1B-1[Omics_revamped]Gene_symbol_update.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## take the Genes from Task2 gene list and check number of invalid gene symbols"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current\n",
      "                                 Dload  Upload   Total   Spent    Left  Speed\n",
      "  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0curl: (6) Could not resolve host: www.genenames.org\n"
     ]
    }
   ],
   "source": [
    "# download the most up-to-date hgnc symbols and aliases\n",
    "## last download on 06/27/2024\n",
    "!bash ./utils/download_genenames.sh"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "from collections import defaultdict\n",
    "import csv\n",
    "class GeneValidator:\n",
    "    def __init__(self, file_path):\n",
    "        self.gene_symbol_set = set()\n",
    "        self.alias_map = defaultdict(str)\n",
    "\n",
    "        with open(file_path, 'r') as file:\n",
    "            reader = csv.reader(file, delimiter='\\t')\n",
    "            next(reader)  # Skip header row\n",
    "            for cells in reader:\n",
    "                if cells[0]:\n",
    "                    gene = cells[0].upper()\n",
    "                    self.gene_symbol_set.add(gene)\n",
    "\n",
    "                    if len(cells) > 1 and cells[1]:\n",
    "                        previous_symbols = cells[1].split(\", \")\n",
    "                        for symbol in previous_symbols:\n",
    "                            self.alias_map[symbol.upper()] = gene\n",
    "\n",
    "                    if len(cells) > 2 and cells[2]:\n",
    "                        alias_symbols = cells[2].split(\", \")\n",
    "                        for alias in alias_symbols:\n",
    "                            self.alias_map[alias.upper()] = gene\n",
    "\n",
    "    def validate_human_genes(self, genes):\n",
    "        official_genes = set()\n",
    "        invalid_genes = set()\n",
    "        updated_genes = {}\n",
    "\n",
    "        for raw_term in genes:\n",
    "            # print(f'validate Hugo symbol for {raw_term}')\n",
    "            term = raw_term.upper()\n",
    "            if term in self.gene_symbol_set:\n",
    "                official_genes.add(term)\n",
    "            elif term in self.alias_map:\n",
    "                official_gene = self.alias_map[term]\n",
    "                official_genes.add(official_gene)\n",
    "                updated_genes[term] = official_gene\n",
    "                invalid_genes.add(term)\n",
    "            else:\n",
    "                invalid_genes.add(term)\n",
    "\n",
    "        return {\n",
    "            'official_genes': official_genes,\n",
    "            'invalid': invalid_genes,\n",
    "            'updated_genes': updated_genes\n",
    "        }\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "6260"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df = pd.read_csv('data/omics_revamped_LLM_DF.tsv', sep='\\t')\n",
    "def get_genes(row):\n",
    "    return row['GeneList'].split(' ')\n",
    "\n",
    "total_genes = df.apply(get_genes, axis=1)\n",
    "total_genes_list = [item for sublist in total_genes for item in sublist]\n",
    "total_genes_set = set(total_genes_list)\n",
    "len(total_genes_set)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "number of invalid genes:  384\n",
      "Invalid gene symbols: ['C14ORF2', 'LOC147004', 'C19ORF52', 'MUM1', 'C2ORF43', 'GNB2L1', 'PQLC3', 'C10ORF10', 'ALS2CR11', 'C9ORF89', 'C8ORF37', 'H2BFS', 'LOC100505650', 'LDOC1L', 'GRAMD3', 'HIST1H2AM', 'LRRC48', 'WDR78', 'C1ORF194', 'LOC400622', 'CASC4', 'LARS', 'TMEM56', 'MAATS1', 'C1ORF213', 'RPS6P6', 'C22ORF24', 'C2ORF70', 'LOC730183', 'LHFP', 'GPR126', 'HIST1H2AH', 'LOC283701', 'HIAT1', 'SEPP1', 'WBP5', 'LOC642852', 'C3ORF58', 'H2AFV', 'KIAA1161', 'KIAA1377', 'TSSC1', 'CENPBD1', 'LOC100288860', 'SLC9A3R1', 'LOC283745', 'C16ORF52', 'PKI55', 'CRAMP1L', 'FAM129C', 'ACRC', 'RFWD2', 'LOC643355', 'WRB', 'C1ORF168', 'PAPD5', 'DNAJC3-AS1', 'ZNF720', 'KIAA0355', 'KIAA1033', 'WARS', 'NUDT16P1', 'ANKRD20A4', 'LOC389831', 'FAM183A', 'ZFYVE20', 'FAM57A', 'LOC349160', 'LOC727916', 'AQPEP', 'FAM63A', 'FAM196B', 'KIAA1244', 'C9ORF16', 'HIST1H2BD', 'DSCR3', 'KIAA1715', 'ZCCHC11', 'C11ORF63', 'FAM71F1', 'CASC10', 'PCDHB18', 'RSG1', 'CCDC94', 'GBA', 'HIST1H4B', 'H3F3C', 'CD97', 'HIST1H4A', 'HIST1H3F', 'TTC18', 'LOC401913', 'ANKRD20A3', 'C9ORF64', 'HRSP12', 'DDX58', 'C14ORF159', 'WBSCR17', 'LOC100505915', 'C8ORF4', 'GPR116', 'LOC646626', 'C15ORF52', 'KIAA1919', 'ATP5O', 'TMEM189', 'HIST1H2AB', 'SEPT6', 'H1FX', 'H2AFZ', 'C19ORF45', 'MESDC2', 'FAM46A', 'C17ORF62', 'GARS', 'C5ORF56', 'FAM173A', 'B3GNT1', 'MST4', 'BAI3', 'TCEB3', 'C2ORF61', 'C11ORF88', 'ICK', 'LOC645984', 'LOC728743', 'LOC100132790', 'CXORF23', 'LRRC16A', 'MUM1L1', 'LOC643085', 'MARCH1', 'GUCY1A3', 'GPR56', 'LOC100506990', 'C16ORF72', 'KIAA1462', 'HIST1H2AI', 'H3F3A', 'LOC730098', 'CCDC67', 'HIST1H3H', 'LRMP', 'C19ORF43', 'ASNA1', 'C17ORF97', 'CSRP2BP', 'LINS', 'ATP5J2', 'NOV', 'FAM102A', 'LOC339803', 'HIST1H3A', 'TMEM110', 'GVQW1', 'METTL7B', 'LOC391020', 'WASH1', 'PPAP2B', 'KIAA0125', 'PROSC', 'MRE11A', 'SEPT2', 'AARS', 'ACPP', 'MARCH3', 'GATSL2', 'C12ORF45', 'KARS', 'KIAA0556', 'FAM64A', 'C12ORF73', 'MFI2', 'DIEXF', 'HIST1H2BG', 'C11ORF95', 'LOC100131150', 'LOC100130331', 'CYR61', 'WDR61', 'FAM96B', 'ISPD', 'MARCH6', 'PP7080', 'DYX1C1', 'LOC100507022', 'METTL21B', 'FAM212B', 'B3GALTL', 'HIST1H2AC', 'C7ORF49', 'DKFZP586K1520', 'C11ORF73', 'MARS', 'C17ORF47', 'CCDC36', 'TCTEX1D4', 'C16ORF45', 'AAED1', 'C1ORF123', 'AIM1', 'TARP', 'IARS', 'LOC100287166', 'PVRL3', 'FAM96A', 'HIST1H2BK', 'RQCD1', 'MARCH10', 'C9ORF84', 'ATPIF1', 'KAL1', 'LOC440934', '1060P11.3', 'FGFR1OP', 'KIAA0100', 'FAM60A', 'HIST2H2BF', 'FAM198B', 'FAM19A5', 'LOC153811', 'PTPLAD1', 'HIST1H1B', 'OCLM', 'C9ORF53', 'MFSD7', 'C14ORF79', 'GAGE3', 'FAM86C1', 'GUCY1B3', 'WDR16', 'KIAA0391', 'C5ORF51', 'RNMTL1', 'FAM126B', 'KIAA1211L', 'FAIM3', 'LOC100507053', 'GATS', 'C14ORF166', 'MARCH8', 'CTGF', 'FAM103A1', 'H1F0', 'TCTEX1D2', 'LOC440434', 'WISP3', 'LOC645752', 'HIST3H2A', 'HIST1H1C', 'FAM84A', 'LOC285692', 'OVOS2', 'LOC284561', 'H2AFY2', 'DKFZP434H168', 'PLA2G16', 'HIST1H2BH', 'UTP11L', 'LOC374443', 'LOC100506469', 'KIAA0226L', 'HIST1H2AJ', 'WHSC1L1', 'C10ORF82', 'DHFRL1', 'QARS', 'HIST1H4K', 'TMEM35', 'CYHR1', 'YARS', 'C17ORF59', 'TARS', 'FAM189A2', 'CXORF57', 'FAM134B', 'C17ORF64', 'LOC100133050', 'SEPW1', 'ZNF788', 'CCDC108', 'LOC554207', 'IGJ', 'HN1', 'CECR1', 'LOC100131929', 'NUPL1', 'FUK', 'LINC00672', 'ZBED6CL', 'ADCK3', 'FAM173B', 'NRD1', 'GPR125', 'PALM2-AKAP2', 'TMEM159', 'LOC93622', 'C4ORF22', 'C11ORF70', 'C11ORF49', 'H2AFX', 'COLCA2', 'GRASP', 'GPR64', 'ATP5A1', 'SQRDL', 'FAM166A', 'HIST1H4C', 'VNN3', 'ATP5G1', 'RARRES3', 'LOC100505878', 'AHSA2', 'KIAA1257', 'GIF', 'STRA13', 'C19ORF10', 'LOC100128002', 'C1ORF204', 'C7ORF55', 'CRIPAK', 'KIAA0247', 'PTPLA', 'LINC00643', 'KIAA1598', 'FAM160B1', 'C11ORF53', 'FAM92B', 'GOLGA8I', 'KIAA0196', 'C19ORF68', 'FAM69A', 'FAM129A', 'C1ORF192', 'KIAA0141', 'TIAF1', 'PYCRL', 'C6ORF48', 'FAM175B', 'FAM134A', 'METTL7A', 'C1ORF106', 'C9ORF9', 'CARS', 'WDR60', 'DFNA5', 'CCDC189', 'ATP5E', 'C4ORF32', 'GPR110', 'SMA4', 'FAM160A2', 'BHLHB9', 'NGFRAP1', 'SGK223', 'H2AFY', 'EFTUD1', 'CCDC129', 'LEPREL1', 'LOC100506098', 'WDR11-AS1', 'C20ORF27', 'FAM134C', 'LOC100287590', 'TWISTNB', 'KIAA1324', 'C17ORF53', 'EFCAB1', 'CXORF67', 'TMEM133', 'C3ORF14', 'LOC100133315', 'GCN1L1', 'GRAMD2', 'FAM189A1', 'KIAA0485', 'LOC401463', 'ERO1L', 'ATP5G3', 'C11ORF85', 'C6ORF201', 'CCDC151', 'SELM', 'HDGFRP3']\n"
     ]
    }
   ],
   "source": [
    "\n",
    "# Usage example:\n",
    "file_path = \"./hgnc_genes.tsv\"\n",
    "\n",
    "validator = GeneValidator(file_path)\n",
    "result = validator.validate_human_genes(total_genes_set)\n",
    "# print(result)\n",
    "\n",
    "updated_gene_symbols = list(result['official_genes'])\n",
    "invalid_gene_symbols = list(result['invalid'])\n",
    "updated_genes_mapping = result['updated_genes']\n",
    "# print(\"Updated gene symbols:\", updated_gene_symbols)\n",
    "print(\"number of invalid genes: \", len(invalid_gene_symbols))\n",
    "print(\"Invalid gene symbols:\", invalid_gene_symbols)\n",
    "# print(\"Updated genes mapping:\", updated_genes_mapping)\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'HIAT1': 'MFSD14A',\n",
       " 'PAPD5': 'TENT4B',\n",
       " 'CASC10': 'MIR1915HG',\n",
       " 'H2AFZ': 'H2AZ1',\n",
       " 'TCEB3': 'ELOA',\n",
       " 'C20ORF27': 'ADISSP',\n",
       " 'KIAA0125': 'FAM30A',\n",
       " 'MARCH3': 'MARCHF3',\n",
       " 'FAM64A': 'PIMREG',\n",
       " 'FAM86C1': 'FAM86C1P',\n",
       " 'KIAA0226L': 'RUBCNL',\n",
       " 'SEPW1': 'SELENOW',\n",
       " 'NUPL1': 'NUP58',\n",
       " 'GRASP': 'TAMALIN',\n",
       " 'GPR64': 'ADGRG2',\n",
       " 'HIST1H4C': 'H4C3',\n",
       " 'VNN3': 'VNN3P',\n",
       " 'C7ORF55': 'FMC1',\n",
       " 'C11ORF95': 'ZFTA',\n",
       " 'C14ORF79': 'CLBA1',\n",
       " 'GNB2L1': 'RACK1',\n",
       " 'LARS': 'LARS1',\n",
       " 'RFWD2': 'COP1',\n",
       " 'C1ORF194': 'CFAP276',\n",
       " 'C19ORF45': 'SAXO5',\n",
       " 'C17ORF97': 'LIAT1',\n",
       " 'C7ORF49': 'CYREN',\n",
       " 'C11ORF73': 'HIKESHI',\n",
       " 'HIST2H2BF': 'H2BC18',\n",
       " 'FAM198B': 'GASK1B',\n",
       " 'C19ORF43': 'TRIR',\n",
       " 'C9ORF53': 'CDKN2A-DT',\n",
       " 'C11ORF63': 'JHY',\n",
       " 'KIAA1211L': 'CRACDL',\n",
       " 'FAM166A': 'CIMIP2A',\n",
       " 'CCDC189': 'CFAP119',\n",
       " 'ATP5E': 'ATP5F1E',\n",
       " 'WDR11-AS1': 'WDR11-DT',\n",
       " 'C19ORF52': 'TIMM29',\n",
       " 'HIST1H2AM': 'H2AC17',\n",
       " 'TSSC1': 'EIPR1',\n",
       " 'FAM63A': 'MINDY1',\n",
       " 'HIST1H2AI': 'H2AC13',\n",
       " 'ATP5J2': 'ATP5MF',\n",
       " 'PPAP2B': 'PLPP3',\n",
       " 'WDR61': 'SKIC8',\n",
       " 'B3GALTL': 'B3GLCT',\n",
       " 'KAL1': 'ANOS1',\n",
       " 'PTPLAD1': 'HACD3',\n",
       " 'HIST1H1B': 'H1-5',\n",
       " 'TCTEX1D2': 'DYNLT2B',\n",
       " 'WHSC1L1': 'NSD3',\n",
       " 'C17ORF59': 'BORCS6',\n",
       " 'IGJ': 'JCHAIN',\n",
       " 'LINC00672': 'LASP1NB',\n",
       " 'ATP5G1': 'ATP5MC1',\n",
       " 'C19ORF10': 'MYDGF',\n",
       " 'KIAA0196': 'WASHC5',\n",
       " 'FAM69A': 'DIPK1A',\n",
       " 'C1ORF106': 'INAVA',\n",
       " 'C4ORF32': 'FAM241A',\n",
       " 'C22ORF24': 'YWHAH-AS1',\n",
       " 'C11ORF70': 'CFAP300',\n",
       " 'WARS': 'WARS1',\n",
       " 'NUDT16P1': 'NUDT16L2P',\n",
       " 'ZCCHC11': 'TUT4',\n",
       " 'PCDHB18': 'PCDHB18P',\n",
       " 'H3F3C': 'H3-5',\n",
       " 'C14ORF159': 'DGLUCY',\n",
       " 'C15ORF52': 'CCDC9B',\n",
       " 'MESDC2': 'MESD',\n",
       " 'NOV': 'RPL10',\n",
       " 'KIAA0556': 'KATNIP',\n",
       " 'AAED1': 'PRXL2C',\n",
       " 'C11ORF88': 'HOATZ',\n",
       " 'IARS': 'IARS1',\n",
       " 'KIAA0100': 'BLTP2',\n",
       " 'GUCY1B3': 'GUCY1B1',\n",
       " 'QARS': 'QARS1',\n",
       " 'TARS': 'TARS1',\n",
       " 'HN1': 'JPT1',\n",
       " 'COLCA2': 'POU2AF3',\n",
       " 'RARRES3': 'PLAAT4',\n",
       " 'LINC00643': 'SERTAD4BP',\n",
       " 'C1ORF192': 'CFAP126',\n",
       " 'FAM175B': 'ABRAXAS2',\n",
       " 'NGFRAP1': 'BEX3',\n",
       " 'H2AFY': 'MACROH2A1',\n",
       " 'C10ORF10': 'DEPP1',\n",
       " 'ACRC': 'GCNA',\n",
       " 'C4ORF22': 'CFAP299',\n",
       " 'MRE11A': 'MRE11',\n",
       " 'C1ORF123': 'CZIB',\n",
       " 'CYR61': 'CCN1',\n",
       " 'DYX1C1': 'DNAAF4',\n",
       " 'HIST1H2BK': 'H2BC12',\n",
       " 'KIAA0391': 'PRORP',\n",
       " 'C9ORF64': 'QNG1',\n",
       " 'UTP11L': 'UTP11',\n",
       " 'C19ORF68': 'ZSWIM9',\n",
       " 'KIAA0141': 'DELE1',\n",
       " 'ERO1L': 'ERO1A',\n",
       " 'PQLC3': 'SLC66A3',\n",
       " 'AQPEP': 'LVRN',\n",
       " 'HIST1H2BD': 'H2BC5',\n",
       " 'RSG1': 'CPLANE2',\n",
       " 'WBSCR17': 'GALNT17',\n",
       " 'MUM1L1': 'PWWP3B',\n",
       " 'CSRP2BP': 'PET117',\n",
       " 'C14ORF166': 'RTRAF',\n",
       " 'H2AFY2': 'MACROH2A2',\n",
       " 'FAM134B': 'RETREG1',\n",
       " 'ADCK3': 'COQ8A',\n",
       " 'METTL7A': 'TMT1A',\n",
       " 'DFNA5': 'GSDME',\n",
       " 'C17ORF64': 'CHCT1',\n",
       " 'EFCAB1': 'CLXN',\n",
       " 'C14ORF2': 'ATP5MJ',\n",
       " 'ALS2CR11': 'C2CD6',\n",
       " 'TMEM56': 'TLCD4',\n",
       " 'SLC9A3R1': 'NHERF1',\n",
       " 'CXORF67': 'EZHIP',\n",
       " 'GPR116': 'ADGRF5',\n",
       " 'SEPT6': 'SEPTIN6',\n",
       " 'B3GNT1': 'B4GAT1',\n",
       " 'ICK': 'CILK1',\n",
       " 'CCDC67': 'DEUP1',\n",
       " 'C1ORF204': 'SNHG28',\n",
       " 'ISPD': 'CRPPA',\n",
       " 'MARCH10': 'MARCHF10',\n",
       " 'NRD1': 'NRDC',\n",
       " 'TMEM159': 'LDAF1',\n",
       " 'WDR60': 'DYNC2I1',\n",
       " 'KIAA1324': 'ELAPOR1',\n",
       " 'GRAMD2': 'GRAMD2A',\n",
       " 'ATP5G3': 'ATP5MC3',\n",
       " 'C2ORF43': 'LDAH',\n",
       " 'C2ORF70': 'CIMIP2C',\n",
       " 'FAM71F1': 'GARIN1B',\n",
       " 'H1FX': 'H1-10',\n",
       " 'C5ORF56': 'IRF1-AS1',\n",
       " 'C11ORF49': 'CSTPP1',\n",
       " 'LRMP': 'IRAG2',\n",
       " 'TMEM110': 'STIMATE',\n",
       " 'WASH1': 'WASHC1',\n",
       " 'DIEXF': 'UTP25',\n",
       " 'CCDC36': 'IHO1',\n",
       " 'FAM103A1': 'RAMAC',\n",
       " 'HIST1H1C': 'H1-2',\n",
       " 'HIST1H4K': 'H4C12',\n",
       " 'YARS': 'YARS1',\n",
       " 'FUK': 'FCSK',\n",
       " 'FAM92B': 'CIBAR2',\n",
       " 'TIAF1': 'MYO18A',\n",
       " 'MUM1': 'PWWP3A',\n",
       " 'LDOC1L': 'RTL6',\n",
       " 'CENPBD1': 'CENPBD1P',\n",
       " 'ZNF720': 'KRBOX5',\n",
       " 'C9ORF16': 'BBLN',\n",
       " 'CD97': 'ADGRE5',\n",
       " 'DDX58': 'RIGI',\n",
       " 'FAM46A': 'TENT5A',\n",
       " 'GPR56': 'ADGRG1',\n",
       " 'MARCH6': 'MARCHF6',\n",
       " 'HIST1H2AC': 'H2AC6',\n",
       " 'PVRL3': 'NECTIN3',\n",
       " 'ATPIF1': 'ATP5IF1',\n",
       " 'FAM60A': 'SINHCAF',\n",
       " 'H1F0': 'H1-0',\n",
       " 'EFTUD1': 'EFL1',\n",
       " 'GRAMD3': 'GRAMD2B',\n",
       " 'WDR78': 'DNAI4',\n",
       " 'WRB': 'GET1',\n",
       " 'FAM183A': 'CFAP144',\n",
       " 'KIAA1244': 'ARFGEF3',\n",
       " 'KIAA1715': 'LNPK',\n",
       " 'HIST1H4B': 'H4C2',\n",
       " 'HIST1H3F': 'H3C7',\n",
       " 'C17ORF62': 'CYBC1',\n",
       " 'BAI3': 'ADGRB3',\n",
       " 'LINS': 'LINS1',\n",
       " 'GATSL2': 'CASTOR2',\n",
       " 'MFI2': 'MELTF',\n",
       " 'GATS': 'CASTOR3P',\n",
       " 'FAM84A': 'LRATD1',\n",
       " 'KIAA0247': 'SUSD6',\n",
       " 'C9ORF9': 'SPACA9',\n",
       " 'CARS': 'CARS1',\n",
       " 'BHLHB9': 'GPRASP3',\n",
       " 'FAM160A2': 'FHIP1B',\n",
       " 'C9ORF89': 'CARD19',\n",
       " 'MAATS1': 'CFAP91',\n",
       " 'H2AFV': 'H2AZ2',\n",
       " 'KIAA1377': 'CEP126',\n",
       " 'CRAMP1L': 'CRAMP1',\n",
       " 'FAM129C': 'NIBAN3',\n",
       " 'KIAA1919': 'MFSD4B',\n",
       " 'HIST1H3A': 'H3C1',\n",
       " 'C3ORF58': 'DIPK2A',\n",
       " 'HIST1H2BG': 'H2BC8',\n",
       " 'METTL21B': 'EEF1AKMT3',\n",
       " 'TCTEX1D4': 'DYNLT4',\n",
       " 'FAM19A5': 'TAFA5',\n",
       " 'HIST3H2A': 'H2AC25',\n",
       " 'HIST1H2AJ': 'H2AC14',\n",
       " 'DHFRL1': 'DHFR2',\n",
       " 'FAM189A2': 'ENTREP1',\n",
       " 'CCDC108': 'CFAP65',\n",
       " 'CECR1': 'ADA2',\n",
       " 'ZBED6CL': 'ZBED10P',\n",
       " 'GPR125': 'ADGRA3',\n",
       " 'KIAA1257': 'CFAP92',\n",
       " 'C2ORF61': 'STPG4',\n",
       " 'GPR110': 'ADGRF1',\n",
       " 'SMA4': 'GUSBP14',\n",
       " 'C17ORF47': 'SEPTIN4',\n",
       " 'TWISTNB': 'POLR1F',\n",
       " 'C11ORF85': 'MAJIN',\n",
       " 'LHFP': 'LHFPL6',\n",
       " 'SEPP1': 'SELENOP',\n",
       " 'WBP5': 'TCEAL9',\n",
       " 'C16ORF52': 'MOSMO',\n",
       " 'KIAA0355': 'GARRE1',\n",
       " 'GBA': 'GBA1',\n",
       " 'TTC18': 'CFAP70',\n",
       " 'TMEM189': 'PEDS1',\n",
       " 'KARS': 'KARS1',\n",
       " 'RQCD1': 'CNOT9',\n",
       " 'FAM126B': 'HYCC2',\n",
       " 'FAIM3': 'FCMR',\n",
       " 'C10ORF82': 'SPMIP5',\n",
       " 'FAM173B': 'ATPSCKMT',\n",
       " 'FAM160B1': 'FHIP2A',\n",
       " 'PYCRL': 'PYCR3',\n",
       " 'LEPREL1': 'P3H2',\n",
       " 'FAM57A': 'TLCD3A',\n",
       " 'HIST1H2AB': 'H2AC4',\n",
       " 'GARS': 'GARS1',\n",
       " 'GUCY1A3': 'GUCY1A1',\n",
       " 'KIAA1462': 'JCAD',\n",
       " 'C12ORF45': 'NOPCHAP1',\n",
       " 'C12ORF73': 'UQCC6',\n",
       " 'C16ORF72': 'HAPSTR1',\n",
       " 'FAM212B': 'INKA2',\n",
       " 'AIM1': 'CRYBG1',\n",
       " 'WDR16': 'CFAP52',\n",
       " 'TMEM35': 'TMEM35A',\n",
       " 'ZNF788': 'ZNF788P',\n",
       " 'H2AFX': 'H2AX',\n",
       " 'ATP5A1': 'ATP5F1A',\n",
       " 'SQRDL': 'SQOR',\n",
       " 'STRA13': 'CENPX',\n",
       " 'GCN1L1': 'GCN1',\n",
       " 'CCDC151': 'ODAD3',\n",
       " 'SELM': 'SELENOM',\n",
       " 'H2BFS': 'H2BC12L',\n",
       " 'CCDC94': 'YJU2',\n",
       " 'MARCH1': 'MARCHF1',\n",
       " 'C1ORF168': 'FYB2',\n",
       " 'H3F3A': 'H3-3A',\n",
       " 'ASNA1': 'GET3',\n",
       " 'FAM102A': 'EEIG1',\n",
       " 'SEPT2': 'SEPTIN6',\n",
       " 'FGFR1OP': 'CEP43',\n",
       " 'RNMTL1': 'MRM3',\n",
       " 'MARCH8': 'MARCHF8',\n",
       " 'WISP3': 'CCN6',\n",
       " 'PLA2G16': 'PLAAT3',\n",
       " 'CYHR1': 'ZFTRAF1',\n",
       " 'PTPLA': 'HACD1',\n",
       " 'GOLGA8I': 'GOLGA8IP',\n",
       " 'C6ORF48': 'SNHG32',\n",
       " 'FAM134C': 'RETREG3',\n",
       " 'C3ORF14': 'CEP15',\n",
       " 'HDGFRP3': 'HDGFL3',\n",
       " 'LRRC48': 'DRC3',\n",
       " 'CASC4': 'GOLM2',\n",
       " 'HIST1H2AH': 'H2AC12',\n",
       " 'KIAA1161': 'MYORG',\n",
       " 'DNAJC3-AS1': 'DNAJC3-DT',\n",
       " 'KIAA1033': 'WASHC4',\n",
       " 'ANKRD20A4': 'ANKRD20A4P',\n",
       " 'ANKRD20A3': 'ANKRD20A3P',\n",
       " 'LRRC16A': 'CARMIL1',\n",
       " 'PROSC': 'PLPBP',\n",
       " 'AARS': 'AARS1',\n",
       " 'ACPP': 'ACP3',\n",
       " 'C17ORF53': 'HROB',\n",
       " 'FAM96B': 'CIAO2B',\n",
       " 'MARS': 'MARS1',\n",
       " 'C16ORF45': 'BMERB1',\n",
       " 'FAM96A': 'CIAO2A',\n",
       " 'MFSD7': 'SLC49A3',\n",
       " 'CTGF': 'CCN2',\n",
       " 'CXORF57': 'RADX',\n",
       " 'CXORF23': 'BCLAF3',\n",
       " 'AHSA2': 'AHSA2P',\n",
       " 'GIF': 'MT3',\n",
       " 'C11ORF53': 'POU2AF2',\n",
       " 'FAM129A': 'NIBAN1',\n",
       " 'SGK223': 'PRAG1',\n",
       " 'TMEM133': 'ARHGAP42',\n",
       " 'C1ORF213': 'ZNF436-AS1',\n",
       " 'GPR126': 'ADGRG6',\n",
       " 'C5ORF51': 'RIMOC1',\n",
       " 'ZFYVE20': 'RBSN',\n",
       " 'FAM196B': 'INSYN2B',\n",
       " 'DSCR3': 'VPS26C',\n",
       " 'HIST1H4A': 'H4C1',\n",
       " 'HRSP12': 'RIDA',\n",
       " 'C8ORF4': 'TCIM',\n",
       " 'ATP5O': 'ATP5PO',\n",
       " 'FAM173A': 'ANTKMT',\n",
       " 'MST4': 'STK26',\n",
       " 'HIST1H3H': 'H3C10',\n",
       " 'METTL7B': 'TMT1B',\n",
       " 'C8ORF37': 'CFAP418',\n",
       " 'PP7080': 'SLC9A3-OT1',\n",
       " 'C6ORF201': 'TEX56P',\n",
       " 'HIST1H2BH': 'H2BC9',\n",
       " 'C9ORF84': 'SHOC1',\n",
       " 'PALM2-AKAP2': 'PALM2AKAP2',\n",
       " 'KIAA1598': 'SHTN1',\n",
       " 'FAM134A': 'RETREG2',\n",
       " 'CCDC129': 'ITPRID1',\n",
       " 'FAM189A1': 'ENTREP2'}"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "updated_genes_mapping"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "def update_gene_list(row):\n",
    "    genes = row['GeneList'].split(' ')\n",
    "    updated_genes = []\n",
    "    updated_status = False\n",
    "    num_updates = 0 \n",
    "    for gene in genes:\n",
    "        if gene in updated_genes_mapping:\n",
    "            updated_genes.append(updated_genes_mapping[gene])\n",
    "            updated_status = True\n",
    "            num_updates += 1\n",
    "        else:\n",
    "            updated_genes.append(gene)\n",
    "\n",
    "    assert len(genes) == len(updated_genes), f\"Length of genes: {len(genes)} and updated_genes: {len(updated_genes)} are not the same\"\n",
    "    return ' '.join(updated_genes), updated_status, num_updates"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Source</th>\n",
       "      <th>GeneSetID</th>\n",
       "      <th>GeneSetName</th>\n",
       "      <th>GeneList</th>\n",
       "      <th>n_Genes</th>\n",
       "      <th>LLM Name</th>\n",
       "      <th>LLM Analysis</th>\n",
       "      <th>Score</th>\n",
       "      <th>updated GeneList</th>\n",
       "      <th>update status</th>\n",
       "      <th>num genes updated</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>292</th>\n",
       "      <td>Viral_Infections</td>\n",
       "      <td>SARS-dORF6_84Hour...137</td>\n",
       "      <td>SARS-dORF6 84Hour...137</td>\n",
       "      <td>HOTTIP NEU1 ARFGAP3 MAPKAPK2 SLC35B4 MIS12 HIN...</td>\n",
       "      <td>99</td>\n",
       "      <td>System of unrelated proteins</td>\n",
       "      <td>The provided list of interacting proteins enco...</td>\n",
       "      <td>0.00</td>\n",
       "      <td>HOTTIP NEU1 ARFGAP3 MAPKAPK2 SLC35B4 MIS12 HIN...</td>\n",
       "      <td>True</td>\n",
       "      <td>12</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>241</th>\n",
       "      <td>L1000</td>\n",
       "      <td>BRD-A41250203_-666_MCF7_6.0_h_10.0_um</td>\n",
       "      <td>BRD-A41250203 -666 MCF7 6.0 h 10.0 um</td>\n",
       "      <td>1060P11.3 ABCC5 AGT AKR1C2 APOC1 APPBP2 ASNS A...</td>\n",
       "      <td>92</td>\n",
       "      <td>Cellular Stress Response and Apoptosis Regulation</td>\n",
       "      <td>1. The proteins in this system are involved in...</td>\n",
       "      <td>0.92</td>\n",
       "      <td>1060P11.3 ABCC5 AGT AKR1C2 APOC1 APPBP2 ASNS A...</td>\n",
       "      <td>True</td>\n",
       "      <td>11</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>NeST</td>\n",
       "      <td>Cluster1-5</td>\n",
       "      <td>Cluster1-5</td>\n",
       "      <td>ANKRD45 BBOF1 C1orf194 C2orf73 C11orf63 C11orf...</td>\n",
       "      <td>93</td>\n",
       "      <td>Ciliogenesis and Ciliary Function</td>\n",
       "      <td>The proteins listed are predominantly associat...</td>\n",
       "      <td>0.92</td>\n",
       "      <td>ANKRD45 BBOF1 C1orf194 C2orf73 C11orf63 C11orf...</td>\n",
       "      <td>True</td>\n",
       "      <td>8</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>283</th>\n",
       "      <td>Viral_Infections</td>\n",
       "      <td>SARS-BatSRBD_0Hour...202</td>\n",
       "      <td>SARS-BatSRBD 0Hour...202</td>\n",
       "      <td>BRSK1 TFPI CHST4 SCARA3 TMEM177 KIF2A HNRNPK G...</td>\n",
       "      <td>95</td>\n",
       "      <td>System of unrelated proteins</td>\n",
       "      <td>The provided list of proteins encompasses a wi...</td>\n",
       "      <td>0.00</td>\n",
       "      <td>BRSK1 TFPI CHST4 SCARA3 TMEM177 KIF2A HNRNPK G...</td>\n",
       "      <td>True</td>\n",
       "      <td>8</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>268</th>\n",
       "      <td>Viral_Infections</td>\n",
       "      <td>A-Vietnam-1203_CIP048_RG4-2004(H5N1)NS1trunc_7...</td>\n",
       "      <td>A-Vietnam-1203 CIP048 RG4-2004(H5N1)NS1trunc 7...</td>\n",
       "      <td>LRRN4 C3ORF20 NELL2 FSTL3 SLC4A9 TAC1 PRB1 CAR...</td>\n",
       "      <td>53</td>\n",
       "      <td>System of unrelated proteins</td>\n",
       "      <td>The provided list of interacting proteins enco...</td>\n",
       "      <td>0.00</td>\n",
       "      <td>LRRN4 C3ORF20 NELL2 FSTL3 SLC4A9 TAC1 PRB1 CAR...</td>\n",
       "      <td>True</td>\n",
       "      <td>8</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>58</th>\n",
       "      <td>NeST</td>\n",
       "      <td>Cluster2-139</td>\n",
       "      <td>Cluster2-139</td>\n",
       "      <td>ACBD6 ACRV1 ACYP1 C4orf48 CAMTA1 CCDC85B CTRL ...</td>\n",
       "      <td>32</td>\n",
       "      <td>Chromatin Organization and Gene Expression Reg...</td>\n",
       "      <td>1. The histone proteins HIST1H2AH, HIST1H2AI, ...</td>\n",
       "      <td>0.85</td>\n",
       "      <td>ACBD6 ACRV1 ACYP1 C4orf48 CAMTA1 CCDC85B CTRL ...</td>\n",
       "      <td>True</td>\n",
       "      <td>8</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>221</th>\n",
       "      <td>L1000</td>\n",
       "      <td>BRD-A35033682_-666_MCF7_6.0_h_10.0_um</td>\n",
       "      <td>BRD-A35033682 -666 MCF7 6.0 h 10.0 um</td>\n",
       "      <td>ABCB6 AK4 AMDHD2 BHLHE41 C1S CD58 CFD CHI3L1 C...</td>\n",
       "      <td>74</td>\n",
       "      <td>System of unrelated proteins</td>\n",
       "      <td>The provided list of proteins encompasses a wi...</td>\n",
       "      <td>0.00</td>\n",
       "      <td>ABCB6 AK4 AMDHD2 BHLHE41 C1S CD58 CFD CHI3L1 C...</td>\n",
       "      <td>True</td>\n",
       "      <td>7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>155</th>\n",
       "      <td>L1000</td>\n",
       "      <td>BRD-A11678676_-666_MCF7_6.0_h_10.0_um</td>\n",
       "      <td>BRD-A11678676 -666 MCF7 6.0 h 10.0 um</td>\n",
       "      <td>1060P11.3 AQP3 BASP1 BNIP3L BTG1 C6ORF48 CCNG2...</td>\n",
       "      <td>75</td>\n",
       "      <td>Cellular Stress Response and Apoptosis Regulation</td>\n",
       "      <td>1. Several proteins in this system, such as BN...</td>\n",
       "      <td>0.85</td>\n",
       "      <td>1060P11.3 AQP3 BASP1 BNIP3L BTG1 SNHG32 CCNG2 ...</td>\n",
       "      <td>True</td>\n",
       "      <td>7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>277</th>\n",
       "      <td>Viral_Infections</td>\n",
       "      <td>Enterovirus 71_8Hour</td>\n",
       "      <td>Enterovirus 71 8Hour</td>\n",
       "      <td>NELL2 PDYN OR7A5 GREB1 PCP4L1 LOC100128002 KRT...</td>\n",
       "      <td>95</td>\n",
       "      <td>System of unrelated proteins</td>\n",
       "      <td>The provided list of proteins encompasses a wi...</td>\n",
       "      <td>0.00</td>\n",
       "      <td>NELL2 PDYN OR7A5 GREB1 PCP4L1 LOC100128002 KRT...</td>\n",
       "      <td>True</td>\n",
       "      <td>7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>271</th>\n",
       "      <td>Viral_Infections</td>\n",
       "      <td>Dhori Virus_24Hour</td>\n",
       "      <td>Dhori Virus 24Hour</td>\n",
       "      <td>SLC39A5 SVEP1 DPYSL5 KIAA1919 GPR89A FAAH2 HEY...</td>\n",
       "      <td>92</td>\n",
       "      <td>System of unrelated proteins</td>\n",
       "      <td>The provided list of proteins encompasses a wi...</td>\n",
       "      <td>0.00</td>\n",
       "      <td>SLC39A5 SVEP1 DPYSL5 MFSD4B GPR89A FAAH2 HEY2 ...</td>\n",
       "      <td>True</td>\n",
       "      <td>7</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "               Source                                          GeneSetID  \\\n",
       "292  Viral_Infections                            SARS-dORF6_84Hour...137   \n",
       "241             L1000              BRD-A41250203_-666_MCF7_6.0_h_10.0_um   \n",
       "14               NeST                                         Cluster1-5   \n",
       "283  Viral_Infections                           SARS-BatSRBD_0Hour...202   \n",
       "268  Viral_Infections  A-Vietnam-1203_CIP048_RG4-2004(H5N1)NS1trunc_7...   \n",
       "58               NeST                                       Cluster2-139   \n",
       "221             L1000              BRD-A35033682_-666_MCF7_6.0_h_10.0_um   \n",
       "155             L1000              BRD-A11678676_-666_MCF7_6.0_h_10.0_um   \n",
       "277  Viral_Infections                               Enterovirus 71_8Hour   \n",
       "271  Viral_Infections                                 Dhori Virus_24Hour   \n",
       "\n",
       "                                           GeneSetName  \\\n",
       "292                            SARS-dORF6 84Hour...137   \n",
       "241              BRD-A41250203 -666 MCF7 6.0 h 10.0 um   \n",
       "14                                          Cluster1-5   \n",
       "283                           SARS-BatSRBD 0Hour...202   \n",
       "268  A-Vietnam-1203 CIP048 RG4-2004(H5N1)NS1trunc 7...   \n",
       "58                                        Cluster2-139   \n",
       "221              BRD-A35033682 -666 MCF7 6.0 h 10.0 um   \n",
       "155              BRD-A11678676 -666 MCF7 6.0 h 10.0 um   \n",
       "277                               Enterovirus 71 8Hour   \n",
       "271                                 Dhori Virus 24Hour   \n",
       "\n",
       "                                              GeneList  n_Genes  \\\n",
       "292  HOTTIP NEU1 ARFGAP3 MAPKAPK2 SLC35B4 MIS12 HIN...       99   \n",
       "241  1060P11.3 ABCC5 AGT AKR1C2 APOC1 APPBP2 ASNS A...       92   \n",
       "14   ANKRD45 BBOF1 C1orf194 C2orf73 C11orf63 C11orf...       93   \n",
       "283  BRSK1 TFPI CHST4 SCARA3 TMEM177 KIF2A HNRNPK G...       95   \n",
       "268  LRRN4 C3ORF20 NELL2 FSTL3 SLC4A9 TAC1 PRB1 CAR...       53   \n",
       "58   ACBD6 ACRV1 ACYP1 C4orf48 CAMTA1 CCDC85B CTRL ...       32   \n",
       "221  ABCB6 AK4 AMDHD2 BHLHE41 C1S CD58 CFD CHI3L1 C...       74   \n",
       "155  1060P11.3 AQP3 BASP1 BNIP3L BTG1 C6ORF48 CCNG2...       75   \n",
       "277  NELL2 PDYN OR7A5 GREB1 PCP4L1 LOC100128002 KRT...       95   \n",
       "271  SLC39A5 SVEP1 DPYSL5 KIAA1919 GPR89A FAAH2 HEY...       92   \n",
       "\n",
       "                                              LLM Name  \\\n",
       "292                       System of unrelated proteins   \n",
       "241  Cellular Stress Response and Apoptosis Regulation   \n",
       "14                   Ciliogenesis and Ciliary Function   \n",
       "283                       System of unrelated proteins   \n",
       "268                       System of unrelated proteins   \n",
       "58   Chromatin Organization and Gene Expression Reg...   \n",
       "221                       System of unrelated proteins   \n",
       "155  Cellular Stress Response and Apoptosis Regulation   \n",
       "277                       System of unrelated proteins   \n",
       "271                       System of unrelated proteins   \n",
       "\n",
       "                                          LLM Analysis  Score  \\\n",
       "292  The provided list of interacting proteins enco...   0.00   \n",
       "241  1. The proteins in this system are involved in...   0.92   \n",
       "14   The proteins listed are predominantly associat...   0.92   \n",
       "283  The provided list of proteins encompasses a wi...   0.00   \n",
       "268  The provided list of interacting proteins enco...   0.00   \n",
       "58   1. The histone proteins HIST1H2AH, HIST1H2AI, ...   0.85   \n",
       "221  The provided list of proteins encompasses a wi...   0.00   \n",
       "155  1. Several proteins in this system, such as BN...   0.85   \n",
       "277  The provided list of proteins encompasses a wi...   0.00   \n",
       "271  The provided list of proteins encompasses a wi...   0.00   \n",
       "\n",
       "                                      updated GeneList  update status  \\\n",
       "292  HOTTIP NEU1 ARFGAP3 MAPKAPK2 SLC35B4 MIS12 HIN...           True   \n",
       "241  1060P11.3 ABCC5 AGT AKR1C2 APOC1 APPBP2 ASNS A...           True   \n",
       "14   ANKRD45 BBOF1 C1orf194 C2orf73 C11orf63 C11orf...           True   \n",
       "283  BRSK1 TFPI CHST4 SCARA3 TMEM177 KIF2A HNRNPK G...           True   \n",
       "268  LRRN4 C3ORF20 NELL2 FSTL3 SLC4A9 TAC1 PRB1 CAR...           True   \n",
       "58   ACBD6 ACRV1 ACYP1 C4orf48 CAMTA1 CCDC85B CTRL ...           True   \n",
       "221  ABCB6 AK4 AMDHD2 BHLHE41 C1S CD58 CFD CHI3L1 C...           True   \n",
       "155  1060P11.3 AQP3 BASP1 BNIP3L BTG1 SNHG32 CCNG2 ...           True   \n",
       "277  NELL2 PDYN OR7A5 GREB1 PCP4L1 LOC100128002 KRT...           True   \n",
       "271  SLC39A5 SVEP1 DPYSL5 MFSD4B GPR89A FAAH2 HEY2 ...           True   \n",
       "\n",
       "     num genes updated  \n",
       "292                 12  \n",
       "241                 11  \n",
       "14                   8  \n",
       "283                  8  \n",
       "268                  8  \n",
       "58                   8  \n",
       "221                  7  \n",
       "155                  7  \n",
       "277                  7  \n",
       "271                  7  "
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df[['updated GeneList', 'update status', 'num genes updated']] = df.apply(lambda row: pd.Series(update_gene_list(row)), axis=1)\n",
    "df.loc[df['update status'] == True, :].sort_values(by='num genes updated', ascending=False).head(10)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(187, 11)"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df.loc[df['update status'] == True,:].shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Index(['Source', 'GeneSetID', 'GeneSetName', 'GeneList', 'n_Genes', 'LLM Name',\n",
       "       'LLM Analysis', 'Score', 'updated GeneList', 'update status',\n",
       "       'num genes updated'],\n",
       "      dtype='object')"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df.columns"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [],
   "source": [
    "df[['Source', 'GeneSetID', 'GeneSetName', 'GeneList','updated GeneList', 'n_Genes', 'LLM Name',\n",
    "       'LLM Analysis', 'Score']].to_csv('data/omics_revamped_LLM_updated_genes_DF.tsv', sep='\\t', index=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "llm_eval",
   "language": "python",
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