Description
Dear authors,
Thanks for sharing the codes! While reproducing your method, I find it difficult to obtain the results presented in the table. Also, the performance is very unstable.
For example, I use the following commands to condense the Cora dataset into a small graph of 140 nodes:
python train_SGDD.py --dataset cora --nlayers=2 --beta 0.1 --r=1.0 --gpu_id=0
The best test accuracy obtained is only about 0.75 at about 400th epoch:
Similarly, I also met the "NAN" loss issue after training a large number of epochs (sometimes it is 400-600th, some times it is after 1000-th).
Another question is about "ogbn-arxiv" dataset. I noticed that the inner_loop is set 0 for ogbn-arxiv dataset. Doesn't it mean that the GNN classifier will not be trained? Also, I failed to obtain a decent performance on ogbn-arxiv dataset using the codes.
My environment is as follows:
absl-py==2.0.0
aiohttp==3.8.6
aiosignal==1.3.1
anndata==0.10.3
anyio @ file:///tmp/build/80754af9/anyio_1644463572971/work/dist
appdirs==1.4.4
argon2-cffi @ file:///opt/conda/conda-bld/argon2-cffi_1645000214183/work
argon2-cffi-bindings @ file:///tmp/build/80754af9/argon2-cffi-bindings_1644569679365/work
array-api-compat==1.4
asttokens @ file:///opt/conda/conda-bld/asttokens_1646925590279/work
async-timeout==4.0.3
attrs @ file:///croot/attrs_1668696182826/work
backcall @ file:///home/ktietz/src/ci/backcall_1611930011877/work
beautifulsoup4 @ file:///opt/conda/conda-bld/beautifulsoup4_1650462163268/work
bleach @ file:///opt/conda/conda-bld/bleach_1641577558959/work
brotlipy==0.7.0
cachetools==5.3.1
cdsapi==0.6.1
certifi @ file:///croot/certifi_1671487769961/work/certifi
cffi @ file:///croot/cffi_1670423208954/work
charset-normalizer @ file:///tmp/build/80754af9/charset-normalizer_1630003229654/work
clean-fid==0.1.35
click==8.1.3
cloudpickle==2.2.1
cmake==3.26.3
comm @ file:///croot/comm_1671231121260/work
contourpy==1.0.7
coolgpus==0.23
cryptography @ file:///croot/cryptography_1677533068310/work
cycler==0.11.0
daal4py==2023.0.2
dask==2023.3.2
debugpy @ file:///tmp/build/80754af9/debugpy_1637091799509/work
decorator @ file:///opt/conda/conda-bld/decorator_1643638310831/work
deeprobust==0.2.9
defusedxml @ file:///tmp/build/80754af9/defusedxml_1615228127516/work
dgl==1.0.1+cu117
entrypoints @ file:///tmp/build/80754af9/entrypoints_1649926439650/work
exceptiongroup==1.1.3
executing @ file:///opt/conda/conda-bld/executing_1646925071911/work
fastjsonschema @ file:///opt/conda/conda-bld/python-fastjsonschema_1661371079312/work
filelock==3.11.0
flit_core @ file:///opt/conda/conda-bld/flit-core_1644941570762/work/source/flit_core
fonttools==4.39.3
frozenlist==1.4.0
fsspec==2023.4.0
gdown==4.7.1
gensim==3.8.3
geomloss==0.2.6
get-annotations==0.1.2
google-auth==2.23.0
google-auth-oauthlib==1.0.0
grpcio==1.58.0
h5py==3.10.0
huggingface-hub==0.13.4
idna @ file:///croot/idna_1666125576474/work
imageio==2.33.0
importlib-metadata==6.3.0
importlib-resources==5.12.0
install==1.3.5
ipykernel @ file:///croot/ipykernel_1671488378391/work
ipython @ file:///croot/ipython_1676582224036/work
ipython-genutils @ file:///tmp/build/80754af9/ipython_genutils_1606773439826/work
ipywidgets==8.0.6
jedi @ file:///tmp/build/80754af9/jedi_1644297102865/work
Jinja2 @ file:///croot/jinja2_1666908132255/work
joblib @ file:///croot/joblib_1666298844297/work
jsonschema @ file:///croot/jsonschema_1676558650973/work
jupyter-server @ file:///croot/jupyter_server_1671707632269/work
jupyter_client @ file:///croot/jupyter_client_1676329080601/work
jupyter_core @ file:///croot/jupyter_core_1676538566912/work
jupyterlab-pygments @ file:///tmp/build/80754af9/jupyterlab_pygments_1601490720602/work
jupyterlab-widgets==3.0.7
keopscore==2.1.2
kiwisolver==1.4.4
lazy_loader==0.3
lightning-bolts==0.7.0
lightning-utilities==0.9.0
littleutils==0.2.2
llvmlite==0.41.1
locket==1.0.0
lxml @ file:///opt/conda/conda-bld/lxml_1657545139709/work
Markdown==3.4.4
MarkupSafe @ file:///opt/conda/conda-bld/markupsafe_1654597864307/work
matplotlib==3.7.1
matplotlib-inline @ file:///opt/conda/conda-bld/matplotlib-inline_1662014470464/work
mistune @ file:///tmp/build/80754af9/mistune_1607364877025/work
mkl-fft==1.3.1
mkl-random @ file:///tmp/build/80754af9/mkl_random_1626186066731/work
mkl-service==2.4.0
multidict==6.0.4
natsort==8.4.0
nb-conda==2.2.1
nb-conda-kernels @ file:///tmp/build/80754af9/nb_conda_kernels_1636035787744/work
nbclassic @ file:///croot/nbclassic_1676902904845/work
nbclient @ file:///tmp/build/80754af9/nbclient_1650290509967/work
nbconvert @ file:///croot/nbconvert_1668450669124/work
nbformat @ file:///croot/nbformat_1670352325207/work
nest-asyncio @ file:///croot/nest-asyncio_1672387112409/work
networkx @ file:///opt/conda/conda-bld/networkx_1657784097507/work
notebook @ file:///croot/notebook_1668179881751/work
notebook_shim @ file:///croot/notebook-shim_1668160579331/work
numba==0.58.1
numpy==1.23.0
oauthlib==3.2.2
ogb==1.3.6
outdated==0.2.2
packaging @ file:///croot/packaging_1671697413597/work
pandas==1.5.3
pandocfilters @ file:///opt/conda/conda-bld/pandocfilters_1643405455980/work
parso @ file:///opt/conda/conda-bld/parso_1641458642106/work
partd==1.4.0
pastel==0.2.1
patsy==0.5.3
pexpect @ file:///tmp/build/80754af9/pexpect_1605563209008/work
pickleshare @ file:///tmp/build/80754af9/pickleshare_1606932040724/work
Pillow==9.4.0
platformdirs @ file:///opt/conda/conda-bld/platformdirs_1662711380096/work
poethepoet==0.10.0
pooch @ file:///tmp/build/80754af9/pooch_1623324770023/work
POT==0.9.1
prometheus-client @ file:///tmp/abs_d3zeliano1/croots/recipe/prometheus_client_1659455100375/work
prompt-toolkit @ file:///croot/prompt-toolkit_1672387306916/work
protobuf==4.24.3
psutil @ file:///opt/conda/conda-bld/psutil_1656431268089/work
ptyprocess @ file:///tmp/build/80754af9/ptyprocess_1609355006118/work/dist/ptyprocess-0.7.0-py2.py3-none-any.whl
pure-eval @ file:///opt/conda/conda-bld/pure_eval_1646925070566/work
pyasn1==0.5.0
pyasn1-modules==0.3.0
pybind11==2.10.4
pycparser @ file:///tmp/build/80754af9/pycparser_1636541352034/work
Pygments @ file:///opt/conda/conda-bld/pygments_1644249106324/work
pykeops==2.1.2
pynndescent==0.5.10
pyOpenSSL @ file:///croot/pyopenssl_1677607685877/work
pyparsing @ file:///opt/conda/conda-bld/pyparsing_1661452539315/work
pyrsistent @ file:///tmp/build/80754af9/pyrsistent_1636110951836/work
PySocks @ file:///tmp/build/80754af9/pysocks_1605305812635/work
python-dateutil @ file:///tmp/build/80754af9/python-dateutil_1626374649649/work
pytorch-lightning==1.9.5
pytz==2023.3
PyYAML==6.0
pyzmq @ file:///opt/conda/conda-bld/pyzmq_1657724186960/work
requests @ file:///opt/conda/conda-bld/requests_1657734628632/work
requests-oauthlib==1.3.1
rsa==4.9
scanpy==1.9.6
scikit-image==0.22.0
scikit-learn @ file:///croot/scikit-learn_1676911643119/work
scikit-learn-intelex==20230228.214108
scipy==1.10.0
scprep==1.2.3
seaborn==0.12.2
Send2Trash @ file:///tmp/build/80754af9/send2trash_1632406701022/work
session-info==1.0.0
six @ file:///tmp/build/80754af9/six_1644875935023/work
smart-open==6.4.0
sniffio @ file:///tmp/build/80754af9/sniffio_1614030464178/work
sortedcontainers==2.1.0
soupsieve @ file:///croot/soupsieve_1666296392845/work
stack-data @ file:///opt/conda/conda-bld/stack_data_1646927590127/work
statsmodels==0.14.0
stdlib-list==0.9.0
tbb==2021.10.0
tensorboard==2.14.0
tensorboard-data-server==0.7.1
tensorboardX==2.6.2.2
terminado @ file:///croot/terminado_1671751832461/work
texttable==1.7.0
threadpoolctl @ file:///Users/ktietz/demo/mc3/conda-bld/threadpoolctl_1629802263681/work
tifffile==2023.9.26
timm==0.6.13
tinycss2 @ file:///croot/tinycss2_1668168815555/work
tomlkit==0.12.2
toolz==0.12.0
torch==1.12.1
torch-cluster @ file:///usr/share/miniconda/envs/test/conda-bld/pytorch-cluster_1656604971222/work
torch-geometric @ file:///usr/share/miniconda/envs/test/conda-bld/pyg_1669879312936/work
torch-scatter @ file:///usr/share/miniconda/envs/test/conda-bld/pytorch-scatter_1669298921716/work
torch-sparse @ file:///usr/share/miniconda/envs/test/conda-bld/pytorch-sparse_1671715073705/work
torchaudio==0.12.1
torchcde==0.2.5
torchcfm==1.0.4
torchdiffeq==0.2.3
torchdyn==1.0.6
torchmetrics==1.2.0
torchsde==0.2.6
torchvision==0.13.1
tornado @ file:///opt/conda/conda-bld/tornado_1662061693373/work
tqdm @ file:///opt/conda/conda-bld/tqdm_1664392687731/work
traitlets @ file:///croot/traitlets_1671143879854/work
trampoline==0.1.2
typing_extensions @ file:///croot/typing_extensions_1669924550328/work
tzdata==2023.3
umap-learn==0.5.4
urllib3 @ file:///croot/urllib3_1673575502006/work
urwid==2.0.1
wcwidth @ file:///Users/ktietz/demo/mc3/conda-bld/wcwidth_1629357192024/work
webencodings==0.5.1
websocket-client @ file:///tmp/build/80754af9/websocket-client_1614803975924/work
Werkzeug==2.3.7
widgetsnbextension==4.0.7
xarray==2023.3.0
yarl==1.9.2
zipp==3.15.0