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Added Madhul-Solutions Directory

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Madhul Sachdeva 5 months ago
parent
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28d56c582e
  1. 298
      week1/community-contributions/day1-article-pdf-reader.ipynb
  2. 353
      week1/day1.ipynb

298
week1/community-contributions/day1-article-pdf-reader.ipynb

@ -24,6 +24,17 @@
"Without further ado, here's the PDF Summarizer!"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "14e98361-f302-423d-87a5-f2f5d570f4ac",
"metadata": {},
"outputs": [],
"source": [
"### Prerequisite - Install below package\n",
"#--> !pip install PyPDF2 --user"
]
},
{
"cell_type": "code",
"execution_count": null,
@ -38,7 +49,8 @@
"from IPython.display import Markdown, display\n",
"from openai import OpenAI\n",
"from io import BytesIO\n",
"from PyPDF2 import PdfReader"
"from PyPDF2 import PdfReader\n",
"import logging"
]
},
{
@ -81,54 +93,104 @@
},
{
"cell_type": "code",
"execution_count": null,
"id": "3a053092-f4f6-4156-8721-39353c8a9367",
"execution_count": 60,
"id": "b6f2967e-4779-458f-aea8-c47147528f77",
"metadata": {},
"outputs": [],
"source": [
"# Step 0: Create article class\n",
"# Step 1: Defince calss for article pdf document\n",
"\n",
"class Article:\n",
" def __init__(self, url):\n",
" \"\"\"\n",
" Create this Article object from the given url using the PyPDF2 library\n",
" \"\"\"\n",
" self.url = url \n",
" response = requests.get(self.url)\n",
" if response.status_code == 200:\n",
" # Configure logging\n",
" logging.basicConfig(level=logging.ERROR)\n",
"\n",
" # Comprehensive headers to mimic browser\n",
" headers = {\n",
" 'User-Agent': 'Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/91.0.4472.124 Safari/537.36',\n",
" 'Accept': 'application/pdf,text/html,application/xhtml+xml,application/xml',\n",
" 'Accept-Language': 'en-US,en;q=0.5',\n",
" 'Referer': self._extract_base_url(url)\n",
" }\n",
"\n",
" try:\n",
" # Enhanced download attempt with multiple strategies\n",
" response = self._download_pdf(url, headers)\n",
" \n",
" # Process PDF\n",
" pdf_bytes = BytesIO(response.content)\n",
" reader = PdfReader(pdf_bytes)\n",
" \n",
" text = \"\"\n",
" for page in reader.pages:\n",
" text += page.extract_text()\n",
" \n",
" self.text = text\n",
" self.title = reader.metadata.get(\"/Title\", \"No title found\")\n",
" else:\n",
" print(f\"Failed to fetch PDF. Status code: {response.status_code}\")\n",
" \n",
" # Efficient text extraction\n",
" self.text = \" \".join(page.extract_text() for page in reader.pages)\n",
" \n",
" # Safe metadata extraction\n",
" self.title = (reader.metadata or {}).get(\"/Title\", \"No title found\") or \"No title found\"\n",
"\n",
" except Exception as error:\n",
" logging.error(f\"PDF Processing Error: {error}\")\n",
" self.text = \"No text found\"\n",
" self.title = \"No title found\""
" self.title = \"No title found\"\n",
"\n",
" def _download_pdf(self, url, headers):\n",
" \"\"\"\n",
" Multiple download strategies to handle different access scenarios\n",
" \"\"\"\n",
" try:\n",
" # Primary download attempt\n",
" response = requests.get(url, headers=headers, timeout=10)\n",
" response.raise_for_status()\n",
" return response\n",
"\n",
" except requests.RequestException as primary_error:\n",
" logging.warning(f\"Primary download failed: {primary_error}\")\n",
" \n",
" try:\n",
" # Fallback strategy: Disable SSL verification\n",
" response = requests.get(url, headers=headers, verify=False, timeout=10)\n",
" response.raise_for_status()\n",
" return response\n",
" \n",
" except requests.RequestException as fallback_error:\n",
" logging.error(f\"All download attempts failed: {fallback_error}\")\n",
" raise\n",
"\n",
" def _extract_base_url(self, url):\n",
" \"\"\"\n",
" Extract base URL for Referer header\n",
" \"\"\"\n",
" from urllib.parse import urlparse\n",
" parsed_url = urlparse(url)\n",
" return f\"{parsed_url.scheme}://{parsed_url.netloc}\""
]
},
{
"cell_type": "markdown",
"id": "95933aab-54df-4afc-a19c-46033f51378f",
"metadata": {},
"source": [
"#####user_prompt_input = input(\"Explain how you would like me to summarise the document? \\n\")"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "adc528f2-25ca-47b5-896e-9d417ba0195f",
"execution_count": 61,
"id": "821acbfa-ad06-4afd-9ac1-b9f68b7a418e",
"metadata": {},
"outputs": [],
"source": [
"# Step 1: Create your prompts\n",
"# General Research Analyst\n",
"#### Step 1: Create your prompts\n",
"\n",
"def craft_user_prompt(article):\n",
" user_prompt = f\"You are looking at a research article titled {article.title}\\n Based on the body of the article, how are micro RNAs produced in the cell? State the function of the proteins \\\n",
" involved. The body of the article is as follows.\"\n",
" user_prompt = f\"You are looking at a document titled {article.title}\\n Based on the body of the document, provide an impactful summary. The body of the article is as follows.\"\n",
" user_prompt += article.text\n",
" return user_prompt\n",
"\n",
"# Step 2: Make the messages list\n",
"### Step 2: Make the messages list\n",
"def craft_messages(article):\n",
" system_prompt = \"You are an assistant that analyses the contents of a research article and provide answers to the question asked by the user in 250 words or less. \\\n",
" Ignore text that doesn't belong to the article, like headers or navigation related text. Respond in markdown. Structure your text in the form of question/answer.\"\n",
" system_prompt = '''You are a research assistant specialising in processing documents. You have been tasked with analysing the contents of the articel and call out the important points as bullets and highlights. \\\n",
" Ignore text that doesn't belong to the article, like headers or navigation related text. Respond in markdown. Structure your text in the form of question/answer.'''\n",
" return [\n",
" {\"role\": \"system\", \"content\": system_prompt},\n",
" {\"role\": \"user\", \"content\": craft_user_prompt(article)}\n",
@ -137,7 +199,7 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 62,
"id": "81ab896e-1ba9-4964-a477-2a0608b7036c",
"metadata": {},
"outputs": [],
@ -152,17 +214,185 @@
" return response.choices[0].message.content"
]
},
{
"cell_type": "markdown",
"id": "ccdfdd33-652f-4ecf-9a0d-355197aba9d5",
"metadata": {},
"source": [
"# Results below:"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "a7a98cdf-0d3b-477d-8e39-a6a4264b9feb",
"execution_count": 63,
"id": "008c03fd-9cc5-4449-a054-7bbef1863b01",
"metadata": {},
"outputs": [],
"outputs": [
{
"name": "stdin",
"output_type": "stream",
"text": [
"Please input the pdf URL: \n",
" https://www.binasss.sa.cr/bibliotecas/bhm/ago22/32.pdf\n"
]
},
{
"data": {
"text/markdown": [
"## Summary of **Bronchiectasis — A Clinical Review**\n",
"\n",
"### What is bronchiectasis?\n",
"- Bronchiectasis is a clinical syndrome characterized by:\n",
" - Chronic cough \n",
" - Sputum production\n",
" - Abnormal thickening and dilation of bronchial walls, visible on lung imaging.\n",
"\n",
"### Historical Background\n",
"- First reported by René Laënnec in 1819.\n",
"- Radiographic characteristics understood more clearly since the 1950s.\n",
"\n",
"### Current Trends\n",
"- Significantly increasing incidence and prevalence over the last 20 years.\n",
"- Diagnosed across a wide age range, with geographic variability in prevalence (as high as 1.5% in some populations).\n",
"- Improved recognition, partly due to advanced imaging technologies like CT scans.\n",
" \n",
"### Clinical Presentation\n",
"- Symptoms include chronic productive cough, chest pain, and shortness of breath.\n",
"- Often misdiagnosed as chronic bronchitis or asthma, leading to delayed diagnosis.\n",
"- Intermittent exacerbations are common, defined by a worsening of cough and sputum characteristics for 48 hours or more.\n",
"\n",
"### Diagnostic Approaches\n",
"- High-resolution CT scans are essential for diagnosis, seeking specific airway abnormalities.\n",
"- A systematic evaluation to identify underlying causes (such as congenital disorders or autoimmune diseases) is critical.\n",
"\n",
"### Pathobiology\n",
"- Multiple factors lead to airway dysfunction, inflammatory responses, and cyclical deterioration.\n",
"- Neutrophils and neutrophil elastase play significant roles in disease progression and exacerbations.\n",
"\n",
"### Microbiological Features\n",
"- **Common pathogens**:\n",
" - Pseudomonas aeruginosa (notably linked to exacerbations and worse prognosis)\n",
" - Staphylococcus aureus and other bacteria.\n",
"- Non-tuberculous mycobacterial infections are reported increasingly.\n",
"\n",
"### Treatment Strategies\n",
"- Emphasizes education about the disease and its management.\n",
"- Goals include symptom management, quality of life improvement, and reduction of exacerbation frequency.\n",
"- Options include:\n",
" - Airway-clearance therapies\n",
" - Antibiotics (macrolides or inhaled antibiotics)\n",
" - Addressing any treatable underlying conditions.\n",
"\n",
"### Prognostic Indicators\n",
"- Disease severity scores like the Bronchiectasis Severity Index and FACED scale are used for predicting outcomes.\n",
"\n",
"### Future Directions\n",
"- Emphasis on research into novel therapies targeting inflamatory pathways and innovative diagnostic tools.\n",
"\n",
"### Conclusion\n",
"- Bronchiectasis represents a complex clinical challenge that requires a multidisciplinary approach for effective management and treatment improvements. Further understanding of the disease mechanisms, enhancing diagnostic processes, and tailored therapies are vital for future advancements in the care of patients."
],
"text/plain": [
"<IPython.core.display.Markdown object>"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"# Step 4: Print the result of an example pdf\n",
"summary = summarize(\"https://www.nature.com/articles/s12276-023-01050-9.pdf\")\n",
"article_url=input('Please input the pdf URL: \\n')\n",
"summary = summarize(article_url)\n",
"display(Markdown(summary))"
]
},
{
"cell_type": "markdown",
"id": "fd2cb395-9e29-438e-9388-5555673b4689",
"metadata": {},
"source": [
"# Financial Report Analyst\n",
"#### Step 1: Create your prompts\n",
"\n",
"def craft_user_prompt(article):\n",
" user_prompt = f\"You are looking at a document titled {article.title}\\n Based on the body of the document, provide an impactful summary. Call out important points as bullets and highlughts . The body of the article is as follows.\"\n",
" user_prompt += article.text\n",
" return user_prompt\n",
"\n",
"#### Step 2: Make the messages list\n",
"def craft_messages(article):\n",
" system_prompt = '''You are a financial report research assistant that specialises in analysing the contents of a financial report and provide summary for investors to \\ \n",
" help adjust investment strategies. Call out important points as bullets and highlights. \\\n",
" Ignore text that doesn't belong to the article, like headers or navigation related text. Respond in markdown. Structure your text in the form of question/answer.'''\n",
" return [\n",
" {\"role\": \"system\", \"content\": system_prompt},\n",
" {\"role\": \"user\", \"content\": craft_user_prompt(article)}\n",
" ]"
]
},
{
"cell_type": "markdown",
"id": "70cbbffd-bf70-47d1-b5d6-5f929bdd89eb",
"metadata": {},
"source": [
"# Medical Report Analyst\n",
"#### Step 1: Create your prompts\n",
"\n",
"def craft_user_prompt(article):\n",
" user_prompt = f\"You are looking at a research article titled {article.title}\\n Based on the body of the article, Summarise the research article while highliting, Introduction, the problem, possible solution and conclusion. The body of the article is as follows.\"\n",
" user_prompt += article.text\n",
" return user_prompt\n",
"\n",
"#### Step 2: Make the messages list\n",
"def craft_messages(article):\n",
" system_prompt = \"You are a medical research assistant that analyses the contents of a research article and provides a summary while calling out important points as bullets and quotes. \\\n",
" Ignore text that doesn't belong to the article, like headers or navigation related text. Respond in markdown. Structure your text in the form of question/answer.\"\n",
" return [\n",
" {\"role\": \"system\", \"content\": system_prompt},\n",
" {\"role\": \"user\", \"content\": craft_user_prompt(article)}\n",
" ]"
]
},
{
"cell_type": "markdown",
"id": "c0bb9579-686a-4277-a139-7dff2c64cc9f",
"metadata": {},
"source": [
"# QA Format\n",
"#### Step 1: Create your prompts\n",
"\n",
"def craft_user_prompt(article):\n",
" user_prompt = f\"You are looking at a research article titled {article.title}\\n Based on the body of the article, how are micro RNAs produced in the cell? State the function of the proteins \\\n",
" involved. The body of the article is as follows.\"\n",
" user_prompt += article.text\n",
" return user_prompt\n",
"\n",
"#### Step 2: Make the messages list\n",
"def craft_messages(article):\n",
" system_prompt = \"You are an assistant that analyses the contents of a research article and provide answers to the question asked by the user in 250 words or less. \\\n",
" Ignore text that doesn't belong to the article, like headers or navigation related text. Respond in markdown. Structure your text in the form of question/answer.\"\n",
" return [\n",
" {\"role\": \"system\", \"content\": system_prompt},\n",
" {\"role\": \"user\", \"content\": craft_user_prompt(article)}\n",
" ]"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "680b45ae-6f3d-43b5-b69a-4e7f4fcca268",
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": null,
"id": "988864cc-08a2-4cfb-a09b-524504ee3803",
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
@ -181,7 +411,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.10"
"version": "3.11.11"
}
},
"nbformat": 4,

353
week1/day1.ipynb

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