Merge pull request #19 from shy982/functional-updates

Finalizing Release

README.md

@@ -5,11 +5,18 @@ of MED 277, UCSD Fall '23
 
 # Overview
 
+**Medimate:** The Medical Q&A App, is a state-of-the-art solution designed as a Proof of Concept (POC) for providing accurate, context-aware answers to medical-related inquiries. Leveraging the power of OpenAI's GPT and self-hosted Retrieval-Augmented Generation (RAG), it integrates sophisticated language models with a specialized medical knowledge base. This application is not only a baseline for building scalable applications in the healthcare domain but also features a user-friendly interface with speech-to-text capabilities and document upload options. Intended for continuous updates, our goal is to enhance its generalization, scalability, and modularity, making it an easily accessible and reliable resource for patients, healthcare professionals, and anyone seeking medical information.
+
+An overview of implementation is given below. 
+
+![Alt text](image.png)
+
 ## Setup:
 
 1. Have ``git`` installed on your system. In a terminal navigate to a directory to save this project.
 2. Do ``git clone [email protected]:shy982/Med-QnA-App.git``.
 3. Do ``cd ./Med-QnA-App`` to enter root directory of project.
+4. Refer to the [Project Hierarchy](https://github.com/shy982/Med-QnA-App/tree/main/ref/ProjectStructure.md) and [API Documentation](https://github.com/shy982/Med-QnA-App/tree/main/ref/APIDocs.md) for related development information.
 
 ## Requirements:
 
@@ -18,7 +25,10 @@ of MED 277, UCSD Fall '23
 
 2. Developing/testing purposes: If you want to have a development environment you'll need to
    install ``npm``, ``node``, ``Python 3.6+`` and follow the README's of the respective
-   directories. ``src/main/marshaller`` has the backend code. ``src/main/ui/web/medi-mate`` has the frontend.
+   directories. ``src/main/marshaler`` has the backend code. ``src/main/ui/web/medi-mate`` has the frontend.
+
+3. Mandatory Requirement: You'll need an `OPENAI_API_KEY` and add that to a .env file.
+   An `env.example` is given in the root directory of the repo. To get the API token follow instructions in [OpenAI API](https://openai.com/blog/openai-api)
 
 ## Running the application:
 
@@ -29,8 +39,20 @@ To run the application (Production build deployment for demo purpose only, not a
 3. Wait a while for frontend and backend containers to spawn.
 4. Go to http://localhost:3000/ to start chatting
 
-# Repository Handling Notes:
+## Repository Handling Notes:
 
 1. Raise PR on separate branch for code updates & request code owner review.
 2. Read env.example to create .env for API tokens.
-3. Mark TODO's as issues.
+3. Mark TODO's as issues.
+
+## Collaboration: 
+
+We appreciate any ideas and contributions from the fellow open-source community. 
+
+We aim to make this application accessible and modularized enough to use as a plug-and-play model for Evidence-based medicine & Closed Domain Question Answering. 
+
+Please feel free to contact the authors if you are interested to contribute or collaborate: 
+
+- [Shyam Renjith](https://www.github.com/shy982)
+- [Sanidhya Singal](https://www.github.com/sayhitosandy)
+- [Hyrum Eddington](https://github.com/hyedd77)

docs/README.md → docs/APIDocs.md

@@ -3,7 +3,7 @@
 # API Documentation
 
 ## Overview
-This document outlines the available endpoints in the MediMate Q&A application. The application provides endpoints for processing user messages using different methods, including simple text processing, OpenAI's GPT-3.5 model, and a Retrieval-Augmented Generation (RAG) approach.
+This document outlines the available endpoints in the MediMate Q&A application. The application provides endpoints for processing user messages using different methods, including simple text processing, OpenAI's GPT-3.5 model, and a Retrieval-Augmented Generation (RAG) approach.
 
 ## Endpoints
 

docs/ProjectStructure.md

@@ -0,0 +1,32 @@
+```
+Med-QnA-App/
+├── src/
+│   ├── main/
+│   │   ├── backend/
+│   │   │   ├── marshaler/
+│   │   │   │   └── chat_io_service.py      # Handles chat input/output operations
+│   │   │   └── qna_service/
+│   │   │       └── open_ai_client.py       # Manages interactions with OpenAI API
+│   │   └── ui/web/medi-mate/               # Main UI codebase
+│   │       ├── components/
+│   │       │   ├── Chat/
+│   │       │   │   └── ...                 # Chat related components
+│   │       │   ├── Layout/
+│   │       │   │   ├── Footer.js           # Footer component
+│   │       │   │   └── Navbar.js           # Navbar component
+│   │       │   ├── ModelSelection/
+│   │       │   │   ├── RAGToggle.js        # Toggle for RAG feature
+│   │       │   │   └── ...                 # Other model selection components
+│   │       │   └── ...
+│   │       ├── App.js                      # Main application component
+│   │       └── index.js                    # Entry point for the React application
+│   |── test/                               # Test files
+│   └── experiments/                        # RAG experiments, evaluations, and results
+├── public/
+│   ├── index.html                          # HTML template
+│   └── ...
+├── .env                                    # Environment configuration file
+├── package.json                            # NPM package configuration
+├── requirements.txt                        # Python dependencies
+└── ...                                     # Docker compose and other files
+```

env.example

@@ -1,6 +1,7 @@
 // README
 // This is a .env example
 // Please use cp env.example .env, then edit .env with your OPENAI_API_KEY etc.
+// Once copied, remove these comments from the .env file 
 
 OPENAI_API_KEY = ""
 GITHUB_USERNAME = ""

ref/README.md

@@ -1 +1,11 @@
-# Add references here
+# Add references here
+
+### Presentation
+
+Our presentation deck can be found at [Medical Q&A App Presentation](https://docs.google.com/presentation/d/1OTjFkpoBCs7I5DemtCoVvvZhMQrcO5r1D2pSYeHlZ1U/edit?usp=sharing). Please request access if you are interested in contributing. 
+
+### Course & Instructors
+
+- [MED 277, UCSD](https://dbmi.ucsd.edu/education/courses/med277.html)
+- [Prof. Shamim Nemati](https://profiles.ucsd.edu/shamim.nemati)
+- [Prof. Michael Hogarth](https://profiles.ucsd.edu/michael.hogarth)

src/experiments/README.md

@@ -0,0 +1,3 @@
+# Experiments
+
+- Our report in [References](https://github.com/shy982/Med-QnA-App/tree/main/ref/README.md) contains the results to these experiments. 

src/main/backend/qna_service/openai_client.py

@@ -19,8 +19,6 @@ def clean_response(response):
 def request_gpt_no_rag(messages, medical_history, model):
     load_dotenv()
     client = openai.OpenAI()
-    # prompt = "\n".join([message["content"] for message in messages])
-    # print(messages)
     conversation_history = "\n".join([message["content"] for message in messages])
     if medical_history != "":
         conversation_history += "\nWhile answering, also consider this as my medical history:\n" + medical_history
@@ -42,7 +40,7 @@ def run_rag_pipeline(messages, medical_history, model="gpt-3.5-turbo-instruct",
     # Load index from file
     loaded_faiss_vs = FAISS.load_local(
         # folder_path=f"src/main/backend/qna_service/datastore/vectordb/faiss/{dataset}/", # Uncomment for dev
-        folder_path=f"./qna_service/datastore/vectordb/faiss/{dataset.lower()}/",
+        folder_path=f"./qna_service/datastore/vectordb/faiss/{dataset.lower()}/",   # Comment for dev
         embeddings=OpenAIEmbeddings())
     retriever = loaded_faiss_vs.as_retriever(search_kwargs={"k": 5})
 
@@ -54,7 +52,7 @@ def run_rag_pipeline(messages, medical_history, model="gpt-3.5-turbo-instruct",
     prompt = ChatPromptTemplate.from_template(template)
 
     # docs_file_path = f"src/main/backend/qna_service/datastore/dataset/{dataset}/documents.pkl" # Uncomment for dev
-    docs_file_path = f"./qna_service/datastore/dataset/{dataset.lower()}/documents.pkl"
+    docs_file_path = f"./qna_service/datastore/dataset/{dataset.lower()}/documents.pkl" # Comment for dev
     with open(docs_file_path, "rb") as file:
         docs = pickle.load(file)
 

src/main/ui/web/medi-mate/.gitignore

@@ -21,3 +21,4 @@
 npm-debug.log*
 yarn-debug.log*
 yarn-error.log*
+.prettier

src/main/ui/web/medi-mate/dependencies.txt

@@ -0,0 +1,13 @@
+[email protected] Med-QnA-App/src/main/ui/web/medi-mate
+├── @tabler/[email protected]
+├── @testing-library/[email protected]
+├── @testing-library/[email protected]
+├── @testing-library/[email protected]
+├── [email protected]
+├── [email protected]
+├── [email protected]
+├── [email protected]
+├── [email protected]
+├── [email protected]
+└── [email protected]
+

src/main/ui/web/medi-mate/package.json

@@ -18,7 +18,8 @@
     "start": "react-scripts start",
     "build": "react-scripts build",
     "test": "react-scripts test",
-    "eject": "react-scripts eject"
+    "eject": "react-scripts eject",
+    "format": "prettier --loglevel warn --write \"{src/components, src/pages}/**/*.{jsx,js}\""
   },
   "eslintConfig": {
     "extends": [
@@ -39,6 +40,7 @@
     ]
   },
   "devDependencies": {
+    "prettier": "3.1.1",
     "tailwindcss": "^3.3.5"
   }
 }

src/main/ui/web/medi-mate/src/components/Chat/Chat.js

@@ -1,51 +1,59 @@
-import React from 'react';
-import ChatInput from './ChatInput';
-import ChatLoader from './ChatLoader';
-import ChatMessage from './ChatMessage';
-import ResetChat from './ResetChat';
-import ModelSelector from '../ModelSelection/ModelSelector';
-import DatasetSelector from '../ModelSelection/DatasetSelector';
-import RAGToggle from '../ModelSelection/RagToggle';
+import React from "react";
+import ChatInput from "./ChatInput";
+import ChatLoader from "./ChatLoader";
+import ChatMessage from "./ChatMessage";
+import ResetChat from "./ResetChat";
+import ModelSelector from "../ModelSelection/ModelSelector";
+import DatasetSelector from "../ModelSelection/DatasetSelector";
+import RAGToggle from "../ModelSelection/RagToggle";
 
 const Chat = ({
-                  messages,
-                  loading,
-                  onSend,
-                  onReset,
-                  onModelChange,
-                  onDatasetChange,
-                  isRAGEnabled,
-                  handleRAGToggle,
-                  setMedicalHistory
-              }) => {
-    return (
-        <>
-            <div className="flex flex-row justify-between items-center mb-4 sm:mb-8">
-                <ResetChat onReset={onReset}/>
-                <ModelSelector onModelChange={onModelChange} handleReset={onReset}/>
-                <RAGToggle isRAGEnabled={isRAGEnabled} handleRAGToggle={handleRAGToggle} handleReset={onReset}/>
-                <DatasetSelector isRAGEnabled={isRAGEnabled} onDatasetChange={onDatasetChange} handleReset={onReset}/>
-            </div>
+  messages,
+  loading,
+  onSend,
+  onReset,
+  onModelChange,
+  onDatasetChange,
+  isRAGEnabled,
+  handleRAGToggle,
+  setMedicalHistory,
+}) => {
+  return (
+    <>
+      <div className="flex flex-row justify-between items-center mb-4 sm:mb-8">
+        <ResetChat onReset={onReset} />
+        <ModelSelector onModelChange={onModelChange} handleReset={onReset} />
+        <RAGToggle
+          isRAGEnabled={isRAGEnabled}
+          handleRAGToggle={handleRAGToggle}
+          handleReset={onReset}
+        />
+        <DatasetSelector
+          isRAGEnabled={isRAGEnabled}
+          onDatasetChange={onDatasetChange}
+          handleReset={onReset}
+        />
+      </div>
 
-            <div className="flex flex-col rounded-lg px-2 sm:p-4 sm:border border-neutral-300">
-                {messages.map((message, index) => (
-                    <div key={index} className="my-1 sm:my-1.5">
-                        <ChatMessage message={message}/>
-                    </div>
-                ))}
+      <div className="flex flex-col rounded-lg px-2 sm:p-4 sm:border border-neutral-300">
+        {messages.map((message, index) => (
+          <div key={index} className="my-1 sm:my-1.5">
+            <ChatMessage message={message} />
+          </div>
+        ))}
 
-                {loading && (
-                    <div className="my-1 sm:my-1.5">
-                        <ChatLoader/>
-                    </div>
-                )}
+        {loading && (
+          <div className="my-1 sm:my-1.5">
+            <ChatLoader />
+          </div>
+        )}
 
-                <div className="mt-4 sm:mt-8 bottom-[56px] left-0 w-full">
-                    <ChatInput onSend={onSend} setMedicalHistory={setMedicalHistory}/>
-                </div>
-            </div>
-        </>
-    );
+        <div className="mt-4 sm:mt-8 bottom-[56px] left-0 w-full">
+          <ChatInput onSend={onSend} setMedicalHistory={setMedicalHistory} />
+        </div>
+      </div>
+    </>
+  );
 };
 
 export default Chat;