[WIP] HDBSCAN C++/CUDA - #3773

Closed

cjnolet wants to merge 87 commits into

NVIDIA:branch-21.06from

cjnolet:fea-020-hdbscan

Commits on Apr 20, 2021

HDBSCAN
cjnolet
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c0a1b8b
Fixing style
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3800f76

Commits on Apr 21, 2021

Progress
cjnolet
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362d429

Commits on Apr 22, 2021

Checking in
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abf2267
Checking in todo stubs of remaining work for initial implementation
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c68bd8d
Creating output condensed hierarchy
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78a8432
Resizing rmm arrays
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b502e1d
Adding missing semicolon
cjnolet
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146ac00

Commits on Apr 23, 2021

initial ideas to compute stabilities
divyegala
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3cee98b
Checking in
cjnolet
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60253ce
Updating
cjnolet
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e4668d3
separating kernels into detail
divyegala
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1e9f557
Merge branch 'fea-020-hdbscan' of github.com:cjnolet/cuml into fea-020-hdbscan
divyegala
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0331697
allocating stabilities through caller
divyegala
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fd77b48
cleaning stabilities a bit
divyegala
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7edb4a3
Initial stub for eom is done.
cjnolet
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0efd58b
Adding data to epilogue
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bbb35db
COuple small updates
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83d8ac3
Adding get_stability scores
cjnolet
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f563aca
tests building
divyegala
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bbe1ffe
cleaning up some comments
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d135645
Fixing style
cjnolet
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0fce1bb
merging
divyegala
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7052836
merge and compile
divyegala
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b6048ce
Updates to get hdbscan to compile
cjnolet
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f05d545
Getting remaining stuff in extract_clusters to compile
cjnolet
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1628a36
Using zip iterators for copy_if
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463f757
compiling compute stabilities
divyegala
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dcc83db
stabilities and merge building
divyegala
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4829b21
Sorry!
cjnolet
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8814181
Renaming and moving a few things around
cjnolet
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025c5d4

Commits on Apr 26, 2021

Debugging mutual reachability through gtest
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5335252
Mutual reachability and dendrogram re-labeling executes
cjnolet
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2844a11
Fixing style
cjnolet
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d4dfc07
Condensed hierarchy executes without error. Output needs to be verified (and is very likely not correct)
cjnolet
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c8c9e55
Fixing formatting
cjnolet
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5619959
Some light prints show the condensing is at least performing the bfs.
cjnolet
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624fdb0
Fixing style
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de4569c

Commits on Apr 27, 2021

condensed clusters
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6cc8d74
Some updates. Fixing off by 1 error
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4865e64
correcting stabilities calculation
divyegala
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aa87e5b
Adding gtest for condensing
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1532e2a
Pushing
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88716d3
condensing *should* be correct
cjnolet
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269d828
Cleaning up cluster condensing. Should be mostly correct
cjnolet
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de0c7b3

Commits on Apr 28, 2021

more updates
divyegala
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741df66
Merge branch 'fea-020-hdbscan' of github.com:cjnolet/cuml into fea-020-hdbscan
divyegala
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52563df
Filling in union find & host-based labeling
cjnolet
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5095f9f
Fixing style
cjnolet
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c389a7a
monotonic parent child and stabilities running
divyegala
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0b5d3e7
merge
divyegala
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071b899
Adding gtest for eom
cjnolet
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13c8672
Adding gtest for eom
cjnolet
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1cc4dbf

Commits on Apr 29, 2021

updated rmm, so removed ->on(stream)
divyegala
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2f17cf8
working stabilities gtest
divyegala
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a9d1058
Adding iris to cluster condensing tests
cjnolet
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68a9344
Code path through stabilities, eom, and labeling seems to work.
cjnolet
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c3dbd8c
Merge branch 'branch-0.20' into fea-020-hdbscan
cjnolet
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89deff8
Fixing reachability
cjnolet
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b143a55
Adding support for max_cluster_size
cjnolet
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dcd590c
Making labels monotonic
cjnolet
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699183d
sketching probabilities
divyegala
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e78b48a
Merge branch 'fea-020-hdbscan' of github.com:cjnolet/cuml into fea-020-hdbscan
divyegala
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b6a85ef

Commits on Apr 30, 2021

passing probabilities gtest
divyegala
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ea759ef
fixing compute-sanitizer issue in excess of mass
cjnolet
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0818d10
Cleaning up API for inputs and outputs
cjnolet
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998c8d4
Fixing memory error
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fb67441

Commits on May 1, 2021

cluster epsilon search start
divyegala
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e000f41

Commits on May 3, 2021

C++ changes for python wrapper
cjnolet
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ebfa61d
C++ changes
cjnolet
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069b1b5
Using rmm allocator directly in thrust for now
cjnolet
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38734d6
Fixing cpp style
cjnolet
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90d7de6
merge
divyegala
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8408c78
Merge branch 'fea-020-hdbscan' of github.com:cjnolet/cuml into fea-020-hdbscan
divyegala
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babf10b

Commits on May 4, 2021

introducing cluster tree creation
divyegala
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ee3c07b
correcting eom test with cluster tree
divyegala
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5f11ea3
Adding labeling for robust single linkage (and dbscan)
cjnolet
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3694173
Small changes to support robust single linkage
cjnolet
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7332199
cluster selection travel upwards working
divyegala
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a4b560c
separating bfs out
divyegala
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6a6a9df
added cluster negation to epsilon search
divyegala
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93c106c
merge
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ee90094
style check
divyegala
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b7d67dd
Separating extract into smaller files.
cjnolet
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bec62e7
styl
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e063a68
leaf selection method
divyegala
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7b57cd0

Commits on May 5, 2021

Cleaning up prints for hdbscan and fixing small segfault
cjnolet
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5e7b850