PDBbind_BAPULM/notebook.ipynb

{"nbformat":4,"nbformat_minor":0,"metadata":{"colab":{"provenance":[],"gpuType":"T4","authorship_tag":"ABX9TyP4lmgEmkwZhdZ2dDp75+pP"},"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/"},"id":"Pb27VJZh53WK","executionInfo":{"status":"ok","timestamp":1754274484649,"user_tz":-345,"elapsed":25815,"user":{"displayName":"Santosh Upreti","userId":"15542637101614503540"}},"outputId":"69a44f8d-d1a5-40ef-9ff5-2e5a02074533"},"outputs":[{"output_type":"stream","name":"stdout","text":["--2025-08-04 02:27:39--  https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh\n","Resolving repo.anaconda.com (repo.anaconda.com)... 104.16.191.158, 104.16.32.241, 2606:4700::6810:bf9e, ...\n","Connecting to repo.anaconda.com (repo.anaconda.com)|104.16.191.158|: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  60.2MB/s    in 2.5s    \n","\n","2025-08-04 02:27:42 (60.2 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/radh55sh/BAPULM.git\n","%cd BAPULM"],"metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"K7ueg7176AZz","executionInfo":{"status":"ok","timestamp":1754274490796,"user_tz":-345,"elapsed":822,"user":{"displayName":"Santosh Upreti","userId":"15542637101614503540"}},"outputId":"3d8828a1-0009-47f7-8f82-1094d7ad6a20"},"execution_count":2,"outputs":[{"output_type":"stream","name":"stdout","text":["Cloning into 'BAPULM'...\n","remote: Enumerating objects: 58, done.\u001b[K\n","remote: Counting objects: 100% (58/58), done.\u001b[K\n","remote: Compressing objects: 100% (57/57), done.\u001b[K\n","remote: Total 58 (delta 25), reused 17 (delta 0), pack-reused 0 (from 0)\u001b[K\n","Receiving objects: 100% (58/58), 248.53 KiB | 3.55 MiB/s, done.\n","Resolving deltas: 100% (25/25), done.\n","/content/BAPULM\n"]}]},{"cell_type":"code","source":["!conda create -n newenv python=3.10"],"metadata":{"colab":{"base_uri":"https://localhost:8080/"},"collapsed":true,"id":"zg8tP83o6HQ1","executionInfo":{"status":"ok","timestamp":1754274548863,"user_tz":-345,"elapsed":27206,"user":{"displayName":"Santosh Upreti","userId":"15542637101614503540"}},"outputId":"33e174c6-74d4-4f22-9042-14e37792d510"},"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","    - python=3.10\n","\n","\n","The following packages will be downloaded:\n","\n","    package                    |            build\n","    ---------------------------|-----------------\n","    ncurses-6.5                |       h7934f7d_0         1.1 MB\n","    openssl-3.0.17             |       h5eee18b_0         5.2 MB\n","    python-3.10.18             |       h1a3bd86_0        26.5 MB\n","    setuptools-78.1.1          |  py310h06a4308_0         1.7 MB\n","    wheel-0.45.1               |  py310h06a4308_0         115 KB\n","    ------------------------------------------------------------\n","                                           Total:        34.7 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","  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","  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","  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","  ncurses            pkgs/main/linux-64::ncurses-6.5-h7934f7d_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-3.10.18-h1a3bd86_0 \n","  readline           pkgs/main/linux-64::readline-8.2-h5eee18b_0 \n","  setuptools         pkgs/main/linux-64::setuptools-78.1.1-py310h06a4308_0 \n","  sqlite             pkgs/main/linux-64::sqlite-3.50.2-hb25bd0a_1 \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-py310h06a4308_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","python-3.10.18       | 26.5 MB   | :   0% 0/1 [00:00<?, ?it/s]\n","openssl-3.0.17       | 5.2 MB    | :   0% 0/1 [00:00<?, ?it/s]\u001b[A\n","\n","setuptools-78.1.1    | 1.7 MB    | :   0% 0/1 [00:00<?, ?it/s]\u001b[A\u001b[A\n","\n","\n","ncurses-6.5          | 1.1 MB    | :   0% 0/1 [00:00<?, ?it/s]\u001b[A\u001b[A\u001b[A\n","\n","\n","\n","wheel-0.45.1         | 115 KB    | :   0% 0/1 [00:00<?, ?it/s]\u001b[A\u001b[A\u001b[A\u001b[A\n","\n","\n","\n","python-3.10.18       | 26.5 MB   | :   2% 0.021777623366973725/1 [00:00<00:04,  4.61s/it]\n","openssl-3.0.17       | 5.2 MB    | :   9% 0.09293115811364591/1 [00:00<00:00,  1.08s/it]\u001b[A\n","\n","setuptools-78.1.1    | 1.7 MB    | :  29% 0.2943653818836784/1 [00:00<00:00,  2.94it/s]\u001b[A\u001b[A\n","\n","\n","ncurses-6.5          | 1.1 MB    | :  95% 0.9505092528701785/1 [00:00<00:00,  9.43it/s]\u001b[A\u001b[A\u001b[A\n","\n","\n","ncurses-6.5          | 1.1 MB    | : 100% 1.0/1 [00:00<00:00,  9.43it/s]               \u001b[A\u001b[A\u001b[A\n","\n","python-3.10.18       | 26.5 MB   | :  21% 0.2148333115931192/1 [00:00<00:00,  1.22it/s]  \n","openssl-3.0.17       | 5.2 MB    | :  88% 0.8753515538446648/1 [00:00<00:00,  4.97it/s] \u001b[A\n","\n","\n","\n","wheel-0.45.1         | 115 KB    | : 100% 1.0/1 [00:00<00:00,  4.42it/s]\u001b[A\u001b[A\u001b[A\u001b[A\n","\n","\n","\n","python-3.10.18       | 26.5 MB   | :  44% 0.44496981798465235/1 [00:00<00:00,  1.71it/s]\n","python-3.10.18       | 26.5 MB   | : 100% 1.0/1 [00:00<00:00,  2.04it/s]               \n","\n","setuptools-78.1.1    | 1.7 MB    | : 100% 1.0/1 [00:01<00:00,  1.13s/it]\u001b[A\u001b[A\n","\n","setuptools-78.1.1    | 1.7 MB    | : 100% 1.0/1 [00:01<00:00,  1.13s/it]\u001b[A\u001b[A\n","openssl-3.0.17       | 5.2 MB    | : 100% 1.0/1 [00:01<00:00,  4.97it/s]\u001b[A\n","\n","\n","                                                                        \n","                                                                        \u001b[A\n","\n","                                                                        \u001b[A\u001b[A\n","\n","\n","                                                                        \u001b[A\u001b[A\u001b[A\n","\n","\n","\n","                                                                        \u001b[A\u001b[A\u001b[A\u001b[A\n","Preparing transaction: - \b\b\\ \b\bdone\n","Verifying transaction: / \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\b- \b\b\\ \b\b| \b\bdone\n","Executing transaction: - \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\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\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\bdone\n","#\n","# To activate this environment, use\n","#\n","#     $ conda activate newenv\n","#\n","# To deactivate an active environment, use\n","#\n","#     $ conda deactivate\n","\n"]}]},{"cell_type":"code","source":["!source /usr/local/bin/activate newenv && pip install -r requirements.txt"],"metadata":{"colab":{"base_uri":"https://localhost:8080/"},"collapsed":true,"id":"sW6ddRy46XmW","executionInfo":{"status":"ok","timestamp":1754274777583,"user_tz":-345,"elapsed":195047,"user":{"displayName":"Santosh Upreti","userId":"15542637101614503540"}},"outputId":"239bb17f-ca56-45cd-bf11-0beb60fca691"},"execution_count":4,"outputs":[{"output_type":"stream","name":"stdout","text":["Collecting torch (from -r requirements.txt (line 1))\n","  Downloading torch-2.7.1-cp310-cp310-manylinux_2_28_x86_64.whl.metadata (29 kB)\n","Collecting tqdm (from -r requirements.txt (line 2))\n","  Downloading tqdm-4.67.1-py3-none-any.whl.metadata (57 kB)\n","Collecting transformers==4.41.0 (from -r requirements.txt (line 3))\n","  Downloading transformers-4.41.0-py3-none-any.whl.metadata (43 kB)\n","Collecting datasets (from -r requirements.txt (line 4))\n","  Downloading datasets-4.0.0-py3-none-any.whl.metadata (19 kB)\n","Collecting numpy==1.24.0 (from -r requirements.txt (line 5))\n","  Downloading numpy-1.24.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.6 kB)\n","Collecting scikit-learn==1.4.2 (from -r requirements.txt (line 6))\n","  Downloading scikit_learn-1.4.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (11 kB)\n","Collecting scipy==1.13.0 (from -r requirements.txt (line 7))\n","  Downloading scipy-1.13.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB)\n","Collecting pandas==1.5.3 (from -r requirements.txt (line 8))\n","  Downloading pandas-1.5.3-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (11 kB)\n","Collecting pyyaml==6.0.1 (from -r requirements.txt (line 9))\n","  Downloading PyYAML-6.0.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB)\n","Collecting filelock (from transformers==4.41.0->-r requirements.txt (line 3))\n","  Downloading filelock-3.18.0-py3-none-any.whl.metadata (2.9 kB)\n","Collecting huggingface-hub<1.0,>=0.23.0 (from transformers==4.41.0->-r requirements.txt (line 3))\n","  Downloading huggingface_hub-0.34.3-py3-none-any.whl.metadata (14 kB)\n","Collecting packaging>=20.0 (from transformers==4.41.0->-r requirements.txt (line 3))\n","  Downloading packaging-25.0-py3-none-any.whl.metadata (3.3 kB)\n","Collecting regex!=2019.12.17 (from transformers==4.41.0->-r requirements.txt (line 3))\n","  Downloading regex-2025.7.34-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (40 kB)\n","Collecting requests (from transformers==4.41.0->-r requirements.txt (line 3))\n","  Downloading requests-2.32.4-py3-none-any.whl.metadata (4.9 kB)\n","Collecting tokenizers<0.20,>=0.19 (from transformers==4.41.0->-r requirements.txt (line 3))\n","  Downloading tokenizers-0.19.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.7 kB)\n","Collecting safetensors>=0.4.1 (from transformers==4.41.0->-r requirements.txt (line 3))\n","  Downloading safetensors-0.5.3-cp38-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.8 kB)\n","Collecting joblib>=1.2.0 (from scikit-learn==1.4.2->-r requirements.txt (line 6))\n","  Downloading joblib-1.5.1-py3-none-any.whl.metadata (5.6 kB)\n","Collecting threadpoolctl>=2.0.0 (from scikit-learn==1.4.2->-r requirements.txt (line 6))\n","  Downloading threadpoolctl-3.6.0-py3-none-any.whl.metadata (13 kB)\n","Collecting python-dateutil>=2.8.1 (from pandas==1.5.3->-r requirements.txt (line 8))\n","  Downloading python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)\n","Collecting pytz>=2020.1 (from pandas==1.5.3->-r requirements.txt (line 8))\n","  Downloading pytz-2025.2-py2.py3-none-any.whl.metadata (22 kB)\n","Collecting fsspec>=2023.5.0 (from huggingface-hub<1.0,>=0.23.0->transformers==4.41.0->-r requirements.txt (line 3))\n","  Downloading fsspec-2025.7.0-py3-none-any.whl.metadata (12 kB)\n","Collecting typing-extensions>=3.7.4.3 (from huggingface-hub<1.0,>=0.23.0->transformers==4.41.0->-r requirements.txt (line 3))\n","  Downloading typing_extensions-4.14.1-py3-none-any.whl.metadata (3.0 kB)\n","Collecting hf-xet<2.0.0,>=1.1.3 (from huggingface-hub<1.0,>=0.23.0->transformers==4.41.0->-r requirements.txt (line 3))\n","  Downloading hf_xet-1.1.5-cp37-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (879 bytes)\n","Collecting sympy>=1.13.3 (from torch->-r requirements.txt (line 1))\n","  Downloading sympy-1.14.0-py3-none-any.whl.metadata (12 kB)\n","Collecting networkx (from torch->-r requirements.txt (line 1))\n","  Downloading networkx-3.4.2-py3-none-any.whl.metadata (6.3 kB)\n","Collecting jinja2 (from torch->-r requirements.txt (line 1))\n","  Downloading jinja2-3.1.6-py3-none-any.whl.metadata (2.9 kB)\n","Collecting nvidia-cuda-nvrtc-cu12==12.6.77 (from torch->-r requirements.txt (line 1))\n","  Downloading nvidia_cuda_nvrtc_cu12-12.6.77-py3-none-manylinux2014_x86_64.whl.metadata (1.5 kB)\n","Collecting nvidia-cuda-runtime-cu12==12.6.77 (from torch->-r requirements.txt (line 1))\n","  Downloading nvidia_cuda_runtime_cu12-12.6.77-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (1.5 kB)\n","Collecting nvidia-cuda-cupti-cu12==12.6.80 (from torch->-r requirements.txt (line 1))\n","  Downloading nvidia_cuda_cupti_cu12-12.6.80-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (1.6 kB)\n","Collecting nvidia-cudnn-cu12==9.5.1.17 (from torch->-r requirements.txt (line 1))\n","  Downloading nvidia_cudnn_cu12-9.5.1.17-py3-none-manylinux_2_28_x86_64.whl.metadata (1.6 kB)\n","Collecting nvidia-cublas-cu12==12.6.4.1 (from torch->-r requirements.txt (line 1))\n","  Downloading nvidia_cublas_cu12-12.6.4.1-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (1.5 kB)\n","Collecting nvidia-cufft-cu12==11.3.0.4 (from torch->-r requirements.txt (line 1))\n","  Downloading 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Upreti","userId":"15542637101614503540"}},"outputId":"1e1b4a99-f315-442d-b783-ac334c2c723f"},"execution_count":8,"outputs":[{"output_type":"stream","name":"stdout","text":["/content/BAPULM\n"]}]},{"cell_type":"code","source":["!source /usr/local/bin/activate newenv && python main.py"],"metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"KMawYgO89Xoh","executionInfo":{"status":"ok","timestamp":1754275809405,"user_tz":-345,"elapsed":251221,"user":{"displayName":"Santosh Upreti","userId":"15542637101614503540"}},"outputId":"fd42e4a5-3365-4699-d618-7e6fba7c66f5"},"execution_count":10,"outputs":[{"output_type":"stream","name":"stdout","text":["Total dataset size: 100000\n","Training data size: 90000\n","Validation data size: 10000\n","Epoch 1/60: 100% 352/352 [00:16<00:00, 20.76batch/s, loss=0.582]\n","Epoch 1, Train Loss: 0.5822758409617976, Validation Loss: 0.47898316457867623\n","Epoch 2/60: 100% 352/352 [00:18<00:00, 19.00batch/s, loss=0.463]\n","Epoch 2, Train Loss: 0.4632116887210445, Validation Loss: 0.4488185353577137\n","Epoch 3/60: 100% 352/352 [00:16<00:00, 21.92batch/s, loss=0.413]\n","Epoch 3, Train Loss: 0.4128318633037535, Validation Loss: 0.4164040111005306\n","Epoch 4/60: 100% 352/352 [00:18<00:00, 19.00batch/s, loss=0.374]\n","Epoch 4, Train Loss: 0.3740186734463681, Validation Loss: 0.38167440742254255\n","Epoch 5/60: 100% 352/352 [00:16<00:00, 21.99batch/s, loss=0.348]\n","Epoch 5, Train Loss: 0.3475755149159919, Validation Loss: 0.3711399342864752\n","Epoch 6/60: 100% 352/352 [00:16<00:00, 20.85batch/s, loss=0.32]\n","Epoch 6, Train Loss: 0.3198107653297484, Validation Loss: 0.3677479259669781\n","Epoch 7/60: 100% 352/352 [00:17<00:00, 19.77batch/s, loss=0.297]\n","Epoch 7, Train Loss: 0.2972728319212117, Validation Loss: 0.34454661086201666\n","Epoch 8/60: 100% 352/352 [00:16<00:00, 20.75batch/s, loss=0.28]\n","Epoch 8, Train Loss: 0.27995874847031454, Validation Loss: 0.33889873065054416\n","Epoch 9/60:  15% 52/352 [00:02<00:12, 23.35batch/s, loss=0.0372]\n","Traceback (most recent call last):\n","  File \"/content/BAPULM/main.py\", line 49, in <module>\n","    main()\n","  File \"/content/BAPULM/main.py\", line 42, in main\n","    model = train(model, train_loader, validation_loader, criterion, optimizer, scheduler, device, num_epochs=config['num_epochs'])\n","  File \"/content/BAPULM/utils/train.py\", line 12, in train\n","  File \"/usr/local/envs/newenv/lib/python3.10/site-packages/tqdm/std.py\", line 1181, in __iter__\n","    for obj in iterable:\n","  File \"/usr/local/envs/newenv/lib/python3.10/site-packages/torch/utils/data/dataloader.py\", line 733, in __next__\n","    data = self._next_data()\n","  File \"/usr/local/envs/newenv/lib/python3.10/site-packages/torch/utils/data/dataloader.py\", line 789, in _next_data\n","    data = self._dataset_fetcher.fetch(index)  # may raise StopIteration\n","  File \"/usr/local/envs/newenv/lib/python3.10/site-packages/torch/utils/data/_utils/fetch.py\", line 50, in fetch\n","    data = self.dataset.__getitems__(possibly_batched_index)\n","  File \"/usr/local/envs/newenv/lib/python3.10/site-packages/torch/utils/data/dataset.py\", line 416, in __getitems__\n","    return [self.dataset[self.indices[idx]] for idx in indices]\n","  File \"/usr/local/envs/newenv/lib/python3.10/site-packages/torch/utils/data/dataset.py\", line 416, in <listcomp>\n","    return [self.dataset[self.indices[idx]] for idx in indices]\n","  File \"/content/BAPULM/data/dataset.py\", line 19, in __getitem__\n","    protein_embedding = torch.tensor(item['prot_embedding'], dtype=torch.float32).squeeze(0)\n","KeyboardInterrupt\n","^C\n"]}]}]}