jajupmochi
578e27bb8c
update .readthedocs.yml.
5 years ago
jajupmochi
3faed9066b
update docs conf.
5 years ago
jajupmochi
d1d0cdfc3b
add PyPI version badge.
5 years ago
jajupmochi
dcccc4e759
update README.md
5 years ago
jajupmochi
e406139447
update docs
5 years ago
jajupmochi
1126b610e2
update .readthedocs.yml
5 years ago
jajupmochi
fc9ccc7769
update readthedocs.
5 years ago
jajupmochi
d6b252a83e
rename library.
5 years ago
jajupmochi
5b91920275
update pre-image method for Letter-h dataset
5 years ago
jajupmochi
461de387b6
add parallel switch for structural sp kernel.
5 years ago
jajupmochi
c38dc97438
add Readthedocs badge.
5 years ago
jajupmochi
933a51a12f
add docs
5 years ago
jajupmochi
f7fcc36d83
add Codecov badge.
5 years ago
jajupmochi
9a9d1d738d
add Codecov.
5 years ago
jajupmochi
956f0a5bcd
add requirements.txt, add a test for travis CI.
5 years ago
jajupmochi
eeebdf9f02
add Travis CI badge in README.
5 years ago
jajupmochi
3728a39015
add Travis CI.
5 years ago
jajupmochi
fd25350bd1
update preimage.
5 years ago
jajupmochi
1a34c9f18e
update preimege/ged.py
5 years ago
jajupmochi
0cc89ae026
add dataset monoterpenoides.
5 years ago
jajupmochi
80e64a44ae
update pre-image
5 years ago
jajupmochi
b7112cd60f
update pre-image.
5 years ago
jajupmochi
e3985c5481
fitDistance.py: print and save results, update codes of quadratic program. This is the last version with edit costs having no other constraints than being no smaller than 0.
5 years ago
jajupmochi
ee6c79603d
1. update fitDistance.py.
1.1 add parallel computation of GEDs.
1.2 randomly initialize edit costs instead of uniform initialization.
1.3 remove the constrain that sum of the edit costs has to be equal to 1, avoiding sparsity.
5 years ago
jajupmochi
2876f7520a
Update fitDistance.py; constrain edit costs (c_i >= 0, sum(c_i) = 1).
5 years ago
jajupmochi
dd810b92da
Update pre-image.
5 years ago
jajupmochi
8c03f1b049
Update the GED method, use new gedlibpy library.
5 years ago
jajupmochi
edc3db457a
1. allow pre-image algorithm based on IAM to use all k nearest graphs as the initials of IAM.
2. fix a bug: in preimage_iam_random_mix function, sort D_k after updating it.
5 years ago
jajupmochi
57e13c9c5d
Update pre-image.
5 years ago
jajupmochi
df1a0c8e66
Changes to be committed:
modified: pygraph/utils/model_selection_precomputed.py
6 years ago
jajupmochi
221b528cb5
Update comments of tool functions.
6 years ago
jajupmochi
344a6f8d4b
Modify function comments of graph kernels.
6 years ago
jajupmochi
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
jajupmochi
73b2b7d279
1. add wl subtree kernel.
2. update datasets.
6 years ago
jajupmochi
6222e1984f
update README
6 years ago
jajupmochi
92c74448ec
add the treelet kernel.
6 years ago
jajupmochi
a13dd94f6a
test of a new preimage algorithm.
6 years ago
jajupmochi
7b75c1fc97
1. add verbose switch.
2. fix two dimension bugs in model selection function when computing std.
6 years ago
jajupmochi
04bc3784cf
deleted: pygraph/kernels/results.md
6 years ago
linlin
d845b8ccd7
Update README.md
6 years ago
jajupmochi
62ede297d6
rearrange notebooks directory.
6 years ago
jajupmochi
ddd921696a
rearrange notebooks directory, correct all scripts.
6 years ago
jajupmochi
6b4738df30
rearrange pygraph/kernels file.
6 years ago
jajupmochi
132e295bb9
add datasets and remove some files not needed.
6 years ago
jajupmochi
123391d3a1
add comments in run_spkernel.py.
6 years ago
jajupmochi
ccec961d2c
* fix the path kernel up to length h.
6 years ago
jajupmochi
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
jajupmochi
8baa21cb67
correct randomness of data split for paralleling.
6 years ago
jajupmochi
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
jajupmochi
834407c262
Modify structural shortest path kernel.
6 years ago