From 036e31ddf0e6543e9ea153a1206c1dc5f995924a Mon Sep 17 00:00:00 2001
From: Adrien Klose <ikenex3@gmail.com>
Date: Fri, 31 May 2024 00:25:39 +0200
Subject: [PATCH] small experiment on handpicked samples
---
ideas_practice/code/.gitignore | 1 +
.../code/bioasq_yesno_chatgpt.ipynb | 89 +++
.../code/bioasq_yesno_handpicked.csv | 108 ++--
.../bioasq_yesno_handpicked_experiment.csv | 81 +++
ideas_practice/code/create_prompts.ipynb | 517 ++++++++++++++++++
ideas_practice/code/prompting_strategies.md | 52 ++
6 files changed, 794 insertions(+), 54 deletions(-)
create mode 100644 ideas_practice/code/bioasq_yesno_chatgpt.ipynb
create mode 100644 ideas_practice/code/bioasq_yesno_handpicked_experiment.csv
create mode 100644 ideas_practice/code/create_prompts.ipynb
create mode 100644 ideas_practice/code/prompting_strategies.md
diff --git a/ideas_practice/code/.gitignore b/ideas_practice/code/.gitignore
index b28b9dd..80eb0a3 100644
--- a/ideas_practice/code/.gitignore
+++ b/ideas_practice/code/.gitignore
@@ -1,2 +1,3 @@
.ipynm_checkpoints/*
.ipynb_checkpoints/*
+*.env
diff --git a/ideas_practice/code/bioasq_yesno_chatgpt.ipynb b/ideas_practice/code/bioasq_yesno_chatgpt.ipynb
new file mode 100644
index 0000000..c211de3
--- /dev/null
+++ b/ideas_practice/code/bioasq_yesno_chatgpt.ipynb
@@ -0,0 +1,89 @@
+{
+ "cells": [
+ {
+ "cell_type": "code",
+ "execution_count": 4,
+ "id": "7209584a-2748-4473-acc8-51a062f7b2cd",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# set up environment\n",
+ "from openai import OpenAI\n",
+ "import os\n",
+ "import dotenv\n",
+ "dotenv.load_dotenv()\n",
+ "client = OpenAI()\n",
+ "#api_key=os.environ.get(\"OPENAI_API_KEY\")"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 5,
+ "id": "6f05f369-af37-45df-8a33-675f177290b4",
+ "metadata": {},
+ "outputs": [
+ {
+ "ename": "RateLimitError",
+ "evalue": "Error code: 429 - {'error': {'message': 'You exceeded your current quota, please check your plan and billing details. For more information on this error, read the docs: https://platform.openai.com/docs/guides/error-codes/api-errors.', 'type': 'insufficient_quota', 'param': None, 'code': 'insufficient_quota'}}",
+ "output_type": "error",
+ "traceback": [
+ "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+ "\u001b[0;31mRateLimitError\u001b[0m Traceback (most recent call last)",
+ "Cell \u001b[0;32mIn[5], line 2\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[38;5;66;03m# first example\u001b[39;00m\n\u001b[0;32m----> 2\u001b[0m completion \u001b[38;5;241m=\u001b[39m \u001b[43mclient\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mchat\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcompletions\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcreate\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 3\u001b[0m \u001b[43m \u001b[49m\u001b[43mmodel\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mgpt-3.5-turbo\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 4\u001b[0m \u001b[43m \u001b[49m\u001b[43mmessages\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m[\u001b[49m\n\u001b[1;32m 5\u001b[0m \u001b[43m \u001b[49m\u001b[43m{\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mrole\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m:\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43msystem\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mcontent\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m:\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mYou are a poetic assistant, skilled in explaining complex programming concepts with creative flair.\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m}\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 6\u001b[0m \u001b[43m \u001b[49m\u001b[43m{\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mrole\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m:\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43muser\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mcontent\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m:\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mCompose a poem that explains the concept of recursion in programming.\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m}\u001b[49m\n\u001b[1;32m 7\u001b[0m \u001b[43m \u001b[49m\u001b[43m]\u001b[49m\n\u001b[1;32m 8\u001b[0m \u001b[43m)\u001b[49m\n\u001b[1;32m 10\u001b[0m \u001b[38;5;28mprint\u001b[39m(completion\u001b[38;5;241m.\u001b[39mchoices[\u001b[38;5;241m0\u001b[39m]\u001b[38;5;241m.\u001b[39mmessage)\n",
+ "File \u001b[0;32m~/.local/lib/python3.10/site-packages/openai/_utils/_utils.py:277\u001b[0m, in \u001b[0;36mrequired_args.<locals>.inner.<locals>.wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 275\u001b[0m msg \u001b[38;5;241m=\u001b[39m \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mMissing required argument: \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mquote(missing[\u001b[38;5;241m0\u001b[39m])\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 276\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mTypeError\u001b[39;00m(msg)\n\u001b[0;32m--> 277\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mfunc\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n",
+ "File \u001b[0;32m~/.local/lib/python3.10/site-packages/openai/resources/chat/completions.py:590\u001b[0m, in \u001b[0;36mCompletions.create\u001b[0;34m(self, messages, model, frequency_penalty, function_call, functions, logit_bias, logprobs, max_tokens, n, presence_penalty, response_format, seed, stop, stream, stream_options, temperature, tool_choice, tools, top_logprobs, top_p, user, extra_headers, extra_query, extra_body, timeout)\u001b[0m\n\u001b[1;32m 558\u001b[0m \u001b[38;5;129m@required_args\u001b[39m([\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mmessages\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mmodel\u001b[39m\u001b[38;5;124m\"\u001b[39m], [\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mmessages\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mmodel\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mstream\u001b[39m\u001b[38;5;124m\"\u001b[39m])\n\u001b[1;32m 559\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mcreate\u001b[39m(\n\u001b[1;32m 560\u001b[0m \u001b[38;5;28mself\u001b[39m,\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 588\u001b[0m timeout: \u001b[38;5;28mfloat\u001b[39m \u001b[38;5;241m|\u001b[39m httpx\u001b[38;5;241m.\u001b[39mTimeout \u001b[38;5;241m|\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m \u001b[38;5;241m|\u001b[39m NotGiven \u001b[38;5;241m=\u001b[39m NOT_GIVEN,\n\u001b[1;32m 589\u001b[0m ) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m ChatCompletion \u001b[38;5;241m|\u001b[39m Stream[ChatCompletionChunk]:\n\u001b[0;32m--> 590\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_post\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 591\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43m/chat/completions\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 592\u001b[0m \u001b[43m \u001b[49m\u001b[43mbody\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mmaybe_transform\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 593\u001b[0m \u001b[43m \u001b[49m\u001b[43m{\u001b[49m\n\u001b[1;32m 594\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mmessages\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m:\u001b[49m\u001b[43m \u001b[49m\u001b[43mmessages\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 595\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mmodel\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m:\u001b[49m\u001b[43m \u001b[49m\u001b[43mmodel\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 596\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mfrequency_penalty\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m:\u001b[49m\u001b[43m \u001b[49m\u001b[43mfrequency_penalty\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 597\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mfunction_call\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m:\u001b[49m\u001b[43m \u001b[49m\u001b[43mfunction_call\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 598\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mfunctions\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m:\u001b[49m\u001b[43m \u001b[49m\u001b[43mfunctions\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 599\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mlogit_bias\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m:\u001b[49m\u001b[43m \u001b[49m\u001b[43mlogit_bias\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 600\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mlogprobs\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m:\u001b[49m\u001b[43m \u001b[49m\u001b[43mlogprobs\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 601\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mmax_tokens\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m:\u001b[49m\u001b[43m \u001b[49m\u001b[43mmax_tokens\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 602\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mn\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m:\u001b[49m\u001b[43m \u001b[49m\u001b[43mn\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 603\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mpresence_penalty\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m:\u001b[49m\u001b[43m \u001b[49m\u001b[43mpresence_penalty\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 604\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mresponse_format\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m:\u001b[49m\u001b[43m \u001b[49m\u001b[43mresponse_format\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 605\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mseed\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m:\u001b[49m\u001b[43m \u001b[49m\u001b[43mseed\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 606\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mstop\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m:\u001b[49m\u001b[43m \u001b[49m\u001b[43mstop\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 607\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mstream\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m:\u001b[49m\u001b[43m \u001b[49m\u001b[43mstream\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 608\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mstream_options\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m:\u001b[49m\u001b[43m \u001b[49m\u001b[43mstream_options\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 609\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mtemperature\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m:\u001b[49m\u001b[43m \u001b[49m\u001b[43mtemperature\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 610\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mtool_choice\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m:\u001b[49m\u001b[43m \u001b[49m\u001b[43mtool_choice\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 611\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mtools\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m:\u001b[49m\u001b[43m \u001b[49m\u001b[43mtools\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 612\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mtop_logprobs\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m:\u001b[49m\u001b[43m \u001b[49m\u001b[43mtop_logprobs\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 613\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mtop_p\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m:\u001b[49m\u001b[43m \u001b[49m\u001b[43mtop_p\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 614\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43muser\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m:\u001b[49m\u001b[43m \u001b[49m\u001b[43muser\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 615\u001b[0m \u001b[43m \u001b[49m\u001b[43m}\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 616\u001b[0m \u001b[43m \u001b[49m\u001b[43mcompletion_create_params\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mCompletionCreateParams\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 617\u001b[0m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 618\u001b[0m \u001b[43m \u001b[49m\u001b[43moptions\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mmake_request_options\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 619\u001b[0m \u001b[43m \u001b[49m\u001b[43mextra_headers\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mextra_headers\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mextra_query\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mextra_query\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mextra_body\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mextra_body\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mtimeout\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mtimeout\u001b[49m\n\u001b[1;32m 620\u001b[0m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 621\u001b[0m \u001b[43m \u001b[49m\u001b[43mcast_to\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mChatCompletion\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 622\u001b[0m \u001b[43m \u001b[49m\u001b[43mstream\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mstream\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;129;43;01mor\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mFalse\u001b[39;49;00m\u001b[43m,\u001b[49m\n\u001b[1;32m 623\u001b[0m \u001b[43m \u001b[49m\u001b[43mstream_cls\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mStream\u001b[49m\u001b[43m[\u001b[49m\u001b[43mChatCompletionChunk\u001b[49m\u001b[43m]\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 624\u001b[0m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m\n",
+ "File \u001b[0;32m~/.local/lib/python3.10/site-packages/openai/_base_client.py:1240\u001b[0m, in \u001b[0;36mSyncAPIClient.post\u001b[0;34m(self, path, cast_to, body, options, files, stream, stream_cls)\u001b[0m\n\u001b[1;32m 1226\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mpost\u001b[39m(\n\u001b[1;32m 1227\u001b[0m \u001b[38;5;28mself\u001b[39m,\n\u001b[1;32m 1228\u001b[0m path: \u001b[38;5;28mstr\u001b[39m,\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 1235\u001b[0m stream_cls: \u001b[38;5;28mtype\u001b[39m[_StreamT] \u001b[38;5;241m|\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m,\n\u001b[1;32m 1236\u001b[0m ) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m ResponseT \u001b[38;5;241m|\u001b[39m _StreamT:\n\u001b[1;32m 1237\u001b[0m opts \u001b[38;5;241m=\u001b[39m FinalRequestOptions\u001b[38;5;241m.\u001b[39mconstruct(\n\u001b[1;32m 1238\u001b[0m method\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mpost\u001b[39m\u001b[38;5;124m\"\u001b[39m, url\u001b[38;5;241m=\u001b[39mpath, json_data\u001b[38;5;241m=\u001b[39mbody, files\u001b[38;5;241m=\u001b[39mto_httpx_files(files), \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39moptions\n\u001b[1;32m 1239\u001b[0m )\n\u001b[0;32m-> 1240\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m cast(ResponseT, \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mrequest\u001b[49m\u001b[43m(\u001b[49m\u001b[43mcast_to\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mopts\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mstream\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mstream\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mstream_cls\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mstream_cls\u001b[49m\u001b[43m)\u001b[49m)\n",
+ "File \u001b[0;32m~/.local/lib/python3.10/site-packages/openai/_base_client.py:921\u001b[0m, in \u001b[0;36mSyncAPIClient.request\u001b[0;34m(self, cast_to, options, remaining_retries, stream, stream_cls)\u001b[0m\n\u001b[1;32m 912\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mrequest\u001b[39m(\n\u001b[1;32m 913\u001b[0m \u001b[38;5;28mself\u001b[39m,\n\u001b[1;32m 914\u001b[0m cast_to: Type[ResponseT],\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 919\u001b[0m stream_cls: \u001b[38;5;28mtype\u001b[39m[_StreamT] \u001b[38;5;241m|\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m,\n\u001b[1;32m 920\u001b[0m ) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m ResponseT \u001b[38;5;241m|\u001b[39m _StreamT:\n\u001b[0;32m--> 921\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_request\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 922\u001b[0m \u001b[43m \u001b[49m\u001b[43mcast_to\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcast_to\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 923\u001b[0m \u001b[43m \u001b[49m\u001b[43moptions\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43moptions\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 924\u001b[0m \u001b[43m \u001b[49m\u001b[43mstream\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mstream\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 925\u001b[0m \u001b[43m \u001b[49m\u001b[43mstream_cls\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mstream_cls\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 926\u001b[0m \u001b[43m \u001b[49m\u001b[43mremaining_retries\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mremaining_retries\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 927\u001b[0m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m\n",
+ "File \u001b[0;32m~/.local/lib/python3.10/site-packages/openai/_base_client.py:1005\u001b[0m, in \u001b[0;36mSyncAPIClient._request\u001b[0;34m(self, cast_to, options, remaining_retries, stream, stream_cls)\u001b[0m\n\u001b[1;32m 1003\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m retries \u001b[38;5;241m>\u001b[39m \u001b[38;5;241m0\u001b[39m \u001b[38;5;129;01mand\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_should_retry(err\u001b[38;5;241m.\u001b[39mresponse):\n\u001b[1;32m 1004\u001b[0m err\u001b[38;5;241m.\u001b[39mresponse\u001b[38;5;241m.\u001b[39mclose()\n\u001b[0;32m-> 1005\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_retry_request\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 1006\u001b[0m \u001b[43m \u001b[49m\u001b[43moptions\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1007\u001b[0m \u001b[43m \u001b[49m\u001b[43mcast_to\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1008\u001b[0m \u001b[43m \u001b[49m\u001b[43mretries\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1009\u001b[0m \u001b[43m \u001b[49m\u001b[43merr\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mresponse\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mheaders\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1010\u001b[0m \u001b[43m \u001b[49m\u001b[43mstream\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mstream\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1011\u001b[0m \u001b[43m \u001b[49m\u001b[43mstream_cls\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mstream_cls\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1012\u001b[0m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1014\u001b[0m \u001b[38;5;66;03m# If the response is streamed then we need to explicitly read the response\u001b[39;00m\n\u001b[1;32m 1015\u001b[0m \u001b[38;5;66;03m# to completion before attempting to access the response text.\u001b[39;00m\n\u001b[1;32m 1016\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m err\u001b[38;5;241m.\u001b[39mresponse\u001b[38;5;241m.\u001b[39mis_closed:\n",
+ "File \u001b[0;32m~/.local/lib/python3.10/site-packages/openai/_base_client.py:1053\u001b[0m, in \u001b[0;36mSyncAPIClient._retry_request\u001b[0;34m(self, options, cast_to, remaining_retries, response_headers, stream, stream_cls)\u001b[0m\n\u001b[1;32m 1049\u001b[0m \u001b[38;5;66;03m# In a synchronous context we are blocking the entire thread. Up to the library user to run the client in a\u001b[39;00m\n\u001b[1;32m 1050\u001b[0m \u001b[38;5;66;03m# different thread if necessary.\u001b[39;00m\n\u001b[1;32m 1051\u001b[0m time\u001b[38;5;241m.\u001b[39msleep(timeout)\n\u001b[0;32m-> 1053\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_request\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 1054\u001b[0m \u001b[43m \u001b[49m\u001b[43moptions\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43moptions\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1055\u001b[0m \u001b[43m \u001b[49m\u001b[43mcast_to\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcast_to\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1056\u001b[0m \u001b[43m \u001b[49m\u001b[43mremaining_retries\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mremaining\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1057\u001b[0m \u001b[43m \u001b[49m\u001b[43mstream\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mstream\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1058\u001b[0m \u001b[43m \u001b[49m\u001b[43mstream_cls\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mstream_cls\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1059\u001b[0m \u001b[43m\u001b[49m\u001b[43m)\u001b[49m\n",
+ "File \u001b[0;32m~/.local/lib/python3.10/site-packages/openai/_base_client.py:1005\u001b[0m, in \u001b[0;36mSyncAPIClient._request\u001b[0;34m(self, cast_to, options, remaining_retries, stream, stream_cls)\u001b[0m\n\u001b[1;32m 1003\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m retries \u001b[38;5;241m>\u001b[39m \u001b[38;5;241m0\u001b[39m \u001b[38;5;129;01mand\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_should_retry(err\u001b[38;5;241m.\u001b[39mresponse):\n\u001b[1;32m 1004\u001b[0m err\u001b[38;5;241m.\u001b[39mresponse\u001b[38;5;241m.\u001b[39mclose()\n\u001b[0;32m-> 1005\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_retry_request\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 1006\u001b[0m \u001b[43m \u001b[49m\u001b[43moptions\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1007\u001b[0m \u001b[43m \u001b[49m\u001b[43mcast_to\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1008\u001b[0m \u001b[43m \u001b[49m\u001b[43mretries\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1009\u001b[0m \u001b[43m \u001b[49m\u001b[43merr\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mresponse\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mheaders\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1010\u001b[0m \u001b[43m \u001b[49m\u001b[43mstream\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mstream\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1011\u001b[0m \u001b[43m \u001b[49m\u001b[43mstream_cls\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mstream_cls\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1012\u001b[0m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1014\u001b[0m \u001b[38;5;66;03m# If the response is streamed then we need to explicitly read the response\u001b[39;00m\n\u001b[1;32m 1015\u001b[0m \u001b[38;5;66;03m# to completion before attempting to access the response text.\u001b[39;00m\n\u001b[1;32m 1016\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m err\u001b[38;5;241m.\u001b[39mresponse\u001b[38;5;241m.\u001b[39mis_closed:\n",
+ "File \u001b[0;32m~/.local/lib/python3.10/site-packages/openai/_base_client.py:1053\u001b[0m, in \u001b[0;36mSyncAPIClient._retry_request\u001b[0;34m(self, options, cast_to, remaining_retries, response_headers, stream, stream_cls)\u001b[0m\n\u001b[1;32m 1049\u001b[0m \u001b[38;5;66;03m# In a synchronous context we are blocking the entire thread. Up to the library user to run the client in a\u001b[39;00m\n\u001b[1;32m 1050\u001b[0m \u001b[38;5;66;03m# different thread if necessary.\u001b[39;00m\n\u001b[1;32m 1051\u001b[0m time\u001b[38;5;241m.\u001b[39msleep(timeout)\n\u001b[0;32m-> 1053\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_request\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 1054\u001b[0m \u001b[43m \u001b[49m\u001b[43moptions\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43moptions\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1055\u001b[0m \u001b[43m \u001b[49m\u001b[43mcast_to\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcast_to\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1056\u001b[0m \u001b[43m \u001b[49m\u001b[43mremaining_retries\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mremaining\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1057\u001b[0m \u001b[43m \u001b[49m\u001b[43mstream\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mstream\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1058\u001b[0m \u001b[43m \u001b[49m\u001b[43mstream_cls\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mstream_cls\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1059\u001b[0m \u001b[43m\u001b[49m\u001b[43m)\u001b[49m\n",
+ "File \u001b[0;32m~/.local/lib/python3.10/site-packages/openai/_base_client.py:1020\u001b[0m, in \u001b[0;36mSyncAPIClient._request\u001b[0;34m(self, cast_to, options, remaining_retries, stream, stream_cls)\u001b[0m\n\u001b[1;32m 1017\u001b[0m err\u001b[38;5;241m.\u001b[39mresponse\u001b[38;5;241m.\u001b[39mread()\n\u001b[1;32m 1019\u001b[0m log\u001b[38;5;241m.\u001b[39mdebug(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mRe-raising status error\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[0;32m-> 1020\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_make_status_error_from_response(err\u001b[38;5;241m.\u001b[39mresponse) \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m\n\u001b[1;32m 1022\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_process_response(\n\u001b[1;32m 1023\u001b[0m cast_to\u001b[38;5;241m=\u001b[39mcast_to,\n\u001b[1;32m 1024\u001b[0m options\u001b[38;5;241m=\u001b[39moptions,\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 1027\u001b[0m stream_cls\u001b[38;5;241m=\u001b[39mstream_cls,\n\u001b[1;32m 1028\u001b[0m )\n",
+ "\u001b[0;31mRateLimitError\u001b[0m: Error code: 429 - {'error': {'message': 'You exceeded your current quota, please check your plan and billing details. For more information on this error, read the docs: https://platform.openai.com/docs/guides/error-codes/api-errors.', 'type': 'insufficient_quota', 'param': None, 'code': 'insufficient_quota'}}"
+ ]
+ }
+ ],
+ "source": [
+ "# first example\n",
+ "completion = client.chat.completions.create(\n",
+ " model=\"gpt-3.5-turbo\",\n",
+ " messages=[\n",
+ " {\"role\": \"system\", \"content\": \"You are a poetic assistant, skilled in explaining complex programming concepts with creative flair.\"},\n",
+ " {\"role\": \"user\", \"content\": \"Compose a poem that explains the concept of recursion in programming.\"}\n",
+ " ]\n",
+ ")\n",
+ "\n",
+ "print(completion.choices[0].message)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "6cf7d4e4-173c-497e-a254-c9278a9c6e13",
+ "metadata": {},
+ "outputs": [],
+ "source": []
+ }
+ ],
+ "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": "3.10.12"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/ideas_practice/code/bioasq_yesno_handpicked.csv b/ideas_practice/code/bioasq_yesno_handpicked.csv
index 4e0172d..2206471 100644
--- a/ideas_practice/code/bioasq_yesno_handpicked.csv
+++ b/ideas_practice/code/bioasq_yesno_handpicked.csv
@@ -5,57 +5,57 @@ bioasq_id,id,rui,s,p,o,nl_resolved,question,ground_truth,source
532f08b8d6d3ac6a34000029,4,R176804338,Pulmonary Embolism,may be treated by,rivaraxoban,Pulmonary Embolism may be treated by Rivaraxoban.,Are there any specific antidotes for rivaroxaban?,no,self
532f08b8d6d3ac6a34000029,4,R176804576,Venous Thrombosis,may be treated by,rivaraxoban,Venous Thrombosis may be treated by Rivaraxoban,Are there any specific antidotes for rivaroxaban?,no,self
532f08b8d6d3ac6a34000029,4,R182894841,Hemorrhage,has contraindicated drug,rivaraxoban,Hemorrhage has the contraindicated drug Rivaraxoban.,Are there any specific antidotes for rivaroxaban?,no,self
-51640b4a298dcd4e51000050,7,R176726757,Pregnancy,has contraindicated drug,isotretinoin,Pregnancy has the contraindicated drug Isotretinoin.,Is it safe to take isotretinoin during pregnancy?,no,
-51640b4a298dcd4e51000050,7,R176812447,isotretinoin,contraindicated with disease,Pregnancy,Isotretinoin contraindicates with pregnancy.,Is it safe to take isotretinoin during pregnancy?,no,
-51640b4a298dcd4e51000050,7,R176810340,Retinoid,parent of,isotretinoin,Retinoid is parent of Isotretinoin in the vocabulary.,Is it safe to take isotretinoin during pregnancy?,no,
-532c147bd6d3ac6a3400001e,9,R32113901,p-(p-(2-aminoethyl)phenoxy)phenol,RN,thyronamine,p-(p-(2-aminoethyl)phenoxy)phenol has a narrower relationship with thyronamine,Have thyronamines effects on fat tissue?,no,
-532c147bd6d3ac6a3400001e,9,R32113902,HCl of thyronamine,RN,thyronamine,HCl of thyronamine has a narrower relationship with Thyronamine.,Have thyronamines effects on fat tissue?,no,
-532c147bd6d3ac6a3400001e,9,R17710985,Brown adipose tissue,is a,Adipose tissue,Brown adipose tissue is a Adipose tissue.,Have thyronamines effects on fat tissue?,no,
-530f685c329f5fcf1e000002,11,R43996771,borna virus,used for,RNA virus,Borna virus is used for RNA virus.,Is there an association between borna virus and brain tumor?,no,
-530f685c329f5fcf1e000002,11,R02836636,borna virus,RB,virus,Borna virus has a broader relationship to virus.,Is there an association between borna virus and brain tumor?,no,
-530f685c329f5fcf1e000002,11,R69762523,Intraventricular Brain Neoplasm,is a,brain tumor,Intraventricular Brain Neoplasm is a brain tumor.,Is there an association between borna virus and brain tumor?,no,
-53124e84e3eabad02100000c,13,R71056477,Collagen Type XVIII,PAR,Endostatins,Collagen Type XVIII is parent of Endostatins in the vocabulary.,Is endostatin a proangiogenic factor?,no,
-53124e84e3eabad02100000c,13,R71368334,Angiostatic Proteins,PAR,Endostatins,Angiostatic Proteins is parent of Endostatins in the vocabulary.,Is endostatin a proangiogenic factor?,no,
-53124e84e3eabad02100000c,13,R28125380,Antineoplastic Agents,inverse is a,Endostatins,Endostatins are antineoplastic agents.,Is endostatin a proangiogenic factor?,no,
-5171833c8ed59a060a00000f,20,R162646180,DNA Cytosine-5-Methylase,has permuted term,DNA Cytosine 5 Methylase,DNA Cytosine-5-Methylase can be permuted to the equivalent DNA Cytosine 5 Methylase.,Are chromomethylases present in animal genomes?,no,
-5171833c8ed59a060a00000f,20,R162764612,DNA Cytosine-5-Methylase,has permuted term,"Cytosine-5-Methylase, DNA","DNA Cytosine-5-Methylase can be permuted to the equivalent Cytosine-5-Methylase, DNA.",Are chromomethylases present in animal genomes?,no,
-5171833c8ed59a060a00000f,20,R174006398,DNA (Cytosine-5-)-Methyltransferase,has sort version,DNA METHYLTRANSFERASE CYTOSINE 05,DNA (Cytosine-5-)-Methyltransferase can be sorted to the equivalent DNA METHYLTRANSFERASE CYTOSINE 05.,Are chromomethylases present in animal genomes?,no,
-52bf1aa503868f1b06000006,33,R157424291,Abatacept,is a,Antirheumatic Agents,Abatacept is a antirheumatic agent.,Is it safe to use Abatacept during pregnancy?,no,
-52bf1aa503868f1b06000006,33,R176834614,Abatacept,has parent,Selective T Cell Costimulation Modulator,Abatacept has the parent Selective T Cell Costimulation Modulator in the vocabulary.,Is it safe to use Abatacept during pregnancy?,no,
-52bf1aa503868f1b06000006,33,R176789004,Abatacept,has parent,A [Preparations],Abatacept has the parent A [Preparations] in the vocabulary.,Is it safe to use Abatacept during pregnancy?,no,
-532f08dcd6d3ac6a3400002a,34,R157427446,Dabigatran,is a,Antithrombins,Dabigatran is an antithrombin .,Are there any specific antidotes for dabigatran?,no,
-532f08dcd6d3ac6a3400002a,34,R176760461,Dabigatran,has parent,D [Preparations],Dabigatran has the parent D [Preparations] in the vocabulary.,Are there any specific antidotes for dabigatran?,no,
-532f08dcd6d3ac6a3400002a,34,C3536847,Dabigatran,has parent,Direct Thrombin Inhibitor,Dabigatran has the parent Direct Thrombin Inhibitor in the vocabulary.,Are there any specific antidotes for dabigatran?,no,
-54f1e781c409818c32000003,36,R176719057,A [Preparations],parent of,armodafinil, A [Preparations]] is parent of armodafinil in the vocabulary.,Is armodafinil used for treatment of insomnia?,no,
-54f1e781c409818c32000003,36,R176742854,Sleep Wake Disorders,may be treated by,armodafinil,Sleep Wake Disorders may be treated by armodafinil.,Is armodafinil used for treatment of insomnia?,no,
-54f1e781c409818c32000003,36,R69828944,CNS Stimulant,inverse is a,armodafinil,Armodafinil is a CNS Stimulant .,Is armodafinil used for treatment of insomnia?,no,
-54e25eaaae9738404b000017,355,R172228926,"papilin, proteoglycan like sulfated glycoprotein",has alias,MGC50452,"Papilin, proteoglycan like sulfated glycoprotein has the alias MGC50452 .",Is the protein Papilin secreted?,yes,
-54e25eaaae9738404b000017,355,R176330815,"PAPILIN, PROTEOGLYCAN-LIKE SULFATED GLYCOPROTEIN",has alias,"PAPILIN, DROSOPHILA, HOMOLOG OF","Papilin, Proteoglycan-like sulfated glycoprotein has the alias papilin, drosophila, homolog of.",Is the protein Papilin secreted?,yes,
-54e25eaaae9738404b000017,355,R176331673,PPN,has expanded form,"PAPILIN, DROSOPHILA, HOMOLOG OF","PPN is a short form for PAPILIN, DROSOPHILA, HOMOLOG OF ",Is the protein Papilin secreted?,yes,
-517395b98ed59a060a00001a,360,R169558438,Transcription,biological process is part of process,Gene Expression,The biological process transcription is part of the process Gene Expression.,Are transcription and splicing connected?,yes,
-517395b98ed59a060a00001a,360,R169238522,Transcription,process includes biological process,Transcription Termination,The process transcription includes the biological process Transcription Termination .,Are transcription and splicing connected?,yes,
-517395b98ed59a060a00001a,360,R168890418,Transcription,process includes biological process,Transcription Initiation,The process transcription includes the biological process Transcription Initiation.,Are transcription and splicing connected?,yes,
-54db1d580f63c58e6e000005,361,R158364010,Hypomethylation,is a,DNA Methylation,Hypomethylation is a DNA Methylation.,Is Alu hypomethylation associated with breast cancer?,yes,
-54db1d580f63c58e6e000005,361,R188854188,Hypomethylation,biological process is part of process,Biochemical Process,The biological process Hypomethylation is part of the process Biochemical Process.,Is Alu hypomethylation associated with breast cancer?,yes,
-54db1d580f63c58e6e000005,361,R169306885,Hypomethylation,biological process is part of process,Epigenetic Process,The biological process Hypomethylation is part of the Epigenetic Process.,Is Alu hypomethylation associated with breast cancer?,yes,
-56bf365eef6e39474100000e,363,R169034691,AKT1 Gene,gene plays role in process,Negative Regulation of Apoptosis,The AKT1 Gene plays a role in the process Negative Regulation of Apoptosis.,Do mutations of AKT1 occur in meningiomas?,yes,
-56bf365eef6e39474100000e,363,R169366166,AKT1 Gene,gene plays role in process,Serine/Threonine Phosphorylation,The AKT1 Gene plays a role in the process Serine/Threonine Phosphorylation.,Do mutations of AKT1 occur in meningiomas?,yes,
-56bf365eef6e39474100000e,363,R169531797,AKT1 Gene,gene plays role in process,Phosphorylation Process,The AKT1 Gene plays a role in the process Phosphorylation Process.,Do mutations of AKT1 occur in meningiomas?,yes,
-571f34ac0fd6f91b68000005,368,R60488665,WEAVER SYNDROME,has manifestation,Talipes equinovarus,The weaver syndrome has the manifestation Talipes equinovarus.,Is Weaver syndrome similar to Sotos?,yes,
-571f34ac0fd6f91b68000005,368,R60605066,WEAVER SYNDROME,has manifestation,Cryptorchidism,The weaver syndrome has the manifestation Cryptorchidism.,Is Weaver syndrome similar to Sotos?,yes,
-571f34ac0fd6f91b68000005,368,R60576105,WEAVER SYNDROME,has manifestation,Loose skin,The weaver syndrome has the manifestation Loose skin.,Is Weaver syndrome similar to Sotos?,yes,
-56c1f029ef6e39474100004a,379,R176829795,valproic acid,may treat,Alzheimer Disease,Valproic acid may treat the Alzheimer Disease.,Is valproic acid effective for glioblastoma treatment?,yes,
-56c1f029ef6e39474100004a,379,R176719689,valproic acid,may treat,Bipolar Disorder,Valproic acid may treat Bipolar Disorder.,Is valproic acid effective for glioblastoma treatment?,yes,
-56c1f029ef6e39474100004a,379,R176733606,valproic acid,may treat,Epilepsy,Valproic acid may treat the Epilepsy.,Is valproic acid effective for glioblastoma treatment?,yes,
-52b2ec744003448f55000001,380,R176798331,levothyroxine sodium,may treat,Thyrotoxicosis,Levothyroxine sodium may treat Thyrotoxicosis.,Can Levoxyl (levothyroxine sodium) cause insomnia?,yes,
-52b2ec744003448f55000001,380,R176784773,levothyroxine sodium,may treat,Goiter,Levothyroxine sodium may treat Goiter.,Can Levoxyl (levothyroxine sodium) cause insomnia?,yes,
-52b2ec744003448f55000001,380,R176753623,levothyroxine sodium,may treat,"Thyroiditis, Autoimmune","Levothyroxine sodium may treat Thyroiditis, Autoimmune.",Can Levoxyl (levothyroxine sodium) cause insomnia?,yes,
-5335b373d6d3ac6a34000050,427,R176753188,ospemifene,may treat,Menopause,Ospemifene may treat Menopause.,Is ospemifene effective for treatment of dyspareunia?,yes,
-5335b373d6d3ac6a34000050,427,R176723366,ospemifene,may treat,Atrophy,Ospemifene may treat Atrophy.,Is ospemifene effective for treatment of dyspareunia?,yes,
-5335b373d6d3ac6a34000050,427,R176754381,ospemifene,may treat,Dyspareunia,Ospemifene may treat Dyspareunia.,Is ospemifene effective for treatment of dyspareunia?,yes,
-5503121de9bde69634000019,430,R168860771,Hirschsprung Disease,disease has associated gene,GDNF Gene,Hirschsprung Disease has the associated gene GDNF.,Is RET the major gene involved in Hirschsprung disease?,yes,
-5503121de9bde69634000019,430,R169160501,Hirschsprung Disease,disease has associated gene,NRTN Gene,Hirschsprung Disease has the associated gene NRTN.,Is RET the major gene involved in Hirschsprung disease?,yes,
-5503121de9bde69634000019,430,R169133845,Hirschsprung Disease,disease has associated gene,NRTN wt Allele,Hirschsprung Disease has the associated gene NRTN wt Allele,Is RET the major gene involved in Hirschsprung disease?,yes,
-56c8318f5795f9a73e00000f,441,R179075784,Sorafenib,is a,Antineoplastic Agents,Sorafenib is an Antineoplastic Agent.,Can sorafenib activate AMPK?,yes,
-56c8318f5795f9a73e00000f,441,R176747430,Sorafenib,has mechanism of action,Kinase Inhibitors,Sorafenib has mechanism of action as Kinase Inhibitors.,Can sorafenib activate AMPK?,yes,
-56c8318f5795f9a73e00000f,441,R188894087,Sorafenib,chemical or drug has mechanism of action,Receptor Tyrosine Kinase Inhibition,Sorafenib is a chemical or drug that has mechanism of action as Receptor Tyrosine Kinase Inhibition.,Can sorafenib activate AMPK?,yes,
+51640b4a298dcd4e51000050,7,R176726757,Pregnancy,has contraindicated drug,isotretinoin,Pregnancy has the contraindicated drug Isotretinoin.,Is it safe to take isotretinoin during pregnancy?,no,self
+51640b4a298dcd4e51000050,7,R176812447,isotretinoin,contraindicated with disease,Pregnancy,Isotretinoin contraindicates with pregnancy.,Is it safe to take isotretinoin during pregnancy?,no,self
+51640b4a298dcd4e51000050,7,R176810340,Retinoid,parent of,isotretinoin,Retinoid is parent of Isotretinoin in the vocabulary.,Is it safe to take isotretinoin during pregnancy?,no,self
+532c147bd6d3ac6a3400001e,9,R32113901,p-(p-(2-aminoethyl)phenoxy)phenol,RN,thyronamine,p-(p-(2-aminoethyl)phenoxy)phenol has a narrower relationship with thyronamine,Have thyronamines effects on fat tissue?,no,self
+532c147bd6d3ac6a3400001e,9,R32113902,HCl of thyronamine,RN,thyronamine,HCl of thyronamine has a narrower relationship with Thyronamine.,Have thyronamines effects on fat tissue?,no,self
+532c147bd6d3ac6a3400001e,9,R17710985,Brown adipose tissue,is a,Adipose tissue,Brown adipose tissue is a Adipose tissue.,Have thyronamines effects on fat tissue?,no,self
+530f685c329f5fcf1e000002,11,R43996771,borna virus,used for,RNA virus,Borna virus is used for RNA virus.,Is there an association between borna virus and brain tumor?,no,self
+530f685c329f5fcf1e000002,11,R02836636,borna virus,RB,virus,Borna virus has a broader relationship to virus.,Is there an association between borna virus and brain tumor?,no,self
+530f685c329f5fcf1e000002,11,R69762523,Intraventricular Brain Neoplasm,is a,brain tumor,Intraventricular Brain Neoplasm is a brain tumor.,Is there an association between borna virus and brain tumor?,no,self
+53124e84e3eabad02100000c,13,R71056477,Collagen Type XVIII,PAR,Endostatins,Collagen Type XVIII is parent of Endostatins in the vocabulary.,Is endostatin a proangiogenic factor?,no,self
+53124e84e3eabad02100000c,13,R71368334,Angiostatic Proteins,PAR,Endostatins,Angiostatic Proteins is parent of Endostatins in the vocabulary.,Is endostatin a proangiogenic factor?,no,self
+53124e84e3eabad02100000c,13,R28125380,Antineoplastic Agents,inverse is a,Endostatins,Endostatins are antineoplastic agents.,Is endostatin a proangiogenic factor?,no,self
+5171833c8ed59a060a00000f,20,R162646180,DNA Cytosine-5-Methylase,has permuted term,DNA Cytosine 5 Methylase,DNA Cytosine-5-Methylase can be permuted to the equivalent DNA Cytosine 5 Methylase.,Are chromomethylases present in animal genomes?,no,self
+5171833c8ed59a060a00000f,20,R162764612,DNA Cytosine-5-Methylase,has permuted term,"Cytosine-5-Methylase, DNA","DNA Cytosine-5-Methylase can be permuted to the equivalent Cytosine-5-Methylase, DNA.",Are chromomethylases present in animal genomes?,no,self
+5171833c8ed59a060a00000f,20,R174006398,DNA (Cytosine-5-)-Methyltransferase,has sort version,DNA METHYLTRANSFERASE CYTOSINE 05,DNA (Cytosine-5-)-Methyltransferase can be sorted to the equivalent DNA METHYLTRANSFERASE CYTOSINE 05.,Are chromomethylases present in animal genomes?,no,self
+52bf1aa503868f1b06000006,33,R157424291,Abatacept,is a,Antirheumatic Agents,Abatacept is a antirheumatic agent.,Is it safe to use Abatacept during pregnancy?,no,self
+52bf1aa503868f1b06000006,33,R176834614,Abatacept,has parent,Selective T Cell Costimulation Modulator,Abatacept has the parent Selective T Cell Costimulation Modulator in the vocabulary.,Is it safe to use Abatacept during pregnancy?,no,self
+52bf1aa503868f1b06000006,33,R176789004,Abatacept,has parent,A [Preparations],Abatacept has the parent A [Preparations] in the vocabulary.,Is it safe to use Abatacept during pregnancy?,no,self
+532f08dcd6d3ac6a3400002a,34,R157427446,Dabigatran,is a,Antithrombins,Dabigatran is an antithrombin .,Are there any specific antidotes for dabigatran?,no,self
+532f08dcd6d3ac6a3400002a,34,R176760461,Dabigatran,has parent,D [Preparations],Dabigatran has the parent D [Preparations] in the vocabulary.,Are there any specific antidotes for dabigatran?,no,self
+532f08dcd6d3ac6a3400002a,34,C3536847,Dabigatran,has parent,Direct Thrombin Inhibitor,Dabigatran has the parent Direct Thrombin Inhibitor in the vocabulary.,Are there any specific antidotes for dabigatran?,no,self
+54f1e781c409818c32000003,36,R176719057,A [Preparations],parent of,armodafinil, A [Preparations]] is parent of armodafinil in the vocabulary.,Is armodafinil used for treatment of insomnia?,no,self
+54f1e781c409818c32000003,36,R176742854,Sleep Wake Disorders,may be treated by,armodafinil,Sleep Wake Disorders may be treated by armodafinil.,Is armodafinil used for treatment of insomnia?,no,self
+54f1e781c409818c32000003,36,R69828944,CNS Stimulant,inverse is a,armodafinil,Armodafinil is a CNS Stimulant .,Is armodafinil used for treatment of insomnia?,no,self
+54e25eaaae9738404b000017,355,R172228926,"papilin, proteoglycan like sulfated glycoprotein",has alias,MGC50452,"Papilin, proteoglycan like sulfated glycoprotein has the alias MGC50452 .",Is the protein Papilin secreted?,yes,self
+54e25eaaae9738404b000017,355,R176330815,"PAPILIN, PROTEOGLYCAN-LIKE SULFATED GLYCOPROTEIN",has alias,"PAPILIN, DROSOPHILA, HOMOLOG OF","Papilin, Proteoglycan-like sulfated glycoprotein has the alias papilin, drosophila, homolog of.",Is the protein Papilin secreted?,yes,self
+54e25eaaae9738404b000017,355,R176331673,PPN,has expanded form,"PAPILIN, DROSOPHILA, HOMOLOG OF","PPN is a short form for PAPILIN, DROSOPHILA, HOMOLOG OF ",Is the protein Papilin secreted?,yes,self
+517395b98ed59a060a00001a,360,R169558438,Transcription,biological process is part of process,Gene Expression,The biological process transcription is part of the process Gene Expression.,Are transcription and splicing connected?,yes,self
+517395b98ed59a060a00001a,360,R169238522,Transcription,process includes biological process,Transcription Termination,The process transcription includes the biological process Transcription Termination .,Are transcription and splicing connected?,yes,self
+517395b98ed59a060a00001a,360,R168890418,Transcription,process includes biological process,Transcription Initiation,The process transcription includes the biological process Transcription Initiation.,Are transcription and splicing connected?,yes,self
+54db1d580f63c58e6e000005,361,R158364010,Hypomethylation,is a,DNA Methylation,Hypomethylation is a DNA Methylation.,Is Alu hypomethylation associated with breast cancer?,yes,self
+54db1d580f63c58e6e000005,361,R188854188,Hypomethylation,biological process is part of process,Biochemical Process,The biological process Hypomethylation is part of the process Biochemical Process.,Is Alu hypomethylation associated with breast cancer?,yes,self
+54db1d580f63c58e6e000005,361,R169306885,Hypomethylation,biological process is part of process,Epigenetic Process,The biological process Hypomethylation is part of the Epigenetic Process.,Is Alu hypomethylation associated with breast cancer?,yes,self
+56bf365eef6e39474100000e,363,R169034691,AKT1 Gene,gene plays role in process,Negative Regulation of Apoptosis,The AKT1 Gene plays a role in the process Negative Regulation of Apoptosis.,Do mutations of AKT1 occur in meningiomas?,yes,self
+56bf365eef6e39474100000e,363,R169366166,AKT1 Gene,gene plays role in process,Serine/Threonine Phosphorylation,The AKT1 Gene plays a role in the process Serine/Threonine Phosphorylation.,Do mutations of AKT1 occur in meningiomas?,yes,self
+56bf365eef6e39474100000e,363,R169531797,AKT1 Gene,gene plays role in process,Phosphorylation Process,The AKT1 Gene plays a role in the process Phosphorylation Process.,Do mutations of AKT1 occur in meningiomas?,yes,self
+571f34ac0fd6f91b68000005,368,R60488665,WEAVER SYNDROME,has manifestation,Talipes equinovarus,The weaver syndrome has the manifestation Talipes equinovarus.,Is Weaver syndrome similar to Sotos?,yes,self
+571f34ac0fd6f91b68000005,368,R60605066,WEAVER SYNDROME,has manifestation,Cryptorchidism,The weaver syndrome has the manifestation Cryptorchidism.,Is Weaver syndrome similar to Sotos?,yes,self
+571f34ac0fd6f91b68000005,368,R60576105,WEAVER SYNDROME,has manifestation,Loose skin,The weaver syndrome has the manifestation Loose skin.,Is Weaver syndrome similar to Sotos?,yes,self
+56c1f029ef6e39474100004a,379,R176829795,valproic acid,may treat,Alzheimer Disease,Valproic acid may treat the Alzheimer Disease.,Is valproic acid effective for glioblastoma treatment?,yes,self
+56c1f029ef6e39474100004a,379,R176719689,valproic acid,may treat,Bipolar Disorder,Valproic acid may treat Bipolar Disorder.,Is valproic acid effective for glioblastoma treatment?,yes,self
+56c1f029ef6e39474100004a,379,R176733606,valproic acid,may treat,Epilepsy,Valproic acid may treat the Epilepsy.,Is valproic acid effective for glioblastoma treatment?,yes,self
+52b2ec744003448f55000001,380,R176798331,levothyroxine sodium,may treat,Thyrotoxicosis,Levothyroxine sodium may treat Thyrotoxicosis.,Can Levoxyl (levothyroxine sodium) cause insomnia?,yes,self
+52b2ec744003448f55000001,380,R176784773,levothyroxine sodium,may treat,Goiter,Levothyroxine sodium may treat Goiter.,Can Levoxyl (levothyroxine sodium) cause insomnia?,yes,self
+52b2ec744003448f55000001,380,R176753623,levothyroxine sodium,may treat,"Thyroiditis, Autoimmune","Levothyroxine sodium may treat Thyroiditis, Autoimmune.",Can Levoxyl (levothyroxine sodium) cause insomnia?,yes,self
+5335b373d6d3ac6a34000050,427,R176753188,ospemifene,may treat,Menopause,Ospemifene may treat Menopause.,Is ospemifene effective for treatment of dyspareunia?,yes,self
+5335b373d6d3ac6a34000050,427,R176723366,ospemifene,may treat,Atrophy,Ospemifene may treat Atrophy.,Is ospemifene effective for treatment of dyspareunia?,yes,self
+5335b373d6d3ac6a34000050,427,R176754381,ospemifene,may treat,Dyspareunia,Ospemifene may treat Dyspareunia.,Is ospemifene effective for treatment of dyspareunia?,yes,self
+5503121de9bde69634000019,430,R168860771,Hirschsprung Disease,disease has associated gene,GDNF Gene,Hirschsprung Disease has the associated gene GDNF.,Is RET the major gene involved in Hirschsprung disease?,yes,self
+5503121de9bde69634000019,430,R169160501,Hirschsprung Disease,disease has associated gene,NRTN Gene,Hirschsprung Disease has the associated gene NRTN.,Is RET the major gene involved in Hirschsprung disease?,yes,self
+5503121de9bde69634000019,430,R169133845,Hirschsprung Disease,disease has associated gene,NRTN wt Allele,Hirschsprung Disease has the associated gene NRTN wt Allele,Is RET the major gene involved in Hirschsprung disease?,yes,self
+56c8318f5795f9a73e00000f,441,R179075784,Sorafenib,is a,Antineoplastic Agents,Sorafenib is an Antineoplastic Agent.,Can sorafenib activate AMPK?,yes,self
+56c8318f5795f9a73e00000f,441,R176747430,Sorafenib,has mechanism of action,Kinase Inhibitors,Sorafenib has mechanism of action as Kinase Inhibitors.,Can sorafenib activate AMPK?,yes,self
+56c8318f5795f9a73e00000f,441,R188894087,Sorafenib,chemical or drug has mechanism of action,Receptor Tyrosine Kinase Inhibition,Sorafenib is a chemical or drug that has mechanism of action as Receptor Tyrosine Kinase Inhibition.,Can sorafenib activate AMPK?,yes,self
diff --git a/ideas_practice/code/bioasq_yesno_handpicked_experiment.csv b/ideas_practice/code/bioasq_yesno_handpicked_experiment.csv
new file mode 100644
index 0000000..c519b2f
--- /dev/null
+++ b/ideas_practice/code/bioasq_yesno_handpicked_experiment.csv
@@ -0,0 +1,81 @@
+id,question,ground_truth,prompt,prompting_strategy,answer,date_time,model
+1,Does metformin interfere thyroxine absorption?,no,,baseline,No,30.05.2024 from 18:00 to 18:30,GPT-3.5
+1,Does metformin interfere thyroxine absorption?,no,,aionr,No,30.05.2024 from 19:55 to 20:05,GPT-3.5
+1,Does metformin interfere thyroxine absorption?,no,,aionlr,No,30.05.2024 from 20:10 to 00:00,GPT-3.5
+1,Does metformin interfere thyroxine absorption?,no,,cot,,,
+4,Are there any specific antidotes for rivaroxaban?,no,,baseline,No,30.05.2024 from 18:00 to 18:30,GPT-3.5
+4,Are there any specific antidotes for rivaroxaban?,no,,aionr,No,30.05.2024 from 19:55 to 20:05,GPT-3.5
+4,Are there any specific antidotes for rivaroxaban?,no,,aionlr,No,30.05.2024 from 20:10 to 00:00,GPT-3.5
+4,Are there any specific antidotes for rivaroxaban?,no,,cot,,,
+7,Is it safe to take isotretinoin during pregnancy?,no,,baseline,No,30.05.2024 from 18:00 to 18:30,GPT-3.5
+7,Is it safe to take isotretinoin during pregnancy?,no,,aionr,No,30.05.2024 from 19:55 to 20:05,GPT-3.5
+7,Is it safe to take isotretinoin during pregnancy?,no,,aionlr,No,30.05.2024 from 20:10 to 00:00,GPT-3.5
+7,Is it safe to take isotretinoin during pregnancy?,no,,cot,,,
+9,Have thyronamines effects on fat tissue?,no,,baseline,Yes,30.05.2024 from 18:00 to 18:30,GPT-3.5
+9,Have thyronamines effects on fat tissue?,no,,aionr,Yes,30.05.2024 from 19:55 to 20:05,GPT-3.5
+9,Have thyronamines effects on fat tissue?,no,,aionlr,Yes,30.05.2024 from 20:10 to 00:00,GPT-3.5
+9,Have thyronamines effects on fat tissue?,no,,cot,,,
+11,Is there an association between borna virus and brain tumor?,no,,baseline,No,30.05.2024 from 18:00 to 18:30,GPT-3.5
+11,Is there an association between borna virus and brain tumor?,no,,aionr,No,30.05.2024 from 19:55 to 20:05,GPT-3.5
+11,Is there an association between borna virus and brain tumor?,no,,aionlr,No,30.05.2024 from 20:10 to 00:00,GPT-3.5
+11,Is there an association between borna virus and brain tumor?,no,,cot,,,
+13,Is endostatin a proangiogenic factor?,no,,baseline,No,30.05.2024 from 18:00 to 18:30,GPT-3.5
+13,Is endostatin a proangiogenic factor?,no,,aionr,No,30.05.2024 from 19:55 to 20:05,GPT-3.5
+13,Is endostatin a proangiogenic factor?,no,,aionlr,No,30.05.2024 from 20:10 to 00:00,GPT-3.5
+13,Is endostatin a proangiogenic factor?,no,,cot,,,
+20,Are chromomethylases present in animal genomes?,no,,baseline,No,30.05.2024 from 18:00 to 18:30,GPT-3.5
+20,Are chromomethylases present in animal genomes?,no,,aionr,Yes,30.05.2024 from 19:55 to 20:05,GPT-3.5
+20,Are chromomethylases present in animal genomes?,no,,aionlr,No,30.05.2024 from 20:10 to 00:00,GPT-3.5
+20,Are chromomethylases present in animal genomes?,no,,cot,,,
+33,Is it safe to use Abatacept during pregnancy?,no,,baseline,No,30.05.2024 from 18:00 to 18:30,GPT-3.5
+33,Is it safe to use Abatacept during pregnancy?,no,,aionr,No,30.05.2024 from 19:55 to 20:05,GPT-3.5
+33,Is it safe to use Abatacept during pregnancy?,no,,aionlr,No,30.05.2024 from 20:10 to 00:00,GPT-3.5
+33,Is it safe to use Abatacept during pregnancy?,no,,cot,,,
+34,Are there any specific antidotes for dabigatran?,no,,baseline,Yes,30.05.2024 from 18:00 to 18:30,GPT-3.5
+34,Are there any specific antidotes for dabigatran?,no,,aionr,No,30.05.2024 from 19:55 to 20:05,GPT-3.5
+34,Are there any specific antidotes for dabigatran?,no,,aionlr,No,30.05.2024 from 20:10 to 00:00,GPT-3.5
+34,Are there any specific antidotes for dabigatran?,no,,cot,,,
+36,Is armodafinil used for treatment of insomnia?,no,,baseline,No,30.05.2024 from 18:00 to 18:30,GPT-3.5
+36,Is armodafinil used for treatment of insomnia?,no,,aionr,Yes,30.05.2024 from 19:55 to 20:05,GPT-3.5
+36,Is armodafinil used for treatment of insomnia?,no,,aionlr,No,30.05.2024 from 20:10 to 00:00,GPT-3.5
+36,Is armodafinil used for treatment of insomnia?,no,,cot,,,
+355,Is the protein Papilin secreted?,yes,,baseline,Yes,30.05.2024 from 18:00 to 18:30,GPT-3.5
+355,Is the protein Papilin secreted?,yes,,aionr,Yes,30.05.2024 from 19:55 to 20:05,GPT-3.5
+355,Is the protein Papilin secreted?,yes,,aionlr,Yes,30.05.2024 from 20:10 to 00:00,GPT-3.5
+355,Is the protein Papilin secreted?,yes,,cot,,,
+360,Are transcription and splicing connected?,yes,,baseline,Yes,30.05.2024 from 18:00 to 18:30,GPT-3.5
+360,Are transcription and splicing connected?,yes,,aionr,No,30.05.2024 from 19:55 to 20:05,GPT-3.5
+360,Are transcription and splicing connected?,yes,,aionlr,Yes,30.05.2024 from 20:10 to 00:00,GPT-3.5
+360,Are transcription and splicing connected?,yes,,cot,,,
+361,Is Alu hypomethylation associated with breast cancer?,yes,,baseline,Yes,30.05.2024 from 18:00 to 18:30,GPT-3.5
+361,Is Alu hypomethylation associated with breast cancer?,yes,,aionr,Yes,30.05.2024 from 19:55 to 20:05,GPT-3.5
+361,Is Alu hypomethylation associated with breast cancer?,yes,,aionlr,Yes,30.05.2024 from 20:10 to 00:00,GPT-3.5
+361,Is Alu hypomethylation associated with breast cancer?,yes,,cot,,,
+363,Do mutations of AKT1 occur in meningiomas?,yes,,baseline,Yes,30.05.2024 from 18:00 to 18:30,GPT-3.5
+363,Do mutations of AKT1 occur in meningiomas?,yes,,aionr,Yes,30.05.2024 from 19:55 to 20:05,GPT-3.5
+363,Do mutations of AKT1 occur in meningiomas?,yes,,aionlr,Yes,30.05.2024 from 20:10 to 00:00,GPT-3.5
+363,Do mutations of AKT1 occur in meningiomas?,yes,,cot,,,
+368,Is Weaver syndrome similar to Sotos?,yes,,baseline,No,30.05.2024 from 18:00 to 18:30,GPT-3.5
+368,Is Weaver syndrome similar to Sotos?,yes,,aionr,No,30.05.2024 from 19:55 to 20:05,GPT-3.5
+368,Is Weaver syndrome similar to Sotos?,yes,,aionlr,No,30.05.2024 from 20:10 to 00:00,GPT-3.5
+368,Is Weaver syndrome similar to Sotos?,yes,,cot,,,
+379,Is valproic acid effective for glioblastoma treatment?,yes,,baseline,No,30.05.2024 from 18:00 to 18:30,GPT-3.5
+379,Is valproic acid effective for glioblastoma treatment?,yes,,aionr,No,30.05.2024 from 19:55 to 20:05,GPT-3.5
+379,Is valproic acid effective for glioblastoma treatment?,yes,,aionlr,No,30.05.2024 from 20:10 to 00:00,GPT-3.5
+379,Is valproic acid effective for glioblastoma treatment?,yes,,cot,,,
+380,Can Levoxyl (levothyroxine sodium) cause insomnia?,yes,,baseline,Yes,30.05.2024 from 18:00 to 18:30,GPT-3.5
+380,Can Levoxyl (levothyroxine sodium) cause insomnia?,yes,,aionr,Yes,30.05.2024 from 19:55 to 20:05,GPT-3.5
+380,Can Levoxyl (levothyroxine sodium) cause insomnia?,yes,,aionlr,Yes,30.05.2024 from 20:10 to 00:00,GPT-3.5
+380,Can Levoxyl (levothyroxine sodium) cause insomnia?,yes,,cot,,,
+427,Is ospemifene effective for treatment of dyspareunia?,yes,,baseline,Yes,30.05.2024 from 18:00 to 18:30,GPT-3.5
+427,Is ospemifene effective for treatment of dyspareunia?,yes,,aionr,Yes,30.05.2024 from 19:55 to 20:05,GPT-3.5
+427,Is ospemifene effective for treatment of dyspareunia?,yes,,aionlr,Yes,30.05.2024 from 20:10 to 00:00,GPT-3.5
+427,Is ospemifene effective for treatment of dyspareunia?,yes,,cot,,,
+430,Is RET the major gene involved in Hirschsprung disease?,yes,,baseline,Yes,30.05.2024 from 18:00 to 18:30,GPT-3.5
+430,Is RET the major gene involved in Hirschsprung disease?,yes,,aionr,Yes,30.05.2024 from 19:55 to 20:05,GPT-3.5
+430,Is RET the major gene involved in Hirschsprung disease?,yes,,aionlr,Yes,30.05.2024 from 20:10 to 00:00,GPT-3.5
+430,Is RET the major gene involved in Hirschsprung disease?,yes,,cot,,,
+441,Can sorafenib activate AMPK?,yes,,baseline,No,30.05.2024 from 18:00 to 18:30,GPT-3.5
+441,Can sorafenib activate AMPK?,yes,,aionr,No,30.05.2024 from 19:55 to 20:05,GPT-3.5
+441,Can sorafenib activate AMPK?,yes,,aionlr,No,30.05.2024 from 20:10 to 00:00,GPT-3.5
+441,Can sorafenib activate AMPK?,yes,,cot,,,
diff --git a/ideas_practice/code/create_prompts.ipynb b/ideas_practice/code/create_prompts.ipynb
new file mode 100644
index 0000000..80bb4ae
--- /dev/null
+++ b/ideas_practice/code/create_prompts.ipynb
@@ -0,0 +1,517 @@
+{
+ "cells": [
+ {
+ "cell_type": "code",
+ "execution_count": 1,
+ "id": "ba3898bb-45d0-42c6-a432-c1c73d9e0498",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "import csv"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 2,
+ "id": "88086cbd-4bfb-47d1-9dd9-4f1dc7b934bb",
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "{'id': '1', 'triples': [('M [Preparations]', 'parent of', 'metformin'), ('Biguanide', 'parent of', 'metformin'), ('Diabetes Mellitus, Type 2', 'may be treated by', 'metformin')], 'question': 'Does metformin interfere thyroxine absorption?', 'nl_resolved': [' M [Preparations] is parent of Metformin in the vocabulary.', 'Biguanide is parent of Metformin in the vocabulary.', 'Diabetes Mellitus Type 2 may be treated by Metformin.']}\n"
+ ]
+ }
+ ],
+ "source": [
+ "## prepare questions for automatic prompt generation\n",
+ "\n",
+ "question_list = []\n",
+ "previous_id = -1\n",
+ "cur_pos = -1\n",
+ "#format bioasq_id, id, rui, s, p, o, nl_resolved, question, ground_truth, source\n",
+ "#assumes that triples for the same question are consecutive in the csv; if they are not use csv tool to sort by rows by column value\n",
+ "with open('bioasq_yesno_handpicked.csv', mode='r') as csv_file:\n",
+ " #heading = next(csv_file) # skip the heading, could check for correct format\n",
+ " csv_reader = csv.DictReader(csv_file)\n",
+ " for row in csv_reader:\n",
+ " if row[\"id\"] != previous_id:\n",
+ " cur_pos += 1\n",
+ " question_list.append({\"id\":row[\"id\"],\"triples\":[(row[\"s\"],row[\"p\"],row[\"o\"])],\"question\":row[\"question\"],\"nl_resolved\":[row[\"nl_resolved\"]]})\n",
+ " else:\n",
+ " question_list[cur_pos][\"triples\"].append((row[\"s\"],row[\"p\"],row[\"o\"]))\n",
+ " question_list[cur_pos][\"nl_resolved\"].append(row[\"nl_resolved\"])\n",
+ " previous_id = row[\"id\"]\n",
+ "print(question_list[0])"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 8,
+ "id": "d9701b91-08f0-4f33-9b69-d8fb7fede75d",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "##TODO write directly to file where copy is easier\n",
+ "#with open(\"./test.csv\", 'w') as csvfile:\n",
+ "# writer = csv.writer(csvfile)\n",
+ "# for question in question_list:\n",
+ "# tmpq = question[\"question\"]\n",
+ "# stri=f\"\"\"You are a helpful medical expert who answers with either yes or no to questions.\n",
+ "#\n",
+ "#Question: {tmpq}\"\"\"\n",
+ "# writer.writerow([stri])"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 3,
+ "id": "82e96bf7-39e9-459d-8b47-1ea318cde1da",
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "You are a helpful medical expert who answers with either yes or no to questions.\n",
+ "\n",
+ "Question: Does metformin interfere thyroxine absorption?\n",
+ "You are a helpful medical expert who answers with either yes or no to questions.\n",
+ "\n",
+ "Question: Are there any specific antidotes for rivaroxaban?\n",
+ "You are a helpful medical expert who answers with either yes or no to questions.\n",
+ "\n",
+ "Question: Is it safe to take isotretinoin during pregnancy?\n",
+ "You are a helpful medical expert who answers with either yes or no to questions.\n",
+ "\n",
+ "Question: Have thyronamines effects on fat tissue?\n",
+ "You are a helpful medical expert who answers with either yes or no to questions.\n",
+ "\n",
+ "Question: Is there an association between borna virus and brain tumor?\n",
+ "You are a helpful medical expert who answers with either yes or no to questions.\n",
+ "\n",
+ "Question: Is endostatin a proangiogenic factor?\n",
+ "You are a helpful medical expert who answers with either yes or no to questions.\n",
+ "\n",
+ "Question: Are chromomethylases present in animal genomes?\n",
+ "You are a helpful medical expert who answers with either yes or no to questions.\n",
+ "\n",
+ "Question: Is it safe to use Abatacept during pregnancy?\n",
+ "You are a helpful medical expert who answers with either yes or no to questions.\n",
+ "\n",
+ "Question: Are there any specific antidotes for dabigatran?\n",
+ "You are a helpful medical expert who answers with either yes or no to questions.\n",
+ "\n",
+ "Question: Is armodafinil used for treatment of insomnia?\n",
+ "You are a helpful medical expert who answers with either yes or no to questions.\n",
+ "\n",
+ "Question: Is the protein Papilin secreted?\n",
+ "You are a helpful medical expert who answers with either yes or no to questions.\n",
+ "\n",
+ "Question: Are transcription and splicing connected?\n",
+ "You are a helpful medical expert who answers with either yes or no to questions.\n",
+ "\n",
+ "Question: Is Alu hypomethylation associated with breast cancer?\n",
+ "You are a helpful medical expert who answers with either yes or no to questions.\n",
+ "\n",
+ "Question: Do mutations of AKT1 occur in meningiomas?\n",
+ "You are a helpful medical expert who answers with either yes or no to questions.\n",
+ "\n",
+ "Question: Is Weaver syndrome similar to Sotos?\n",
+ "You are a helpful medical expert who answers with either yes or no to questions.\n",
+ "\n",
+ "Question: Is valproic acid effective for glioblastoma treatment?\n",
+ "You are a helpful medical expert who answers with either yes or no to questions.\n",
+ "\n",
+ "Question: Can Levoxyl (levothyroxine sodium) cause insomnia?\n",
+ "You are a helpful medical expert who answers with either yes or no to questions.\n",
+ "\n",
+ "Question: Is ospemifene effective for treatment of dyspareunia?\n",
+ "You are a helpful medical expert who answers with either yes or no to questions.\n",
+ "\n",
+ "Question: Is RET the major gene involved in Hirschsprung disease?\n",
+ "You are a helpful medical expert who answers with either yes or no to questions.\n",
+ "\n",
+ "Question: Can sorafenib activate AMPK?\n"
+ ]
+ }
+ ],
+ "source": [
+ "# generate the prompts for baseline\n",
+ "for question in question_list:\n",
+ " tmpq = question[\"question\"]\n",
+ " print(f\"\"\"You are a helpful medical expert who answers with either yes or no to questions.\n",
+ "\n",
+ "Question: {tmpq}\"\"\")"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 4,
+ "id": "d2e14820-91c7-4ce0-81aa-30e3f600fb7f",
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "You are a helpful medical expert who answers with either yes or no. Consider the information in triple quotes as factual knowledge.\n",
+ "\n",
+ "\"\"\"M [Preparations] has relationshsip parent of to metformin\"\"\"\n",
+ "\"\"\"Biguanide has relationshsip parent of to metformin\"\"\"\n",
+ "\"\"\"Diabetes Mellitus, Type 2 has relationshsip may be treated by to metformin\"\"\"\n",
+ "\n",
+ "Question: Does metformin interfere thyroxine absorption?\n",
+ "You are a helpful medical expert who answers with either yes or no. Consider the information in triple quotes as factual knowledge.\n",
+ "\n",
+ "\"\"\"Pulmonary Embolism has relationshsip may be treated by to rivaraxoban\"\"\"\n",
+ "\"\"\"Venous Thrombosis has relationshsip may be treated by to rivaraxoban\"\"\"\n",
+ "\"\"\"Hemorrhage has relationshsip has contraindicated drug to rivaraxoban\"\"\"\n",
+ "\n",
+ "Question: Are there any specific antidotes for rivaroxaban?\n",
+ "You are a helpful medical expert who answers with either yes or no. Consider the information in triple quotes as factual knowledge.\n",
+ "\n",
+ "\"\"\"Pregnancy has relationshsip has contraindicated drug to isotretinoin\"\"\"\n",
+ "\"\"\"isotretinoin has relationshsip contraindicated with disease to Pregnancy\"\"\"\n",
+ "\"\"\"Retinoid has relationshsip parent of to isotretinoin\"\"\"\n",
+ "\n",
+ "Question: Is it safe to take isotretinoin during pregnancy?\n",
+ "You are a helpful medical expert who answers with either yes or no. Consider the information in triple quotes as factual knowledge.\n",
+ "\n",
+ "\"\"\"p-(p-(2-aminoethyl)phenoxy)phenol has relationshsip RN to thyronamine\"\"\"\n",
+ "\"\"\"HCl of thyronamine has relationshsip RN to thyronamine\"\"\"\n",
+ "\"\"\"Brown adipose tissue has relationshsip is a to Adipose tissue\"\"\"\n",
+ "\n",
+ "Question: Have thyronamines effects on fat tissue?\n",
+ "You are a helpful medical expert who answers with either yes or no. Consider the information in triple quotes as factual knowledge.\n",
+ "\n",
+ "\"\"\"borna virus has relationshsip used for to RNA virus\"\"\"\n",
+ "\"\"\"borna virus has relationshsip RB to virus\"\"\"\n",
+ "\"\"\"Intraventricular Brain Neoplasm has relationshsip is a to brain tumor\"\"\"\n",
+ "\n",
+ "Question: Is there an association between borna virus and brain tumor?\n",
+ "You are a helpful medical expert who answers with either yes or no. Consider the information in triple quotes as factual knowledge.\n",
+ "\n",
+ "\"\"\"Collagen Type XVIII has relationshsip PAR to Endostatins\"\"\"\n",
+ "\"\"\"Angiostatic Proteins has relationshsip PAR to Endostatins\"\"\"\n",
+ "\"\"\"Antineoplastic Agents has relationshsip inverse is a to Endostatins\"\"\"\n",
+ "\n",
+ "Question: Is endostatin a proangiogenic factor?\n",
+ "You are a helpful medical expert who answers with either yes or no. Consider the information in triple quotes as factual knowledge.\n",
+ "\n",
+ "\"\"\"DNA Cytosine-5-Methylase has relationshsip has permuted term to DNA Cytosine 5 Methylase\"\"\"\n",
+ "\"\"\"DNA Cytosine-5-Methylase has relationshsip has permuted term to Cytosine-5-Methylase, DNA\"\"\"\n",
+ "\"\"\"DNA (Cytosine-5-)-Methyltransferase has relationshsip has sort version to DNA METHYLTRANSFERASE CYTOSINE 05\"\"\"\n",
+ "\n",
+ "Question: Are chromomethylases present in animal genomes?\n",
+ "You are a helpful medical expert who answers with either yes or no. Consider the information in triple quotes as factual knowledge.\n",
+ "\n",
+ "\"\"\"Abatacept has relationshsip is a to Antirheumatic Agents\"\"\"\n",
+ "\"\"\"Abatacept has relationshsip has parent to Selective T Cell Costimulation Modulator\"\"\"\n",
+ "\"\"\"Abatacept has relationshsip has parent to A [Preparations]\"\"\"\n",
+ "\n",
+ "Question: Is it safe to use Abatacept during pregnancy?\n",
+ "You are a helpful medical expert who answers with either yes or no. Consider the information in triple quotes as factual knowledge.\n",
+ "\n",
+ "\"\"\"Dabigatran has relationshsip is a to Antithrombins\"\"\"\n",
+ "\"\"\"Dabigatran has relationshsip has parent to D [Preparations]\"\"\"\n",
+ "\"\"\"Dabigatran has relationshsip has parent to Direct Thrombin Inhibitor\"\"\"\n",
+ "\n",
+ "Question: Are there any specific antidotes for dabigatran?\n",
+ "You are a helpful medical expert who answers with either yes or no. Consider the information in triple quotes as factual knowledge.\n",
+ "\n",
+ "\"\"\"A [Preparations] has relationshsip parent of to armodafinil\"\"\"\n",
+ "\"\"\"Sleep Wake Disorders has relationshsip may be treated by to armodafinil\"\"\"\n",
+ "\"\"\"CNS Stimulant has relationshsip inverse is a to armodafinil\"\"\"\n",
+ "\n",
+ "Question: Is armodafinil used for treatment of insomnia?\n",
+ "You are a helpful medical expert who answers with either yes or no. Consider the information in triple quotes as factual knowledge.\n",
+ "\n",
+ "\"\"\"papilin, proteoglycan like sulfated glycoprotein has relationshsip has alias to MGC50452\"\"\"\n",
+ "\"\"\"PAPILIN, PROTEOGLYCAN-LIKE SULFATED GLYCOPROTEIN has relationshsip has alias to PAPILIN, DROSOPHILA, HOMOLOG OF\"\"\"\n",
+ "\"\"\"PPN has relationshsip has expanded form to PAPILIN, DROSOPHILA, HOMOLOG OF\"\"\"\n",
+ "\n",
+ "Question: Is the protein Papilin secreted?\n",
+ "You are a helpful medical expert who answers with either yes or no. Consider the information in triple quotes as factual knowledge.\n",
+ "\n",
+ "\"\"\"Transcription has relationshsip biological process is part of process to Gene Expression\"\"\"\n",
+ "\"\"\"Transcription has relationshsip process includes biological process to Transcription Termination\"\"\"\n",
+ "\"\"\"Transcription has relationshsip process includes biological process to Transcription Initiation\"\"\"\n",
+ "\n",
+ "Question: Are transcription and splicing connected?\n",
+ "You are a helpful medical expert who answers with either yes or no. Consider the information in triple quotes as factual knowledge.\n",
+ "\n",
+ "\"\"\"Hypomethylation has relationshsip is a to DNA Methylation\"\"\"\n",
+ "\"\"\"Hypomethylation has relationshsip biological process is part of process to Biochemical Process\"\"\"\n",
+ "\"\"\"Hypomethylation has relationshsip biological process is part of process to Epigenetic Process\"\"\"\n",
+ "\n",
+ "Question: Is Alu hypomethylation associated with breast cancer?\n",
+ "You are a helpful medical expert who answers with either yes or no. Consider the information in triple quotes as factual knowledge.\n",
+ "\n",
+ "\"\"\"AKT1 Gene has relationshsip gene plays role in process to Negative Regulation of Apoptosis\"\"\"\n",
+ "\"\"\"AKT1 Gene has relationshsip gene plays role in process to Serine/Threonine Phosphorylation\"\"\"\n",
+ "\"\"\"AKT1 Gene has relationshsip gene plays role in process to Phosphorylation Process\"\"\"\n",
+ "\n",
+ "Question: Do mutations of AKT1 occur in meningiomas?\n",
+ "You are a helpful medical expert who answers with either yes or no. Consider the information in triple quotes as factual knowledge.\n",
+ "\n",
+ "\"\"\"WEAVER SYNDROME has relationshsip has manifestation to Talipes equinovarus\"\"\"\n",
+ "\"\"\"WEAVER SYNDROME has relationshsip has manifestation to Cryptorchidism\"\"\"\n",
+ "\"\"\"WEAVER SYNDROME has relationshsip has manifestation to Loose skin\"\"\"\n",
+ "\n",
+ "Question: Is Weaver syndrome similar to Sotos?\n",
+ "You are a helpful medical expert who answers with either yes or no. Consider the information in triple quotes as factual knowledge.\n",
+ "\n",
+ "\"\"\"valproic acid has relationshsip may treat to Alzheimer Disease\"\"\"\n",
+ "\"\"\"valproic acid has relationshsip may treat to Bipolar Disorder\"\"\"\n",
+ "\"\"\"valproic acid has relationshsip may treat to Epilepsy\"\"\"\n",
+ "\n",
+ "Question: Is valproic acid effective for glioblastoma treatment?\n",
+ "You are a helpful medical expert who answers with either yes or no. Consider the information in triple quotes as factual knowledge.\n",
+ "\n",
+ "\"\"\"levothyroxine sodium has relationshsip may treat to Thyrotoxicosis\"\"\"\n",
+ "\"\"\"levothyroxine sodium has relationshsip may treat to Goiter\"\"\"\n",
+ "\"\"\"levothyroxine sodium has relationshsip may treat to Thyroiditis, Autoimmune\"\"\"\n",
+ "\n",
+ "Question: Can Levoxyl (levothyroxine sodium) cause insomnia?\n",
+ "You are a helpful medical expert who answers with either yes or no. Consider the information in triple quotes as factual knowledge.\n",
+ "\n",
+ "\"\"\"ospemifene has relationshsip may treat to Menopause\"\"\"\n",
+ "\"\"\"ospemifene has relationshsip may treat to Atrophy\"\"\"\n",
+ "\"\"\"ospemifene has relationshsip may treat to Dyspareunia\"\"\"\n",
+ "\n",
+ "Question: Is ospemifene effective for treatment of dyspareunia?\n",
+ "You are a helpful medical expert who answers with either yes or no. Consider the information in triple quotes as factual knowledge.\n",
+ "\n",
+ "\"\"\"Hirschsprung Disease has relationshsip disease has associated gene to GDNF Gene\"\"\"\n",
+ "\"\"\"Hirschsprung Disease has relationshsip disease has associated gene to NRTN Gene\"\"\"\n",
+ "\"\"\"Hirschsprung Disease has relationshsip disease has associated gene to NRTN wt Allele\"\"\"\n",
+ "\n",
+ "Question: Is RET the major gene involved in Hirschsprung disease?\n",
+ "You are a helpful medical expert who answers with either yes or no. Consider the information in triple quotes as factual knowledge.\n",
+ "\n",
+ "\"\"\"Sorafenib has relationshsip is a to Antineoplastic Agents\"\"\"\n",
+ "\"\"\"Sorafenib has relationshsip has mechanism of action to Kinase Inhibitors\"\"\"\n",
+ "\"\"\"Sorafenib has relationshsip chemical or drug has mechanism of action to Receptor Tyrosine Kinase Inhibition\"\"\"\n",
+ "\n",
+ "Question: Can sorafenib activate AMPK?\n"
+ ]
+ }
+ ],
+ "source": [
+ "# generate the prompts for All in One None Resolve\n",
+ "for question in question_list:\n",
+ " tmpq = question[\"question\"]\n",
+ " tmptrip = \"\"\n",
+ " for triple in question[\"triples\"]:\n",
+ " s = triple[0] \n",
+ " p = triple[1]\n",
+ " o = triple[2]\n",
+ " tmptrip = tmptrip + f'\"\"\"{s} has relationshsip {p} to {o}\"\"\"\\n'\n",
+ " tmptrip = tmptrip.rstrip()\n",
+ " print(f\"\"\"You are a helpful medical expert who answers with either yes or no. Consider the information in triple quotes as factual knowledge.\n",
+ "\n",
+ "{tmptrip}\n",
+ "\n",
+ "Question: {tmpq}\"\"\")"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 5,
+ "id": "085e3ac0-bd77-4686-94c3-68e3da1f15b4",
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "You are a helpful medical expert who answers with either yes or no. Consider the information in triple quotes as factual knowledge.\n",
+ "\n",
+ "\"\"\" M [Preparations] is parent of Metformin in the vocabulary.\"\"\"\n",
+ "\"\"\"Biguanide is parent of Metformin in the vocabulary.\"\"\"\n",
+ "\"\"\"Diabetes Mellitus Type 2 may be treated by Metformin.\"\"\"\n",
+ "\n",
+ "Question: Does metformin interfere thyroxine absorption?\n",
+ "You are a helpful medical expert who answers with either yes or no. Consider the information in triple quotes as factual knowledge.\n",
+ "\n",
+ "\"\"\"Pulmonary Embolism may be treated by Rivaraxoban.\"\"\"\n",
+ "\"\"\"Venous Thrombosis may be treated by Rivaraxoban\"\"\"\n",
+ "\"\"\"Hemorrhage has the contraindicated drug Rivaraxoban.\"\"\"\n",
+ "\n",
+ "Question: Are there any specific antidotes for rivaroxaban?\n",
+ "You are a helpful medical expert who answers with either yes or no. Consider the information in triple quotes as factual knowledge.\n",
+ "\n",
+ "\"\"\"Pregnancy has the contraindicated drug Isotretinoin.\"\"\"\n",
+ "\"\"\"Isotretinoin contraindicates with pregnancy.\"\"\"\n",
+ "\"\"\"Retinoid is parent of Isotretinoin in the vocabulary.\"\"\"\n",
+ "\n",
+ "Question: Is it safe to take isotretinoin during pregnancy?\n",
+ "You are a helpful medical expert who answers with either yes or no. Consider the information in triple quotes as factual knowledge.\n",
+ "\n",
+ "\"\"\"p-(p-(2-aminoethyl)phenoxy)phenol has a narrower relationship with thyronamine\"\"\"\n",
+ "\"\"\"HCl of thyronamine has a narrower relationship with Thyronamine.\"\"\"\n",
+ "\"\"\"Brown adipose tissue is a Adipose tissue.\"\"\"\n",
+ "\n",
+ "Question: Have thyronamines effects on fat tissue?\n",
+ "You are a helpful medical expert who answers with either yes or no. Consider the information in triple quotes as factual knowledge.\n",
+ "\n",
+ "\"\"\"Borna virus is used for RNA virus.\"\"\"\n",
+ "\"\"\"Borna virus has a broader relationship to virus.\"\"\"\n",
+ "\"\"\"Intraventricular Brain Neoplasm is a brain tumor.\"\"\"\n",
+ "\n",
+ "Question: Is there an association between borna virus and brain tumor?\n",
+ "You are a helpful medical expert who answers with either yes or no. Consider the information in triple quotes as factual knowledge.\n",
+ "\n",
+ "\"\"\"Collagen Type XVIII is parent of Endostatins in the vocabulary.\"\"\"\n",
+ "\"\"\"Angiostatic Proteins is parent of Endostatins in the vocabulary.\"\"\"\n",
+ "\"\"\"Endostatins are antineoplastic agents.\"\"\"\n",
+ "\n",
+ "Question: Is endostatin a proangiogenic factor?\n",
+ "You are a helpful medical expert who answers with either yes or no. Consider the information in triple quotes as factual knowledge.\n",
+ "\n",
+ "\"\"\"DNA Cytosine-5-Methylase can be permuted to the equivalent DNA Cytosine 5 Methylase.\"\"\"\n",
+ "\"\"\"DNA Cytosine-5-Methylase can be permuted to the equivalent Cytosine-5-Methylase, DNA.\"\"\"\n",
+ "\"\"\"DNA (Cytosine-5-)-Methyltransferase can be sorted to the equivalent DNA METHYLTRANSFERASE CYTOSINE 05.\"\"\"\n",
+ "\n",
+ "Question: Are chromomethylases present in animal genomes?\n",
+ "You are a helpful medical expert who answers with either yes or no. Consider the information in triple quotes as factual knowledge.\n",
+ "\n",
+ "\"\"\"Abatacept is a antirheumatic agent.\"\"\"\n",
+ "\"\"\"Abatacept has the parent Selective T Cell Costimulation Modulator in the vocabulary.\"\"\"\n",
+ "\"\"\"Abatacept has the parent A [Preparations] in the vocabulary.\"\"\"\n",
+ "\n",
+ "Question: Is it safe to use Abatacept during pregnancy?\n",
+ "You are a helpful medical expert who answers with either yes or no. Consider the information in triple quotes as factual knowledge.\n",
+ "\n",
+ "\"\"\"Dabigatran is an antithrombin .\"\"\"\n",
+ "\"\"\"Dabigatran has the parent D [Preparations] in the vocabulary.\"\"\"\n",
+ "\"\"\"Dabigatran has the parent Direct Thrombin Inhibitor in the vocabulary.\"\"\"\n",
+ "\n",
+ "Question: Are there any specific antidotes for dabigatran?\n",
+ "You are a helpful medical expert who answers with either yes or no. Consider the information in triple quotes as factual knowledge.\n",
+ "\n",
+ "\"\"\" A [Preparations]] is parent of armodafinil in the vocabulary.\"\"\"\n",
+ "\"\"\"Sleep Wake Disorders may be treated by armodafinil.\"\"\"\n",
+ "\"\"\"Armodafinil is a CNS Stimulant .\"\"\"\n",
+ "\n",
+ "Question: Is armodafinil used for treatment of insomnia?\n",
+ "You are a helpful medical expert who answers with either yes or no. Consider the information in triple quotes as factual knowledge.\n",
+ "\n",
+ "\"\"\"Papilin, proteoglycan like sulfated glycoprotein has the alias MGC50452 .\"\"\"\n",
+ "\"\"\"Papilin, Proteoglycan-like sulfated glycoprotein has the alias papilin, drosophila, homolog of.\"\"\"\n",
+ "\"\"\"PPN is a short form for PAPILIN, DROSOPHILA, HOMOLOG OF \"\"\"\n",
+ "\n",
+ "Question: Is the protein Papilin secreted?\n",
+ "You are a helpful medical expert who answers with either yes or no. Consider the information in triple quotes as factual knowledge.\n",
+ "\n",
+ "\"\"\"The biological process transcription is part of the process Gene Expression.\"\"\"\n",
+ "\"\"\"The process transcription includes the biological process Transcription Termination .\"\"\"\n",
+ "\"\"\"The process transcription includes the biological process Transcription Initiation.\"\"\"\n",
+ "\n",
+ "Question: Are transcription and splicing connected?\n",
+ "You are a helpful medical expert who answers with either yes or no. Consider the information in triple quotes as factual knowledge.\n",
+ "\n",
+ "\"\"\"Hypomethylation is a DNA Methylation.\"\"\"\n",
+ "\"\"\"The biological process Hypomethylation is part of the process Biochemical Process.\"\"\"\n",
+ "\"\"\"The biological process Hypomethylation is part of the Epigenetic Process.\"\"\"\n",
+ "\n",
+ "Question: Is Alu hypomethylation associated with breast cancer?\n",
+ "You are a helpful medical expert who answers with either yes or no. Consider the information in triple quotes as factual knowledge.\n",
+ "\n",
+ "\"\"\"The AKT1 Gene plays a role in the process Negative Regulation of Apoptosis.\"\"\"\n",
+ "\"\"\"The AKT1 Gene plays a role in the process Serine/Threonine Phosphorylation.\"\"\"\n",
+ "\"\"\"The AKT1 Gene plays a role in the process Phosphorylation Process.\"\"\"\n",
+ "\n",
+ "Question: Do mutations of AKT1 occur in meningiomas?\n",
+ "You are a helpful medical expert who answers with either yes or no. Consider the information in triple quotes as factual knowledge.\n",
+ "\n",
+ "\"\"\"The weaver syndrome has the manifestation Talipes equinovarus.\"\"\"\n",
+ "\"\"\"The weaver syndrome has the manifestation Cryptorchidism.\"\"\"\n",
+ "\"\"\"The weaver syndrome has the manifestation Loose skin.\"\"\"\n",
+ "\n",
+ "Question: Is Weaver syndrome similar to Sotos?\n",
+ "You are a helpful medical expert who answers with either yes or no. Consider the information in triple quotes as factual knowledge.\n",
+ "\n",
+ "\"\"\"Valproic acid may treat the Alzheimer Disease.\"\"\"\n",
+ "\"\"\"Valproic acid may treat Bipolar Disorder.\"\"\"\n",
+ "\"\"\"Valproic acid may treat the Epilepsy.\"\"\"\n",
+ "\n",
+ "Question: Is valproic acid effective for glioblastoma treatment?\n",
+ "You are a helpful medical expert who answers with either yes or no. Consider the information in triple quotes as factual knowledge.\n",
+ "\n",
+ "\"\"\"Levothyroxine sodium may treat Thyrotoxicosis.\"\"\"\n",
+ "\"\"\"Levothyroxine sodium may treat Goiter.\"\"\"\n",
+ "\"\"\"Levothyroxine sodium may treat Thyroiditis, Autoimmune.\"\"\"\n",
+ "\n",
+ "Question: Can Levoxyl (levothyroxine sodium) cause insomnia?\n",
+ "You are a helpful medical expert who answers with either yes or no. Consider the information in triple quotes as factual knowledge.\n",
+ "\n",
+ "\"\"\"Ospemifene may treat Menopause.\"\"\"\n",
+ "\"\"\"Ospemifene may treat Atrophy.\"\"\"\n",
+ "\"\"\"Ospemifene may treat Dyspareunia.\"\"\"\n",
+ "\n",
+ "Question: Is ospemifene effective for treatment of dyspareunia?\n",
+ "You are a helpful medical expert who answers with either yes or no. Consider the information in triple quotes as factual knowledge.\n",
+ "\n",
+ "\"\"\"Hirschsprung Disease has the associated gene GDNF.\"\"\"\n",
+ "\"\"\"Hirschsprung Disease has the associated gene NRTN.\"\"\"\n",
+ "\"\"\"Hirschsprung Disease has the associated gene NRTN wt Allele\"\"\"\n",
+ "\n",
+ "Question: Is RET the major gene involved in Hirschsprung disease?\n",
+ "You are a helpful medical expert who answers with either yes or no. Consider the information in triple quotes as factual knowledge.\n",
+ "\n",
+ "\"\"\"Sorafenib is an Antineoplastic Agent.\"\"\"\n",
+ "\"\"\"Sorafenib has mechanism of action as Kinase Inhibitors.\"\"\"\n",
+ "\"\"\"Sorafenib is a chemical or drug that has mechanism of action as Receptor Tyrosine Kinase Inhibition.\"\"\"\n",
+ "\n",
+ "Question: Can sorafenib activate AMPK?\n"
+ ]
+ }
+ ],
+ "source": [
+ "for question in question_list:\n",
+ " tmpq = question[\"question\"]\n",
+ " tmptrip = \"\"\n",
+ " for sent in question[\"nl_resolved\"]:\n",
+ " tmptrip = tmptrip + f'\"\"\"{sent}\"\"\"\\n'\n",
+ " tmptrip = tmptrip.rstrip()\n",
+ " print(f\"\"\"You are a helpful medical expert who answers with either yes or no. Consider the information in triple quotes as factual knowledge.\n",
+ "\n",
+ "{tmptrip}\n",
+ "\n",
+ "Question: {tmpq}\"\"\")"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "b24de3a0-a683-47ee-8a8a-4f68e5d6a5b1",
+ "metadata": {},
+ "outputs": [],
+ "source": []
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+ "kernelspec": {
+ "display_name": "Python 3 (ipykernel)",
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+ "name": "python3"
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+ "name": "ipython",
+ "version": 3
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diff --git a/ideas_practice/code/prompting_strategies.md b/ideas_practice/code/prompting_strategies.md
new file mode 100644
index 0000000..20b026e
--- /dev/null
+++ b/ideas_practice/code/prompting_strategies.md
@@ -0,0 +1,52 @@
+This file describes the different strategies used for the prompting process and how the prompts are created. We considered the guidlines offered by OpenAI https://platform.openai.com/docs/guides/prompt-engineering/
+
+## Baseline (baseline):
+The questions will be given to the model as is without any additional context.
+Prompts have the following format:
+"""
+You are a helpful medical expert who answers with either yes or no to questions.
+
+Question: <question>
+"""
+
+## All in One None Resolve (aionr):
+The questions will be given to the model as is with additional triples in their raw format.
+Prompts have the following format:
+"""
+You are a helpful medical expert who answers with either yes or no. Consider the information in triple quotes as factual knowledge.
+
+"""<s1> has relationshsip <r1> to <o1>"""
+"""<s2> has relationshsip <r2> to <o2>"""
+
+Question: <question>
+"""
+
+## All in One NL Resolve (aionlr):
+The questions will be given to the model as is with additional triples in the form of natural sentences.
+Prompts have the following format:
+"""
+You are a helpful medical expert who answers with either yes or no. Consider the information in triple quotes as factual knowledge.
+
+"""<NL sentence for s1r1o1>"""
+"""<NL sentence for s2r2o2>"""
+
+Question: <question>
+"""
+
+## Chain of Thought (cot):
+The questions will be given to the model as is. After the answer the model will be iteratively asked to reevaluate their answer given a triple in NL sentence form.
+"""
+You are a helpful medical expert who answers with either yes or no. Consider the information in triple quotes as factual knowledge.
+
+Question: <question>
+"""
+
+"""
+Given our previous conversation and the following information in triple quotes reevaluate your answer.
+"""<NL sentence for s1r1o1>"""
+"""
+
+"""
+Given our previous conversation and the following information in triple quotes reevaluate your answer.
+"""<NL sentence for s2r2o2>"""
+"""
--
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