jupyter_nb/Geneformer_Skin.ipynb

{
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  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "279964df-65b9-4c26-ad0a-3875f773ee1a",
   "metadata": {},
   "outputs": [],
   "source": [
    "import os, scanpy as sc, warnings\n",
    "from geneformer import TranscriptomeTokenizer, EmbExtractor\n",
    "warnings.filterwarnings('ignore', category=FutureWarning)\n",
    "warnings.filterwarnings('ignore', category=UserWarning)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "e761c6b0-1127-43db-ac49-9b16b57cc8b3",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "AnnData object with n_obs × n_vars = 48981 × 29673\n",
       "    obs: 'biosample_id', 'donor_id', 'cell_type_ontology_term_id', 'organism_ontology_term_id', 'disease_ontology_term_id', 'tissue_ontology_term_id', 'assay_ontology_term_id', 'cell_type__custom', 'development_stage_ontology_term_id', 'sex_ontology_term_id', 'suspension_type', 'is_primary_data', 'age', 'self_reported_ethnicity_ontology_term_id', 'cell_type', 'assay', 'disease', 'organism', 'sex', 'tissue', 'self_reported_ethnicity', 'development_stage', 'n_counts', 'n_genes', '_scvi_batch', '_scvi_labels', 'conditions_combined'\n",
       "    var: 'feature_is_filtered', 'feature_name', 'feature_reference', 'feature_biotype', 'n_cells'\n",
       "    uns: '_scvi_manager_uuid', '_scvi_uuid', 'cell_type_colors', 'log1p', 'neighbors', 'pca', 'schema_version', 'title', 'tsne', 'umap'\n",
       "    obsm: 'Geneformer', 'Geneformer_UMAP', 'Harmony', 'Harmony_UMAP', 'Islander', 'Islander_SCL', 'Islander_SCL_UMAP', 'Islander_TRI', 'Islander_TRI_UMAP', 'Islander_UMAP', 'Provided_x_umap', 'Scanorama', 'Scanorama_UMAP', 'X_bbknn', 'X_pca', 'X_pca_UMAP', 'X_scANVI', 'X_scANVI_UMAP', 'X_scGPT', 'X_scGPT_FT', 'X_scGPT_FT_UMAP', 'X_scGPT_UMAP', 'X_scVI', 'X_scVI_UMAP', 'X_tsne', 'X_umap', 'scPoli', 'scPoli_UMAP'\n",
       "    varm: 'PCs'\n",
       "    layers: 'raw_counts'\n",
       "    obsp: 'connectivities', 'distances'"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "dataset = \"eye\"\n",
    "DATA_DIR = \"/home/wangh256/Islander_dev/data/%s/\" % dataset\n",
    "adata = sc.read_h5ad(rf\"{DATA_DIR}/emb.h5ad\")\n",
    "adata.X = adata.layers[\"raw_counts\"]\n",
    "adata"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "ad0e54c8-fb4e-42cf-a5e2-ca725b550b71",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>feature_is_filtered</th>\n",
       "      <th>feature_name</th>\n",
       "      <th>feature_reference</th>\n",
       "      <th>feature_biotype</th>\n",
       "      <th>n_cells</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>gene_ids</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>ENSG00000243485</th>\n",
       "      <td>False</td>\n",
       "      <td>MIR1302-2HG</td>\n",
       "      <td>NCBITaxon:9606</td>\n",
       "      <td>gene</td>\n",
       "      <td>113</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000237613</th>\n",
       "      <td>False</td>\n",
       "      <td>FAM138A</td>\n",
       "      <td>NCBITaxon:9606</td>\n",
       "      <td>gene</td>\n",
       "      <td>17</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000238009</th>\n",
       "      <td>False</td>\n",
       "      <td>RP11-34P13.7</td>\n",
       "      <td>NCBITaxon:9606</td>\n",
       "      <td>gene</td>\n",
       "      <td>254</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000241860</th>\n",
       "      <td>False</td>\n",
       "      <td>RP11-34P13.13</td>\n",
       "      <td>NCBITaxon:9606</td>\n",
       "      <td>gene</td>\n",
       "      <td>646</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000241599</th>\n",
       "      <td>False</td>\n",
       "      <td>RP11-34P13.9</td>\n",
       "      <td>NCBITaxon:9606</td>\n",
       "      <td>gene</td>\n",
       "      <td>13</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                 feature_is_filtered   feature_name feature_reference  \\\n",
       "gene_ids                                                                \n",
       "ENSG00000243485                False    MIR1302-2HG    NCBITaxon:9606   \n",
       "ENSG00000237613                False        FAM138A    NCBITaxon:9606   \n",
       "ENSG00000238009                False   RP11-34P13.7    NCBITaxon:9606   \n",
       "ENSG00000241860                False  RP11-34P13.13    NCBITaxon:9606   \n",
       "ENSG00000241599                False   RP11-34P13.9    NCBITaxon:9606   \n",
       "\n",
       "                feature_biotype  n_cells  \n",
       "gene_ids                                  \n",
       "ENSG00000243485            gene      113  \n",
       "ENSG00000237613            gene       17  \n",
       "ENSG00000238009            gene      254  \n",
       "ENSG00000241860            gene      646  \n",
       "ENSG00000241599            gene       13  "
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "adata.var.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "a162d940-a08e-4f6b-87d7-204807bca637",
   "metadata": {},
   "outputs": [],
   "source": [
    "adata.var['ensembl_id'] = adata.var.index.tolist()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "e94e7e16-3160-4044-ba43-ea8fa2289da0",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Tokenizing /home/wangh256/Islander_dev/data/eye/GeneformerRaw/local.h5ad\n",
      "/home/wangh256/Islander_dev/data/eye/GeneformerRaw/local.h5ad has no column attribute 'filter_pass'; tokenizing all cells.\n",
      "Creating dataset.\n"
     ]
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "f271c88c7384414e8d32a71c35dbe01f",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "Map (num_proc=16):   0%|          | 0/48981 [00:00<?, ? examples/s]"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "b76c3cab4bc94cd4b1e75248f2f09803",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "Map (num_proc=16):   0%|          | 0/48981 [00:00<?, ? examples/s]"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "edce5b7f313f4ad7a23a29636f888398",
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       "version_minor": 0
      },
      "text/plain": [
       "Saving the dataset (0/1 shards):   0%|          | 0/48981 [00:00<?, ? examples/s]"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "os.makedirs(rf\"{DATA_DIR}/Geneformer\", exist_ok=True)\n",
    "os.makedirs(rf\"{DATA_DIR}/GeneformerRaw\", exist_ok=True)\n",
    "adata.write_h5ad(rf\"{DATA_DIR}/GeneformerRaw/local.h5ad\", compression=\"gzip\")\n",
    "\n",
    "tk = TranscriptomeTokenizer({}, nproc=16)\n",
    "tk.tokenize_data(rf\"{DATA_DIR}/GeneformerRaw\", \n",
    "                 rf\"{DATA_DIR}/Geneformer\", \n",
    "                 dataset, \n",
    "                 file_format=\"h5ad\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "0da2d53e-c8bc-44e7-8587-c2d770761890",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "609fbc5c4ddd407f93d6f446ffdf099d",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "  0%|          | 0/383 [00:00<?, ?it/s]"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "embex = EmbExtractor(model_type=\"Pretrained\",\n",
    "                     num_classes=0,\n",
    "                     max_ncells=None,\n",
    "                     forward_batch_size=128,\n",
    "                     nproc=16)\n",
    "\n",
    "embs = embex.extract_embs(\"/home/wangh256/GeneDataEngine_dev/Geneformer-main/geneformer-12L-30M\",\n",
    "                          rf\"{DATA_DIR}/Geneformer/{dataset}.dataset\",\n",
    "                          rf\"{DATA_DIR}/\",\n",
    "                          \"Geneformer\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "97cb10b0",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "      <td>-0.019582</td>\n",
       "      <td>-0.009240</td>\n",
       "      <td>-0.034118</td>\n",
       "      <td>0.034324</td>\n",
       "      <td>...</td>\n",
       "      <td>0.013263</td>\n",
       "      <td>0.030504</td>\n",
       "      <td>0.018553</td>\n",
       "      <td>0.031204</td>\n",
       "      <td>0.014214</td>\n",
       "      <td>-0.021961</td>\n",
       "      <td>-0.029018</td>\n",
       "      <td>-0.011996</td>\n",
       "      <td>0.002177</td>\n",
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       "      <th>1</th>\n",
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       "      <td>0.009877</td>\n",
       "      <td>0.003998</td>\n",
       "      <td>0.020734</td>\n",
       "      <td>0.058412</td>\n",
       "      <td>0.005678</td>\n",
       "      <td>-0.015380</td>\n",
       "      <td>-0.017890</td>\n",
       "      <td>0.046616</td>\n",
       "      <td>...</td>\n",
       "      <td>0.037718</td>\n",
       "      <td>0.019069</td>\n",
       "      <td>-0.005409</td>\n",
       "      <td>0.045154</td>\n",
       "      <td>0.023234</td>\n",
       "      <td>-0.031534</td>\n",
       "      <td>-0.020503</td>\n",
       "      <td>-0.043775</td>\n",
       "      <td>0.013293</td>\n",
       "      <td>-0.039457</td>\n",
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       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>-0.005619</td>\n",
       "      <td>-0.027241</td>\n",
       "      <td>-0.005561</td>\n",
       "      <td>-0.003682</td>\n",
       "      <td>0.008809</td>\n",
       "      <td>0.041009</td>\n",
       "      <td>0.022319</td>\n",
       "      <td>0.007139</td>\n",
       "      <td>-0.032794</td>\n",
       "      <td>0.090452</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.007362</td>\n",
       "      <td>0.028629</td>\n",
       "      <td>0.006897</td>\n",
       "      <td>0.019762</td>\n",
       "      <td>0.045937</td>\n",
       "      <td>-0.044144</td>\n",
       "      <td>-0.022708</td>\n",
       "      <td>-0.043145</td>\n",
       "      <td>0.029624</td>\n",
       "      <td>-0.026715</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>0.000959</td>\n",
       "      <td>-0.027369</td>\n",
       "      <td>-0.008465</td>\n",
       "      <td>0.001370</td>\n",
       "      <td>-0.003953</td>\n",
       "      <td>0.037561</td>\n",
       "      <td>-0.024571</td>\n",
       "      <td>-0.015594</td>\n",
       "      <td>-0.039167</td>\n",
       "      <td>0.046891</td>\n",
       "      <td>...</td>\n",
       "      <td>0.015203</td>\n",
       "      <td>-0.003330</td>\n",
       "      <td>0.029155</td>\n",
       "      <td>0.016561</td>\n",
       "      <td>0.021866</td>\n",
       "      <td>-0.002586</td>\n",
       "      <td>-0.003752</td>\n",
       "      <td>-0.045425</td>\n",
       "      <td>0.005103</td>\n",
       "      <td>-0.016290</td>\n",
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       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>-0.011275</td>\n",
       "      <td>-0.019907</td>\n",
       "      <td>-0.019691</td>\n",
       "      <td>0.003722</td>\n",
       "      <td>0.011628</td>\n",
       "      <td>0.033808</td>\n",
       "      <td>-0.027955</td>\n",
       "      <td>0.018790</td>\n",
       "      <td>-0.029486</td>\n",
       "      <td>0.048524</td>\n",
       "      <td>...</td>\n",
       "      <td>0.023187</td>\n",
       "      <td>0.003533</td>\n",
       "      <td>0.019235</td>\n",
       "      <td>0.018353</td>\n",
       "      <td>0.032400</td>\n",
       "      <td>-0.021172</td>\n",
       "      <td>-0.030966</td>\n",
       "      <td>-0.018062</td>\n",
       "      <td>0.012432</td>\n",
       "      <td>-0.030218</td>\n",
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       "      <th>...</th>\n",
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       "      <td>...</td>\n",
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       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
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       "      <th>48976</th>\n",
       "      <td>0.025174</td>\n",
       "      <td>-0.001727</td>\n",
       "      <td>0.026214</td>\n",
       "      <td>0.000973</td>\n",
       "      <td>-0.003128</td>\n",
       "      <td>0.021305</td>\n",
       "      <td>-0.009780</td>\n",
       "      <td>0.018237</td>\n",
       "      <td>0.001709</td>\n",
       "      <td>-0.021251</td>\n",
       "      <td>...</td>\n",
       "      <td>0.028916</td>\n",
       "      <td>0.018966</td>\n",
       "      <td>0.000022</td>\n",
       "      <td>0.022634</td>\n",
       "      <td>-0.005928</td>\n",
       "      <td>-0.014672</td>\n",
       "      <td>-0.011444</td>\n",
       "      <td>0.014179</td>\n",
       "      <td>-0.002151</td>\n",
       "      <td>-0.016365</td>\n",
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       "    <tr>\n",
       "      <th>48977</th>\n",
       "      <td>0.029809</td>\n",
       "      <td>-0.030063</td>\n",
       "      <td>0.022909</td>\n",
       "      <td>-0.000005</td>\n",
       "      <td>0.005120</td>\n",
       "      <td>0.033246</td>\n",
       "      <td>-0.011090</td>\n",
       "      <td>0.025449</td>\n",
       "      <td>-0.024464</td>\n",
       "      <td>-0.005825</td>\n",
       "      <td>...</td>\n",
       "      <td>0.015554</td>\n",
       "      <td>0.032800</td>\n",
       "      <td>0.021001</td>\n",
       "      <td>0.011944</td>\n",
       "      <td>-0.004278</td>\n",
       "      <td>-0.015013</td>\n",
       "      <td>-0.016721</td>\n",
       "      <td>0.010995</td>\n",
       "      <td>-0.001858</td>\n",
       "      <td>-0.030193</td>\n",
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       "      <th>48978</th>\n",
       "      <td>0.028608</td>\n",
       "      <td>0.002319</td>\n",
       "      <td>0.024588</td>\n",
       "      <td>-0.000784</td>\n",
       "      <td>-0.004131</td>\n",
       "      <td>0.021955</td>\n",
       "      <td>0.008164</td>\n",
       "      <td>0.027745</td>\n",
       "      <td>0.007088</td>\n",
       "      <td>-0.001086</td>\n",
       "      <td>...</td>\n",
       "      <td>0.026314</td>\n",
       "      <td>0.020785</td>\n",
       "      <td>0.002720</td>\n",
       "      <td>0.016647</td>\n",
       "      <td>0.002657</td>\n",
       "      <td>-0.010621</td>\n",
       "      <td>-0.020980</td>\n",
       "      <td>0.012103</td>\n",
       "      <td>0.006307</td>\n",
       "      <td>-0.033755</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>48979</th>\n",
       "      <td>0.030072</td>\n",
       "      <td>-0.023417</td>\n",
       "      <td>0.014408</td>\n",
       "      <td>0.001479</td>\n",
       "      <td>-0.019943</td>\n",
       "      <td>0.023076</td>\n",
       "      <td>-0.008544</td>\n",
       "      <td>0.023940</td>\n",
       "      <td>-0.014923</td>\n",
       "      <td>-0.008359</td>\n",
       "      <td>...</td>\n",
       "      <td>0.007809</td>\n",
       "      <td>0.022821</td>\n",
       "      <td>0.019562</td>\n",
       "      <td>0.010346</td>\n",
       "      <td>-0.005769</td>\n",
       "      <td>-0.009558</td>\n",
       "      <td>-0.017058</td>\n",
       "      <td>0.028475</td>\n",
       "      <td>-0.006424</td>\n",
       "      <td>-0.008761</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>48980</th>\n",
       "      <td>0.024469</td>\n",
       "      <td>0.005690</td>\n",
       "      <td>0.028882</td>\n",
       "      <td>0.000791</td>\n",
       "      <td>0.000841</td>\n",
       "      <td>0.017281</td>\n",
       "      <td>0.000444</td>\n",
       "      <td>0.016459</td>\n",
       "      <td>-0.002022</td>\n",
       "      <td>-0.002702</td>\n",
       "      <td>...</td>\n",
       "      <td>0.036611</td>\n",
       "      <td>0.030911</td>\n",
       "      <td>-0.001970</td>\n",
       "      <td>0.030680</td>\n",
       "      <td>-0.021220</td>\n",
       "      <td>-0.020431</td>\n",
       "      <td>-0.014993</td>\n",
       "      <td>0.017867</td>\n",
       "      <td>0.001403</td>\n",
       "      <td>-0.032011</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>48981 rows × 512 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "            0         1         2         3         4         5         6    \\\n",
       "0     -0.002395 -0.013618 -0.009898  0.003715  0.027983  0.044488 -0.019582   \n",
       "1      0.007458 -0.033755  0.009877  0.003998  0.020734  0.058412  0.005678   \n",
       "2     -0.005619 -0.027241 -0.005561 -0.003682  0.008809  0.041009  0.022319   \n",
       "3      0.000959 -0.027369 -0.008465  0.001370 -0.003953  0.037561 -0.024571   \n",
       "4     -0.011275 -0.019907 -0.019691  0.003722  0.011628  0.033808 -0.027955   \n",
       "...         ...       ...       ...       ...       ...       ...       ...   \n",
       "48976  0.025174 -0.001727  0.026214  0.000973 -0.003128  0.021305 -0.009780   \n",
       "48977  0.029809 -0.030063  0.022909 -0.000005  0.005120  0.033246 -0.011090   \n",
       "48978  0.028608  0.002319  0.024588 -0.000784 -0.004131  0.021955  0.008164   \n",
       "48979  0.030072 -0.023417  0.014408  0.001479 -0.019943  0.023076 -0.008544   \n",
       "48980  0.024469  0.005690  0.028882  0.000791  0.000841  0.017281  0.000444   \n",
       "\n",
       "            7         8         9    ...       502       503       504  \\\n",
       "0     -0.009240 -0.034118  0.034324  ...  0.013263  0.030504  0.018553   \n",
       "1     -0.015380 -0.017890  0.046616  ...  0.037718  0.019069 -0.005409   \n",
       "2      0.007139 -0.032794  0.090452  ... -0.007362  0.028629  0.006897   \n",
       "3     -0.015594 -0.039167  0.046891  ...  0.015203 -0.003330  0.029155   \n",
       "4      0.018790 -0.029486  0.048524  ...  0.023187  0.003533  0.019235   \n",
       "...         ...       ...       ...  ...       ...       ...       ...   \n",
       "48976  0.018237  0.001709 -0.021251  ...  0.028916  0.018966  0.000022   \n",
       "48977  0.025449 -0.024464 -0.005825  ...  0.015554  0.032800  0.021001   \n",
       "48978  0.027745  0.007088 -0.001086  ...  0.026314  0.020785  0.002720   \n",
       "48979  0.023940 -0.014923 -0.008359  ...  0.007809  0.022821  0.019562   \n",
       "48980  0.016459 -0.002022 -0.002702  ...  0.036611  0.030911 -0.001970   \n",
       "\n",
       "            505       506       507       508       509       510       511  \n",
       "0      0.031204  0.014214 -0.021961 -0.029018 -0.011996  0.002177 -0.025248  \n",
       "1      0.045154  0.023234 -0.031534 -0.020503 -0.043775  0.013293 -0.039457  \n",
       "2      0.019762  0.045937 -0.044144 -0.022708 -0.043145  0.029624 -0.026715  \n",
       "3      0.016561  0.021866 -0.002586 -0.003752 -0.045425  0.005103 -0.016290  \n",
       "4      0.018353  0.032400 -0.021172 -0.030966 -0.018062  0.012432 -0.030218  \n",
       "...         ...       ...       ...       ...       ...       ...       ...  \n",
       "48976  0.022634 -0.005928 -0.014672 -0.011444  0.014179 -0.002151 -0.016365  \n",
       "48977  0.011944 -0.004278 -0.015013 -0.016721  0.010995 -0.001858 -0.030193  \n",
       "48978  0.016647  0.002657 -0.010621 -0.020980  0.012103  0.006307 -0.033755  \n",
       "48979  0.010346 -0.005769 -0.009558 -0.017058  0.028475 -0.006424 -0.008761  \n",
       "48980  0.030680 -0.021220 -0.020431 -0.014993  0.017867  0.001403 -0.032011  \n",
       "\n",
       "[48981 rows x 512 columns]"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "embs"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "6ef56895-9e52-4a10-9bd2-004e9168eda5",
   "metadata": {},
   "outputs": [],
   "source": [
    "adata.obsm[\"Geneformer\"] = embs.values"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "abc46e11",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Geneformer",
   "language": "python",
   "name": "python3"
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  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
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   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
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 },
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