rapidjson/internal/biginteger.h +0 -290
- data/vendor/cereal/include/cereal/external/rapidjson/internal/diyfp.h +0 -271
- data/vendor/cereal/include/cereal/external/rapidjson/internal/dtoa.h +0 -245
- data/vendor/cereal/include/cereal/external/rapidjson/internal/ieee754.h +0 -78
- data/vendor/cereal/include/cereal/external/rapidjson/internal/itoa.h +0 -308
- data/vendor/cereal/include/cereal/external/rapidjson/internal/meta.h +0 -186
- data/vendor/cereal/include/cereal/external/rapidjson/internal/pow10.h +0 -55
- data/vendor/cereal/include/cereal/external/rapidjson/internal/regex.h +0 -740
- data/vendor/cereal/include/cereal/external/rapidjson/internal/stack.h +0 -232
- data/vendor/cereal/include/cereal/external/rapidjson/internal/strfunc.h +0 -69
- data/vendor/cereal/include/cereal/external/rapidjson/internal/strtod.h +0 -290
- data/vendor/cereal/include/cereal/external/rapidjson/internal/swap.h +0 -46
- data/vendor/cereal/include/cereal/external/rapidjson/istreamwrapper.h +0 -128
- data/vendor/cereal/include/cereal/external/rapidjson/memorybuffer.h +0 -70
- data/vendor/cereal/include/cereal/external/rapidjson/memorystream.h +0 -71
- data/vendor/cereal/include/cereal/external/rapidjson/msinttypes/inttypes.h +0 -316
- data/vendor/cereal/include/cereal/external/rapidjson/msinttypes/stdint.h +0 -300
- data/vendor/cereal/include/cereal/external/rapidjson/ostreamwrapper.h +0 -81
- data/vendor/cereal/include/cereal/external/rapidjson/pointer.h +0 -1414
- data/vendor/cereal/include/cereal/external/rapidjson/prettywriter.h +0 -277
- data/vendor/cereal/include/cereal/external/rapidjson/rapidjson.h +0 -656
- data/vendor/cereal/include/cereal/external/rapidjson/reader.h +0 -2230
- data/vendor/cereal/include/cereal/external/rapidjson/schema.h +0 -2497
- data/vendor/cereal/include/cereal/external/rapidjson/stream.h +0 -223
- data/vendor/cereal/include/cereal/external/rapidjson/stringbuffer.h +0 -121
- data/vendor/cereal/include/cereal/external/rapidjson/writer.h +0 -709
- data/vendor/cereal/include/cereal/external/rapidxml/license.txt +0 -52
- data/vendor/cereal/include/cereal/external/rapidxml/manual.html +0 -406
- data/vendor/cereal/include/cereal/external/rapidxml/rapidxml.hpp +0 -2624
- data/vendor/cereal/include/cereal/external/rapidxml/rapidxml_iterators.hpp +0 -175
- data/vendor/cereal/include/cereal/external/rapidxml/rapidxml_print.hpp +0 -428
- data/vendor/cereal/include/cereal/external/rapidxml/rapidxml_utils.hpp +0 -123
- data/vendor/cereal/include/cereal/macros.hpp +0 -154
- data/vendor/cereal/include/cereal/specialize.hpp +0 -139
- data/vendor/cereal/include/cereal/types/array.hpp +0 -79
- data/vendor/cereal/include/cereal/types/atomic.hpp +0 -55
- data/vendor/cereal/include/cereal/types/base_class.hpp +0 -203
- data/vendor/cereal/include/cereal/types/bitset.hpp +0 -176
- data/vendor/cereal/include/cereal/types/boost_variant.hpp +0 -164
- data/vendor/cereal/include/cereal/types/chrono.hpp +0 -72
- data/vendor/cereal/include/cereal/types/common.hpp +0 -129
- data/vendor/cereal/include/cereal/types/complex.hpp +0 -56
- data/vendor/cereal/include/cereal/types/concepts/pair_associative_container.hpp +0 -73
- data/vendor/cereal/include/cereal/types/deque.hpp +0 -62
- data/vendor/cereal/include/cereal/types/forward_list.hpp +0 -68
- data/vendor/cereal/include/cereal/types/functional.hpp +0 -43
- data/vendor/cereal/include/cereal/types/list.hpp +0 -62
- data/vendor/cereal/include/cereal/types/map.hpp +0 -36
- data/vendor/cereal/include/cereal/types/memory.hpp +0 -425
- data/vendor/cereal/include/cereal/types/optional.hpp +0 -66
- data/vendor/cereal/include/cereal/types/polymorphic.hpp +0 -483
- data/vendor/cereal/include/cereal/types/queue.hpp +0 -132
- data/vendor/cereal/include/cereal/types/set.hpp +0 -103
- data/vendor/cereal/include/cereal/types/stack.hpp +0 -76
- data/vendor/cereal/include/cereal/types/string.hpp +0 -61
- data/vendor/cereal/include/cereal/types/tuple.hpp +0 -123
- data/vendor/cereal/include/cereal/types/unordered_map.hpp +0 -36
- data/vendor/cereal/include/cereal/types/unordered_set.hpp +0 -99
- data/vendor/cereal/include/cereal/types/utility.hpp +0 -47
- data/vendor/cereal/include/cereal/types/valarray.hpp +0 -89
- data/vendor/cereal/include/cereal/types/variant.hpp +0 -109
- data/vendor/cereal/include/cereal/types/vector.hpp +0 -112
- data/vendor/cereal/include/cereal/version.hpp +0 -52
- data/vendor/isotree/src/Makevars +0 -4
- data/vendor/isotree/src/crit.cpp +0 -912
- data/vendor/isotree/src/dist.cpp +0 -749
- data/vendor/isotree/src/extended.cpp +0 -790
- data/vendor/isotree/src/fit_model.cpp +0 -1090
- data/vendor/isotree/src/helpers_iforest.cpp +0 -324
- data/vendor/isotree/src/isoforest.cpp +0 -771
- data/vendor/isotree/src/mult.cpp +0 -607
- data/vendor/isotree/src/predict.cpp +0 -853
- data/vendor/isotree/src/utils.cpp +0 -1566
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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.
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* "Distance approximation using Isolation Forests."
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* arXiv preprint arXiv:1910.12362 (2019).
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* [9] Cortes, David.
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* "Imputing missing values with unsupervised random trees."
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* arXiv preprint arXiv:1911.06646 (2019).
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* [10] https://math.stackexchange.com/questions/3333220/expected-average-depth-in-random-binary-tree-constructed-top-to-bottom
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* [11] Cortes, David.
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* "Revisiting randomized choices in isolation forests."
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* arXiv preprint arXiv:2110.13402 (2021).
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* [12] Guha, Sudipto, et al.
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* "Robust random cut forest based anomaly detection on streams."
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* International conference on machine learning. PMLR, 2016.
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* [13] Cortes, David.
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* "Isolation forests: looking beyond tree depth."
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* arXiv preprint arXiv:2111.11639 (2021).
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* [14] Ting, Kai Ming, Yue Zhu, and Zhi-Hua Zhou.
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* "Isolation kernel and its effect on SVM"
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* Proceedings of the 24th ACM SIGKDD
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* International Conference on Knowledge Discovery & Data Mining. 2018.
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*
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* BSD 2-Clause License
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* Copyright (c) 2019-2022, 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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static inline bool is_terminal_node(const IsoTree &node)
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{
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return node.tree_left == 0;
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}
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static inline bool is_terminal_node(const IsoHPlane &node)
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{
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return node.hplane_left == 0;
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}
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template <class Tree>
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void build_terminal_node_mappings_single_tree(std::vector<size_t> &mappings, size_t &n_terminal, const std::vector<Tree> &tree)
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{
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mappings.resize(tree.size());
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mappings.shrink_to_fit();
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std::fill(mappings.begin(), mappings.end(), (size_t)0);
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n_terminal = 0;
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for (size_t node = 0; node < tree.size(); node++)
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{
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if (is_terminal_node(tree[node]))
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{
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mappings[node] = n_terminal;
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n_terminal++;
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}
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}
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}
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void build_terminal_node_mappings_single_tree(std::vector<size_t> &mappings, size_t &n_terminal, const std::vector<IsoTree> &tree)
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{
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build_terminal_node_mappings_single_tree<IsoTree>(mappings, n_terminal, tree);
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}
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void build_terminal_node_mappings_single_tree(std::vector<size_t> &mappings, size_t &n_terminal, const std::vector<IsoHPlane> &tree)
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{
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build_terminal_node_mappings_single_tree<IsoHPlane>(mappings, n_terminal, tree);
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}
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static inline const std::vector<IsoTree>& get_tree(const IsoForest &model, size_t tree)
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{
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return model.trees[tree];
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}
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static inline const std::vector<IsoHPlane>& get_tree(const ExtIsoForest &model, size_t tree)
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{
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return model.hplanes[tree];
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}
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template <class Model>
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void build_terminal_node_mappings(TreesIndexer &indexer, const Model &model)
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{
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indexer.indices.resize(get_ntrees(model));
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indexer.indices.shrink_to_fit();
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if (!indexer.indices.empty() && !indexer.indices.front().reference_points.empty())
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{
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for (auto &ind : indexer.indices)
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{
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ind.reference_points.clear();
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ind.reference_indptr.clear();
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ind.reference_mapping.clear();
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}
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}
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for (size_t tree = 0; tree < indexer.indices.size(); tree++)
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{
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build_terminal_node_mappings_single_tree(indexer.indices[tree].terminal_node_mappings,
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indexer.indices[tree].n_terminal,
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get_tree(model, tree));
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}
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}
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static inline size_t get_idx_tree_left(const IsoTree &node)
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{
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return node.tree_left;
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}
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static inline size_t get_idx_tree_left(const IsoHPlane &node)
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{
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return node.hplane_left;
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}
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static inline size_t get_idx_tree_right(const IsoTree &node)
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{
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return node.tree_right;
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}
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static inline size_t get_idx_tree_right(const IsoHPlane &node)
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{
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return node.hplane_right;
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}
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template <class Node>
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void build_dindex_recursive
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(
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const size_t curr_node,
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const size_t n_terminal, const size_t ncomb,
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const size_t st, const size_t end,
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std::vector<size_t> &restrict node_indices, /* array with all terminal indices in 'tree' */
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const std::vector<size_t> &restrict node_mappings, /* tree_index : terminal_index */
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std::vector<double> &restrict node_distances, /* indexed by terminal_index */
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std::vector<double> &restrict node_depths, /* indexed by terminal_index */
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size_t curr_depth,
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const std::vector<Node> &tree
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)
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{
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if (end > st)
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{
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size_t i, j;
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for (size_t el1 = st; el1 < end; el1++)
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{
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for (size_t el2 = el1 + 1; el2 <= end; el2++)
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{
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i = node_mappings[node_indices[el1]];
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j = node_mappings[node_indices[el2]];
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node_distances[ix_comb(i, j, n_terminal, ncomb)]++;
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}
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}
|
183
|
+
}
|
184
|
+
|
185
|
+
if (!is_terminal_node(tree[curr_node]))
|
186
|
+
{
|
187
|
+
const size_t delim = get_idx_tree_right(tree[curr_node]);
|
188
|
+
size_t frontier = st;
|
189
|
+
size_t temp;
|
190
|
+
for (size_t ix = st; ix <= end; ix++)
|
191
|
+
{
|
192
|
+
if (node_indices[ix] < delim)
|
193
|
+
{
|
194
|
+
temp = node_indices[frontier];
|
195
|
+
node_indices[frontier] = node_indices[ix];
|
196
|
+
node_indices[ix] = temp;
|
197
|
+
frontier++;
|
198
|
+
}
|
199
|
+
}
|
200
|
+
|
201
|
+
if (unlikely(frontier == st)) unexpected_error();
|
202
|
+
|
203
|
+
curr_depth++;
|
204
|
+
build_dindex_recursive<Node>(get_idx_tree_left(tree[curr_node]),
|
205
|
+
n_terminal, ncomb,
|
206
|
+
st, frontier-1,
|
207
|
+
node_indices,
|
208
|
+
node_mappings,
|
209
|
+
node_distances,
|
210
|
+
node_depths,
|
211
|
+
curr_depth,
|
212
|
+
tree);
|
213
|
+
build_dindex_recursive<Node>(get_idx_tree_right(tree[curr_node]),
|
214
|
+
n_terminal, ncomb,
|
215
|
+
frontier, end,
|
216
|
+
node_indices,
|
217
|
+
node_mappings,
|
218
|
+
node_distances,
|
219
|
+
node_depths,
|
220
|
+
curr_depth,
|
221
|
+
tree);
|
222
|
+
}
|
223
|
+
|
224
|
+
else
|
225
|
+
{
|
226
|
+
node_depths[node_mappings[curr_node]] = curr_depth;
|
227
|
+
}
|
228
|
+
}
|
229
|
+
|
230
|
+
template <class Node>
|
231
|
+
void build_dindex
|
232
|
+
(
|
233
|
+
std::vector<size_t> &restrict node_indices, /* empty, but correctly sized */
|
234
|
+
const std::vector<size_t> &restrict node_mappings, /* tree_index : terminal_index */
|
235
|
+
std::vector<double> &restrict node_distances, /* indexed by terminal_index */
|
236
|
+
std::vector<double> &restrict node_depths, /* indexed by terminal_index */
|
237
|
+
const size_t n_terminal,
|
238
|
+
const std::vector<Node> &tree
|
239
|
+
)
|
240
|
+
{
|
241
|
+
if (tree.size() <= 1) return;
|
242
|
+
|
243
|
+
std::fill(node_distances.begin(), node_distances.end(), 0.);
|
244
|
+
|
245
|
+
node_indices.clear();
|
246
|
+
for (size_t node = 0; node < tree.size(); node++)
|
247
|
+
{
|
248
|
+
if (is_terminal_node(tree[node]))
|
249
|
+
node_indices.push_back(node);
|
250
|
+
}
|
251
|
+
|
252
|
+
node_depths.resize(n_terminal);
|
253
|
+
|
254
|
+
build_dindex_recursive<Node>(
|
255
|
+
(size_t)0,
|
256
|
+
node_indices.size(), calc_ncomb(node_indices.size()),
|
257
|
+
0, node_indices.size()-1,
|
258
|
+
node_indices,
|
259
|
+
node_mappings,
|
260
|
+
node_distances,
|
261
|
+
node_depths,
|
262
|
+
(size_t)0,
|
263
|
+
tree
|
264
|
+
);
|
265
|
+
}
|
266
|
+
|
267
|
+
void build_dindex
|
268
|
+
(
|
269
|
+
std::vector<size_t> &restrict node_indices, /* empty, but correctly sized */
|
270
|
+
const std::vector<size_t> &restrict node_mappings, /* tree_index : terminal_index */
|
271
|
+
std::vector<double> &restrict node_distances, /* indexed by terminal_index */
|
272
|
+
std::vector<double> &restrict node_depths, /* indexed by terminal_index */
|
273
|
+
const size_t n_terminal,
|
274
|
+
const std::vector<IsoTree> &tree
|
275
|
+
)
|
276
|
+
{
|
277
|
+
build_dindex<IsoTree>(
|
278
|
+
node_indices,
|
279
|
+
node_mappings,
|
280
|
+
node_distances,
|
281
|
+
node_depths,
|
282
|
+
n_terminal,
|
283
|
+
tree
|
284
|
+
);
|
285
|
+
}
|
286
|
+
|
287
|
+
void build_dindex
|
288
|
+
(
|
289
|
+
std::vector<size_t> &restrict node_indices, /* empty, but correctly sized */
|
290
|
+
const std::vector<size_t> &restrict node_mappings, /* tree_index : terminal_index */
|
291
|
+
std::vector<double> &restrict node_distances, /* indexed by terminal_index */
|
292
|
+
std::vector<double> &restrict node_depths, /* indexed by terminal_index */
|
293
|
+
const size_t n_terminal,
|
294
|
+
const std::vector<IsoHPlane> &tree
|
295
|
+
)
|
296
|
+
{
|
297
|
+
build_dindex<IsoHPlane>(
|
298
|
+
node_indices,
|
299
|
+
node_mappings,
|
300
|
+
node_distances,
|
301
|
+
node_depths,
|
302
|
+
n_terminal,
|
303
|
+
tree
|
304
|
+
);
|
305
|
+
}
|
306
|
+
|
307
|
+
template <class Model>
|
308
|
+
void build_distance_mappings(TreesIndexer &indexer, const Model &model, int nthreads)
|
309
|
+
{
|
310
|
+
build_terminal_node_mappings(indexer, model);
|
311
|
+
SignalSwitcher ss = SignalSwitcher();
|
312
|
+
|
313
|
+
size_t ntrees = get_ntrees(model);
|
314
|
+
std::vector<size_t> n_terminal(ntrees);
|
315
|
+
for (size_t tree = 0; tree < ntrees; tree++)
|
316
|
+
n_terminal[tree] = indexer.indices[tree].n_terminal;
|
317
|
+
|
318
|
+
size_t max_n_terminal = *std::max_element(n_terminal.begin(), n_terminal.end());
|
319
|
+
check_interrupt_switch(ss);
|
320
|
+
if (max_n_terminal <= 1) return;
|
321
|
+
|
322
|
+
#ifndef _OPENMP
|
323
|
+
nthreads = 1;
|
324
|
+
#endif
|
325
|
+
std::vector<std::vector<size_t>> thread_buffer_indices(nthreads);
|
326
|
+
for (std::vector<size_t> &v : thread_buffer_indices)
|
327
|
+
v.reserve(max_n_terminal);
|
328
|
+
check_interrupt_switch(ss);
|
329
|
+
|
330
|
+
|
331
|
+
|
332
|
+
bool threw_exception = false;
|
333
|
+
std::exception_ptr ex = NULL;
|
334
|
+
#pragma omp parallel for schedule(dynamic) num_threads(nthreads) shared(indexer, model, n_terminal, threw_exception, ex)
|
335
|
+
for (size_t_for tree = 0; tree < (decltype(tree))ntrees; tree++)
|
336
|
+
{
|
337
|
+
if (interrupt_switch || threw_exception) continue;
|
338
|
+
|
339
|
+
try
|
340
|
+
{
|
341
|
+
size_t n_terminal_this = n_terminal[tree];
|
342
|
+
size_t ncomb = calc_ncomb(n_terminal_this);
|
343
|
+
indexer.indices[tree].node_distances.assign(ncomb, 0.);
|
344
|
+
indexer.indices[tree].node_distances.shrink_to_fit();
|
345
|
+
build_dindex(
|
346
|
+
thread_buffer_indices[omp_get_thread_num()],
|
347
|
+
indexer.indices[tree].terminal_node_mappings,
|
348
|
+
indexer.indices[tree].node_distances,
|
349
|
+
indexer.indices[tree].node_depths,
|
350
|
+
n_terminal_this,
|
351
|
+
get_tree(model, tree)
|
352
|
+
);
|
353
|
+
}
|
354
|
+
|
355
|
+
catch (...)
|
356
|
+
{
|
357
|
+
#pragma omp critical
|
358
|
+
{
|
359
|
+
if (!threw_exception)
|
360
|
+
{
|
361
|
+
threw_exception = true;
|
362
|
+
ex = std::current_exception();
|
363
|
+
}
|
364
|
+
}
|
365
|
+
}
|
366
|
+
}
|
367
|
+
|
368
|
+
if (interrupt_switch || threw_exception)
|
369
|
+
{
|
370
|
+
indexer.indices.clear();
|
371
|
+
}
|
372
|
+
|
373
|
+
check_interrupt_switch(ss);
|
374
|
+
if (threw_exception) std::rethrow_exception(ex);
|
375
|
+
}
|
376
|
+
|
377
|
+
template <class Model>
|
378
|
+
void build_tree_indices(TreesIndexer &indexer, const Model &model, int nthreads, const bool with_distances)
|
379
|
+
{
|
380
|
+
if (!indexer.indices.empty() && !indexer.indices.front().reference_points.empty())
|
381
|
+
{
|
382
|
+
for (auto &ind : indexer.indices)
|
383
|
+
{
|
384
|
+
ind.reference_points.clear();
|
385
|
+
ind.reference_indptr.clear();
|
386
|
+
ind.reference_mapping.clear();
|
387
|
+
}
|
388
|
+
}
|
389
|
+
|
390
|
+
|
391
|
+
try
|
392
|
+
{
|
393
|
+
if (with_distances) {
|
394
|
+
build_distance_mappings(indexer, model, nthreads);
|
395
|
+
}
|
396
|
+
|
397
|
+
else {
|
398
|
+
if (!indexer.indices.empty() && !indexer.indices.front().node_distances.empty())
|
399
|
+
{
|
400
|
+
for (auto &ind : indexer.indices)
|
401
|
+
{
|
402
|
+
ind.node_distances.clear();
|
403
|
+
ind.node_depths.clear();
|
404
|
+
}
|
405
|
+
}
|
406
|
+
|
407
|
+
build_terminal_node_mappings(indexer, model);
|
408
|
+
}
|
409
|
+
}
|
410
|
+
|
411
|
+
catch (...)
|
412
|
+
{
|
413
|
+
indexer.indices.clear();
|
414
|
+
throw;
|
415
|
+
}
|
416
|
+
}
|
417
|
+
|
418
|
+
void build_tree_indices(TreesIndexer &indexer, const IsoForest &model, int nthreads, const bool with_distances)
|
419
|
+
{
|
420
|
+
if (model.trees.empty())
|
421
|
+
throw std::runtime_error("Cannot build indexed for unfitted model.\n");
|
422
|
+
if (model.missing_action == Divide)
|
423
|
+
throw std::runtime_error("Cannot build tree indexer with 'missing_action=Divide'.\n");
|
424
|
+
if (model.new_cat_action == Weighted && model.cat_split_type == SubSet)
|
425
|
+
{
|
426
|
+
for (const std::vector<IsoTree> &tree : model.trees)
|
427
|
+
{
|
428
|
+
for (const IsoTree &node : tree)
|
429
|
+
{
|
430
|
+
if (!is_terminal_node(node) && node.col_type == Categorical)
|
431
|
+
throw std::runtime_error("Cannot build tree indexer with 'new_cat_action=Weighted'.\n");
|
432
|
+
}
|
433
|
+
}
|
434
|
+
}
|
435
|
+
|
436
|
+
build_tree_indices<IsoForest>(indexer, model, nthreads, with_distances);
|
437
|
+
}
|
438
|
+
|
439
|
+
void build_tree_indices(TreesIndexer &indexer, const ExtIsoForest &model, int nthreads, const bool with_distances)
|
440
|
+
{
|
441
|
+
if (model.hplanes.empty())
|
442
|
+
throw std::runtime_error("Cannot build indexed for unfitted model.\n");
|
443
|
+
build_tree_indices<ExtIsoForest>(indexer, model, nthreads, with_distances);
|
444
|
+
}
|
445
|
+
|
446
|
+
/* Build indexer for faster terminal node predictions and/or distance calculations
|
447
|
+
*
|
448
|
+
* Parameters
|
449
|
+
* ==========
|
450
|
+
* - indexer
|
451
|
+
* Pointer or reference to an indexer object which will be associated to a fitted model and in
|
452
|
+
* which indices for terminal nodes and potentially node distances will be stored.
|
453
|
+
* - model / model_outputs / model_outputs_ext
|
454
|
+
* Pointer or reference to a fitted model object for which an indexer will be built.
|
455
|
+
* - nthreads
|
456
|
+
* Number of parallel threads to use. This operation will only be multi-threaded when passing
|
457
|
+
* 'with_distances=true'.
|
458
|
+
* - with_distances
|
459
|
+
* Whether to also pre-calculate node distances in order to speed up 'calc_similarity' (distances).
|
460
|
+
* Note that this will consume a lot more memory and make the resulting object significantly
|
461
|
+
* heavier.
|
462
|
+
*/
|
463
|
+
void build_tree_indices
|
464
|
+
(
|
465
|
+
TreesIndexer *indexer,
|
466
|
+
const IsoForest *model_outputs,
|
467
|
+
const ExtIsoForest *model_outputs_ext,
|
468
|
+
int nthreads,
|
469
|
+
const bool with_distances
|
470
|
+
)
|
471
|
+
{
|
472
|
+
if (model_outputs != NULL)
|
473
|
+
build_tree_indices(*indexer, *model_outputs, nthreads, with_distances);
|
474
|
+
else
|
475
|
+
build_tree_indices(*indexer, *model_outputs_ext, nthreads, with_distances);
|
476
|
+
}
|
477
|
+
|
478
|
+
/* Gets the number of reference points stored in an indexer object */
|
479
|
+
size_t get_number_of_reference_points(const TreesIndexer &indexer) noexcept
|
480
|
+
{
|
481
|
+
if (indexer.indices.empty()) return 0;
|
482
|
+
return indexer.indices.front().reference_points.size();
|
483
|
+
}
|
484
|
+
|
485
|
+
/* This assumes it already has the indexer and 'reference_points' were just added.
|
486
|
+
It builds up 'reference_mapping' and 'reference_indptr' from it. */
|
487
|
+
void build_ref_node(SingleTreeIndex &node)
|
488
|
+
{
|
489
|
+
node.reference_mapping.resize(node.reference_points.size());
|
490
|
+
node.reference_mapping.shrink_to_fit();
|
491
|
+
std::iota(node.reference_mapping.begin(), node.reference_mapping.end(), (size_t)0);
|
492
|
+
std::sort(node.reference_mapping.begin(), node.reference_mapping.end(),
|
493
|
+
[&node](const size_t a, const size_t b)
|
494
|
+
{return node.reference_points[a] < node.reference_points[b];});
|
495
|
+
|
496
|
+
size_t n_terminal = node.n_terminal;
|
497
|
+
node.reference_indptr.assign(n_terminal+1, (size_t)0);
|
498
|
+
node.reference_indptr.shrink_to_fit();
|
499
|
+
|
500
|
+
std::vector<size_t>::iterator curr_begin = node.reference_mapping.begin();
|
501
|
+
std::vector<size_t>::iterator new_begin;
|
502
|
+
size_t curr_node;
|
503
|
+
while (curr_begin != node.reference_mapping.end())
|
504
|
+
{
|
505
|
+
curr_node = node.reference_points[*curr_begin];
|
506
|
+
new_begin = std::upper_bound(curr_begin, node.reference_mapping.end(), curr_node,
|
507
|
+
[&node](const size_t a, const size_t b)
|
508
|
+
{return a < node.reference_points[b];});
|
509
|
+
node.reference_indptr[curr_node+1] = std::distance(curr_begin, new_begin);
|
510
|
+
curr_begin = new_begin;
|
511
|
+
}
|
512
|
+
|
513
|
+
for (size_t ix = 1; ix < n_terminal; ix++)
|
514
|
+
node.reference_indptr[ix+1] += node.reference_indptr[ix];
|
515
|
+
}
|
@@ -0,0 +1,118 @@
|
|
1
|
+
/* Isolation forests and variations thereof, with adjustments for incorporation
|
2
|
+
* of categorical variables and missing values.
|
3
|
+
* Writen for C++11 standard and aimed at being used in R and Python.
|
4
|
+
*
|
5
|
+
* This library is based on the following works:
|
6
|
+
* [1] Liu, Fei Tony, Kai Ming Ting, and Zhi-Hua Zhou.
|
7
|
+
* "Isolation forest."
|
8
|
+
* 2008 Eighth IEEE International Conference on Data Mining. IEEE, 2008.
|
9
|
+
* [2] Liu, Fei Tony, Kai Ming Ting, and Zhi-Hua Zhou.
|
10
|
+
* "Isolation-based anomaly detection."
|
11
|
+
* ACM Transactions on Knowledge Discovery from Data (TKDD) 6.1 (2012): 3.
|
12
|
+
* [3] Hariri, Sahand, Matias Carrasco Kind, and Robert J. Brunner.
|
13
|
+
* "Extended Isolation Forest."
|
14
|
+
* arXiv preprint arXiv:1811.02141 (2018).
|
15
|
+
* [4] Liu, Fei Tony, Kai Ming Ting, and Zhi-Hua Zhou.
|
16
|
+
* "On detecting clustered anomalies using SCiForest."
|
17
|
+
* Joint European Conference on Machine Learning and Knowledge Discovery in Databases. Springer, Berlin, Heidelberg, 2010.
|
18
|
+
* [5] https://sourceforge.net/projects/iforest/
|
19
|
+
* [6] https://math.stackexchange.com/questions/3388518/expected-number-of-paths-required-to-separate-elements-in-a-binary-tree
|
20
|
+
* [7] Quinlan, J. Ross. C4. 5: programs for machine learning. Elsevier, 2014.
|
21
|
+
* [8] Cortes, David.
|
22
|
+
* "Distance approximation using Isolation Forests."
|
23
|
+
* arXiv preprint arXiv:1910.12362 (2019).
|
24
|
+
* [9] Cortes, David.
|
25
|
+
* "Imputing missing values with unsupervised random trees."
|
26
|
+
* arXiv preprint arXiv:1911.06646 (2019).
|
27
|
+
* [10] https://math.stackexchange.com/questions/3333220/expected-average-depth-in-random-binary-tree-constructed-top-to-bottom
|
28
|
+
* [11] Cortes, David.
|
29
|
+
* "Revisiting randomized choices in isolation forests."
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* arXiv preprint arXiv:2110.13402 (2021).
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31
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+
* [12] Guha, Sudipto, et al.
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32
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+
* "Robust random cut forest based anomaly detection on streams."
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33
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+
* International conference on machine learning. PMLR, 2016.
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34
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+
* [13] Cortes, David.
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35
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+
* "Isolation forests: looking beyond tree depth."
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36
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+
* arXiv preprint arXiv:2111.11639 (2021).
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37
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+
* [14] Ting, Kai Ming, Yue Zhu, and Zhi-Hua Zhou.
|
38
|
+
* "Isolation kernel and its effect on SVM"
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39
|
+
* Proceedings of the 24th ACM SIGKDD
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40
|
+
* International Conference on Knowledge Discovery & Data Mining. 2018.
|
41
|
+
*
|
42
|
+
* BSD 2-Clause License
|
43
|
+
* Copyright (c) 2019-2022, David Cortes
|
44
|
+
* All rights reserved.
|
45
|
+
* Redistribution and use in source and binary forms, with or without
|
46
|
+
* modification, are permitted provided that the following conditions are met:
|
47
|
+
* * Redistributions of source code must retain the above copyright notice, this
|
48
|
+
* list of conditions and the following disclaimer.
|
49
|
+
* * Redistributions in binary form must reproduce the above copyright notice,
|
50
|
+
* this list of conditions and the following disclaimer in the documentation
|
51
|
+
* and/or other materials provided with the distribution.
|
52
|
+
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
|
53
|
+
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
|
54
|
+
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
|
55
|
+
* DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
|
56
|
+
* FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
|
57
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+
* DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
|
58
|
+
* SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
|
59
|
+
* CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
|
60
|
+
* OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
|
61
|
+
* OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
|
62
|
+
*/
|
63
|
+
|
64
|
+
/* Note: the R and Python versions calls the 'sort_csc_indices' templated function,
|
65
|
+
so it's not enough to just include 'isotree_exportable.hpp' under them and let
|
66
|
+
this same file instantiate all supported templated types.
|
67
|
+
Also, Cython makes it hard to use overloaded functions since they have to
|
68
|
+
be declared multiple times. */
|
69
|
+
|
70
|
+
#if !defined(_FOR_R) && !defined(_FOR_PYTHON)
|
71
|
+
|
72
|
+
#include "headers_joined.hpp"
|
73
|
+
|
74
|
+
#define real_t double
|
75
|
+
#define sparse_ix int
|
76
|
+
#include "instantiate_template_headers.hpp"
|
77
|
+
#undef real_t
|
78
|
+
#undef sparse_ix
|
79
|
+
|
80
|
+
#ifndef NO_TEMPLATED_VERSIONS
|
81
|
+
|
82
|
+
#define real_t double
|
83
|
+
#define sparse_ix int64_t
|
84
|
+
#include "instantiate_template_headers.hpp"
|
85
|
+
#undef real_t
|
86
|
+
#undef sparse_ix
|
87
|
+
|
88
|
+
#define real_t double
|
89
|
+
#define sparse_ix size_t
|
90
|
+
#include "instantiate_template_headers.hpp"
|
91
|
+
#undef real_t
|
92
|
+
#undef sparse_ix
|
93
|
+
|
94
|
+
#define _NO_REAL_T
|
95
|
+
|
96
|
+
#define real_t float
|
97
|
+
#define sparse_ix int
|
98
|
+
#include "instantiate_template_headers.hpp"
|
99
|
+
#undef real_t
|
100
|
+
#undef sparse_ix
|
101
|
+
|
102
|
+
#define real_t float
|
103
|
+
#define sparse_ix int64_t
|
104
|
+
#include "instantiate_template_headers.hpp"
|
105
|
+
#undef real_t
|
106
|
+
#undef sparse_ix
|
107
|
+
|
108
|
+
#define real_t float
|
109
|
+
#define sparse_ix size_t
|
110
|
+
#include "instantiate_template_headers.hpp"
|
111
|
+
#undef real_t
|
112
|
+
#undef sparse_ix
|
113
|
+
|
114
|
+
#undef _NO_REAL_T
|
115
|
+
|
116
|
+
#endif /* NO_TEMPLATED_VERSIONS */
|
117
|
+
|
118
|
+
#endif
|