{
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  {
   "cell_type": "code",
   "execution_count": null,
   "id": "e10ac0c9-40ce-41fb-b6fa-3d62b76f2e57",
   "metadata": {},
   "outputs": [],
   "source": [
    "from geneformer import InSilicoPerturber\n",
    "from geneformer import InSilicoPerturberStats"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "67b44366-f255-4415-a865-6a27a8ffcce7",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "# in silico perturbation in deletion mode to determine genes whose \n",
    "# deletion in the dilated cardiomyopathy (dcm) state significantly shifts\n",
    "# the embedding towards non-failing (nf) state\n",
    "isp = InSilicoPerturber(perturb_type=\"delete\",\n",
    "                        perturb_rank_shift=None,\n",
    "                        genes_to_perturb=\"all\",\n",
    "                        combos=0,\n",
    "                        anchor_gene=None,\n",
    "                        model_type=\"CellClassifier\",\n",
    "                        num_classes=3,\n",
    "                        emb_mode=\"cell\",\n",
    "                        cell_emb_style=\"mean_pool\",\n",
    "                        filter_data={\"cell_type\":[\"Cardiomyocyte1\",\"Cardiomyocyte2\",\"Cardiomyocyte3\"]},\n",
    "                        cell_states_to_model={\"disease\":([\"dcm\"],[\"nf\"],[\"hcm\"])},\n",
    "                        max_ncells=2000,\n",
    "                        emb_layer=0,\n",
    "                        forward_batch_size=400,\n",
    "                        nproc=16)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "0525a663-871a-4ce0-a135-cc203817ffa9",
   "metadata": {},
   "outputs": [],
   "source": [
    "# outputs intermediate files from in silico perturbation\n",
    "isp.perturb_data(\"path/to/model\",\n",
    "                 \"path/to/input_data\",\n",
    "                 \"path/to/output_directory\",\n",
    "                 \"output_prefix\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "f8aadabb-516a-4dc0-b307-6de880e64e26",
   "metadata": {},
   "outputs": [],
   "source": [
    "ispstats = InSilicoPerturberStats(mode=\"goal_state_shift\",\n",
    "                                  genes_perturbed=\"all\",\n",
    "                                  combos=0,\n",
    "                                  anchor_gene=None,\n",
    "                                  cell_states_to_model={\"disease\":([\"dcm\"],[\"nf\"],[\"hcm\"])})"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "ffecfae6-e737-43e3-99e9-fa37ff46610b",
   "metadata": {},
   "outputs": [],
   "source": [
    "# extracts data from intermediate files and processes stats to output in final .csv\n",
    "ispstats.get_stats(\"path/to/input_data\",\n",
    "                   None,\n",
    "                   \"path/to/output_directory\",\n",
    "                   \"output_prefix\")"
   ]
  }
 ],
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