add dataset

.ipynb

@@ -1,277 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "code",
-   "execution_count": 9,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "import pandas as pd\n",
-    "a = pd.read_parquet(\"data/test.parquet\")\n",
-    "b = pd.read_parquet(\"data/passages.parquet\")"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 13,
-   "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>question</th>\n",
-       "      <th>answer</th>\n",
-       "      <th>relevant_passage_ids</th>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>id</th>\n",
-       "      <th></th>\n",
-       "      <th></th>\n",
-       "      <th></th>\n",
-       "    </tr>\n",
-       "  </thead>\n",
-       "  <tbody>\n",
-       "    <tr>\n",
-       "      <th>0</th>\n",
-       "      <td>Is Hirschsprung disease a mendelian or a multi...</td>\n",
-       "      <td>Coding sequence mutations in RET, GDNF, EDNRB,...</td>\n",
-       "      <td>[20598273, 6650562, 15829955, 15617541, 230011...</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>1</th>\n",
-       "      <td>List signaling molecules (ligands) that intera...</td>\n",
-       "      <td>The 7 known EGFR ligands  are: epidermal growt...</td>\n",
-       "      <td>[23821377, 24323361, 23382875, 22247333, 23787...</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>2</th>\n",
-       "      <td>Is the protein Papilin secreted?</td>\n",
-       "      <td>Yes,  papilin is a secreted protein</td>\n",
-       "      <td>[21784067, 19297413, 15094122, 7515725, 332004...</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>3</th>\n",
-       "      <td>Are long non coding RNAs spliced?</td>\n",
-       "      <td>Long non coding RNAs appear to be spliced thro...</td>\n",
-       "      <td>[22955974, 21622663, 22707570, 22955988, 24285...</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>4</th>\n",
-       "      <td>Is RANKL secreted from the cells?</td>\n",
-       "      <td>Receptor activator of nuclear factor κB ligand...</td>\n",
-       "      <td>[22867712, 23827649, 21618594, 23835909, 24265...</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>...</th>\n",
-       "      <td>...</td>\n",
-       "      <td>...</td>\n",
-       "      <td>...</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>4714</th>\n",
-       "      <td>Is PPROM a condition that occurs in males or f...</td>\n",
-       "      <td>Preterm premature rupture of fetal membranes (...</td>\n",
-       "      <td>[23599878, 23573382, 24304137, 18301713, 23179...</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>4715</th>\n",
-       "      <td>What is EpiMethylTag?</td>\n",
-       "      <td>EpiMethylTag is a fast, low-input, low sequenc...</td>\n",
-       "      <td>[31752933]</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>4716</th>\n",
-       "      <td>What is the target of Sutimlimab?</td>\n",
-       "      <td>Sutimlimab is a novel humanized monoclonal ant...</td>\n",
-       "      <td>[30635392, 31229501, 33826820, 32176765, 31114...</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>4717</th>\n",
-       "      <td>Can parasite infections by Schistosoma japonic...</td>\n",
-       "      <td>A peptide named as SJMHE1 from Schistosoma jap...</td>\n",
-       "      <td>[26840774, 34703270, 28614408, 31496071, 18654...</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>4718</th>\n",
-       "      <td>Describe Multilocus Inherited Neoplasia Allele...</td>\n",
-       "      <td>Genetic testing of hereditary cancer using com...</td>\n",
-       "      <td>[30580288]</td>\n",
-       "    </tr>\n",
-       "  </tbody>\n",
-       "</table>\n",
-       "<p>4719 rows × 3 columns</p>\n",
-       "</div>"
-      ],
-      "text/plain": [
-       "                                               question  \\\n",
-       "id                                                        \n",
-       "0     Is Hirschsprung disease a mendelian or a multi...   \n",
-       "1     List signaling molecules (ligands) that intera...   \n",
-       "2                      Is the protein Papilin secreted?   \n",
-       "3                     Are long non coding RNAs spliced?   \n",
-       "4                     Is RANKL secreted from the cells?   \n",
-       "...                                                 ...   \n",
-       "4714  Is PPROM a condition that occurs in males or f...   \n",
-       "4715                              What is EpiMethylTag?   \n",
-       "4716                  What is the target of Sutimlimab?   \n",
-       "4717  Can parasite infections by Schistosoma japonic...   \n",
-       "4718  Describe Multilocus Inherited Neoplasia Allele...   \n",
-       "\n",
-       "                                                 answer  \\\n",
-       "id                                                        \n",
-       "0     Coding sequence mutations in RET, GDNF, EDNRB,...   \n",
-       "1     The 7 known EGFR ligands  are: epidermal growt...   \n",
-       "2                   Yes,  papilin is a secreted protein   \n",
-       "3     Long non coding RNAs appear to be spliced thro...   \n",
-       "4     Receptor activator of nuclear factor κB ligand...   \n",
-       "...                                                 ...   \n",
-       "4714  Preterm premature rupture of fetal membranes (...   \n",
-       "4715  EpiMethylTag is a fast, low-input, low sequenc...   \n",
-       "4716  Sutimlimab is a novel humanized monoclonal ant...   \n",
-       "4717  A peptide named as SJMHE1 from Schistosoma jap...   \n",
-       "4718  Genetic testing of hereditary cancer using com...   \n",
-       "\n",
-       "                                   relevant_passage_ids  \n",
-       "id                                                       \n",
-       "0     [20598273, 6650562, 15829955, 15617541, 230011...  \n",
-       "1     [23821377, 24323361, 23382875, 22247333, 23787...  \n",
-       "2     [21784067, 19297413, 15094122, 7515725, 332004...  \n",
-       "3     [22955974, 21622663, 22707570, 22955988, 24285...  \n",
-       "4     [22867712, 23827649, 21618594, 23835909, 24265...  \n",
-       "...                                                 ...  \n",
-       "4714  [23599878, 23573382, 24304137, 18301713, 23179...  \n",
-       "4715                                         [31752933]  \n",
-       "4716  [30635392, 31229501, 33826820, 32176765, 31114...  \n",
-       "4717  [26840774, 34703270, 28614408, 31496071, 18654...  \n",
-       "4718                                         [30580288]  \n",
-       "\n",
-       "[4719 rows x 3 columns]"
-      ]
-     },
-     "execution_count": 13,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "a"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 11,
-   "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>passage</th>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>id</th>\n",
-       "      <th></th>\n",
-       "    </tr>\n",
-       "  </thead>\n",
-       "  <tbody>\n",
-       "    <tr>\n",
-       "      <th>21495810</th>\n",
-       "      <td>OBJECT: Factors determining choice of an acade...</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>26869762</th>\n",
-       "      <td>Castleman disease (CD) is a rare, heterogeneou...</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>28049410</th>\n",
-       "      <td>BACKGROUND: Data extraction and integration me...</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>24510469</th>\n",
-       "      <td>Flecainide is recommended as a first-line anti...</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>8650761</th>\n",
-       "      <td>Primary intestinal lymphangiectasia (PIL), fir...</td>\n",
-       "    </tr>\n",
-       "  </tbody>\n",
-       "</table>\n",
-       "</div>"
-      ],
-      "text/plain": [
-       "                                                    passage\n",
-       "id                                                         \n",
-       "21495810  OBJECT: Factors determining choice of an acade...\n",
-       "26869762  Castleman disease (CD) is a rare, heterogeneou...\n",
-       "28049410  BACKGROUND: Data extraction and integration me...\n",
-       "24510469  Flecainide is recommended as a first-line anti...\n",
-       "8650761   Primary intestinal lymphangiectasia (PIL), fir..."
-      ]
-     },
-     "execution_count": 11,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "b"
-   ]
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "env",
-   "language": "python",
-   "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.10.12"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 2
-}

data/passages.parquet/part.0.parquet

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:c288905f142dde9c3c21207333380a81d3f34603584851be02ccf7e543041934
-size 12581
+oid sha256:93afd23506e6ab65451a43a411fd6481b6378a00fef7983b44cc8c3ddbb37c84
+size 24470604

generate.py

@@ -73,6 +73,7 @@ if __name__ == "__main__":
 
         # intermediate save
         if i % 1000 == 0:
+            passages.index.name = "id"
             dd.from_pandas(passages, npartitions=1).to_parquet(PATH_TO_PASSAGE_DATASET)