Request for ’data‘ folder

[CDchenlin]

Hello,

I wanted to express my gratitude for the outstanding work you’ve done! I must apologize if I’ve missed it, but I was unable to locate the ‘data’ folder in this repository, which is supposed to contain the ‘/pubmed/search_query.csv’ file and ‘/textbook/pdf_files’. Could you kindly let me know if there are any plans to release these pertinent resources?

Best Regards,
Chenlin

[chanwkimlab]

Hi, thanks for your interest in our work! We've updated the repo to include the pubmed/search_query.csv file. As for other data, since they are raw data, we do not have plans to redistribute them.

[CDchenlin]

Dear @chanwkimlab,

I greatly appreciate your response and nice work. It has been immensely helpful. However, I encountered an issue when executing scripts/preprocess/preprocess_pubmed.sh. The error message displayed is ModuleNotFoundError: No module named 'MONET'.

To the best of my knowledge, I have installed all necessary packages following the instructions in the Read Me file. I also attempted to resolve the issue by running pip install MONET, but the error remains.

For your reference, I have attached the package information from my Anaconda environment. I would be grateful if you could review it and let me know if I have missed anything.

_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
anndata                   0.10.7                   pypi_0    pypi
anyio                     4.3.0                    pypi_0    pypi
argon2-cffi               23.1.0                   pypi_0    pypi
argon2-cffi-bindings      21.2.0                   pypi_0    pypi
array-api-compat          1.6                      pypi_0    pypi
arrow                     1.3.0                    pypi_0    pypi
asttokens                 2.4.1                    pypi_0    pypi
async-lru                 2.0.4                    pypi_0    pypi
attrs                     23.2.0                   pypi_0    pypi
babel                     2.15.0                   pypi_0    pypi
beautifulsoup4            4.12.3                   pypi_0    pypi
bleach                    6.1.0                    pypi_0    pypi
bzip2                     1.0.8                hd590300_5    conda-forge
ca-certificates           2024.2.2             hbcca054_0    conda-forge
certifi                   2024.2.2                 pypi_0    pypi
cffi                      1.16.0                   pypi_0    pypi
charset-normalizer        3.3.2                    pypi_0    pypi
click                     7.1.2                    pypi_0    pypi
clip                      1.0                      pypi_0    pypi
comm                      0.2.2                    pypi_0    pypi
contourpy                 1.2.1                    pypi_0    pypi
cycler                    0.12.1                   pypi_0    pypi
cython                    0.29.37                  pypi_0    pypi
debugpy                   1.8.1                    pypi_0    pypi
decorator                 5.1.1                    pypi_0    pypi
defusedxml                0.7.1                    pypi_0    pypi
exceptiongroup            1.2.1                    pypi_0    pypi
executing                 2.0.1                    pypi_0    pypi
fastjsonschema            2.19.1                   pypi_0    pypi
filelock                  3.14.0                   pypi_0    pypi
fonttools                 4.51.0                   pypi_0    pypi
fqdn                      1.5.1                    pypi_0    pypi
fsspec                    2024.3.1                 pypi_0    pypi
ftfy                      6.2.0                    pypi_0    pypi
get-annotations           0.1.2                    pypi_0    pypi
h11                       0.14.0                   pypi_0    pypi
h5py                      3.11.0                   pypi_0    pypi
httpcore                  1.0.5                    pypi_0    pypi
httpx                     0.27.0                   pypi_0    pypi
huggingface-hub           0.22.0                   pypi_0    pypi
idna                      3.7                      pypi_0    pypi
importlib-metadata        7.1.0                    pypi_0    pypi
importlib-resources       6.4.0                    pypi_0    pypi
ipykernel                 6.29.4                   pypi_0    pypi
ipython                   8.18.1                   pypi_0    pypi
ipywidgets                8.1.2                    pypi_0    pypi
isoduration               20.11.0                  pypi_0    pypi
jedi                      0.19.1                   pypi_0    pypi
jinja2                    3.1.4                    pypi_0    pypi
joblib                    1.4.2                    pypi_0    pypi
json5                     0.9.25                   pypi_0    pypi
jsonpointer               2.4                      pypi_0    pypi
jsonschema                4.22.0                   pypi_0    pypi
jsonschema-specifications 2023.12.1                pypi_0    pypi
jupyter                   1.0.0                    pypi_0    pypi
jupyter-client            8.6.1                    pypi_0    pypi
jupyter-console           6.6.3                    pypi_0    pypi
jupyter-core              5.7.2                    pypi_0    pypi
jupyter-events            0.10.0                   pypi_0    pypi
jupyter-lsp               2.2.5                    pypi_0    pypi
jupyter-server            2.14.0                   pypi_0    pypi
jupyter-server-terminals  0.5.3                    pypi_0    pypi
jupyterlab                4.1.8                    pypi_0    pypi
jupyterlab-pygments       0.3.0                    pypi_0    pypi
jupyterlab-server         2.27.1                   pypi_0    pypi
jupyterlab-widgets        3.0.10                   pypi_0    pypi
kiwisolver                1.4.5                    pypi_0    pypi
ld_impl_linux-64          2.40                 h55db66e_0    conda-forge
legacy-api-wrap           1.4                      pypi_0    pypi
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 13.2.0               h77fa898_7    conda-forge
libgomp                   13.2.0               h77fa898_7    conda-forge
libnsl                    2.0.1                hd590300_0    conda-forge
libsqlite                 3.45.3               h2797004_0    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libzlib                   1.2.13               hd590300_5    conda-forge
llvmlite                  0.42.0                   pypi_0    pypi
markupsafe                2.1.5                    pypi_0    pypi
matplotlib                3.8.4                    pypi_0    pypi
matplotlib-inline         0.1.7                    pypi_0    pypi
mistune                   3.0.2                    pypi_0    pypi
monet                     0.3.1                    pypi_0    pypi
mpmath                    1.3.0                    pypi_0    pypi
natsort                   8.4.0                    pypi_0    pypi
nbclient                  0.10.0                   pypi_0    pypi
nbconvert                 7.16.4                   pypi_0    pypi
nbformat                  5.10.4                   pypi_0    pypi
ncurses                   6.5                  h59595ed_0    conda-forge
nest-asyncio              1.6.0                    pypi_0    pypi
networkx                  3.2.1                    pypi_0    pypi
notebook                  7.1.3                    pypi_0    pypi
notebook-shim             0.2.4                    pypi_0    pypi
numba                     0.59.1                   pypi_0    pypi
numpy                     1.26.4                   pypi_0    pypi
nvidia-cublas-cu12        12.1.3.1                 pypi_0    pypi
nvidia-cuda-cupti-cu12    12.1.105                 pypi_0    pypi
nvidia-cuda-nvrtc-cu12    12.1.105                 pypi_0    pypi
nvidia-cuda-runtime-cu12  12.1.105                 pypi_0    pypi
nvidia-cudnn-cu12         8.9.2.26                 pypi_0    pypi
nvidia-cufft-cu12         11.0.2.54                pypi_0    pypi
nvidia-curand-cu12        10.3.2.106               pypi_0    pypi
nvidia-cusolver-cu12      11.4.5.107               pypi_0    pypi
nvidia-cusparse-cu12      12.1.0.106               pypi_0    pypi
nvidia-nccl-cu12          2.20.5                   pypi_0    pypi
nvidia-nvjitlink-cu12     12.4.127                 pypi_0    pypi
nvidia-nvtx-cu12          12.1.105                 pypi_0    pypi
openssl                   3.3.0                hd590300_0    conda-forge
overrides                 7.7.0                    pypi_0    pypi
packaging                 24.0                     pypi_0    pypi
pandas                    2.2.2                    pypi_0    pypi
pandocfilters             1.5.1                    pypi_0    pypi
parso                     0.8.4                    pypi_0    pypi
patsy                     0.5.6                    pypi_0    pypi
pexpect                   4.9.0                    pypi_0    pypi
pillow                    10.3.0                   pypi_0    pypi
pip                       24.0               pyhd8ed1ab_0    conda-forge
platformdirs              4.2.1                    pypi_0    pypi
plotly                    5.22.0                   pypi_0    pypi
prometheus-client         0.20.0                   pypi_0    pypi
prompt-toolkit            3.0.43                   pypi_0    pypi
psutil                    5.9.8                    pypi_0    pypi
ptyprocess                0.7.0                    pypi_0    pypi
pure-eval                 0.2.2                    pypi_0    pypi
pycparser                 2.22                     pypi_0    pypi
pygments                  2.18.0                   pypi_0    pypi
pynndescent               0.5.12                   pypi_0    pypi
pyparsing                 3.1.2                    pypi_0    pypi
python                    3.9.15          hba424b6_0_cpython    conda-forge
python-dateutil           2.9.0.post0              pypi_0    pypi
python-json-logger        2.0.7                    pypi_0    pypi
pytz                      2024.1                   pypi_0    pypi
pyyaml                    6.0.1                    pypi_0    pypi
pyzmq                     26.0.3                   pypi_0    pypi
qtconsole                 5.5.2                    pypi_0    pypi
qtpy                      2.4.1                    pypi_0    pypi
readline                  8.2                  h8228510_1    conda-forge
referencing               0.35.1                   pypi_0    pypi
regex                     2024.5.10                pypi_0    pypi
requests                  2.31.0                   pypi_0    pypi
rfc3339-validator         0.1.4                    pypi_0    pypi
rfc3986-validator         0.1.1                    pypi_0    pypi
rpds-py                   0.18.1                   pypi_0    pypi
safetensors               0.4.3                    pypi_0    pypi
scanpy                    1.10.1                   pypi_0    pypi
scikit-learn              1.4.2                    pypi_0    pypi
scipy                     1.13.0                   pypi_0    pypi
seaborn                   0.13.2                   pypi_0    pypi
send2trash                1.8.3                    pypi_0    pypi
session-info              1.0.0                    pypi_0    pypi
setuptools                69.5.1             pyhd8ed1ab_0    conda-forge
six                       1.16.0                   pypi_0    pypi
sniffio                   1.3.1                    pypi_0    pypi
soupsieve                 2.5                      pypi_0    pypi
stack-data                0.6.3                    pypi_0    pypi
statsmodels               0.14.2                   pypi_0    pypi
stdlib-list               0.10.0                   pypi_0    pypi
sympy                     1.12                     pypi_0    pypi
tenacity                  8.3.0                    pypi_0    pypi
terminado                 0.18.1                   pypi_0    pypi
threadpoolctl             3.5.0                    pypi_0    pypi
tinycss2                  1.3.0                    pypi_0    pypi
tk                        8.6.13          noxft_h4845f30_101    conda-forge
tokenizers                0.15.2                   pypi_0    pypi
tomli                     2.0.1                    pypi_0    pypi
torch                     2.3.0                    pypi_0    pypi
torchaudio                2.3.0                    pypi_0    pypi
torchvision               0.18.0                   pypi_0    pypi
tornado                   6.4                      pypi_0    pypi
tqdm                      4.66.4                   pypi_0    pypi
traitlets                 5.14.3                   pypi_0    pypi
transformers              4.39.1                   pypi_0    pypi
triton                    2.3.0                    pypi_0    pypi
types-python-dateutil     2.9.0.20240316           pypi_0    pypi
typing-extensions         4.11.0                   pypi_0    pypi
tzdata                    2024.1                   pypi_0    pypi
umap-learn                0.5.6                    pypi_0    pypi
uri-template              1.3.0                    pypi_0    pypi
urllib3                   2.2.1                    pypi_0    pypi
wcwidth                   0.2.13                   pypi_0    pypi
webcolors                 1.13                     pypi_0    pypi
webencodings              0.5.1                    pypi_0    pypi
websocket-client          1.8.0                    pypi_0    pypi
wheel                     0.43.0             pyhd8ed1ab_1    conda-forge
widgetsnbextension        4.0.10                   pypi_0    pypi
xlmhg                     2.5.4                    pypi_0    pypi
xz                        5.2.6                h166bdaf_0    conda-forge
zipp                      3.18.1                   pypi_0    pypi

Thank you once again for your invaluable assistance!

Best Regards,
Chenlin