344a6f8d4b
Modify function comments of graph kernels.
6 years ago
b7eef40edf
1. add parallelization choice into the treelet kernel, including "imap_unordered" and None.
2. modify the treelet kernel, use tuples to store canonkeys instead of strings in case that some labels strings contain more than 1 character.
6 years ago
73b2b7d279
1. add wl subtree kernel.
2. update datasets.
6 years ago
6222e1984f
update README
6 years ago
92c74448ec
add the treelet kernel.
6 years ago
a13dd94f6a
test of a new preimage algorithm.
6 years ago
7b75c1fc97
1. add verbose switch.
2. fix two dimension bugs in model selection function when computing std.
6 years ago
04bc3784cf
deleted: pygraph/kernels/results.md
6 years ago
d845b8ccd7
Update README.md
6 years ago
62ede297d6
rearrange notebooks directory.
6 years ago
ddd921696a
rearrange notebooks directory, correct all scripts.
6 years ago
6b4738df30
rearrange pygraph/kernels file.
6 years ago
132e295bb9
add datasets and remove some files not needed.
6 years ago
123391d3a1
add comments in run_spkernel.py.
6 years ago
ccec961d2c
* fix the path kernel up to length h.
6 years ago
1566139883
* use global variable to tackle big read-only variables when they are used in subprocesses.
* rewrite the implementation of the marginalized kernel.
* implement four computing methods of the generalized random walk kernel.
* in the path kernel up to length h, use trie to save all paths, saving tremendous memories; use the Deep-first search to get paths from graphs.
* in model_selection_for_precomputed_kernel method, complete the part to do cross validation when Gram matrices are read from file.
* in get_dataset_attributes methods, correct three sub-methods about getting node degrees, add sub-methods to get fill factors of graphs.
* change default chunksize of pool.imap_unordered parallel method to 100.
* remove try... except blocks in case they hidden bugs.
6 years ago
8baa21cb67
correct randomness of data split for paralleling.
6 years ago
ef19fcba5a
1. fix bug when computing kernels between non-symbolic node attributes of the spkernel and the ssp kernel, add a gaussian kernel implementation.
2. update pygraph.utils.graphdatasets.get_dataset_attributes function, so that if a dataset has missing attributes it can still read the dimension of attributes.
6 years ago
834407c262
Modify structural shortest path kernel.
6 years ago
347b44cdd9
A lot of things changed...
6 years ago
68772ba4b4
1. [IMPORTANT] correct an error in dataset split section in function cross_validation_pre_computed. DON NOT use previous versions. They are all wrong.
2. save gram matrices and relative data when using function cross_validation_pre_computed, before cross validation step, in case that something goes wrong with CV. Parameter read_gm_from_file can be used to choose whether to read gram matrices from file.
3. add some test code to check if a gram matrix is symmetric and positive semi-definite.
6 years ago
06b32cdf8a
1. apply multiprocessing.Pool.imap_unordered method instead of the map method, so that tqdm could be applied to track progress.
2. apply part of the Fast Computation of Shortest Path Kernel (FCSP) to speed up the sp kernel.
7 years ago
22a1f1e8d8
1. add parallel computing scheme to spkernel and model_selection_precomputed.
2. modify model_selection_precomputed so that all results are written into memory and then to a file at last section of code, in case that on cpu/disk seperated systems the IO takes too much time.
3. correct utils.floyd_warshall_numpy function. DONNOT use the last version.
7 years ago
6aac5b2981
1. add Sylvester Equation Methods for the generalized random walk kernel.
2. correct an error in the common walk kernel. DON NOT use the old one.
3. improve the method to construct fully-labeled direct product graphs, much faster for sparse graphs.
7 years ago
efca08fb30
1. upgrate spkernel, now supporting symbolic and non-symbolic node labels, directed and undirected graphs, and allowing user-defined node kernels.
2. model_selection_precomputed can now save all results as human readable text.
3. modify pygraph.utils.utils.floydTransformation and pygraph.utils.graphdataset.get_dataset_attributes.
7 years ago
4fa6f373f3
Merge branch 'ljia' of https://git.litislab.fr/bgauzere/py-graph into ljia
7 years ago
bc93c0f80b
I am dead...
7 years ago
ff2201d42b
Merge branch 'ljia' of https://github.com/jajupmochi/py-graph into ljia
7 years ago
f684f51ad1
delete useless results.
7 years ago
1ee3ee0cba
Merge branch 'ljia' of https://github.com/jajupmochi/py-graph into ljia
7 years ago
3fd31d48ec
delete useless results files.
7 years ago
503187dc3f
delete useless results files.
7 years ago
8e4f0aba58
Merge branch 'ljia' of https://git.litislab.fr/bgauzere/py-graph into ljia
7 years ago
609a7a0124
Merge branch 'ljia' of https://git.litislab.fr/bgauzere/py-graph into ljia
7 years ago
38d66d8ae3
Plus de choses sont changées...
7 years ago
b0f6470c35
Plus de choses sont changées...
7 years ago
2db913b7eb
MOD extend marginalized kernel, remove tottering.
MOD modify tree pattern kernel, remove tottering.
MOD save output in function model_selection_precpmputed.
7 years ago
51f034a4a0
MOD extend marginalized kernel, remove tottering.
MOD modify tree pattern kernel, remove tottering.
MOD save output in function model_selection_precpmputed.
7 years ago
c2cc1336dc
MOD extend marginalized kernel, remove tottering.
MOD modify tree pattern kernel, remove tottering.
MOD save output in function model_selection_precpmputed.
7 years ago
c615605b08
MOD extend marginalized kernel, remove tottering.
MOD modify tree pattern kernel, remove tottering.
MOD save output in function model_selection_precpmputed.
7 years ago
b683eb9e5e
remove unnecessary files.
7 years ago
522ab84d1c
remove unnecessary files.
7 years ago
15b6a97053
modifié : README.md
modifié : notebooks/run_treepatternkernel.ipynb
modifié : notebooks/run_untilnwalkkernel.ipynb
7 years ago
521b91ff0f
modifié : README.md
modifié : notebooks/run_treepatternkernel.ipynb
modifié : notebooks/run_untilnwalkkernel.ipynb
7 years ago
338f8ba326
modifié : README.md
modifié : notebooks/run_cyclicpatternkernel.ipynb
modifié : notebooks/run_marginalizedkernel_acyclic.ipynb
modifié : notebooks/run_pathkernel_acyclic.ipynb
modifié : notebooks/run_spkernel_acyclic.ipynb
modifié : notebooks/run_treeletkernel_acyclic.ipynb
modifié : notebooks/run_treepatternkernel.ipynb
modifié : notebooks/run_untildpathkernel_acyclic.ipynb
nouveau fichier : notebooks/run_untilnwalkkernel.ipynb
modifié : notebooks/run_weisfeilerLehmankernel_acyclic.ipynb
modifié : pygraph/kernels/treePatternKernel.py
modifié : pygraph/kernels/untildPathKernel.py
nouveau fichier : pygraph/kernels/untilnWalkKernel.py
nouveau fichier : pygraph/utils/model_selection_precomputed.py
modifié : pygraph/utils/utils.py
7 years ago
4b7e8f5522
modifié : README.md
modifié : notebooks/run_cyclicpatternkernel.ipynb
modifié : notebooks/run_marginalizedkernel_acyclic.ipynb
modifié : notebooks/run_pathkernel_acyclic.ipynb
modifié : notebooks/run_spkernel_acyclic.ipynb
modifié : notebooks/run_treeletkernel_acyclic.ipynb
modifié : notebooks/run_treepatternkernel.ipynb
modifié : notebooks/run_untildpathkernel_acyclic.ipynb
nouveau fichier : notebooks/run_untilnwalkkernel.ipynb
modifié : notebooks/run_weisfeilerLehmankernel_acyclic.ipynb
modifié : pygraph/kernels/treePatternKernel.py
modifié : pygraph/kernels/untildPathKernel.py
nouveau fichier : pygraph/kernels/untilnWalkKernel.py
nouveau fichier : pygraph/utils/model_selection_precomputed.py
modifié : pygraph/utils/utils.py
7 years ago
0d82ebe6b8
copié : notebooks/run_weisfeilerLehmankernel_acyclic.ipynb -> .ipynb_checkpoints/run_weisfeilerLehmankernel_acyclic-checkpoint.ipynb
modifié : README.md
nouveau fichier : notebooks/run_cyclicpatternkernel.ipynb
modifié : notebooks/run_marginalizedkernel_acyclic.ipynb
modifié : notebooks/run_pathkernel_acyclic.ipynb
modifié : notebooks/run_spkernel_acyclic.ipynb
modifié : notebooks/run_treeletkernel_acyclic.ipynb
nouveau fichier : notebooks/run_treepatternkernel.ipynb
modifié : notebooks/run_weisfeilerLehmankernel_acyclic.ipynb
nouveau fichier : pygraph/kernels/cyclicPatternKernel.py
modifié : pygraph/kernels/deltaKernel.py
modifié : pygraph/kernels/pathKernel.py
modifié : pygraph/kernels/results.md
modifié : pygraph/kernels/spKernel.py
nouveau fichier : pygraph/kernels/treePatternKernel.py
modifié : pygraph/kernels/treeletKernel.py
modifié : pygraph/kernels/untildPathKernel.py
modifié : pygraph/kernels/weisfeilerLehmanKernel.py
modifié : pygraph/utils/graphfiles.py
modifié : pygraph/utils/utils.py
nouveau fichier : run_cyclic.py
7 years ago
122ba2ae06
copié : notebooks/run_weisfeilerLehmankernel_acyclic.ipynb -> .ipynb_checkpoints/run_weisfeilerLehmankernel_acyclic-checkpoint.ipynb
modifié : README.md
nouveau fichier : notebooks/run_cyclicpatternkernel.ipynb
modifié : notebooks/run_marginalizedkernel_acyclic.ipynb
modifié : notebooks/run_pathkernel_acyclic.ipynb
modifié : notebooks/run_spkernel_acyclic.ipynb
modifié : notebooks/run_treeletkernel_acyclic.ipynb
nouveau fichier : notebooks/run_treepatternkernel.ipynb
modifié : notebooks/run_weisfeilerLehmankernel_acyclic.ipynb
nouveau fichier : pygraph/kernels/cyclicPatternKernel.py
modifié : pygraph/kernels/deltaKernel.py
modifié : pygraph/kernels/pathKernel.py
modifié : pygraph/kernels/results.md
modifié : pygraph/kernels/spKernel.py
nouveau fichier : pygraph/kernels/treePatternKernel.py
modifié : pygraph/kernels/treeletKernel.py
modifié : pygraph/kernels/untildPathKernel.py
modifié : pygraph/kernels/weisfeilerLehmanKernel.py
modifié : pygraph/utils/graphfiles.py
modifié : pygraph/utils/utils.py
nouveau fichier : run_cyclic.py
7 years ago
24eae65154
* ADD *path kernel up to depth d* and its result on dataset Asyclic.
* MOD treelet kernel, retrieve canonkeys of all graphs before calculate kernels, wildly speed it up.
7 years ago
58e7456f6b
* ADD *path kernel up to depth d* and its result on dataset Asyclic.
* MOD treelet kernel, retrieve canonkeys of all graphs before calculate kernels, wildly speed it up.
7 years ago
jajupmochi