{ "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": [ "
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pubidquestioncontextlong_answerfinal_decision
021645374Do mitochondria play a role in remodelling lac...{'contexts': ['Programmed cell death (PCD) is ...Results depicted mitochondrial dynamics in viv...yes
116418930Landolt C and snellen e acuity: differences in...{'contexts': ['Assessment of visual acuity dep...Using the charts described, there was only a s...no
29488747Syncope during bathing in infants, a pediatric...{'contexts': ['Apparent life-threatening event...\"Aquagenic maladies\" could be a pediatric form...yes
317208539Are the long-term results of the transanal pul...{'contexts': ['The transanal endorectal pull-t...Our long-term study showed significantly bette...no
410808977Can tailored interventions increase mammograph...{'contexts': ['Telephone counseling and tailor...The effects of the intervention were most pron...yes
..................
9958921484Does gestational age misclassification explain...{'contexts': ['After 34 weeks gestation, summa...Gestational age misclassification is an unlike...no
99616564683Is there any interest to perform ultrasonograp...{'contexts': ['To evaluate the accuracy of ult...Sonography has no place in the diagnosis of un...no
99723147106Is peak concentration needed in therapeutic dr...{'contexts': ['We analyzed the pharmacokinetic...These results suggest little need to use peak ...no
99821550158Can autologous platelet-rich plasma gel enhanc...{'contexts': ['This investigation assesses the...The PRP group recorded reduced pain, swelling,...yes
99917559449Are sugars-free medicines more erosive than su...{'contexts': ['The reduced use of sugars-conta...Paediatric SF medicines were not more erosive ...no
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" ], "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 }