Chameleon_CoED/notebook.ipynb

{"nbformat":4,"nbformat_minor":0,"metadata":{"colab":{"provenance":[],"gpuType":"T4","authorship_tag":"ABX9TyMOvBKZooVqxDCgOWSyf49O"},"kernelspec":{"name":"python3","display_name":"Python 3"},"language_info":{"name":"python"},"accelerator":"GPU"},"cells":[{"cell_type":"code","execution_count":1,"metadata":{"colab":{"base_uri":"https://localhost:8080/"},"collapsed":true,"id":"G7iNrauQz5tm","executionInfo":{"status":"ok","timestamp":1754306504406,"user_tz":-345,"elapsed":27944,"user":{"displayName":"Santosh Upreti","userId":"01961227760879466523"}},"outputId":"d7bc9bff-2090-4389-8f57-a5a18e865e52"},"outputs":[{"output_type":"stream","name":"stdout","text":["--2025-08-04 11:21:16--  https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh\n","Resolving repo.anaconda.com (repo.anaconda.com)... 104.16.32.241, 104.16.191.158, 2606:4700::6810:20f1, ...\n","Connecting to repo.anaconda.com (repo.anaconda.com)|104.16.32.241|:443... connected.\n","HTTP request sent, awaiting response... 200 OK\n","Length: 160039710 (153M) [application/octet-stream]\n","Saving to: ‘Miniconda3-latest-Linux-x86_64.sh’\n","\n","Miniconda3-latest-L 100%[===================>] 152.62M   319MB/s    in 0.5s    \n","\n","2025-08-04 11:21:17 (319 MB/s) - ‘Miniconda3-latest-Linux-x86_64.sh’ saved [160039710/160039710]\n","\n","PREFIX=/usr/local\n","Unpacking payload ...\n","entry_point.py:256: DeprecationWarning: Python 3.14 will, by default, filter extracted tar archives and reject files or modify their metadata. Use the filter argument to control this behavior.\n","entry_point.py:256: DeprecationWarning: Python 3.14 will, by default, filter extracted tar archives and reject files or modify their metadata. Use the filter argument to control this behavior.\n","\n","Installing base environment...\n","\n","Preparing transaction: ...working... done\n","Executing transaction: ...working... done\n","entry_point.py:256: DeprecationWarning: Python 3.14 will, by default, filter extracted tar archives and reject files or modify their metadata. Use the filter argument to control this behavior.\n","installation finished.\n","WARNING:\n","    You currently have a PYTHONPATH environment variable set. This may cause\n","    unexpected behavior when running the Python interpreter in Miniconda3.\n","    For best results, please verify that your PYTHONPATH only points to\n","    directories of packages that are compatible with the Python interpreter\n","    in Miniconda3: /usr/local\n","accepted Terms of Service for \u001b[4;94mhttps://repo.anaconda.com/pkgs/main\u001b[0m\n","accepted Terms of Service for \u001b[4;94mhttps://repo.anaconda.com/pkgs/r\u001b[0m\n"]}],"source":["!wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh\n","!chmod +x Miniconda3-latest-Linux-x86_64.sh\n","!bash ./Miniconda3-latest-Linux-x86_64.sh -b -f -p /usr/local\n","\n","import sys\n","sys.path.append('/usr/local/lib/python3.9/site-packages')\n","\n","!conda tos accept --override-channels --channel https://repo.anaconda.com/pkgs/main\n","!conda tos accept --override-channels --channel https://repo.anaconda.com/pkgs/r"]},{"cell_type":"code","source":["!git clone https://github.com/hormoz-lab/coed-gnn.git\n","%cd coed-gnn"],"metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"KWIhjdXM0SJW","executionInfo":{"status":"ok","timestamp":1754306544187,"user_tz":-345,"elapsed":3619,"user":{"displayName":"Santosh Upreti","userId":"01961227760879466523"}},"outputId":"f3b03a0f-5a4f-48ed-ba92-cd906b3125a8"},"execution_count":2,"outputs":[{"output_type":"stream","name":"stdout","text":["Cloning into 'coed-gnn'...\n","remote: Enumerating objects: 202, done.\u001b[K\n","remote: Counting objects: 100% (29/29), done.\u001b[K\n","remote: Compressing objects: 100% (25/25), done.\u001b[K\n","remote: Total 202 (delta 11), reused 10 (delta 4), pack-reused 173 (from 2)\u001b[K\n","Receiving objects: 100% (202/202), 43.19 MiB | 25.71 MiB/s, done.\n","Resolving deltas: 100% (38/38), done.\n","/content/coed-gnn\n"]}]},{"cell_type":"code","source":["!conda create -n newenv python=3.11 scipy numpy"],"metadata":{"colab":{"base_uri":"https://localhost:8080/"},"collapsed":true,"id":"REc_Al4F0YvU","executionInfo":{"status":"ok","timestamp":1754306592148,"user_tz":-345,"elapsed":27281,"user":{"displayName":"Santosh Upreti","userId":"01961227760879466523"}},"outputId":"248ec269-4eaf-493f-8f6f-912aa2de006a"},"execution_count":3,"outputs":[{"output_type":"stream","name":"stdout","text":["\u001b[1;32m2\u001b[0m\u001b[1;32m channel Terms of Service accepted\u001b[0m\n","Channels:\n"," - defaults\n","Platform: linux-64\n","Collecting package metadata (repodata.json): - \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\bdone\n","Solving environment: | \b\bdone\n","\n","## Package Plan ##\n","\n","  environment location: /usr/local/envs/newenv\n","\n","  added / updated specs:\n","    - numpy\n","    - python=3.11\n","    - scipy\n","\n","\n","The following packages will be downloaded:\n","\n","    package                    |            build\n","    ---------------------------|-----------------\n","    blas-1.0                   |              mkl           6 KB\n","    intel-openmp-2023.1.0      |   hdb19cb5_46306        17.2 MB\n","    libgfortran-ng-11.2.0      |       h00389a5_1          20 KB\n","    libgfortran5-11.2.0        |       h1234567_1         2.0 MB\n","    mkl-2023.1.0               |   h213fc3f_46344       171.5 MB\n","    mkl-service-2.4.0          |  py311h5eee18b_2          69 KB\n","    mkl_fft-1.3.11             |  py311h5eee18b_0         207 KB\n","    mkl_random-1.2.8           |  py311ha02d727_0         328 KB\n","    ncurses-6.5                |       h7934f7d_0         1.1 MB\n","    numpy-2.3.1                |  py311h2470af2_0          11 KB\n","    numpy-base-2.3.1           |  py311h06ae042_0         9.2 MB\n","    openssl-3.0.17             |       h5eee18b_0         5.2 MB\n","    python-3.11.13             |       h1a3bd86_0        32.6 MB\n","    scipy-1.16.0               |  py311h0cc6016_0        25.0 MB\n","    setuptools-72.1.0          |  py311h06a4308_0         3.0 MB\n","    tbb-2021.8.0               |       hdb19cb5_0         1.6 MB\n","    wheel-0.45.1               |  py311h06a4308_0         151 KB\n","    ------------------------------------------------------------\n","                                           Total:       269.3 MB\n","\n","The following NEW packages will be INSTALLED:\n","\n","  _libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main \n","  _openmp_mutex      pkgs/main/linux-64::_openmp_mutex-5.1-1_gnu \n","  blas               pkgs/main/linux-64::blas-1.0-mkl \n","  bzip2              pkgs/main/linux-64::bzip2-1.0.8-h5eee18b_6 \n","  ca-certificates    pkgs/main/linux-64::ca-certificates-2025.2.25-h06a4308_0 \n","  expat              pkgs/main/linux-64::expat-2.7.1-h6a678d5_0 \n","  intel-openmp       pkgs/main/linux-64::intel-openmp-2023.1.0-hdb19cb5_46306 \n","  ld_impl_linux-64   pkgs/main/linux-64::ld_impl_linux-64-2.40-h12ee557_0 \n","  libffi             pkgs/main/linux-64::libffi-3.4.4-h6a678d5_1 \n","  libgcc-ng          pkgs/main/linux-64::libgcc-ng-11.2.0-h1234567_1 \n","  libgfortran-ng     pkgs/main/linux-64::libgfortran-ng-11.2.0-h00389a5_1 \n","  libgfortran5       pkgs/main/linux-64::libgfortran5-11.2.0-h1234567_1 \n","  libgomp            pkgs/main/linux-64::libgomp-11.2.0-h1234567_1 \n","  libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-11.2.0-h1234567_1 \n","  libuuid            pkgs/main/linux-64::libuuid-1.41.5-h5eee18b_0 \n","  libxcb             pkgs/main/linux-64::libxcb-1.17.0-h9b100fa_0 \n","  mkl                pkgs/main/linux-64::mkl-2023.1.0-h213fc3f_46344 \n","  mkl-service        pkgs/main/linux-64::mkl-service-2.4.0-py311h5eee18b_2 \n","  mkl_fft            pkgs/main/linux-64::mkl_fft-1.3.11-py311h5eee18b_0 \n","  mkl_random         pkgs/main/linux-64::mkl_random-1.2.8-py311ha02d727_0 \n","  ncurses            pkgs/main/linux-64::ncurses-6.5-h7934f7d_0 \n","  numpy              pkgs/main/linux-64::numpy-2.3.1-py311h2470af2_0 \n","  numpy-base         pkgs/main/linux-64::numpy-base-2.3.1-py311h06ae042_0 \n","  openssl            pkgs/main/linux-64::openssl-3.0.17-h5eee18b_0 \n","  pip                pkgs/main/noarch::pip-25.1-pyhc872135_2 \n","  pthread-stubs      pkgs/main/linux-64::pthread-stubs-0.3-h0ce48e5_1 \n","  python             pkgs/main/linux-64::python-3.11.13-h1a3bd86_0 \n","  readline           pkgs/main/linux-64::readline-8.2-h5eee18b_0 \n","  scipy              pkgs/main/linux-64::scipy-1.16.0-py311h0cc6016_0 \n","  setuptools         pkgs/main/linux-64::setuptools-72.1.0-py311h06a4308_0 \n","  sqlite             pkgs/main/linux-64::sqlite-3.50.2-hb25bd0a_1 \n","  tbb                pkgs/main/linux-64::tbb-2021.8.0-hdb19cb5_0 \n","  tk                 pkgs/main/linux-64::tk-8.6.14-h993c535_1 \n","  tzdata             pkgs/main/noarch::tzdata-2025b-h04d1e81_0 \n","  wheel              pkgs/main/linux-64::wheel-0.45.1-py311h06a4308_0 \n","  xorg-libx11        pkgs/main/linux-64::xorg-libx11-1.8.12-h9b100fa_1 \n","  xorg-libxau        pkgs/main/linux-64::xorg-libxau-1.0.12-h9b100fa_0 \n","  xorg-libxdmcp      pkgs/main/linux-64::xorg-libxdmcp-1.1.5-h9b100fa_0 \n","  xorg-xorgproto     pkgs/main/linux-64::xorg-xorgproto-2024.1-h5eee18b_1 \n","  xz                 pkgs/main/linux-64::xz-5.6.4-h5eee18b_1 \n","  zlib               pkgs/main/linux-64::zlib-1.2.13-h5eee18b_1 \n","\n","\n","Proceed ([y]/n)? y\n","\n","\n","Downloading and Extracting Packages:\n","mkl-2023.1.0         | 171.5 MB  | :   0% 0/1 [00:00<?, ?it/s]\n","python-3.11.13       | 32.6 MB   | :   0% 0/1 [00:00<?, ?it/s]\u001b[A\n","\n","scipy-1.16.0         | 25.0 MB   | :   0% 0/1 [00:00<?, ?it/s]\u001b[A\u001b[A\n","\n","\n","intel-openmp-2023.1. | 17.2 MB   | :   0% 0/1 [00:00<?, ?it/s]\u001b[A\u001b[A\u001b[A\n","\n","\n","\n","numpy-base-2.3.1     | 9.2 MB    | :   0% 0/1 [00:00<?, ?it/s]\u001b[A\u001b[A\u001b[A\u001b[A\n","\n","\n","\n","\n","openssl-3.0.17       | 5.2 MB    | :   0% 0/1 [00:00<?, ?it/s]\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n","\n","\n","\n","\n","\n","setuptools-72.1.0    | 3.0 MB    | :   0% 0/1 [00:00<?, ?it/s]\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n","\n","\n","\n","\n","\n","\n","libgfortran5-11.2.0  | 2.0 MB    | :   0% 0/1 [00:00<?, ?it/s]\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n","\n","\n","\n","\n","\n","\n","\n","tbb-2021.8.0         | 1.6 MB    | :   0% 0/1 [00:00<?, ?it/s]\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n","\n","\n","\n","\n","\n","\n","\n","\n","ncurses-6.5          | 1.1 MB    | :   0% 0/1 [00:00<?, ?it/s]\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n","\n","\n","\n","\n","\n","\n","\n","\n","\n","mkl_random-1.2.8     | 328 KB    | :   0% 0/1 [00:00<?, ?it/s]\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n","\n","\n","\n","\n","\n","\n","\n","\n","\n","\n","mkl_fft-1.3.11       | 207 KB    | :   0% 0/1 [00:00<?, ?it/s]\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n","\n","\n","\n","\n","\n","\n","\n","\n","\n","\n","\n","wheel-0.45.1         | 151 KB    | :   0% 0/1 [00:00<?, ?it/s]\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n","\n","\n","\n","\n","\n","\n","\n","\n","\n","\n","\n","\n","mkl-service-2.4.0    | 69 KB     | :   0% 0/1 [00:00<?, ?it/s]\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n","\n","\n","\n","\n","\n","\n","\n","\n","\n","\n","\n","\n","\n","libgfortran-ng-11.2. | 20 KB     | :   0% 0/1 [00:00<?, ?it/s]\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n","\n","\n","\n","\n","\n","\n","\n","\n","\n","\n","\n","\n","\n","\n","numpy-2.3.1          | 11 KB     | :   0% 0/1 [00:00<?, ?it/s]\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n","\n","\n","\n","\n","\n","\n","\n","\n","\n","\n","\n","\n","\n","\n","\n","mkl-2023.1.0         | 171.5 MB  | :   1% 0.007104816987772907/1 [00:00<00:14, 14.11s/it]\n","python-3.11.13       | 32.6 MB   | :   4% 0.041177877657027434/1 [00:00<00:02,  2.43s/it]\u001b[A\n","\n","scipy-1.16.0         | 25.0 MB   | :   5% 0.054895976915081794/1 [00:00<00:01,  1.83s/it]\u001b[A\u001b[A\n","\n","\n","intel-openmp-2023.1. | 17.2 MB   | :   5% 0.04820923921959562/1 [00:00<00:01,  2.08s/it]\u001b[A\u001b[A\u001b[A\n","\n","\n","\n","mkl-2023.1.0         | 171.5 MB  | :   2% 0.024866859457205175/1 [00:00<00:07,  7.51s/it]\n","python-3.11.13       | 32.6 MB   | :  16% 0.1565716976028834/1 [00:00<00:00,  1.18s/it]  \u001b[A\n","\n","scipy-1.16.0         | 25.0 MB   | :  20% 0.19650264463921324/1 [00:00<00:00,  1.06it/s] \u001b[A\u001b[A\n","\n","\n","intel-openmp-2023.1. | 17.2 MB   | :  31% 0.305628384486493/1 [00:00<00:00,  1.71it/s]  \u001b[A\u001b[A\u001b[A\n","\n","\n","\n","mkl-2023.1.0         | 171.5 MB  | :   4% 0.04335760110487056/1 [00:00<00:06,  6.39s/it] \n","python-3.11.13       | 32.6 MB   | :  26% 0.260952829338139/1 [00:00<00:00,  1.07s/it] \u001b[A\n","\n","scipy-1.16.0         | 25.0 MB   | :  39% 0.38614329216404125/1 [00:00<00:00,  1.44it/s]\u001b[A\u001b[A\n","\n","\n","intel-openmp-2023.1. | 17.2 MB   | :  61% 0.611256768972986/1 [00:00<00:00,  2.32it/s]\u001b[A\u001b[A\u001b[A\n","mkl-2023.1.0         | 171.5 MB  | :   7% 0.0706838202886125/1 [00:00<00:04,  4.96s/it] \n","\n","scipy-1.16.0         | 25.0 MB   | :  59% 0.5882602980786606/1 [00:00<00:00,  1.67it/s] \u001b[A\u001b[A\n","\n","\n","intel-openmp-2023.1. | 17.2 MB   | :  87% 0.8732239556756942/1 [00:00<00:00,  2.44it/s]\u001b[A\u001b[A\u001b[A\n","\n","\n","\n","numpy-base-2.3.1     | 9.2 MB    | : 100% 1.0/1 [00:00<00:00,  2.28it/s]               \u001b[A\u001b[A\u001b[A\u001b[A\n","\n","\n","\n","numpy-base-2.3.1     | 9.2 MB    | : 100% 1.0/1 [00:00<00:00,  2.28it/s]\u001b[A\u001b[A\u001b[A\u001b[A\n","\n","\n","\n","\n","mkl-2023.1.0         | 171.5 MB  | :   9% 0.0908141350873024/1 [00:00<00:04,  4.97s/it]\n","python-3.11.13       | 32.6 MB   | :  61% 0.6119224144846636/1 [00:00<00:00,  1.41it/s]\u001b[A\n","\n","scipy-1.16.0         | 25.0 MB   | :  75% 0.7548196825823746/1 [00:00<00:00,  1.63it/s]\u001b[A\u001b[A\n","\n","\n","\n","\n","mkl-2023.1.0         | 171.5 MB  | :  11% 0.1111266246805506/1 [00:00<00:04,  4.95s/it]\n","\n","scipy-1.16.0         | 25.0 MB   | :  93% 0.9326077896369009/1 [00:00<00:00,  1.67it/s]\u001b[A\u001b[A\n","python-3.11.13       | 32.6 MB   | :  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mpmath-1.3.0 networkx-3.3 nvidia-cublas-cu12-12.1.3.1 nvidia-cuda-cupti-cu12-12.1.105 nvidia-cuda-nvrtc-cu12-12.1.105 nvidia-cuda-runtime-cu12-12.1.105 nvidia-cudnn-cu12-8.9.2.26 nvidia-cufft-cu12-11.0.2.54 nvidia-curand-cu12-10.3.2.106 nvidia-cusolver-cu12-11.4.5.107 nvidia-cusparse-cu12-12.1.0.106 nvidia-nccl-cu12-2.19.3 nvidia-nvjitlink-cu12-12.1.105 nvidia-nvtx-cu12-12.1.105 pillow-11.0.0 sympy-1.13.3 torch-2.2.2+cu121 torchaudio-2.2.2+cu121 torchvision-0.17.2+cu121 triton-2.2.0 typing-extensions-4.12.2\n"]}]},{"cell_type":"code","source":["!source /usr/local/bin/activate newenv && pip install torch_geometric"],"metadata":{"colab":{"base_uri":"https://localhost:8080/"},"collapsed":true,"id":"suncvLl81uaz","executionInfo":{"status":"ok","timestamp":1754306927878,"user_tz":-345,"elapsed":10546,"user":{"displayName":"Santosh Upreti","userId":"01961227760879466523"}},"outputId":"c1936dff-12e7-4af2-f3a0-2b859c1d3150"},"execution_count":5,"outputs":[{"output_type":"stream","name":"stdout","text":["Collecting torch_geometric\n","  Downloading torch_geometric-2.6.1-py3-none-any.whl.metadata (63 kB)\n","Collecting aiohttp (from torch_geometric)\n","  Downloading aiohttp-3.12.15-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (7.7 kB)\n","Requirement already satisfied: fsspec in /usr/local/envs/newenv/lib/python3.11/site-packages (from torch_geometric) (2024.6.1)\n","Requirement already satisfied: jinja2 in /usr/local/envs/newenv/lib/python3.11/site-packages (from torch_geometric) (3.1.4)\n","Requirement already satisfied: numpy in /usr/local/envs/newenv/lib/python3.11/site-packages (from torch_geometric) (2.3.1)\n","Collecting psutil>=5.8.0 (from torch_geometric)\n","  Downloading 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tqdm-4.67.1 urllib3-2.5.0 yarl-1.20.1\n"]}]},{"cell_type":"code","source":["!source /usr/local/bin/activate newenv && pip install pyg_lib torch_scatter torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-2.2.2+cu121.html\n"],"metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"a8nRJhW213Fz","executionInfo":{"status":"ok","timestamp":1754306948666,"user_tz":-345,"elapsed":3840,"user":{"displayName":"Santosh Upreti","userId":"01961227760879466523"}},"outputId":"f74477a1-7a49-4a6e-d797-0264d4caaddb"},"execution_count":6,"outputs":[{"output_type":"stream","name":"stdout","text":["Looking in links: https://data.pyg.org/whl/torch-2.2.2+cu121.html\n","Collecting pyg_lib\n","  Downloading https://data.pyg.org/whl/torch-2.2.0%2Bcu121/pyg_lib-0.4.0%2Bpt22cu121-cp311-cp311-linux_x86_64.whl (2.5 MB)\n","\u001b[2K     \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m2.5/2.5 MB\u001b[0m \u001b[31m31.2 MB/s\u001b[0m eta 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Upreti","userId":"01961227760879466523"}},"outputId":"1aa4192c-9210-4420-dfbe-7187cac2ab3f"},"execution_count":16,"outputs":[{"output_type":"stream","name":"stdout","text":["Requirement already satisfied: PyYAML in /usr/local/envs/newenv/lib/python3.11/site-packages (6.0.2)\n","Requirement already satisfied: jax in /usr/local/envs/newenv/lib/python3.11/site-packages (0.7.0)\n","Requirement already satisfied: jaxlib in /usr/local/envs/newenv/lib/python3.11/site-packages (0.7.0)\n","Requirement already satisfied: numpy in /usr/local/envs/newenv/lib/python3.11/site-packages (2.3.1)\n","Requirement already satisfied: ml_dtypes>=0.5.0 in /usr/local/envs/newenv/lib/python3.11/site-packages (from jax) (0.5.3)\n","Requirement already satisfied: opt_einsum in /usr/local/envs/newenv/lib/python3.11/site-packages (from jax) (3.4.0)\n","Requirement already satisfied: scipy>=1.12 in /usr/local/envs/newenv/lib/python3.11/site-packages (from jax) (1.16.0)\n"]}]},{"cell_type":"code","source":["!source /usr/local/bin/activate newenv && pip uninstall numpy --yes\n","!source /usr/local/bin/activate newenv && pip install numpy<2"],"metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"-oASIPhe3qDN","executionInfo":{"status":"ok","timestamp":1754307468740,"user_tz":-345,"elapsed":1717,"user":{"displayName":"Santosh Upreti","userId":"01961227760879466523"}},"outputId":"78835eb2-cd81-4f5b-fd13-f3fe127a1bde"},"execution_count":19,"outputs":[{"output_type":"stream","name":"stdout","text":["Found existing installation: numpy 2.3.1\n","Uninstalling numpy-2.3.1:\n","  Successfully uninstalled numpy-2.3.1\n","/bin/bash: line 1: 2: No such file or directory\n"]}]},{"cell_type":"code","source":["!bash -c \"source /usr/local/bin/activate newenv && pip uninstall numpy -y && pip install 'numpy<2'\""],"metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"9OIcbxXo4As8","executionInfo":{"status":"ok","timestamp":1754307579890,"user_tz":-345,"elapsed":5421,"user":{"displayName":"Santosh Upreti","userId":"01961227760879466523"}},"outputId":"ba7147d6-abe9-4b06-a28d-4d1a238585ed"},"execution_count":22,"outputs":[{"output_type":"stream","name":"stdout","text":["\u001b[33mWARNING: Skipping numpy as it is not installed.\u001b[0m\u001b[33m\n","\u001b[0mCollecting numpy<2\n","  Downloading numpy-1.26.4-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (61 kB)\n","Downloading numpy-1.26.4-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (18.3 MB)\n","\u001b[2K   \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m18.3/18.3 MB\u001b[0m \u001b[31m35.7 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n","\u001b[?25hInstalling collected packages: numpy\n","Successfully installed numpy-1.26.4\n"]}]},{"cell_type":"code","source":["!source /usr/local/bin/activate newenv && python classification.py \\\n","    --dataset chameleon \\\n","    --dataset-directory ./data \\\n","    --model GCN \\\n","    --hidden-dimension 128 \\\n","    --num-layers 2 \\\n","    --dropout-rate 0.5 \\\n","    --learning-rate 0.01 \\\n","    --weight-decay 5e-4 \\\n","    --patience 100 \\\n","    --normalize \\\n","    --self-loop \\\n","    --gpu-idx 0"],"metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"XnBBl3Gp2RZN","executionInfo":{"status":"ok","timestamp":1754307710575,"user_tz":-345,"elapsed":128375,"user":{"displayName":"Santosh Upreti","userId":"01961227760879466523"}},"outputId":"2e7d287e-5fde-441d-df5d-325344e6f660"},"execution_count":23,"outputs":[{"output_type":"stream","name":"stdout","text":["index: 0 | Epoch: 050, Loss: 0.18343, Train: 0.95055, Val: 0.58985, Best: 0.6118, early_stopping: 41\n","index: 0 | Epoch: 100, Loss: 0.24476, Train: 0.93315, Val: 0.60357, Best: 0.6118, early_stopping: 91\n","index: 1 | Epoch: 050, Loss: 0.20863, Train: 0.92125, Val: 0.53909, Best: 0.6162, early_stopping: 42\n","index: 1 | Epoch: 100, Loss: 0.19254, Train: 0.93681, Val: 0.55007, Best: 0.6162, early_stopping: 92\n","index: 2 | Epoch: 050, Loss: 0.17640, Train: 0.95055, Val: 0.57613, Best: 0.5592, early_stopping: 39\n","index: 2 | Epoch: 100, Loss: 0.16595, Train: 0.95879, Val: 0.58162, Best: 0.5592, early_stopping: 89\n","index: 2 | Epoch: 150, Loss: 0.15965, Train: 0.95879, Val: 0.59259, Best: 0.5636, early_stopping: 18\n","index: 2 | Epoch: 200, Loss: 0.16358, Train: 0.92766, Val: 0.59808, Best: 0.5877, early_stopping: 11\n","index: 2 | Epoch: 250, Loss: 0.14793, Train: 0.92857, Val: 0.60905, Best: 0.5877, early_stopping: 61\n","index: 2 | Epoch: 300, Loss: 0.17109, Train: 0.96062, Val: 0.63237, Best: 0.5899, early_stopping: 29\n","index: 2 | Epoch: 350, Loss: 0.14975, Train: 0.91667, Val: 0.61454, Best: 0.5899, early_stopping: 79\n","index: 3 | Epoch: 050, Loss: 0.19507, Train: 0.94689, Val: 0.59671, Best: 0.6009, early_stopping: 39\n","index: 3 | Epoch: 100, Loss: 0.19419, Train: 0.94872, Val: 0.61454, Best: 0.6009, early_stopping: 89\n","index: 3 | Epoch: 150, Loss: 0.16036, Train: 0.93590, Val: 0.61043, Best: 0.5855, early_stopping: 34\n","index: 3 | Epoch: 200, Loss: 0.16628, Train: 0.94597, Val: 0.61180, Best: 0.6206, early_stopping: 19\n","index: 3 | Epoch: 250, Loss: 0.16335, Train: 0.93407, Val: 0.62826, Best: 0.6096, early_stopping: 24\n","index: 3 | Epoch: 300, Loss: 0.15540, Train: 0.94780, Val: 0.62826, Best: 0.6206, early_stopping: 2\n","index: 3 | Epoch: 350, Loss: 0.16083, Train: 0.96795, Val: 0.65295, Best: 0.625, early_stopping: 0\n","index: 3 | Epoch: 400, Loss: 0.18060, Train: 0.95421, Val: 0.63237, Best: 0.6228, early_stopping: 46\n","index: 3 | Epoch: 450, Loss: 0.18801, Train: 0.95330, Val: 0.65021, Best: 0.6228, early_stopping: 19\n","index: 3 | Epoch: 500, Loss: 0.21619, Train: 0.92766, Val: 0.62963, Best: 0.6228, early_stopping: 69\n","index: 4 | Epoch: 050, Loss: 0.19132, Train: 0.93407, Val: 0.56927, Best: 0.5877, early_stopping: 32\n","index: 4 | Epoch: 100, Loss: 0.16184, Train: 0.95604, Val: 0.56241, Best: 0.5877, early_stopping: 82\n","index: 5 | Epoch: 050, Loss: 0.24247, Train: 0.92766, Val: 0.55830, Best: 0.6184, early_stopping: 41\n","index: 5 | Epoch: 100, Loss: 0.18442, Train: 0.92857, Val: 0.57888, Best: 0.6184, early_stopping: 91\n","index: 6 | Epoch: 050, Loss: 0.21708, Train: 0.93956, Val: 0.56790, Best: 0.5592, early_stopping: 38\n","index: 6 | Epoch: 100, Loss: 0.18676, Train: 0.89103, Val: 0.56241, Best: 0.5592, early_stopping: 88\n","index: 7 | Epoch: 050, Loss: 0.18292, Train: 0.94231, Val: 0.55693, Best: 0.5899, early_stopping: 42\n","index: 7 | Epoch: 100, Loss: 0.16064, Train: 0.92033, Val: 0.57064, Best: 0.5899, early_stopping: 92\n","index: 8 | Epoch: 050, Loss: 0.19932, Train: 0.94597, Val: 0.57339, Best: 0.5987, early_stopping: 39\n","index: 8 | Epoch: 100, Loss: 0.17601, Train: 0.94322, Val: 0.57202, Best: 0.5987, early_stopping: 89\n","index: 9 | Epoch: 050, Loss: 0.19550, Train: 0.94231, Val: 0.55556, Best: 0.6228, early_stopping: 39\n","index: 9 | Epoch: 100, Loss: 0.16515, Train: 0.95513, Val: 0.56516, Best: 0.6228, early_stopping: 89\n","test acc: 60.17544 +/- 1.94224\n"]}]}]}