utils.py

import urllib.request, urllib.error, urllib.parse
import json
import pandas as pd
import ssl
import torch
import re
from pprint import pprint
from captum.attr import visualization

REST_URL = "http://data.bioontology.org"
API_KEY = "604a90bc-ef14-4c26-a347-f4928fa086ea"
ssl._create_default_https_context = ssl._create_unverified_context

class PyTMinMaxScalerVectorized(object):
    """
    From https://discuss.pytorch.org/t/using-scikit-learns-scalers-for-torchvision/53455
    Transforms each channel to the range [0, 1].
    """
    def __call__(self, tensor):
        scale = 1.0 / (tensor.max(dim=0, keepdim=True)[0] - tensor.min(dim=0, keepdim=True)[0]) 
        tensor.mul_(scale).sub_(tensor.min(dim=0, keepdim=True)[0])
        return tensor
    
def get_diseases(text, pipe):
    results = pipe(text)
    diseases = []
    disease_span = []
    for result in results:
        ent = result['entity']
        # start of a new entity
        if ent == 'B-DISEASE':
            disease_span = result['start'], result['end']
        elif ent == 'I-DISEASE':
            if len(disease_span) == 0:
                disease_span = []
            else:
                disease_span = disease_span[0], result['end']
        else:
            if len(disease_span) > 1:
                disease = text[disease_span[0]: disease_span[1]]
                if len(disease) > 2:
                    diseases.append(disease)
            disease_span = []
    if len(disease_span) > 1:
        disease = text[disease_span[0]: disease_span[1]]
        diseases.append(disease)
    return diseases    

def find_end(text):
    """Find the end of the report."""
    ends = [len(text)]
    patterns = [
        re.compile(r'BY ELECTRONICALLY SIGNING THIS REPORT', re.I),
        re.compile(r'\n {3,}DR.', re.I),
        re.compile(r'[ ]{1,}RADLINE ', re.I),
        re.compile(r'.*electronically signed on', re.I),
        re.compile(r'M\[0KM\[0KM')
    ]
    for pattern in patterns:
        matchobj = pattern.search(text)
        if matchobj:
            ends.append(matchobj.start())
    return min(ends)

def pattern_repl(matchobj):
    """
    Return a replacement string to be used for match object
    """
    return ' '.rjust(len(matchobj.group(0)))

def clean_text(text):
    """
    Clean text
    """

    # Replace [**Patterns**] with spaces.
    text = re.sub(r'\[\*\*.*?\*\*\]', pattern_repl, text)
    # Replace `_` with spaces.
    text = re.sub(r'_', ' ', text)

    start = 0
    end = find_end(text)
    new_text = ''
    if start > 0:
        new_text += ' ' * start
    new_text = text[start:end]

    # make sure the new text has the same length of old text.
    if len(text) - end > 0:
        new_text += ' ' * (len(text) - end)
    return new_text

def get_drg_link(drg_code):
    drg_code = str(drg_code)
    if len(drg_code) == 1:
        drg_code = '00' + drg_code
    elif len(drg_code) == 2:
        drg_code = '0' + drg_code
    return f'https://www.findacode.com/code.php?set=DRG&c={drg_code}'

def prettify(dict_list, k):
    li = [di[k] for di in dict_list]
    result = "\n".join(l for l in li)
    return result

def get_json(text_to_annotate):
    url = REST_URL + "/annotator?text=" + urllib.parse.quote(text_to_annotate) + "&ontologies=ICD9CM" +\
        "&longest_only=false" + "&exclude_numbers=false" + "&whole_word_only=true" + '&exclude_synonyms=false'
    opener = urllib.request.build_opener()
    opener.addheaders = [('Authorization', 'apikey token=' + API_KEY)]
    try:
        return json.loads(opener.open(url).read())
    except:
        return []

def parse_results(results):
    if len(results) == 0:
        return []
    rlist = []
    for result in results:
        annotations = result['annotations']
        for annotation in annotations:
            start = annotation['from']-1
            end = annotation['to'] - 1
            text = annotation['text']
            rlist.append({
                'start': start,
                'end': end,
                'text': text,
                'link': result['annotatedClass']['@id']
            })
    return rlist

def get_icd_annotations(text):
    response = get_json(text)
    annotation_list = parse_results(response)
    return annotation_list

def subfinder(mylist, pattern):
    mylist = mylist.tolist()
    pattern = pattern.tolist()
    return list(filter(lambda x: x in pattern, mylist))

def tokenize_icds(tokenizer, annotations, token_ids):
    icd_tokens = torch.zeros(token_ids.shape)
    for annotation in annotations:
        icd = annotation['text']
        icd_token_ids = tokenizer(icd, add_special_tokens=False, return_tensors='pt').input_ids[0]
        # find index of the beginning icd token
        starting_indices = (token_ids==icd_token_ids[0]).nonzero(as_tuple=False)
        num_icd_tokens = icd_token_ids.shape[0]

        # if there's more than 1 icd token for the given annotation
        if num_icd_tokens > 1:
            # if there's only one starting index
            if starting_indices.shape[0] == 1:
                starting_index = starting_indices.item()
                icd_tokens[starting_index: starting_index + num_icd_tokens] = 1
            # if there's more than 1 starting index, determine which is the appropriate
            else:
                for starting_index in starting_indices:
                    if token_ids[starting_index + num_icd_tokens] == icd_token_ids:
                        icd_tokens[starting_index: starting_index + num_icd_tokens] = 1
        
        # otherwise, set the corresponding index to a value of 1
        else:
            icd_tokens[starting_indices] = 1
    return icd_tokens

def get_attribution(text, tokenizer, model_outputs, inputs, k=7):
    tokens = tokenizer.convert_ids_to_tokens(inputs.input_ids[0])
    padding_idx = tokens.index('[PAD]')
    tokens = tokens[:padding_idx][1:-1]
    attn = model_outputs[-1][0]
    agg_attn, final_text = reconstruct_text(tokenizer=tokenizer, tokens=tokens, attn=attn)
    return agg_attn, final_text
    
def reconstruct_text(tokenizer, tokens, attn):
    """
    find a word -> token_id mapping that allows you to
    perform an aggregation on the sub-tokens' attention
    values
    """
    reconstructed_text = tokenizer.convert_tokens_to_string(tokens)
    num_subtokens = len([t for t in tokens if t.startswith('#')])
    aggregated_attn = torch.zeros(len(tokens) - num_subtokens)
    token_indices = [0]
    token_idx = 0
    reconstructed_tokens = []
    for i, token in enumerate(tokens[1:], start=1):
        # case when a token is a subtoken
        if token.startswith('#'):
            token_indices.append(i)    
        else:
            # reconstruct the tokens to make sure you're doing this correctly
            reconstructed_token = ''.join(tokens[i].replace('#', '') for i in token_indices)
            reconstructed_tokens.append(reconstructed_token)
            # find the corresponding attention vectors
            aggregated_attn[token_idx] = torch.mean(attn[token_indices])
            # create new index list
            token_indices = [i]
            token_idx += 1
    # reconstruct the tokens to make sure you're doing this correctly
    reconstructed_token = ''.join(tokens[i].replace('#', '') for i in token_indices)
    reconstructed_tokens.append(reconstructed_token)
    # find the corresponding attention vectors
    aggregated_attn[token_idx] = torch.mean(attn[token_indices])   

    # final representation of text
    final_text = ' '.join(reconstructed_tokens).replace(' .', '.')
    final_text = final_text.replace(' ,', ',')
    # final_text == reconstructed_text
    return aggregated_attn, reconstructed_tokens

def load_rule(path):
    rule_df = pd.read_csv(path)
    
    # remove MDC 15 - neonate and couple other codes related to postcare
    if 'MS' in path:
        msk = (rule_df['MDC']!='15') & (~rule_df['MS-DRG'].isin([945, 946, 949, 950, 998, 999])) 
        space = sorted(rule_df[msk]['DRG_CODE'].unique())
    elif 'APR' in path:
        msk = (rule_df['MDC']!='15') & (~rule_df['APR-DRG'].isin([860, 863])) 
        space = sorted(rule_df[msk]['DRG_CODE'].unique())
        
    drg2idx = {}
    for d in space:
        drg2idx[d] = len(drg2idx)
    i2d = {v:k for k,v in drg2idx.items()}

    d2mdc, d2w = {}, {}
    for _, r in rule_df.iterrows():
        drg = r['DRG_CODE']
        mdc = r['MDC']
        w = r['WEIGHT']
        d2mdc[drg] = mdc
        d2w[drg] = w
        
    return rule_df, drg2idx, i2d, d2mdc, d2w

def visualize_attn(model_results):
    class_id = model_results['class_dsc']
    prob = model_results['prob']
    attn = model_results['attn']
    tokens = model_results['tokens']
    scaler = PyTMinMaxScalerVectorized()
    normalized_attn = scaler(attn)
    viz_record = visualization.VisualizationDataRecord(
        word_attributions=normalized_attn,
        pred_prob=prob,
        pred_class=class_id,
        true_class=class_id,
        attr_class=0,
        attr_score=1,
        raw_input_ids=tokens,
        convergence_score=1
    )
    return visualize_text(
        viz_record,
        drg_link=model_results['drg_link'],
        icd_annotations=model_results['icd_results'],
        diseases=model_results['diseases']
    )


def modify_attn_html(attn_html):
    attn_split = attn_html.split('<mark')
    htmls = [attn_split[0]]
    for html in attn_split[1:]:
        # wrap around href tag
        href_html = f'<a href="https://" \
            <mark{html} \
            </a>'
        htmls.append(href_html)
    return "".join(htmls)

def modify_code_html(html, link, icd=False):
    html = html.split('<td>')[1].split('</td>')[0]
    href_html = f'<td><a href="{link}"{html}</a></td>'
    if icd:
        href_html = href_html.replace('<td>', '').replace('</td>', '')
    return href_html

def modify_drg_html(html, drg_link):
    return modify_code_html(html=html, link=drg_link, icd=False)

def get_icd_html(icd_list):
    if len(icd_list) == 0:
        return '<td><text style="padding-right:2em"><b>N/A</b></text></td>'
    final_html = '<td>'
    icd_set = set()
    for icd_dict in icd_list:
        text, link = icd_dict['text'], icd_dict['link']
        if text in icd_set:
            continue
        tmp_html = visualization.format_classname(classname=text)
        html = modify_code_html(html=tmp_html, link=link, icd=True)
        final_html += html
        icd_set.add(text)
    return final_html + '</td>'


def get_disease_html(diseases):
    if len(diseases) == 0:
        return '<td><text style="padding-right:2em"><b>N/A</b></text></td>'
    diseases = list(set(diseases))
    diseases_str = ', '.join(diseases)
    html = visualization.format_classname(classname=diseases_str)
    return html + '</td>'

    

# copied out of captum because we need raw html instead of a jupyter widget
def visualize_text(datarecord, drg_link, icd_annotations, diseases):
    dom = ["<table width: 100%>"]
    rows = [
        "<th style='text-align: left'>Predicted DRG</th>"
        "<th style='text-align: left'>Word Importance</th>"
        "<th style='text-align: left'>Diseases</th>"
        "<th style='text-align: left'>ICD Codes</th>"
    ]
    pred_class_html = visualization.format_classname(datarecord.pred_class)
    icd_class_html = get_icd_html(icd_annotations)
    disease_html = get_disease_html(diseases)
    pred_class_html = modify_drg_html(html=pred_class_html, drg_link=drg_link)
    word_attn_html = visualization.format_word_importances(
        datarecord.raw_input_ids, datarecord.word_attributions
    )
    rows.append(
        "".join(
            [
                "<tr>",
                pred_class_html,
                word_attn_html,
                disease_html,
                icd_class_html,
                "<tr>",
            ]
        )
    )

    dom.append("".join(rows))
    dom.append("</table>")
    html = "".join(dom)

    return html