File size: 12,115 Bytes
5374a2d | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 | {
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"id": "b0ea2822",
"metadata": {},
"outputs": [],
"source": [
"import pandas as pd\n",
"\n",
"df = pd.read_parquet(\"hf://datasets/qiaojin/PubMedQA/pqa_artificial/train-00000-of-00001.parquet\")"
]
},
{
"cell_type": "code",
"execution_count": 6,
"id": "532fb572",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'Chronic rhinosinusitis (CRS) is a heterogeneous disease with an uncertain pathogenesis. Group 2 innate lymphoid cells (ILC2s) represent a recently discovered cell population which has been implicated in driving Th2 inflammation in CRS; however, their relationship with clinical disease characteristics has yet to be investigated.\\nThe aim of this study was to identify ILC2s in sinus mucosa in patients with CRS and controls and compare ILC2s across characteristics of disease.\\nA cross-sectional study of patients with CRS undergoing endoscopic sinus surgery was conducted. Sinus mucosal biopsies were obtained during surgery and control tissue from patients undergoing pituitary tumour resection through transphenoidal approach. ILC2s were identified as CD45(+) Lin(-) CD127(+) CD4(-) CD8(-) CRTH2(CD294)(+) CD161(+) cells in single cell suspensions through flow cytometry. ILC2 frequencies, measured as a percentage of CD45(+) cells, were compared across CRS phenotype, endotype, inflammatory CRS subtype and other disease characteristics including blood eosinophils, serum IgE, asthma status and nasal symptom score.\\n35 patients (40% female, age 48 ± 17 years) including 13 with eosinophilic CRS (eCRS), 13 with non-eCRS and 9 controls were recruited. ILC2 frequencies were associated with the presence of nasal polyps (P = 0.002) as well as high tissue eosinophilia (P = 0.004) and eosinophil-dominant CRS (P = 0.001) (Mann-Whitney U). They were also associated with increased blood eosinophilia (P = 0.005). There were no significant associations found between ILC2s and serum total IgE and allergic disease. In the CRS with nasal polyps (CRSwNP) population, ILC2s were increased in patients with co-existing asthma (P = 0.03). ILC2s were also correlated with worsening nasal symptom score in CRS (P = 0.04).'"
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"'\\n'.join(df.loc[0]['context']['contexts'])"
]
},
{
"cell_type": "code",
"execution_count": 8,
"id": "273a2b36",
"metadata": {},
"outputs": [],
"source": [
"df.to_json(\"pubmedqa_train.json\", orient='records', indent=4)"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "bbb50950",
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": 10,
"id": "9be45340",
"metadata": {},
"outputs": [],
"source": [
"import pandas as pd\n",
"\n",
"df = pd.read_parquet(\"hf://datasets/qiaojin/PubMedQA/pqa_labeled/train-00000-of-00001.parquet\")"
]
},
{
"cell_type": "code",
"execution_count": 14,
"id": "77730f3e",
"metadata": {},
"outputs": [],
"source": [
"df.to_json(\"pubmedqa_label.json\", orient='records', indent=4)"
]
},
{
"cell_type": "code",
"execution_count": 15,
"id": "c6471fbd",
"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>pubid</th>\n",
" <th>question</th>\n",
" <th>context</th>\n",
" <th>long_answer</th>\n",
" <th>final_decision</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>21645374</td>\n",
" <td>Do mitochondria play a role in remodelling lac...</td>\n",
" <td>{'contexts': ['Programmed cell death (PCD) is ...</td>\n",
" <td>Results depicted mitochondrial dynamics in viv...</td>\n",
" <td>yes</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>16418930</td>\n",
" <td>Landolt C and snellen e acuity: differences in...</td>\n",
" <td>{'contexts': ['Assessment of visual acuity dep...</td>\n",
" <td>Using the charts described, there was only a s...</td>\n",
" <td>no</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>9488747</td>\n",
" <td>Syncope during bathing in infants, a pediatric...</td>\n",
" <td>{'contexts': ['Apparent life-threatening event...</td>\n",
" <td>\"Aquagenic maladies\" could be a pediatric form...</td>\n",
" <td>yes</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>17208539</td>\n",
" <td>Are the long-term results of the transanal pul...</td>\n",
" <td>{'contexts': ['The transanal endorectal pull-t...</td>\n",
" <td>Our long-term study showed significantly bette...</td>\n",
" <td>no</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>10808977</td>\n",
" <td>Can tailored interventions increase mammograph...</td>\n",
" <td>{'contexts': ['Telephone counseling and tailor...</td>\n",
" <td>The effects of the intervention were most pron...</td>\n",
" <td>yes</td>\n",
" </tr>\n",
" <tr>\n",
" <th>...</th>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>995</th>\n",
" <td>8921484</td>\n",
" <td>Does gestational age misclassification explain...</td>\n",
" <td>{'contexts': ['After 34 weeks gestation, summa...</td>\n",
" <td>Gestational age misclassification is an unlike...</td>\n",
" <td>no</td>\n",
" </tr>\n",
" <tr>\n",
" <th>996</th>\n",
" <td>16564683</td>\n",
" <td>Is there any interest to perform ultrasonograp...</td>\n",
" <td>{'contexts': ['To evaluate the accuracy of ult...</td>\n",
" <td>Sonography has no place in the diagnosis of un...</td>\n",
" <td>no</td>\n",
" </tr>\n",
" <tr>\n",
" <th>997</th>\n",
" <td>23147106</td>\n",
" <td>Is peak concentration needed in therapeutic dr...</td>\n",
" <td>{'contexts': ['We analyzed the pharmacokinetic...</td>\n",
" <td>These results suggest little need to use peak ...</td>\n",
" <td>no</td>\n",
" </tr>\n",
" <tr>\n",
" <th>998</th>\n",
" <td>21550158</td>\n",
" <td>Can autologous platelet-rich plasma gel enhanc...</td>\n",
" <td>{'contexts': ['This investigation assesses the...</td>\n",
" <td>The PRP group recorded reduced pain, swelling,...</td>\n",
" <td>yes</td>\n",
" </tr>\n",
" <tr>\n",
" <th>999</th>\n",
" <td>17559449</td>\n",
" <td>Are sugars-free medicines more erosive than su...</td>\n",
" <td>{'contexts': ['The reduced use of sugars-conta...</td>\n",
" <td>Paediatric SF medicines were not more erosive ...</td>\n",
" <td>no</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"<p>1000 rows × 5 columns</p>\n",
"</div>"
],
"text/plain": [
" pubid question \\\n",
"0 21645374 Do mitochondria play a role in remodelling lac... \n",
"1 16418930 Landolt C and snellen e acuity: differences in... \n",
"2 9488747 Syncope during bathing in infants, a pediatric... \n",
"3 17208539 Are the long-term results of the transanal pul... \n",
"4 10808977 Can tailored interventions increase mammograph... \n",
".. ... ... \n",
"995 8921484 Does gestational age misclassification explain... \n",
"996 16564683 Is there any interest to perform ultrasonograp... \n",
"997 23147106 Is peak concentration needed in therapeutic dr... \n",
"998 21550158 Can autologous platelet-rich plasma gel enhanc... \n",
"999 17559449 Are sugars-free medicines more erosive than su... \n",
"\n",
" context \\\n",
"0 {'contexts': ['Programmed cell death (PCD) is ... \n",
"1 {'contexts': ['Assessment of visual acuity dep... \n",
"2 {'contexts': ['Apparent life-threatening event... \n",
"3 {'contexts': ['The transanal endorectal pull-t... \n",
"4 {'contexts': ['Telephone counseling and tailor... \n",
".. ... \n",
"995 {'contexts': ['After 34 weeks gestation, summa... \n",
"996 {'contexts': ['To evaluate the accuracy of ult... \n",
"997 {'contexts': ['We analyzed the pharmacokinetic... \n",
"998 {'contexts': ['This investigation assesses the... \n",
"999 {'contexts': ['The reduced use of sugars-conta... \n",
"\n",
" long_answer final_decision \n",
"0 Results depicted mitochondrial dynamics in viv... yes \n",
"1 Using the charts described, there was only a s... no \n",
"2 \"Aquagenic maladies\" could be a pediatric form... yes \n",
"3 Our long-term study showed significantly bette... no \n",
"4 The effects of the intervention were most pron... yes \n",
".. ... ... \n",
"995 Gestational age misclassification is an unlike... no \n",
"996 Sonography has no place in the diagnosis of un... no \n",
"997 These results suggest little need to use peak ... no \n",
"998 The PRP group recorded reduced pain, swelling,... yes \n",
"999 Paediatric SF medicines were not more erosive ... no \n",
"\n",
"[1000 rows x 5 columns]"
]
},
"execution_count": 15,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"df"
]
},
{
"cell_type": "code",
"execution_count": 16,
"id": "c0f1ab25",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"/gpfs/radev/pi/ying_rex/tl688/selfevolve/EvoAgentX/examples/pubmedqa\r\n"
]
}
],
"source": [
"!pwd"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"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": "3.11.13"
}
},
"nbformat": 4,
"nbformat_minor": 5
}
|