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  • 6222e19 update README by jajupmochi 2019-05-21 17:22:14 +0200
  • 92c7444 add the treelet kernel. by jajupmochi 2019-05-21 16:46:38 +0200
  • a13dd94 test of a new preimage algorithm. by jajupmochi 2019-05-12 17:38:56 +0200
  • 7b75c1f 1. add verbose switch. 2. fix two dimension bugs in model selection function when computing std. by jajupmochi 2019-04-18 11:30:51 +0200
  • 04bc378 deleted: pygraph/kernels/results.md by jajupmochi 2019-03-27 14:38:16 +0100
  • d845b8c Update README.md by linlin 2019-03-27 14:21:02 +0100
  • 62ede29 rearrange notebooks directory. by jajupmochi 2019-03-26 16:17:00 +0100
  • ddd9216 rearrange notebooks directory, correct all scripts. by jajupmochi 2019-03-26 16:10:14 +0100
  • 6b4738d rearrange pygraph/kernels file. by jajupmochi 2019-03-19 11:26:25 +0100
  • 132e295 add datasets and remove some files not needed. by jajupmochi 2019-02-19 18:38:17 +0100
  • 123391d add comments in run_spkernel.py. by jajupmochi 2019-02-19 18:21:32 +0100
  • ccec961 * fix the path kernel up to length h. by jajupmochi 2019-02-01 11:00:45 +0100
  • 1566139 * 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. by jajupmochi 2019-01-31 17:04:15 +0100
  • 8baa21c correct randomness of data split for paralleling. by jajupmochi 2018-10-25 19:17:13 +0200
  • ef19fcb 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. by jajupmochi 2018-10-18 19:33:35 +0200
  • 834407c Modify structural shortest path kernel. by jajupmochi 2018-10-16 20:18:14 +0200
  • 347b44c A lot of things changed... by jajupmochi 2018-10-15 15:42:26 +0200
  • 68772ba 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. by jajupmochi 2018-09-21 18:31:12 +0200
  • 06b32cd 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. by jajupmochi 2018-07-23 16:35:14 +0200
  • 22a1f1e 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. by jajupmochi 2018-07-11 15:27:10 +0200
  • 6aac5b2 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. by jajupmochi 2018-06-29 17:41:16 +0200
  • efca08f 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. by jajupmochi 2018-06-14 14:37:00 +0200
  • 4fa6f37 Merge branch 'ljia' of https://git.litislab.fr/bgauzere/py-graph into ljia by jajupmochi 2018-06-05 18:42:49 +0200
  • bc93c0f I am dead... by jajupmochi 2018-06-05 17:52:08 +0200
  • ff2201d Merge branch 'ljia' of https://github.com/jajupmochi/py-graph into ljia by jajupmochi 2018-06-05 17:48:24 +0200
  • f684f51 delete useless results. by jajupmochi 2018-06-05 17:35:53 +0200
  • 1ee3ee0 Merge branch 'ljia' of https://github.com/jajupmochi/py-graph into ljia by jajupmochi 2018-06-05 17:34:53 +0200
  • 3fd31d4 delete useless results files. by jajupmochi 2018-06-05 17:07:26 +0200
  • 503187d delete useless results files. by jajupmochi 2018-06-05 17:07:26 +0200
  • 8e4f0ab Merge branch 'ljia' of https://git.litislab.fr/bgauzere/py-graph into ljia by jajupmochi 2018-06-05 16:53:09 +0200
  • 609a7a0 Merge branch 'ljia' of https://git.litislab.fr/bgauzere/py-graph into ljia by jajupmochi 2018-06-05 16:53:09 +0200
  • 38d66d8 Plus de choses sont changées... by jajupmochi 2018-06-05 15:29:40 +0200
  • b0f6470 Plus de choses sont changées... by jajupmochi 2018-06-05 15:29:40 +0200
  • 51f034a MOD extend marginalized kernel, remove tottering. MOD modify tree pattern kernel, remove tottering. MOD save output in function model_selection_precpmputed. by jajupmochi 2018-04-03 15:19:34 +0200
  • 2db913b MOD extend marginalized kernel, remove tottering. MOD modify tree pattern kernel, remove tottering. MOD save output in function model_selection_precpmputed. by jajupmochi 2018-04-03 15:19:34 +0200
  • c2cc133 MOD extend marginalized kernel, remove tottering. MOD modify tree pattern kernel, remove tottering. MOD save output in function model_selection_precpmputed. by jajupmochi 2018-04-03 15:19:34 +0200
  • c615605 MOD extend marginalized kernel, remove tottering. MOD modify tree pattern kernel, remove tottering. MOD save output in function model_selection_precpmputed. by jajupmochi 2018-04-03 15:19:34 +0200
  • 522ab84 remove unnecessary files. by jajupmochi 2018-03-05 18:14:18 +0100
  • b683eb9 remove unnecessary files. by jajupmochi 2018-03-05 18:14:18 +0100
  • 521b91f modifié : README.md modifié : notebooks/run_treepatternkernel.ipynb modifié : notebooks/run_untilnwalkkernel.ipynb by jajupmochi 2018-02-28 19:50:38 +0100
  • 15b6a97 modifié : README.md modifié : notebooks/run_treepatternkernel.ipynb modifié : notebooks/run_untilnwalkkernel.ipynb by jajupmochi 2018-02-28 19:50:38 +0100
  • 4b7e8f5 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 by jajupmochi 2018-02-28 19:30:42 +0100
  • 338f8ba 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 by jajupmochi 2018-02-28 19:30:42 +0100
  • 122ba2a 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 by jajupmochi 2018-02-08 15:37:56 +0100
  • 0d82ebe 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 by jajupmochi 2018-02-08 15:37:56 +0100
  • 58e7456 * 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. by jajupmochi 2018-01-24 18:43:48 +0100
  • 24eae65 * 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. by jajupmochi 2018-01-24 18:43:48 +0100
  • 8f6f78f ADD comments to code of treelet kernel. by jajupmochi 2018-01-17 17:06:57 +0100
  • 713edf2 ADD comments to code of treelet kernel. by jajupmochi 2018-01-17 17:06:57 +0100
  • e7c5e82 * ADD *treelet kernel* and its result on dataset Asyclic. - linlin * MOD the way to calculate WL subtree kernel, correct its results. - linlin * ADD *kernel_train_test* and *split_train_test* to wrap training and testing process. - linlin * MOD readme.md file, add detailed results of each kernel. - linlin by jajupmochi 2018-01-16 18:04:28 +0100
  • a719ac6 * ADD *treelet kernel* and its result on dataset Asyclic. - linlin * MOD the way to calculate WL subtree kernel, correct its results. - linlin * ADD *kernel_train_test* and *split_train_test* to wrap training and testing process. - linlin * MOD readme.md file, add detailed results of each kernel. - linlin by jajupmochi 2018-01-16 18:04:28 +0100
  • 62a0d26 * ADD *treelet kernel* and its result on dataset Asyclic. - linlin * MOD the way to calculate WL subtree kernel, correct its results. - linlin * ADD *kernel_train_test* and *split_train_test* to wrap training and testing process. - linlin * MOD readme.md file, add detailed results of each kernel. - linlin by jajupmochi 2018-01-16 18:03:38 +0100
  • 5d0d9e3 * ADD *treelet kernel* and its result on dataset Asyclic. - linlin * MOD the way to calculate WL subtree kernel, correct its results. - linlin * ADD *kernel_train_test* and *split_train_test* to wrap training and testing process. - linlin * MOD readme.md file, add detailed results of each kernel. - linlin by jajupmochi 2018-01-16 18:03:38 +0100
  • 7e2a15d * ADD calculation of the time spend to acquire kernel matrices for each kernel. - linlin * MOD floydTransformation function, calculate shortest paths taking into consideration user-defined edge weight. - linlin * MOD implementation of nodes and edges attributes genericity for all kernels. - linlin * ADD detailed results file results.md. - linlin * MOD Weisfeiler-Lehman subtree kernel and the test code. - linlin by jajupmochi 2017-12-22 14:14:45 +0100
  • 460e846 * ADD calculation of the time spend to acquire kernel matrices for each kernel. - linlin * MOD floydTransformation function, calculate shortest paths taking into consideration user-defined edge weight. - linlin * MOD implementation of nodes and edges attributes genericity for all kernels. - linlin * ADD detailed results file results.md. - linlin * MOD Weisfeiler-Lehman subtree kernel and the test code. - linlin by jajupmochi 2017-12-22 14:14:45 +0100
  • 323590e * MOD Implementation of attributes genericity for both gxl and ct functions by jajupmochi 2017-12-21 13:51:09 +0100
  • 6e70980 * MOD Implementation of attributes genericity for both gxl and ct functions by jajupmochi 2017-12-21 13:51:09 +0100
  • 4ede969 * ADD Weisfeiler-Lehman subtree kernel and its result on dataset Asyclic. by jajupmochi 2017-12-20 21:26:02 +0100
  • 1cac6d2 * ADD Weisfeiler-Lehman subtree kernel and its result on dataset Asyclic. by jajupmochi 2017-12-20 21:26:02 +0100
  • 2bd2325 * ADD mean average path kernel and its result on dataset Asyclic. - linlin * ADD delta kernel. - linlin * MOD reconstruction the code of marginalized kernel. - linlin by jajupmochi 2017-12-07 16:14:33 +0100
  • 0184a2a * ADD mean average path kernel and its result on dataset Asyclic. - linlin * ADD delta kernel. - linlin * MOD reconstruction the code of marginalized kernel. - linlin by jajupmochi 2017-12-07 16:14:33 +0100
  • c567c73 change of file structure. by jajupmochi 2017-12-05 17:52:54 +0100
  • a74c201 change of file structure. by jajupmochi 2017-12-05 17:52:54 +0100
  • 1f2d94d initial by jajupmochi 2017-12-05 17:51:56 +0100
  • 51911e8 initial by jajupmochi 2017-12-05 17:51:56 +0100
  • 1dbe663 Merge branch 'ljia' of https://git.litislab.fr/bgauzere/py-graph into ljia by jajupmochi 2017-12-05 17:48:12 +0100
  • 8ef5931 Merge branch 'ljia' of https://git.litislab.fr/bgauzere/py-graph into ljia by jajupmochi 2017-12-05 17:48:12 +0100
  • a287df8 initial by jajupmochi 2017-12-05 11:03:17 +0100
  • 4f71b86 Initial commit by linlin 2017-12-05 16:47:59 +0100
  • 5fa8e5a initial by jajupmochi 2017-12-05 11:03:17 +0100
  • f7fad1a Initial commit by linlin 2017-12-05 16:47:59 +0100
  • d6abcc2 Minor bug on traversal of shortest path list inutils.py by Benoit GAUZERE 2017-11-30 15:37:51 +0100
  • 4cd3654 Remove non pertinent files by Benoit GAUZERE 2017-11-27 21:05:23 +0100
  • d8a96ce Merge branch 'master' of https://git.litislab.fr/bgauzere/py-graph by jajupmochi 2017-11-24 11:14:11 +0100
  • 4ade070 commit by jajupmochi 2017-11-24 10:54:05 +0100
  • e1c2c3a Add of tests repository to play with pygraph. Use of virtualenv by Benoit GAUZERE 2017-11-23 15:15:17 +0100
  • 0b2e8ce Correction of minor bug on shortest paths computations by Benoit GAUZERE 2017-11-23 15:11:56 +0100
  • 66129a6 Update to NetworkX 2.0 by Benoit GAUZERE 2017-11-17 16:42:21 +0100
  • 595e09c Add of __init__.py files by Benoit GAUZERE 2017-11-17 16:41:54 +0100
  • 24a8ec3 Re structuration of project by Benoit GAUZERE 2017-11-17 10:46:50 +0100
  • eda8604 Re structuration of project by Benoit GAUZERE 2017-11-17 10:45:52 +0100
  • d9dfc8e Update of costfunctions hierarchy to distinguish cost function for ged and for cost matrix by Benoit GAUZERE 2017-11-17 10:40:14 +0100
  • a3e75c8 This notebook compute ged approx using 2 methods and 2 solvers by Benoit GAUZERE 2017-11-16 17:49:03 +0100
  • 755c174 Adding a generic lsap solver as parameter by Benoit GAUZERE 2017-11-16 17:47:14 +0100
  • 46c21bf Add of a first binder to C++ implementations of LSAP algorithms by Benoit GAUZERE 2017-11-16 17:46:39 +0100
  • 51a0f0b Minor bug on comparaison between sub and del costs for edges by Benoit GAUZERE 2017-11-16 17:09:27 +0100
  • 91cb5d2 First init - may contains some errors... by Benoit GAUZERE 2017-11-10 14:57:02 +0100
  • 1defa32 add README by Benoit GAUZERE 2017-11-10 14:38:33 +0100