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Can't reproduce my results #77

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yunbokai opened this issue Jul 12, 2023 · 3 comments
Open

Can't reproduce my results #77

yunbokai opened this issue Jul 12, 2023 · 3 comments

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@yunbokai
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Hi,
I use the easy mode to my data with code below:

#Set seed
r_seed=t_seed=n_seed=100
#Search for suitable resolution
#Set seed
random.seed(r_seed)
torch.manual_seed(t_seed)
np.random.seed(n_seed)
#Run SpaGCN
adata.obs["pred"]= spg.detect_spatial_domains_ez_mode(adata, img, x_array, y_array, x_pixel, y_pixel, n_clusters=7, histology=True, s=1, b=49, p=0.5, r_seed=100, t_seed=100, n_seed=100)
adata.obs["pred"]=adata.obs["pred"].astype('category')
#Refine domains (optional)
#shape="hexagon" for Visium data, "square" for ST data.
adata.obs["refined_pred"]=spg.spatial_domains_refinement_ez_mode(sample_id=adata.obs.index.tolist(), pred=adata.obs["pred"].tolist(), x_array=x_array, y_array=y_array, shape="hexagon")
adata.obs["refined_pred"]=adata.obs["refined_pred"].astype('category')

However, each time I ran the same code, I got a similar but different domain result. I want to make the result reproducible. Do you have some advice?

Best wishes,
18k
@jianhuupenn
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Owner

Thanks for your interest in SpaGCN.
I have tested our method on 3 OS with Intel chips (https://github.com/jianhuupenn/SpaGCN#versions-the-software-has-been-tested-on), and setting the same seed will generate exactly the same results. I suspect that your issue results from the hardware. Are you using a machine with M1/2 chip?

@yunbokai
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Author

Thanks for your quick reply!
I use 20.04.1-Ubuntu and Anaconda whith python==3.9, because lower version was difficult to install. I got SpaGCN version 1.2.7. Here is my env version:

# packages in environment at /home/data/ybk/.conda/envs/SpaGCN:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                        main    defaults
_openmp_mutex             5.1                       1_gnu    defaults
anndata                   0.9.1                    pypi_0    pypi
asttokens                 2.0.5              pyhd3eb1b0_0    defaults
backcall                  0.2.0              pyhd3eb1b0_0    defaults
ca-certificates           2023.05.30           h06a4308_0    defaults
certifi                   2022.12.7                pypi_0    pypi
charset-normalizer        2.1.1                    pypi_0    pypi
comm                      0.1.2            py39h06a4308_0    defaults
contourpy                 1.1.0                    pypi_0    pypi
cycler                    0.11.0                   pypi_0    pypi
debugpy                   1.5.1            py39h295c915_0    defaults
decorator                 5.1.1              pyhd3eb1b0_0    defaults
executing                 0.8.3              pyhd3eb1b0_0    defaults
filelock                  3.9.0                    pypi_0    pypi
fonttools                 4.40.0                   pypi_0    pypi
h5py                      3.9.0                    pypi_0    pypi
idna                      3.4                      pypi_0    pypi
igraph                    0.10.5                   pypi_0    pypi
importlib-metadata        6.0.0            py39h06a4308_0    defaults
importlib-resources       6.0.0                    pypi_0    pypi
importlib_metadata        6.0.0                hd3eb1b0_0    defaults
ipykernel                 6.19.2           py39hb070fc8_0    defaults
ipython                   8.12.0           py39h06a4308_0    defaults
jedi                      0.18.1           py39h06a4308_1    defaults
jinja2                    3.1.2                    pypi_0    pypi
joblib                    1.3.1                    pypi_0    pypi
jupyter_client            8.1.0            py39h06a4308_0    defaults
jupyter_core              5.3.0            py39h06a4308_0    defaults
kiwisolver                1.4.4                    pypi_0    pypi
ld_impl_linux-64          2.38                 h1181459_1    defaults
libffi                    3.4.4                h6a678d5_0    defaults
libgcc-ng                 11.2.0               h1234567_1    defaults
libgomp                   11.2.0               h1234567_1    defaults
libsodium                 1.0.18               h7b6447c_0    defaults
libstdcxx-ng              11.2.0               h1234567_1    defaults
llvmlite                  0.40.1                   pypi_0    pypi
louvain                   0.8.0                    pypi_0    pypi
markupsafe                2.1.2                    pypi_0    pypi
matplotlib                3.7.2                    pypi_0    pypi
matplotlib-inline         0.1.6            py39h06a4308_0    defaults
mpmath                    1.2.1                    pypi_0    pypi
natsort                   8.4.0                    pypi_0    pypi
ncurses                   6.4                  h6a678d5_0    defaults
nest-asyncio              1.5.6            py39h06a4308_0    defaults
networkx                  3.0                      pypi_0    pypi
numba                     0.57.1                   pypi_0    pypi
numpy                     1.24.0                   pypi_0    pypi
opencv-python             4.8.0.74                 pypi_0    pypi
openssl                   3.0.9                h7f8727e_0    defaults
packaging                 23.1                     pypi_0    pypi
pandas                    2.0.3                    pypi_0    pypi
parso                     0.8.3              pyhd3eb1b0_0    defaults
patsy                     0.5.3                    pypi_0    pypi
pexpect                   4.8.0              pyhd3eb1b0_3    defaults
pickleshare               0.7.5           pyhd3eb1b0_1003    defaults
pillow                    9.3.0                    pypi_0    pypi
pip                       23.1.2           py39h06a4308_0    defaults
platformdirs              2.5.2            py39h06a4308_0    defaults
prompt-toolkit            3.0.36           py39h06a4308_0    defaults
psutil                    5.9.0            py39h5eee18b_0    defaults
ptyprocess                0.7.0              pyhd3eb1b0_2    defaults
pure_eval                 0.2.2              pyhd3eb1b0_0    defaults
pygments                  2.15.1           py39h06a4308_1    defaults
pynndescent               0.5.10                   pypi_0    pypi
pyparsing                 3.0.9                    pypi_0    pypi
python                    3.9.17               h955ad1f_0    defaults
python-dateutil           2.8.2              pyhd3eb1b0_0    defaults
python-igraph             0.10.5                   pypi_0    pypi
pytz                      2023.3                   pypi_0    pypi
pyzmq                     25.1.0           py39h6a678d5_0    defaults
readline                  8.2                  h5eee18b_0    defaults
requests                  2.28.1                   pypi_0    pypi
scanpy                    1.9.3                    pypi_0    pypi
scikit-learn              1.3.0                    pypi_0    pypi
scipy                     1.11.1                   pypi_0    pypi
seaborn                   0.12.2                   pypi_0    pypi
session-info              1.0.0                    pypi_0    pypi
setuptools                67.8.0           py39h06a4308_0    defaults
six                       1.16.0             pyhd3eb1b0_1    defaults
sqlite                    3.41.2               h5eee18b_0    defaults
stack_data                0.2.0              pyhd3eb1b0_0    defaults
statsmodels               0.14.0                   pypi_0    pypi
stdlib-list               0.9.0                    pypi_0    pypi
sympy                     1.11.1                   pypi_0    pypi
texttable                 1.6.7                    pypi_0    pypi
threadpoolctl             3.1.0                    pypi_0    pypi
tk                        8.6.12               h1ccaba5_0    defaults
torch                     2.0.1+cpu                pypi_0    pypi
torchaudio                2.0.2+cpu                pypi_0    pypi
torchvision               0.15.2+cpu               pypi_0    pypi
tornado                   6.2              py39h5eee18b_0    defaults
tqdm                      4.65.0                   pypi_0    pypi
traitlets                 5.7.1            py39h06a4308_0    defaults
typing-extensions         4.4.0                    pypi_0    pypi
typing_extensions         4.6.3            py39h06a4308_0    defaults
tzdata                    2023.3                   pypi_0    pypi
umap-learn                0.5.3                    pypi_0    pypi
urllib3                   1.26.13                  pypi_0    pypi
wcwidth                   0.2.5              pyhd3eb1b0_0    defaults
wheel                     0.38.4           py39h06a4308_0    defaults
xz                        5.4.2                h5eee18b_0    defaults
zeromq                    4.3.4                h2531618_0    defaults
zipp                      3.16.0                   pypi_0    pypi
zlib                      1.2.13               h5eee18b_0    defaults

Do you think I must use the env you offered ? thanks.

@WJPina
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WJPina commented Apr 17, 2024

I got the same issue, did you find the solution?

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@jianhuupenn @WJPina @yunbokai