app.py

import re
import gradio as gr
import pandas as pd
import torch

from model import MimicTransformer
from utils import load_rule, get_attribution, get_diseases, get_drg_link, get_icd_annotations, visualize_attn, clean_text
from transformers import AutoTokenizer, AutoModel, set_seed, pipeline

torch.manual_seed(0)
set_seed(34)
if torch.cuda.is_available():
    torch.cuda.manual_seed_all(0)

model_path = 'checkpoint_0_9113.bin'
related_tensor = torch.load('discharge_embeddings.pt')
all_summaries = pd.read_csv('all_summaries.csv')['SUMMARIES'].to_list()

similarity_tokenizer = AutoTokenizer.from_pretrained('kamalkraj/BioSimCSE-BioLinkBERT-BASE')
similarity_model = AutoModel.from_pretrained('kamalkraj/BioSimCSE-BioLinkBERT-BASE')
similarity_model.eval()

def read_model(model, path):
    # model.load_state_dict(torch.load(path, map_location=torch.device('cpu')))
    state_dict = torch.load(path, map_location='cpu')
    model.load_state_dict({"model."+k: v for k, v in state_dict.items()}, strict=False)
    return model

mimic = MimicTransformer(cutoff=512)
mimic = read_model(model=mimic, path=model_path)
tokenizer = mimic.tokenizer
mimic.eval()

# disease ner model
pipe = pipeline("token-classification", model="alvaroalon2/biobert_diseases_ner")

# default DRG summary examples
ex1 = """HEAD CT:  Head CT showed no intracranial hemorrhage or mass effect, but old infarction consistent with past medical history."""
ex2 = """Radiologic studies also included a chest CT, which confirmed cavitary lesions in the left lung apex consistent with infectious tuberculosis. This also moderate-sized left pleural effusion."""
ex3 = """We have discharged Mrs Smith on regular oral Furosemide (40mg OD) and we have requested an outpatient ultrasound of her renal tract which will be performed in the next few weeks. We will review Mrs Smith in the Cardiology Outpatient Clinic in 6 weeks time."""
ex4 = """Blood tests revealed a raised BNP. An ECG showed evidence of left-ventricular hypertrophy and echocardiography revealed grossly impaired ventricular function (ejection fraction 35%). A chest X-ray demonstrated bilateral pleural effusions, with evidence of upper lobe diversion."""
ex5 = """Mrs Smith presented to A&E with worsening shortness of breath and ankle swelling. On arrival, she was tachypnoeic and hypoxic (oxygen saturation 82% on air). Clinical examination revealed reduced breath sounds and dullness to percussion in both lung bases. There was also a significant degree of lower limb oedema extending up to the mid-thigh bilaterally."""
examples = [ex1, ex2, ex3, ex4, ex5]
related_summaries = [[ex1]]
related_chosen = []
related_attn = []
related_clr_bts = []
correct_drg_text_list = []
correct_salient_words_list = []

rule_df, drg2idx, i2d, d2mdc, d2w = load_rule('MSDRG_RULE13.csv')

def mean_pooling(model_output, attention_mask):
    token_embeddings = model_output[0] #First element of model_output contains all token embeddings
    input_mask_expanded = attention_mask.unsqueeze(-1).expand(token_embeddings.size()).float()
    return torch.sum(token_embeddings * input_mask_expanded, 1) / torch.clamp(input_mask_expanded.sum(1), min=1e-9)


def get_model_results(text):
    text = clean_text(text)
    inputs = tokenizer(text, return_tensors='pt', padding='max_length', max_length=512, truncation=True)
    with torch.no_grad():
        outputs = mimic(input_ids=inputs.input_ids, attention_mask=inputs.attention_mask, drg_labels=None)
    attribution, reconstructed_text = get_attribution(text=text, tokenizer=tokenizer, model_outputs=outputs, inputs=inputs, k=10)
    logits = outputs[0][0]
    out = logits.detach().cpu()[0]
    drg_code = i2d[out.argmax().item()]
    print(out.topk(5))
    prob = torch.nn.functional.softmax(out).max()
    return {
        'class': drg_code,
        'prob': prob,
        'attn': attribution,
        'tokens': reconstructed_text,
        'logits': logits
    }

def find_related_summaries(text):
    inputs = similarity_tokenizer(
        text, padding='max_length', truncation=True, return_tensors='pt', max_length=512
    )
    outputs = similarity_model(**inputs)
    embedding = mean_pooling(outputs, attention_mask=inputs.attention_mask)
    embedding = torch.nn.functional.normalize(embedding)
    scores = torch.mm(related_tensor, embedding.transpose(1,0))
    scores_indices = scores.topk(k=50, dim=0)
    indices, scores = scores_indices[-1], torch.round(100 * scores_indices[0], decimals=2)
    summary_score_list = []
    score_set = set()
    for summary_idx, score in zip(indices, scores):
        score = score.item()
        if len(summary_score_list) == 5:
            break
        corresp_summary = all_summaries[summary_idx]
        if score in score_set or score >= 99: # potential duplicate
            continue
        summary_score_list.append(
            [round(score,2), corresp_summary])
        score_set.add(score)
    return summary_score_list



def run(text, related_discharges=False):
    torch.manual_seed(0)
    set_seed(34)
    if torch.cuda.is_available():
        torch.cuda.manual_seed_all(0)
    # initial drg results

    model_results = get_model_results(text=text)
    drg_code = model_results['class']

    # find diseases
    diseases = get_diseases(text=text, pipe=pipe)
    model_results['diseases'] = diseases
    drg_link = get_drg_link(drg_code=drg_code)
    icd_results = get_icd_annotations(text=text)
    row = rule_df[rule_df['DRG_CODE'] == drg_code]
    drg_description = row['DESCRIPTION'].values[0]
    model_results['class_dsc'] = drg_description
    model_results['drg_link'] = drg_link
    model_results['icd_results'] = icd_results
    global related_summaries    
    # related_summaries = generate_similar_summeries()
    related_summaries = find_related_summaries(text=text)
    if related_discharges:
        return visualize_attn(model_results=model_results)
    return (
        visualize_attn(model_results=model_results),
        # gr.Dataset.update(samples=related_summaries, visible=True, label='Related Discharge Summaries'),
        gr.DataFrame.update(value=related_summaries, visible=True),
        gr.ClearButton.update(visible=True),
        gr.TextArea.update(visible=True),
        gr.Button.update(visible=True),
        gr.Button.update(visible=True),
        gr.TextArea.update(visible=True),
        gr.TextArea.update(visible=True)
    )



def run_related():
    global related_chosen
    attn_list = []
    clr_bts = []
    correct_drg_list = []
    correct_salient_list = []
    for related in related_chosen:
        text = related[0]
        attn_html = run(text=text, related_discharges=True)
        attn_list.append(gr.HTML.update(value=attn_html))
        clr_bts.append(gr.ClearButton.update(visible=True))
        correct_drg_list.append(gr.Textbox.update(visible=True))
        correct_salient_list.append(gr.Textbox.update(visible=True))
    if len(attn_list) != 3:
        # find difference
        diff = 3 - len(attn_list)
        for i in range(diff):
            attn_list.append(gr.HTML.update(value=''))
            clr_bts.append(gr.ClearButton.update(visible=False))
            correct_drg_list.append(gr.Textbox.update(visible=False))
            correct_salient_list.append(gr.Textbox.update(visible=False))
    return attn_list + clr_bts + correct_drg_list + correct_salient_list
        


def load_example(example_id):
    global related_summaries
    global related_chosen
    sample = related_summaries[example_id][0]
    cleaned_sample = sample.split('% Similarity Rate for the following Discharge Summary:\n\n')[1:]
    related_chosen.append(cleaned_sample)
    return prettify_text(related_chosen)
    # return related_chosen

def load_df_example(df, event: gr.SelectData):
    global related_chosen
    discharge_summary = event.value
    related_chosen.append([discharge_summary])
    return prettify_text(related_chosen)

def save_results(text):
    return gr.Textbox.update(value='Thank you for your input!')

def prettify_text(nested_list):
    string = ''
    for li in nested_list:
        striped = re.sub(' +', ' ', li[0]).strip()
        delimiters = 99 * '='
        string += f'{striped}\n{delimiters}\n'
    return string.strip()

def remove_most_recent():
    global related_chosen
    related_chosen = related_chosen[:-1]
    if len(related_chosen) == 0:
        return ''
    return prettify_text(related_chosen)

def clr_btn():
    return gr.ClearButton.update(visible=False), gr.Textbox.update(visible=False), gr.Textbox.update(visible=False)

def main():
    with gr.Blocks() as demo:
        gr.Markdown("""
        # DRGCoder
        This interface outlines DRGCoder, an explainable clinical coding for the early prediction of diagnostic-related groups (DRGs). Please note all summaries will be truncated to 512 words if longer. 
        """)
        with gr.Row() as row:
            input = gr.Textbox(
                label="Input Discharge Summary Here", placeholder='sample discharge summary',
                text_align='left', interactive=True
            )
        with gr.Row() as row:
            gr.Examples(examples, [input])
        with gr.Row() as row:
            btn = gr.Button(value="Submit")
        with gr.Row() as row:
            attn_viz = gr.HTML() 
        with gr.Row() as row:
            with gr.Column() as col:
                correct_drg_text = gr.Textbox(visible=False, label="Input Correct DRG", interactive=True)
                correct_drg_text.submit(save_results, inputs=correct_drg_text, outputs=correct_drg_text)            
            with gr.Column() as col:
                salient_words_box = gr.Textbox(visible=False, label="Input Salient Words (comma separated)", interactive=True)
                salient_words_box.submit(save_results, inputs=salient_words_box, outputs=salient_words_box)
            attn_clr_btn = gr.ClearButton(value='Remove DRG Results', visible=False, components=[attn_viz]) 
            attn_clr_btn.click(clr_btn, outputs=[attn_clr_btn, correct_drg_text, salient_words_box])        
        
        # related row 1
        with gr.Row() as row:
            attn_1 = gr.HTML()
            related_attn.append(attn_1)
        with gr.Row() as row:
            with gr.Column() as col:
                correct_drg_text_1 = gr.Textbox(visible=False, label="Input Correct DRG", interactive=True)
                correct_drg_text_1.submit(save_results, inputs=correct_drg_text_1, outputs=correct_drg_text_1)
                correct_drg_text_list.append(correct_drg_text_1)            
            with gr.Column() as col:
                salient_words_box_1 = gr.Textbox(visible=False, label="Input Salient Words (comma separated)", interactive=True)
                salient_words_box_1.submit(save_results, inputs=salient_words_box_1, outputs=salient_words_box_1)
                correct_salient_words_list.append(salient_words_box_1)
            attn_clr_1 = gr.ClearButton(value='Remove DRG Results', visible=False, components=[attn_1])    
            related_clr_bts.append(attn_clr_1)
            attn_clr_1.click(clr_btn, outputs=[attn_clr_1, correct_drg_text_1, salient_words_box_1]) 

        # related row 2
        with gr.Row() as row:
            attn_2 = gr.HTML()
            related_attn.append(attn_2)
        with gr.Row() as row:
            with gr.Column() as col:
                correct_drg_text_2 = gr.Textbox(visible=False, label="Input Correct DRG", interactive=True)
                correct_drg_text_2.submit(save_results, inputs=correct_drg_text_2, outputs=correct_drg_text_2)
                correct_drg_text_list.append(correct_drg_text_2)            
            with gr.Column() as col:
                salient_words_box_2 = gr.Textbox(visible=False, label="Input Salient Words (comma separated)", interactive=True)
                salient_words_box_2.submit(save_results, inputs=salient_words_box_2, outputs=salient_words_box_2)
                correct_salient_words_list.append(salient_words_box_2)
            attn_clr_2 = gr.ClearButton(value='Remove DRG Results', visible=False, components=[attn_2])    
            related_clr_bts.append(attn_clr_2)
            attn_clr_2.click(clr_btn, outputs=[attn_clr_2, correct_drg_text_2, salient_words_box_2]) 


        # related row 3
        with gr.Row() as row:
            attn_3 = gr.HTML()
            related_attn.append(attn_3)
        with gr.Row() as row:
            with gr.Column() as col:
                correct_drg_text_3 = gr.Textbox(visible=False, label="Input Correct DRG", interactive=True)
                correct_drg_text_3.submit(save_results, inputs=correct_drg_text_3, outputs=correct_drg_text_3)
                correct_drg_text_list.append(correct_drg_text_3)            
            with gr.Column() as col:
                salient_words_box_3 = gr.Textbox(visible=False, label="Input Salient Words (comma separated)", interactive=True)
                salient_words_box_3.submit(save_results, inputs=salient_words_box_3, outputs=salient_words_box_3)
                correct_salient_words_list.append(salient_words_box_3)
            attn_clr_3 = gr.ClearButton(value='Remove DRG Results', visible=False, components=[attn_3])    
            related_clr_bts.append(attn_clr_3)
            attn_clr_3.click(clr_btn, outputs=[attn_clr_3, correct_drg_text_3, salient_words_box_3]) 


        # input to related summaries
        with gr.Row() as row:
            input_related = gr.TextArea(label="Input up to 3 Related Discharge Summaries Here", visible=False, text_align='left', min_width=300)
        with gr.Row() as row:
            rmv_related_btn = gr.Button(value='Remove Related Summary', visible=False)
            sbm_btn = gr.Button(value="Submit Related Summaries", components=[input_related], visible=False)                              
        
        with gr.Row() as row:
            related = gr.DataFrame(
                value=None, headers=['Similarity Score', 'Related Discharge Summary'], max_rows=5,
                datatype=['number', 'str'], col_count=(2, 'fixed'), visible=False
            )
        # initial run
        btn.click(run, inputs=[input], outputs=[
            attn_viz, related, attn_clr_btn, input_related,
            sbm_btn, rmv_related_btn, correct_drg_text, salient_words_box
        ])
        # find related summaries
        # related.click(load_example, inputs=[related], outputs=[input_related])
        related.select(load_df_example, inputs=[related], outputs=[input_related])
        # remove related summaries
        rmv_related_btn.click(remove_most_recent, outputs=[input_related])

        # perform attribution on related summaries
        sbm_btn.click(run_related, outputs=related_attn + related_clr_bts + correct_drg_text_list + correct_salient_words_list)

        
    demo.launch()

if __name__ == "__main__":
    main()