app.py

import streamlit as st
import gradio as gr
import shap
import numpy as np
import scipy as sp
import torch
import transformers
from transformers import pipeline
from transformers import AutoTokenizer, AutoModelForSequenceClassification, AutoModelForTokenClassification

import matplotlib.pyplot as plt
import sys
import csv

csv.field_size_limit(sys.maxsize)

device = "cuda:0" if torch.cuda.is_available() else "cpu"

tokenizer = AutoTokenizer.from_pretrained("jschwaller/ADRv2024")  
model = AutoModelForSequenceClassification.from_pretrained("jschwaller/ADRv2024")

# Build a pipeline object for predictions
pred = transformers.pipeline("text-classification", model=model, 
                             tokenizer=tokenizer, top_k=None)

explainer = shap.Explainer(pred)

ner_tokenizer = AutoTokenizer.from_pretrained("d4data/biomedical-ner-all")
ner_model = AutoModelForTokenClassification.from_pretrained("d4data/biomedical-ner-all")

ner_pipe = pipeline("ner", model=ner_model, tokenizer=ner_tokenizer, aggregation_strategy="simple") # pass device=0 if using gpu
#

entity_colors = {
    'Severity': '#E63946',  # a vivid red
    'Sign_symptom': '#2A9D8F',  # a deep teal
    'Medication': '#457B9D',  # a dusky blue
    'Age': '#F4A261',  # a sandy orange
    'Sex': '#F4A261',  # same sandy orange for consistency with 'Age'
    'Diagnostic_procedure': '#9C6644',  # a brown
    'Biological_structure': '#BDB2FF',  # a light pastel purple
}

def adr_predict(x):
    encoded_input = tokenizer(x, return_tensors='pt')
    output = model(**encoded_input)
    scores = output[0][0].detach()
    scores = torch.nn.functional.softmax(scores)
   
    shap_values = explainer([str(x).lower()])
    local_plot = shap.plots.text(shap_values[0], display=False)

    res = ner_pipe(x)

    htext = ""
    prev_end = 0
    for entity in res:
        start = entity['start']
        end = entity['end']
        word = entity['word'].replace("##", "")
        color = entity_colors[entity['entity_group']]
        
        htext += f"{x[prev_end:start]}<mark style='background-color:{color};'>{word}</mark>"
        prev_end = end
    htext += x[prev_end:]
   
    return {"Severe Reaction": float(scores.numpy()[1]), "Non-severe Reaction": float(scores.numpy()[0])}, local_plot, htext


def main(prob1):
    text = str(prob1).lower()
    obj = adr_predict(text)
    return obj[0], obj[1], obj[2]
    
# Define HTML for the legend
legend_html = """
<div style='margin-top: 20px; color: white;'>  <!-- Ensure the legend text is white for visibility -->
    <h3>NER Legend</h3>
    <ul style='list-style-type:none; padding-left: 0;'>  <!-- Remove padding from the list -->
"""

for entity, color in entity_colors.items():
    legend_html += f"<li><span style='color: white; background-color: {color}; padding: 5px 10px; margin-right: 5px; border-radius: 5px;'>{entity}</span></li>"

legend_html += "</ul></div>"

# Create a Gradio HTML component to display the legend
ner_legend = gr.HTML(value=legend_html)

title = "Welcome to **ADR Tracker**"
description1 = "This app takes text (up to a few sentences) and predicts to what extent the text describes severe (or non-severe) adverse reaction to medications. Please do NOT use for medical diagnosis."

css = """
body { font-family: 'Roboto', sans-serif; background-color: #333; color: #163E64; }
h1, h2, h3, h4, h5, h6, p, label, .markdown { color: #163E64; } /* Ensuring that all text elements are consistently light blue */
.textbox { width: 100%; border-radius: 10px; border: 1px solid #ccc; background-color: white; color: black; }
.button { background-color: #FF6347; color: white; border: none; border-radius: 10px; padding: 10px 20px; cursor: pointer; }
"""

with gr.Blocks(css=css) as demo:
    gr.Markdown(f"## {title}")
    gr.Markdown(description1)
    gr.Markdown("---")
    prob1 = gr.Textbox(label="Enter Your Text Here:", lines=2, placeholder="Type it here...")
    submit_btn = gr.Button("Analyze")

    with gr.Row():
        with gr.Column(visible=True):
            label = gr.Label(label="Predicted Label")
        with gr.Column(visible=True):
            local_plot = gr.HTML(label='Shap:')
            htext = gr.HTML(label="NER")

    submit_btn.click(
        main,
        [prob1],
        [label, local_plot, htext],
        api_name="adr"
    )

    # Display the NER Legend below the buttons
    ner_legend  # Assuming you've defined this component above as shown

    with gr.Row():
        gr.Markdown("### Click on any of the examples below to see how it works:")
        gr.Examples([["A 35 year-old female had suicidal ideation after taking Prednisone."],
                     ["A 23 year-old male had minor nausea after taking Acetaminophen."]], 
                    [prob1], [label, local_plot, htext], main, cache_examples=True)

demo.launch()