[FEA] All points membership vector for HDBSCAN #4800
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tarang-jain
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Jul 5, 2022
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tarang-jain
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- All points distance membership vector
- All points outlier membership vector
- All points probability in some cluster
- All points membership vector
- Tests
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cjnolet
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Aug 11, 2022
cpp/include/cuml/cluster/hdbscan.hpp
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| */ | ||
| void hdbscan(const raft::handle_t& handle, | ||
| const float* X, | ||
| size_t m, | ||
| size_t n, | ||
| raft::distance::DistanceType metric, | ||
| HDBSCAN::Common::HDBSCANParams& params, | ||
| HDBSCAN::Common::hdbscan_output<int, float>& out); | ||
| HDBSCAN::Common::hdbscan_output<int, float>& out, | ||
| bool prediction_data, |
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Why not add prediction_data to params? Ideally we'd use std::optional for prediction_data_
cpp/src/hdbscan/hdbscan.cu
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| exemplar_label_offsets.resize(n_selected_clusters_ + 1, handle.get_stream()); | ||
| deaths.resize(n_clusters, handle.get_stream()); | ||
| selected_clusters.resize(n_selected_clusters, handle.get_stream()); | ||
| raft::copy(exemplar_idx.begin(), exemplar_idx_, n_exemplars_, handle.get_stream()); |
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This is expensive in both memory usage and runtime. Rather than accepting raw pointers in cache, I would suggest creating an allocate() function that will resize the device_uvector members and then using the getters for the underlying pointers inside build_prediction_data to have the computations populate the values directly. That would remove the additional memory usage.
cpp/src/hdbscan/runner.h
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| @@ -255,6 +258,15 @@ void _fit_hdbscan(const raft::handle_t& handle, | |||
| * starting at 0 even in the presence of noise (-1) | |||
| */ | |||
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| if (prediction_data) { | |||
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if(params.prediction_data) or you could also do if(prediction_data_.has_value()) if you use std::optional.
cpp/test/sg/hdbscan_test.cu
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| params = ::testing::TestWithParam<SoftClusteringInputs<T, IdxT>>::GetParam(); | ||
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| Logger::get().setLevel(CUML_LEVEL_DEBUG); |
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rerun tests |
…points-membership-vector-hdbscan
…:tarang-jain/cuml into fea-all-points-membership-vector-hdbscan
…points-membership-vector-hdbscan
Codecov Report
@@ Coverage Diff @@
## branch-22.10 #4800 +/- ##
================================================
+ Coverage 78.02% 78.04% +0.01%
================================================
Files 180 180
Lines 11385 11422 +37
================================================
+ Hits 8883 8914 +31
- Misses 2502 2508 +6
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cjnolet
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Aug 26, 2022
|
@gpucibot merge |
This was referenced Aug 29, 2022
divyegala
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Sep 2, 2022
- [x] All points distance membership vector - [x] All points outlier membership vector - [x] All points probability in some cluster - [x] All points membership vector - [x] Tests Authors: - Tarang Jain (https://github.com/tarang-jain) Approvers: - Corey J. Nolet (https://github.com/cjnolet) URL: rapidsai#4800
ajschmidt8
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that referenced
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Feb 13, 2023
- [x] All points distance membership vector - [x] All points outlier membership vector - [x] All points probability in some cluster - [x] All points membership vector - [x] Tests Authors: - Tarang Jain (https://github.com/tarang-jain) Approvers: - Corey J. Nolet (https://github.com/cjnolet) URL: #4800
jakirkham
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Feb 27, 2023
- [x] All points distance membership vector - [x] All points outlier membership vector - [x] All points probability in some cluster - [x] All points membership vector - [x] Tests Authors: - Tarang Jain (https://github.com/tarang-jain) Approvers: - Corey J. Nolet (https://github.com/cjnolet) URL: rapidsai#4800
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