The project doesn't run

[alighasemi78]

Hi. I'm following the instructions in the readme to run the project. However, I encounter errors in the data generation process. Could you try to run the project yourself and update the readme accordingly? some libraries have been deprecated and some functionalities have been changed. For example, when generating the SPMotif datasets, the code throws an error when we're trying to use

np.save(f'../data/SPMotif-{global_b}/raw/train.npy', (edge_index_list, label_list, ground_truth_list, role_id_list, pos_list))

Regards.

[LFhase]

Hi, thanks for your interest in our project. Apologize it has been 3 years since the project was developed. The error should be related to the numpy version, which was 1.20.3. Could you try to install the corresponding requirements as per https://github.com/LFhase/GMT/requirements.txt ? Indeed I would recommend https://github.com/LFhase/GALA to run the experiments with the environment of the GMT project.

For your reference, here is a screening of the packages in the environment where I developed the CIGA project.

Package                           Version               Location
--------------------------------- --------------------- ---------------------------
absl-py                           1.0.0
addict                            2.4.0
alabaster                         0.7.12
alembic                           1.6.5
antlr4-python3-runtime            4.9.3
astroid                           2.9.0
attrs                             21.2.0
autopage                          0.4.0
autopep8                          1.5.7
Babel                             2.9.1
backcall                          0.2.0
backpack                          0.1
backpack-for-pytorch              1.3.0
backports.entry-points-selectable 1.1.0
beautifulsoup4                    4.10.0
blessings                         1.7
brokenaxes                        0.5.0
Brotli                            1.0.9
brotlipy                          0.7.0
cachetools                        5.0.0
captum                            0.2.0
certifi                           2021.5.30
cffi                              1.14.6
cfgv                              3.3.1
chardet                           4.0.0
charset-normalizer                2.0.0
chex                              0.1.3
cilog                             1.3.0
click                             8.0.1
cliff                             3.9.0
cloudpickle                       2.0.0
cmaes                             0.8.2
cmd2                              2.1.2
cogdl                             0.4.1
colorama                          0.4.4
colorlog                          6.4.1
commonmark                        0.9.1
coverage                          7.6.1
cryptography                      3.4.7
cvxopt                            1.3.0
cvxpy                             1.2.0
cycler                            0.11.0
Cython                            3.0.0a10
debugpy                           1.4.1
decorator                         4.4.2
deeprobust                        0.2.4
dgl                               0.7.0
dgl-cu110                         0.6.1
dgllife                           0.2.9
distlib                           0.3.2
dive-into-graphs                  1.1.0
dm-tree                           0.1.7
docker-pycreds                    0.4.0
docutils                          0.17.1
drugood                           0.0.1                 /data2/home/yqchen/DrugOOD
ecos                              2.0.10
einops                            0.4.1
emoji                             1.4.2
entrypoints                       0.3
et-xmlfile                        1.1.0
execnet                           2.1.1
filelock                          3.0.12
flake8                            3.9.2
flatbuffers                       2.0
fonttools                         4.37.1
future                            0.18.2
fuzzywuzzy                        0.18.0
gdown                             5.2.0
gensim                            3.8.3
gitdb                             4.0.9
GitPython                         3.1.27
google-auth                       2.6.2
google-auth-oauthlib              0.4.6
googledrivedownloader             0.4
gpustat                           0.6.0
graph-ood                         1.1.1                 /data2/home/yqchen/BrainOOD
grave                             0.0.3
grb                               0.1.0
greenlet                          1.1.1
grpcio                            1.44.0
gurobipy                          9.5.1
h5py                              3.7.0
huggingface-hub                   0.0.12
hydra-core                        1.3.2
hyperopt                          0.2.7
identify                          2.2.13
idna                              3.1
imageio                           2.10.3
imagesize                         1.4.1
importlib-metadata                4.11.3
importlib_resources               6.4.4
iniconfig                         2.0.0
ipykernel                         6.2.0
ipython                           7.26.0
ipython-genutils                  0.2.0
isodate                           0.6.1
isort                             5.10.1
jax                               0.3.13
jaxlib                            0.3.10+cuda11.cudnn82
jedi                              0.18.0
Jinja2                            3.0.1
joblib                            1.0.1
jupyter-client                    7.0.1
jupyter-core                      4.7.1
kiwisolver                        1.3.2
lazy-object-proxy                 1.6.0
littleutils                       0.2.2
llvmlite                          0.37.0
Mako                              1.1.5
Markdown                          3.3.6
MarkupSafe                        2.0.1
matplotlib                        3.5.2
matplotlib-inline                 0.1.2
mccabe                            0.6.1
mkl-fft                           1.3.0
mkl-random                        1.2.2
mkl-service                       2.4.0
mmcv                              1.4.6
mpmath                            1.3.0
munch                             2.5.0
mypy-extensions                   1.0.0
nest-asyncio                      1.5.1
networkx                          2.8
nodeenv                           1.6.0
numba                             0.54.0
numpy                             1.20.3
nvidia-ml-py3                     7.352.0
oauthlib                          3.2.0
ogb                               1.3.6
olefile                           0.46
omegaconf                         2.3.0
opencv-python                     4.5.5.64
openpyxl                          3.1.5
opt-einsum                        3.3.0
optax                             0.1.2
optuna                            2.4.0
osqp                              0.6.2.post5
outdated                          0.2.1
packaging                         21.0
pandas                            1.3.0
parso                             0.8.2
pathtools                         0.1.2
pbr                               5.6.0
pexpect                           4.8.0
pickleshare                       0.7.5
Pillow                            8.4.0
pip                               21.2.2
platformdirs                      2.2.0
pluggy                            1.5.0
pre-commit                        2.14.0
prettytable                       2.2.0
promise                           2.3
prompt-toolkit                    3.0.17
protobuf                          3.20.1
psutil                            6.0.0
ptyprocess                        0.7.0
py                                1.11.0
py4j                              0.10.9.5
pyasn1                            0.4.8
pyasn1-modules                    0.2.8
pycairo                           1.20.1
pycodestyle                       2.7.0
pycparser                         2.20
pyflakes                          2.3.1
Pygments                          2.18.0
pylint                            2.12.2
pynvml                            11.5.3
pyOpenSSL                         20.0.1
pyparsing                         2.4.7
pyperclip                         1.8.2
pyscf                             2.6.2
PySocks                           1.7.1
PyTDC                             0.3.6
pytest                            7.1.2
pytest-cov                        3.0.0
pytest-forked                     1.6.0
pytest-xdist                      2.5.0
python-dateutil                   2.8.2
python-editor                     1.0.4
python-louvain                    0.15
pytz                              2021.1
PyWavelets                        1.2.0
PyYAML                            6.0
pyzmq                             22.2.1
qdldl                             0.1.5.post2
rdflib                            6.1.1
rdkit-pypi                        2021.9.5.1
recommonmark                      0.7.1
regex                             2021.8.28
reportlab                         3.5.68
requests                          2.26.0
requests-oauthlib                 1.3.1
rsa                               4.8
ruamel.yaml                       0.17.21
ruamel.yaml.clib                  0.2.8
sacremoses                        0.0.45
SciencePlots                      1.0.9
scikit-image                      0.19.1
scikit-learn                      0.24.2
scipy                             1.6.2
scs                               3.2.0
seaborn                           0.11.2
sentencepiece                     0.1.96
sentry-sdk                        1.9.8
setproctitle                      1.3.2
setuptools                        59.5.0
shap                              0.44.1
shortuuid                         1.0.9
simplejson                        3.17.6
six                               1.16.0
slicer                            0.0.7
smart-open                        5.2.1
smmap                             5.0.0
snowballstemmer                   2.1.0
soupsieve                         2.3.1
Sphinx                            5.3.0
sphinx-rtd-theme                  1.0.0
sphinxcontrib-applehelp           1.0.2
sphinxcontrib-devhelp             1.0.2
sphinxcontrib-htmlhelp            2.0.0
sphinxcontrib-jsmath              1.0.1
sphinxcontrib-qthelp              1.0.3
sphinxcontrib-serializinghtml     1.1.5
SQLAlchemy                        1.4.23
stevedore                         3.4.0
sympy                             1.13.2
tabulate                          0.8.9
tensorboard                       2.8.0
tensorboard-data-server           0.6.1
tensorboard-plugin-wit            1.8.1
tensorboardX                      2.4
texttable                         1.6.4
threadpoolctl                     2.2.0
tifffile                          2021.11.2
tokenizers                        0.10.3
toml                              0.10.2
tomli                             2.0.1
toolz                             0.11.2
torch                             1.9.0
torch-cluster                     1.5.9
torch-geometric                   2.0.3
torch-scatter                     2.0.8
torch-sparse                      0.6.11
torch-spline-conv                 1.2.1
torchaudio                        0.9.0a0+33b2469
torchvision                       0.10.0
tornado                           6.1
tqdm                              4.64.0
traitlets                         5.0.5
transformers                      4.9.2
typed-argument-parser             1.7.2
typing-extensions                 3.10.0.0
typing-inspect                    0.9.0
urllib3                           1.26.19
virtualenv                        20.7.2
wandb                             0.13.3
wcwidth                           0.2.5
Werkzeug                          2.0.3
wheel                             0.37.0
wilds                             2.0.0
wrapt                             1.13.3
yacs                              0.1.6
yapf                              0.31.0
zipp                              3.7.0