05_jax_predict.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 48,
   "id": "5c0aebf6",
   "metadata": {},
   "outputs": [],
   "source": [
    "import scanpy as sc\n",
    "import numpy as np\n",
    "import pandas as pd\n",
    "import matplotlib as mpl\n",
    "import matplotlib.pyplot as plt\n",
    "import seaborn as sns\n",
    "import anndata\n",
    "import sc_utils\n",
    "import scvi\n",
    "import catboost\n",
    "import pickle"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "7b550858-e0ba-4c1f-9810-d3a1291bc53a",
   "metadata": {},
   "outputs": [],
   "source": [
    "import h5py\n",
    "import hdf5plugin"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "78547514",
   "metadata": {},
   "outputs": [],
   "source": [
    "pd.options.display.max_rows = 200"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "8baa9c3b-50a2-4d47-bfd4-ce5d767c823a",
   "metadata": {},
   "outputs": [],
   "source": [
    "%config InlineBackend.figure_format = \"retina\""
   ]
  },
  {
   "cell_type": "markdown",
   "id": "77c713ab",
   "metadata": {},
   "source": [
    "## 1. Load data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "1e9e3576-b4c7-455c-9de8-160050e34be3",
   "metadata": {},
   "outputs": [],
   "source": [
    "ds = sc.read_h5ad(\"../data/h5ad/jax_rna.h5ad\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "a573a5e1-c7a9-4005-aa0d-bc3fd4373c1c",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "AnnData object with n_obs × n_vars = 119651 × 2000\n",
       "    obs: 'day', 'donor', 'cell_type', 'technology', 'batch', 'n_genes_by_counts', 'total_counts', 'total_counts_mito', 'pct_counts_mito', 'sample', 'leiden', 'diff_leiden', 'dpt_pseudotime', 'jax_leiden'\n",
       "    var: 'ensembl_id', 'mito', 'n_cells_by_counts', 'mean_counts', 'pct_dropout_by_counts', 'total_counts', 'highly_variable', 'means', 'dispersions', 'dispersions_norm'\n",
       "    uns: 'cell_type_colors', 'day_colors', 'diff_leiden_colors', 'diff_leiden_sizes', 'diff_neighbors', 'diffmap_evals', 'donor_colors', 'hvg', 'iroot', 'jax_leiden_colors', 'jax_neighbors', 'leiden', 'leiden_colors', 'leiden_sizes', 'neighbors', 'paga', 'pca', 'rank_genes_groups', 'sample_colors', 'umap'\n",
       "    obsm: 'X_diffmap', 'X_jax', 'X_pca', 'X_umap'\n",
       "    obsp: 'connectivities', 'diff_neighbors_connectivities', 'diff_neighbors_distances', 'distances', 'jax_neighbors_connectivities', 'jax_neighbors_distances'"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ds"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "76841fe5-4bca-4b53-88e0-1acfcc2c6c2d",
   "metadata": {},
   "source": [
    "## 2. Load targets"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "0be588d1-9ec1-45bd-8c9f-8c8bceac1cf9",
   "metadata": {},
   "outputs": [],
   "source": [
    "meta = pd.read_csv(\"../data/metadata.csv\", index_col=0)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "25dc633c-6363-4e29-9fac-690b5b183613",
   "metadata": {},
   "outputs": [],
   "source": [
    "f = h5py.File(\"\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "id": "0746e0c8-380d-48d1-be78-4f1d9198168e",
   "metadata": {},
   "outputs": [],
   "source": [
    "def read_h5_as_df(path, meta, key=\"train_cite_inputs\"):\n",
    "    f = h5py.File(path)\n",
    "    expr = f[key][\"block0_values\"][:]\n",
    "    genes = f[key][\"axis0\"].asstr()[:]\n",
    "    cells = f[key][\"axis1\"].asstr()[:]\n",
    "    return pd.DataFrame(expr, index=cells, columns=genes)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "91075f34-9998-481e-96a8-ddbdadd371c4",
   "metadata": {},
   "outputs": [],
   "source": [
    "targets = read_h5_as_df(\"../data/train_cite_targets.h5\", meta, key=\"train_cite_targets\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "id": "cd7270d2-87b1-4d58-aea5-73550c915a7b",
   "metadata": {},
   "outputs": [
    {
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       "...                ...       ...       ...       ...       ...       ...   \n",
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       "\n",
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       "...                 ...       ...       ...       ...  ...       ...   \n",
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       "\n",
       "                  CD162     CD85j      CD23     CD328     HLA-E       CD82  \\\n",
       "45006fe3e4c8   3.220174 -0.533004  0.674956 -0.006187  0.682148   1.398105   \n",
       "d02759a80ba2   8.407108  0.131301  0.047607 -0.243628  0.547864   1.832587   \n",
       "c016c6b0efa5   4.888579 -0.279483 -0.131097 -0.177604 -0.689188   9.013709   \n",
       "ba7f733a4f75  12.391979  0.511394  0.587863 -0.752638  1.714851   3.893782   \n",
       "fbcf2443ffb2   6.496499  0.279898 -0.841950 -0.869419  0.675092   5.259685   \n",
       "...                 ...       ...       ...       ...       ...        ...   \n",
       "650ee456f0f3   3.092832  0.003275  0.278930 -0.272002  0.249477   3.789460   \n",
       "cc506e7707f5   5.029233  0.909861  0.057322  2.633387  1.340077  11.456146   \n",
       "a91f1b55a520   5.027534 -0.703609  1.139491 -0.078092  1.592960   9.358179   \n",
       "3a9882c98205  12.883892  1.579381 -0.382835 -0.065286 -0.021458   7.372662   \n",
       "c91b6b2ccd3d   7.204354  2.410788  0.459688 -0.241992  1.508021   7.803446   \n",
       "\n",
       "                 CD101      CD88     CD224  \n",
       "45006fe3e4c8  0.414292  1.780314  0.548070  \n",
       "d02759a80ba2  0.982308  2.736507  2.184063  \n",
       "c016c6b0efa5 -1.182975  3.958148  2.868600  \n",
       "ba7f733a4f75  1.799661  1.537249  4.407671  \n",
       "fbcf2443ffb2 -0.835379  9.631781  1.765445  \n",
       "...                ...       ...       ...  \n",
       "650ee456f0f3  0.138330  1.466193  4.278504  \n",
       "cc506e7707f5 -1.431453  5.275882  2.510530  \n",
       "a91f1b55a520  0.981883  6.911032  3.415310  \n",
       "3a9882c98205  1.010247  1.864805  3.449289  \n",
       "c91b6b2ccd3d  0.618852  7.220644  3.234360  \n",
       "\n",
       "[70988 rows x 140 columns]"
      ]
     },
     "execution_count": 21,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "targets"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "5f9ebe6c",
   "metadata": {},
   "source": [
    "## 2. Catboost model"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "id": "0860cb8b-5f41-4d76-b83b-82d054c08bb1",
   "metadata": {},
   "outputs": [],
   "source": [
    "ds.obs_names = ds.obs_names.str.replace(\"-\\d+$\", \"\", regex=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "id": "598df830-8d4d-4c88-8c97-bd3e414fad6f",
   "metadata": {},
   "outputs": [],
   "source": [
    "train_x = ds[targets.index, :].obsm[\"X_jax\"]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 36,
   "id": "5aa36ef3-e730-4d50-b262-7c60225aa9f5",
   "metadata": {},
   "outputs": [],
   "source": [
    "model = catboost.CatBoostRegressor(\n",
    "    iterations=1000,\n",
    "    # task_type=\"GPU\",\n",
    "    loss_function=\"MultiRMSE\",\n",
    "    eval_metric=\"MultiRMSE\"\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 37,
   "id": "5c8393dd-8c62-48dd-86f9-e9a12e9b51ea",
   "metadata": {
    "collapsed": true,
    "jupyter": {
     "outputs_hidden": true
    },
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
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      "999:\tlearn: 19.0796620\ttotal: 20m 31s\tremaining: 0us\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "<catboost.core.CatBoostRegressor at 0x2b13bc29f730>"
      ]
     },
     "execution_count": 37,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "model.fit(train_x, targets)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 38,
   "id": "833699e6-9bf7-4a0b-bd14-479a39aa904c",
   "metadata": {},
   "outputs": [],
   "source": [
    "def correlation_score(y_true, y_pred):\n",
    "    if type(y_true) == pd.DataFrame: y_true = y_true.values\n",
    "    if type(y_pred) == pd.DataFrame: y_pred = y_pred.values\n",
    "    corrsum = 0\n",
    "    for i in range(len(y_true)):\n",
    "        corrsum += np.corrcoef(y_true[i], y_pred[i])[1, 0]\n",
    "    return corrsum / len(y_true)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 39,
   "id": "9e353ff8-0d77-4e0a-94c0-0e82a16bb044",
   "metadata": {},
   "outputs": [],
   "source": [
    "y_pred = model.predict(train_x)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 40,
   "id": "e5442c28-05dc-49fd-9a3f-91800b9034a0",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "0.8963400960239647"
      ]
     },
     "execution_count": 40,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "correlation_score(targets, y_pred)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 43,
   "id": "db7449a8-8a50-4567-95e8-f59c0de766ff",
   "metadata": {},
   "outputs": [],
   "source": [
    "model.save_model(\"05jax_catboost.model\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 44,
   "id": "f3633f7b-3c04-44bf-b320-02bd771c7c3f",
   "metadata": {},
   "outputs": [],
   "source": [
    "test_x = ds[~ds.obs_names.isin(targets.index), :].obsm[\"X_jax\"]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 45,
   "id": "f4922aff-a1ac-43f1-a1d9-b2e77e9833ad",
   "metadata": {},
   "outputs": [],
   "source": [
    "test_pred = model.predict(test_x)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 46,
   "id": "2e7e3fa5-e2de-4818-bfe7-0d90f5e4c044",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(48663, 140)"
      ]
     },
     "execution_count": 46,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "test_pred.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 49,
   "id": "e7e21d12-8e3c-49f6-9991-5a4d862cdf7d",
   "metadata": {},
   "outputs": [],
   "source": [
    "with open(\"05_jax_preds/cite_test_preds.pickle\", \"wb\") as f:\n",
    "    pickle.dump(test_pred, f)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 50,
   "id": "2913a763-e691-47e5-b630-26e1333c3d09",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "row_id\n",
       "0           0.273072\n",
       "1           0.293944\n",
       "2           0.658493\n",
       "3           4.448602\n",
       "4           4.789261\n",
       "              ...   \n",
       "65744175    7.271666\n",
       "65744176    0.017597\n",
       "65744177    0.025040\n",
       "65744178    1.933743\n",
       "65744179    5.111444\n",
       "Name: target, Length: 65744180, dtype: float64"
      ]
     },
     "execution_count": 50,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "with open(\"05_jax_preds/partial_submission_multi.pickle\", \"rb\") as f:\n",
    "    submission = pickle.load(f)\n",
    "\n",
    "submission.iloc[:len(test_pred.ravel())] = test_pred.ravel()\n",
    "assert not submission.isna().any()\n",
    "submission = submission.round(6) # reduce the size of the csv\n",
    "submission.to_csv(\"05_jax_preds/submission.csv\")\n",
    "submission"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "7a657c79-da38-448c-90bd-35b816b50ab2",
   "metadata": {},
   "source": [
    "This submission scores 0.794"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "eee1cd40-9d4e-4538-b2d3-50fec22147fc",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "d3c7b939-3926-45bb-a881-8579359415dc",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "29946762-c33d-4e7b-8e2f-583dfd6719aa",
   "metadata": {},
   "outputs": [],
   "source": [
    "# from https://www.kaggle.com/code/geraseva/magic-correlation\n",
    "cite_cols_important={'CD86': ['ENSG00000114013_CD86'],\n",
    "             'CD274': ['ENSG00000120217_CD274'],\n",
    "             'CD270': ['ENSG00000157873_TNFRSF14'],\n",
    "             'CD155': ['ENSG00000073008_PVR'],\n",
    "             'CD112': ['ENSG00000130202_NECTIN2'],\n",
    "             'CD47': ['ENSG00000196776_CD47'],\n",
    "             'CD48': ['ENSG00000117091_CD48'],\n",
    "             'CD40': ['ENSG00000101017_CD40'],\n",
    "             'CD154': ['ENSG00000102245_CD40LG'],\n",
    "             'CD52': ['ENSG00000169442_CD52'],\n",
    "             'CD3': ['ENSG00000167286_CD3D'],\n",
    "             'CD8': [],\n",
    "             'CD56': ['ENSG00000149294_NCAM1'],\n",
    "             'CD19': ['ENSG00000177455_CD19'],\n",
    "             'CD33': ['ENSG00000105383_CD33'],\n",
    "             'CD11c': ['ENSG00000140678_ITGAX'],\n",
    "             'HLA-A-B-C': ['ENSG00000204525_HLA-C',\n",
    "              'ENSG00000206503_HLA-A',\n",
    "              'ENSG00000234745_HLA-B'],\n",
    "             'CD45RA': ['ENSG00000081237_PTPRC'],\n",
    "             'CD123': ['ENSG00000185291_IL3RA'],\n",
    "             'CD7': ['ENSG00000173762_CD7'],\n",
    "             'CD105': ['ENSG00000106991_ENG'],\n",
    "             'CD49f': ['ENSG00000091409_ITGA6'],\n",
    "             'CD194': ['ENSG00000183813_CCR4'],\n",
    "             'CD4': ['ENSG00000010610_CD4'],\n",
    "             'CD44': ['ENSG00000026508_CD44'],\n",
    "             'CD14': ['ENSG00000170458_CD14'],\n",
    "             'CD16': [],\n",
    "             'CD25': ['ENSG00000134460_IL2RA'],\n",
    "             'CD45RO': ['ENSG00000081237_PTPRC'],\n",
    "             'CD279': [],\n",
    "             'TIGIT': [],\n",
    "             'Mouse-IgG1': [],\n",
    "             'Mouse-IgG2a': [],\n",
    "             'Mouse-IgG2b': [],\n",
    "             'Rat-IgG2b': [],\n",
    "             'CD20': ['ENSG00000156738_MS4A1'],\n",
    "             'CD335': ['ENSG00000189430_NCR1'],\n",
    "             'CD31': ['ENSG00000261371_PECAM1'],\n",
    "             'Podoplanin': [],\n",
    "             'CD146': ['ENSG00000076706_MCAM'],\n",
    "             'IgM': ['ENSG00000211899_IGHM'],\n",
    "             'CD5': [],\n",
    "             'CD195': ['ENSG00000160791_CCR5'],\n",
    "             'CD32': ['ENSG00000143226_FCGR2A'],\n",
    "             'CD196': [],\n",
    "             'CD185': ['ENSG00000160683_CXCR5'],\n",
    "             'CD103': ['ENSG00000083457_ITGAE'],\n",
    "             'CD69': ['ENSG00000110848_CD69'],\n",
    "             'CD62L': ['ENSG00000188404_SELL'],\n",
    "             'CD161': ['ENSG00000111796_KLRB1'],\n",
    "             'CD152': [],\n",
    "             'CD223': ['ENSG00000089692_LAG3'],\n",
    "             'KLRG1': ['ENSG00000139187_KLRG1'],\n",
    "             'CD27': ['ENSG00000139193_CD27'],\n",
    "             'CD107a': ['ENSG00000185896_LAMP1'],\n",
    "             'CD95': ['ENSG00000026103_FAS'],\n",
    "             'CD134': ['ENSG00000186827_TNFRSF4'],\n",
    "             'HLA-DR': ['ENSG00000204287_HLA-DRA'],\n",
    "             'CD1c': ['ENSG00000158481_CD1C'],\n",
    "             'CD11b': ['ENSG00000169896_ITGAM'],\n",
    "             'CD64': ['ENSG00000150337_FCGR1A'],\n",
    "             'CD141': ['ENSG00000178726_THBD'],\n",
    "             'CD1d': ['ENSG00000158473_CD1D'],\n",
    "             'CD314': [],\n",
    "             'CD35': ['ENSG00000203710_CR1'],\n",
    "             'CD57': [],\n",
    "             'CD272': [],\n",
    "             'CD278': ['ENSG00000163600_ICOS'],\n",
    "             'CD58': ['ENSG00000116815_CD58'],\n",
    "             'CD39': ['ENSG00000138185_ENTPD1'],\n",
    "             'CX3CR1': ['ENSG00000168329_CX3CR1'],\n",
    "             'CD24': ['ENSG00000272398_CD24'],\n",
    "             'CD21': ['ENSG00000117322_CR2'],\n",
    "             'CD11a': ['ENSG00000005844_ITGAL'],\n",
    "             'CD79b': ['ENSG00000007312_CD79B'],\n",
    "             'CD244': ['ENSG00000122223_CD244'],\n",
    "             'CD169': [],\n",
    "             'integrinB7': ['ENSG00000139626_ITGB7'],\n",
    "             'CD268': ['ENSG00000159958_TNFRSF13C'],\n",
    "             'CD42b': ['ENSG00000185245_GP1BA'],\n",
    "             'CD54': ['ENSG00000090339_ICAM1'],\n",
    "             'CD62P': ['ENSG00000174175_SELP'],\n",
    "             'CD119': ['ENSG00000027697_IFNGR1'],\n",
    "             'TCR': [],\n",
    "             'Rat-IgG1': [],\n",
    "             'Rat-IgG2a': [],\n",
    "             'CD192': ['ENSG00000121807_CCR2'],\n",
    "             'CD122': ['ENSG00000100385_IL2RB'],\n",
    "             'FceRIa': ['ENSG00000179639_FCER1A'],\n",
    "             'CD41': ['ENSG00000005961_ITGA2B'],\n",
    "             'CD137': ['ENSG00000049249_TNFRSF9'],\n",
    "             'CD163': ['ENSG00000177575_CD163'],\n",
    "             'CD83': ['ENSG00000112149_CD83'],\n",
    "             'CD124': ['ENSG00000077238_IL4R'],\n",
    "             'CD13': ['ENSG00000166825_ANPEP'],\n",
    "             'CD2': ['ENSG00000116824_CD2'],\n",
    "             'CD226': ['ENSG00000150637_CD226'],\n",
    "             'CD29': ['ENSG00000150093_ITGB1'],\n",
    "             'CD303': ['ENSG00000198178_CLEC4C'],\n",
    "             'CD49b': ['ENSG00000164171_ITGA2'],\n",
    "             'CD81': ['ENSG00000110651_CD81'],\n",
    "             'IgD': ['ENSG00000211898_IGHD'],\n",
    "             'CD18': ['ENSG00000160255_ITGB2'],\n",
    "             'CD28': [],\n",
    "             'CD38': ['ENSG00000004468_CD38'],\n",
    "             'CD127': ['ENSG00000168685_IL7R'],\n",
    "             'CD45': ['ENSG00000081237_PTPRC'],\n",
    "             'CD22': ['ENSG00000012124_CD22'],\n",
    "             'CD71': ['ENSG00000072274_TFRC'],\n",
    "             'CD26': ['ENSG00000197635_DPP4'],\n",
    "             'CD115': ['ENSG00000182578_CSF1R'],\n",
    "             'CD63': ['ENSG00000135404_CD63'],\n",
    "             'CD304': ['ENSG00000099250_NRP1'],\n",
    "             'CD36': ['ENSG00000135218_CD36'],\n",
    "             'CD172a': ['ENSG00000198053_SIRPA'],\n",
    "             'CD72': ['ENSG00000137101_CD72'],\n",
    "             'CD158': [],\n",
    "             'CD93': ['ENSG00000125810_CD93'],\n",
    "             'CD49a': ['ENSG00000213949_ITGA1'],\n",
    "             'CD49d': ['ENSG00000115232_ITGA4'],\n",
    "             'CD73': [],\n",
    "             'CD9': ['ENSG00000010278_CD9'],\n",
    "             'TCRVa7.2': [],\n",
    "             'TCRVd2': [],\n",
    "             'LOX-1': ['ENSG00000173391_OLR1'],\n",
    "             'CD158b': [],\n",
    "             'CD158e1': [],\n",
    "             'CD142': ['ENSG00000117525_F3'],\n",
    "             'CD319': ['ENSG00000026751_SLAMF7'],\n",
    "             'CD352': ['ENSG00000162739_SLAMF6'],\n",
    "             'CD94': ['ENSG00000134539_KLRD1'],\n",
    "             'CD162': ['ENSG00000110876_SELPLG'],\n",
    "             'CD85j': ['ENSG00000104972_LILRB1'],\n",
    "             'CD23': ['ENSG00000104921_FCER2'],\n",
    "             'CD328': ['ENSG00000168995_SIGLEC7'],\n",
    "             'HLA-E': ['ENSG00000204592_HLA-E'],\n",
    "             'CD82': ['ENSG00000085117_CD82'],\n",
    "             'CD101': ['ENSG00000134256_CD101'],\n",
    "             'CD88': ['ENSG00000197405_C5AR1'],\n",
    "             'CD224': ['ENSG00000100031_GGT1']}"
   ]
  },
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   "id": "102dc5ce-3bae-4b29-9536-527cf9ad1acd",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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