app.py

import torch
from torch import nn
import pandas as pd
import numpy as np
import gradio as gr
from LongLAT.models.modeling import CodingModel as LongLATCodingModel, CodingModelConfig as LongLATCodingModelConfig
from HiLATmain.models.modeling import CodingModel, CodingModelConfig
from LongHiLATmain.models.modeling import CodingModel as LongHiLATCodingModel, CodingModelConfig as LongHiLATCodingModelConfig
from run_coding import ModelArguments, DataTrainingArguments
from LongLAT.models.utils import segment_tokenize_dataset
from transformers import (
    AutoConfig,
    AutoTokenizer,
    DataCollatorWithPadding,
    EvalPrediction,
    HfArgumentParser,
    Trainer,
    TrainingArguments,
    AutoModel,
    default_data_collator,
    set_seed,
    AutoModelForSequenceClassification
)


import hashlib
import colorsys

def hash_to_color(label):
    hash_val = int(hashlib.sha256(label.encode('utf-8')).hexdigest(), 16)
    hue = hash_val % 256 / 256.0
    rgb = colorsys.hsv_to_rgb(hue, 0.3, 0.9) 
    hex_color = '#%02x%02x%02x' % tuple(int(c * 255) for c in rgb)
    return hex_color


def get_coding_model_config(model_name, model_args, data_args, label_dict, num_labels):
    model_config_mapping = {
        "HiLAT": (CodingModelConfig, CodingModel),
        "Long-HiLAT": (LongHiLATCodingModelConfig, LongHiLATCodingModel),
        "Long-LAT": (LongLATCodingModelConfig, LongLATCodingModel)
    }

    config_class, model_class = model_config_mapping.get(model_name)
    if config_class is None or model_class is None:
        raise ValueError("Invalid model name")

    config = config_class(
        model_args.model_name_or_path,
        model_args.tokenizer_name,
        model_args.transformer_layer_update_strategy,
        model_args.num_chunks_per_document,
        data_args.max_seq_length,
        model_args.dropout,
        model_args.dropout_att,
        model_args.d_model,
        label_dict,
        num_labels,
        model_args.use_code_representation,
        data_args.code_max_seq_length,
        data_args.code_batch_size,
        model_args.multi_head_attention,
        model_args.chunk_attention,
        model_args.linear_init_mean,
        model_args.linear_init_std,
        model_args.document_pooling_strategy,
        model_args.multi_head_chunk_attention,
        model_args.num_hidden_layers
    )
    return config, model_class


def predict_icd(text_input, model_name, label_count):
    labels = []
    values = []
    if label_count == "50":
        labels  = ['038.9', '244.9', '250.00', '272.0', '272.4', '276.1', '276.2', '285.1', '285.9', '287.5', '305.1', '311', '33.24', '36.15', '37.22', '38.91', '38.93', '39.61', '39.95', '401.9', '403.90', '410.71', '412', '414.01', '424.0', '427.31', '428.0', '45.13', '486', '496', '507.0', '511.9', '518.81', '530.81', '584.9', '585.9', '599.0', '88.56', '88.72', '93.9', '96.04', '96.6', '96.71', '96.72', '99.04', '99.15', '995.92', 'V15.82', 'V45.81', 'V58.61']
        values = [0, 0, 0, 0, 0, 1, 0, 0, 1, 1, 1, 0, 1, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0]
    if label_count == "5":
        labels = ['38.93', '401.9', '414.01', '427.31', '428.0']
        values = [1, 0, 0, 0, 0]
    label_map = {i: label for i, label in enumerate(labels)}
    data_dict = {label: [] for label in labels}
    
    for label, value in zip(labels, values):
        data_dict[label].append(value)

    data = pd.DataFrame(data_dict)
    labels = data.iloc[:, 0:].apply(lambda x: [seg for seg in x], axis=1).tolist()
   
    if 'text' not in data:
        data.insert(0, 'text', text_input)
    else:
        data['text'] = text_input
    text = data["text"].tolist()
    
    model_path = "meghanaraok/"+model_name+"_"+label_count
    #change
    label_dict = pd.read_csv("data/mimic3/"+label_count+"/labels_dictionary_"+label_count+"_level_1.csv")
    num_labels = label_dict.shape[0]
    
    if model_name != "ClinicalLongformer":
        config_json = "config/"+model_name+"_"+label_count+"/config.json"
        parser = HfArgumentParser((ModelArguments, DataTrainingArguments, TrainingArguments))
        model_args, data_args, training_args = parser.parse_json_file(json_file=config_json)
        coding_model_config, model_class = get_coding_model_config(model_name, model_args, data_args, label_dict, label_dict.shape[0])
        kwargs = {
            "coding_model_config": coding_model_config,
            "args": training_args
        }
        model = model_class.from_pretrained(model_path, **kwargs)
        tokenizer = AutoTokenizer.from_pretrained(model_args.tokenizer_name,  padding_side="right")
        results = segment_tokenize_dataset(tokenizer, text, labels,
                                           data_args.max_seq_length,
                                           model_args.num_chunks_per_document)


        input_ids = torch.tensor(results['input_ids'])
        attention_mask = torch.tensor(results['attention_mask'])
        token_type_ids = torch.tensor(results['token_type_ids'])
        targets = torch.tensor(results['targets'])
        targets = targets.float()


        with torch.no_grad():
            # input_ids = input_ids.to(torch.device("cuda:0"))
            # attention_mask = attention_mask.to(torch.device("cuda:0"))
            # token_type_ids = token_type_ids.to(torch.device("cuda:0"))
            # targets = targets.to(torch.device("cuda:0"))
            model_inputs = {
                            "input_ids": input_ids,
                            "attention_mask": attention_mask,
                            "token_type_ids": token_type_ids,
                            "targets": targets
                            }
            outputs = model(**model_inputs)
            
    else:
        tokenizer = AutoTokenizer.from_pretrained('yikuan8/Clinical-Longformer',
                                          padding='max_length',
                                          truncation=False,
                                          max_length=4096,
                                          padding_side="right")
        if label_count == "5":
            model_path = "meghanaraok/ClinicalLongformer_5"
        else:
            model_path = "meghanaraok/ClinicalLongformer_50"
        
        model = AutoModelForSequenceClassification.from_pretrained(model_path)
        single_input_df = pd.DataFrame({'CombinedChunk': [text_input], 'labels': [[]]})
        inputs = tokenizer(single_input_df['CombinedChunk'].tolist(), return_tensors='pt', padding=True, truncation=True, max_length=4096)

        with torch.no_grad():
            outputs = model(**inputs)
        

    probabilities = nn.functional.sigmoid(outputs['logits'])
    predictions = (probabilities >= 0.5).cpu().numpy().astype(int)
    predicted_labels = [label_map[i] for i, pred in enumerate(predictions[0]) if pred == 1]
    label_probabilities = {label_map[i]: prob * 100 for i, prob in enumerate(probabilities[0]) if label_map[i] in predicted_labels}
    y_pred = np.array(predicted_labels)
    y_pred = "\n".join(y_pred)
    label_dict_df = pd.read_csv("data/mimic3/50/labels_dictionary_50_level_1.csv")

    label_dict = label_dict_df.set_index('icd9_code')['long_title'].to_dict()
    predicted_labels_with_titles = [(label, label_dict.get(str(label), "Not Found")) for label in predicted_labels]

    html_output ="<h2>ICD Codes</h2>"
    for label, title in predicted_labels_with_titles:
        label = str(label)
        color = hash_to_color(label)
        html_output += f"<div style='background-color: {color}; padding: 5px; margin-bottom: 5px;'>{label} - {title} <span style='float:right;'>{label_probabilities.get(label, 0):.2f}%</span></div>"


    
    return html_output

sample_texts = {"Sample summary 1": "date of birth:               sex:   m service surgery allergies patient recorded as having no known allergies to drugs attending chief complaint found down unresponsive major surgical or invasive procedure percutaneous cholecystostomy tube placement diagnostic laparoscopy with washout and drain placement percutaneous cholecystostomy tube placement exploratory laparoscopy picc line placement flexiseal placement history of present illness 82yo m without known medical hx presents from osh following finding of r sah on head ct per limited report the patient was found down on his lawn by a neighbor brought to where head ct reveal r temporal sah and small sdh without mass effect the patient was aphasic at the osh and unable to provide hx pt transferred to for further care the patient at present is not cooperative and unable provide any further history past medical history pmhx syncope glaucoma htn social history lives alone proxy is year old cousin family history non contributory physical exam physical exam on discharge 99ra gen nad drowsy but arousable cv rrr pulm ctab anteriorly abd soft mildly distended incision c d i perc chole tube in place ext wwp dopplerable pt dp on lle and rle edema bilaterally neuro fluctuating mental status at times will not respond to any questions other times will say his name and make jokes eomib moves all extremities but only strength pertinent results imaging ct head slight interval increase in right temporoparietal subdural and subarachnoid hemorrhages with developing contusions slightly more prominent foci of extra axial blood at the anterior left frontal and temporal lobes likely representing contre coup injury cta head less conspicuous subarachnoid hemorrhage with overall stable right and smaller left subdural hematomas intraventricular hemorrhage more evident now may reflect redistribution no change in venticular size stable hypodensity in the superior right frontal lobe may be an area of infarct or contusion whose chronicity is unclear hemodynamically significant stenosis occlusion nor aneurysm of the intracranial anterior or posterior circulation probable infundibulum at the left sca origin ct head expected interval evolution of multiple foci of intracranial hemorrhage including small right subdural hematoma foci of subarachnoid hemorrhage right temporal and left frontal hemorrhagic contusions and intraventricular hemorrhage no evidence of new hemorrhage or hydrocephalus apparent developing bilateral subdural hygromas recommend attention on follow up ct head bilateral subdural hygromas evolving since but stable since the most recent study of these are slightly hyperattenuating likely reflecting admixture with a small amount of pre existent blood in the subdural space expected evolution of multiple foci of subarachnoid hemorrhage small right subdural hematoma and several parenchymal contusions no new hemorrhage or hydrocephalus is detected ct head no significant interval change in the appearance of the brain since the recent study of right temporal hemorrhagic contusions and the surrounding edema small foci of sah intraventricular hemorrhage and bilateral subdural hygromas are stable since the recent study ct head decreased small bilateral intraventricular hemorrhage with stable bilateral subdural hygromas right temporal contusions have evolved a left frontal lobe hypodensity may represent a contusion or infarction unchanged since ct head bilateral predomitly chronic subdural hematomas minimal intraventricular blood right temporal contusion and left frontal contusion vs infarct are again noted without superimposed acute process compared to prior study slight enlargement of the right subdural fluid collection ct abd pelvis findings concerning for acute cholecystitis as described above no evidence of pe bibasilar atelectasis and trace left pleural effusions are noted minimally dilated small bowel in the left upper quadrant with collapsed distal small bowel raises concern for evolving small bowel obstruction perc chole tube placement successful ultrasound guided percutaneous cholecystostomy tube placement with fr catheter echo mild concentric left ventricular hypertrophy with preserved biventricular function no valvular vegetations identified low average technical quality if clinically suggested the absence of a vegetation by 2d echocardiography does not exclude endocarditis lvef micro pm blood culture source venipuncture blood culture routine final escherichia coli identification and sensitivities performed on culture 0613m anaerobic bottle gram stain final gram negative rod s am blood culture source line central line blood culture routine final escherichia coli final sensitivities sensitivities mic expressed in mcg ml escherichia coli ampicillin i ampicillin sulbactam s cefazolin s cefepime s ceftazidime s ceftriaxone s ciprofloxacin s gentamicin s meropenem s piperacillin tazo s tobramycin s trimethoprim sulfa s anaerobic bottle gram stain final gram negative rod s reported by phone to on 745pm am bile gram stain final no polymorphonuclear leukocytes seen per 1000x field gram negative rod s fluid culture final escherichia coli moderate growth klebsiella pneumoniae sparse growth sensitivities mic expressed in mcg ml escherichia coli klebsiella pneumoniae ampicillin i ampicillin sulbactam s s cefazolin s s cefepime s s ceftazidime s s ceftriaxone s s ciprofloxacin s s gentamicin s s meropenem s s piperacillin tazo s s tobramycin s s trimethoprim sulfa s s anaerobic culture final no anaerobes isolated pm peritoneal fluid gram stain final per 1000x field polymorphonuclear leukocytes no microorganisms seen fungal culture final no fungus isolated wound culture final a swab is not the optimal specimen collection to evaluate body fluids escherichia coli rare growth sensitivities mic expressed in mcg ml escherichia coli ampicillin s ampicillin sulbactam s cefazolin s cefepime s ceftazidime s ceftriaxone s ciprofloxacin s gentamicin s meropenem s piperacillin tazo s tobramycin s trimethoprim sulfa s anaerobic culture final no anaerobes isolated am sputum source endotracheal gram stain final pmns and epithelial cells 100x field no microorganisms seen respiratory culture final rare growth commensal respiratory flora staph aureus coag rare growth staphylococcus species may develop resistance during prolonged therapy with quinolones therefore isolates that are initially susceptible may become resistant within three to four days after initiation of therapy testing of repeat isolates may be warranted sensitivities mic expressed in mcg ml staph aureus coag clindamycin s erythromycin s gentamicin s levofloxacin s oxacillin s trimethoprim sulfa s am blood culture x blood culture routine final no growth am stool consistency not applicable source stool clostridium difficile toxin a b test final feces negative for c difficile toxin a b by eia reference range negative am stool consistency watery source stool clostridium difficile toxin a b test final feces negative for c difficile toxin a b by eia reference range negative laboratories 00am blood wbc rbc hgb hct mcv mch mchc rdw plt ct 19am blood pt ptt inr pt 19am blood glucose urean creat na k cl hco3 angap 19am blood calcium phos mg brief hospital course per report the patient was found down by his neighbor on the ground outside his home confused after being evaluated at osh he was transferred to for evaluation and treatment in the ed workup was significant for exam without evidence of trauma ct head with r sah sm r sdh bifrontal contusion exam in ed was significant for mae but he was not following commands he also displayed subtle l hemineglect and favoring of the r side he was admitted initially to the icu by neurosurgery and later transferred to the stepdown unit the following day after ct demonstrated stability of the bleed his mental status has remained limited noted for spontaneous movement of his extremities but without following command on he developed fever to followed by rapid afib electrical cardioversion was unsuccessful he was transferred to the icu as he became hypotensive and required pressors he was intubated shortly after arrival to sicu a ct abd pelvis was obtained to identify the source for his presumed sepsis and showed evidence of cholecystitis given the patient s unstable condition a percutaneous cholecystostomy tube was placed and broad spectrum antibiotics were initiated bile and blood cultures revealed klebsiella and e coli and antibiotics were narrowed to cipro vancomycin was re added later for cellulitis of the right flank following the attempted cardioversion the patient s r foot became blue cold and pulseless vascular surgery was consulted and they felt that this likely was an exacerbation of chronic vascular disease made worse by his pressor requirements given his condition they felt that it would be unwise to perform an angiogram at that time and preferred to see him as an outpatient a heparin gtt was started after clearance with neurosurgery as the heparin gtt was started and the levo was weaned the foot became pinker warm and gained doppler signals in the pt and dp his right hand also transiently became blue and cold but this resolved on its own within hours the patient s labs demonstrated a rising lactate during this time and the patient underwent an exploratory laparoscopy to evaluate for ischemic gut the ex laparoscopy was negative and he did not undergo a laparotomy the patient began doing better in terms of vital signs and he was able to be weaned off of all pressors the patient was then diuresed aggressively and his ventilator weaned coumadin was started after a discussion with vascular surgery and neurosurgery after discussion the health care proxy decided against a trach peg and the patient was made dni he was then given a breathing trial which he tolerated well his mental status improved off the ventilator and he was transferred to the floor on the floor the patient continued to improve moving all extremities and becoming more alert he demonstrated a fluctuating mental status but overall improved in terms of answering questions a final repeat head ct showed no new bleeds his foley was removed and he voided spontaneously the day before discharge the patient failed a speech and swallow test and his proxy refused a peg tube a post pyloric feeding tube was placed by ir so that tube feeds could continue at rehabilitation tube feeds had been started in the sicu and were continued on the floor throughout his stay his final cultures obtained on for his fluctuating mental status are currently pending the blood cultures prior to these were negative his antibiotics were discontinued on the day of discharge on the day of discharge the patient was in stable condition afebrile and with stable vital signs he was tolerating tube feeds at goal through a post pyloric dobhoff tube voiding spontaneously and having bowel movements he had been out of bed but not ambulating he was on coumadin for his previously cold right foot follow up instructions from general surgery vascular surgery and neurosurgery were obtained and documented in his transfer materials to rehabilitation medications on admission unknown discharge medications docusate sodium mg ml liquid sig ten ml po bid times a day through dobhoff tube senna mg tablet sig one tablet po bid times a day as needed for constipation through tube ipratropium albuterol mcg actuation aerosol sig puffs inhalation q6h every hours as needed for increased wob hypoxia bisacodyl mg tablet delayed release e c sig two tablet delayed release e c po daily daily albuterol sulfate mg ml solution for nebulization sig one neb inhalation q6h every hours as needed for wheezing acetaminophen mg ml solution sig one solution po q6h every hours insulin regular human unit ml solution sig one sliding scale injection asdir as directed folic acid mg tablet sig one tablet po daily daily thiamine hcl mg tablet sig one tablet po daily daily famotidine mg tablet sig one tablet po bid times a day multivitamin tablet sig one tablet po daily daily acetylcysteine mg ml solution sig one ml miscellaneous q6h every hours as needed for thick secretions nystatin unit g cream sig one appl topical times a day coumadin mg tablet sig one tablet po once a day please dose according to inr goal enoxaparin mg ml syringe sig one subcutaneous q12h every hours disp 80mg 8ml refills discharge disposition extended care facility discharge diagnosis traumatic brain injury acute cholecystitis sepsis discharge condition mental status confused always level of consciousness lethargic but arousable activity status bedbound activity status bed chairbound discharge instructions please call your doctor or nurse practitioner if you experience the following you experience new chest pain pressure squeezing or tightness new or worsening cough shortness of breath or wheeze if you are vomiting and cannot keep down fluids or your medications you are getting dehydrated due to continued vomiting diarrhea or other reasons signs of dehydration include dry mouth rapid heartbeat or feeling dizzy or faint when standing you see blood or dark black material when you vomit or have a bowel movement you experience burning when you urinate have blood in your urine or experience a discharge your pain is not improving within hours or is not gone within hours call or return immediately if your pain is getting worse or changes location or moving to your chest or back you have shaking chills or fever greater than degrees fahrenheit or degrees celsius any change in your symptoms or any new symptoms that concern you please resume all regular home medications unless specifically advised not to take a particular medication also please take any new medications as prescribed please get plenty of rest continue to ambulate several times per day and drink adequate amounts of fluids avoid lifting weights greater than lbs until you follow up with your surgeon who will instruct you further regarding activity restrictions avoid driving or operating heavy machinery while taking pain medications please follow up with your surgeon and primary care provider pcp as advised incision care you may shower but do not bathe dry dressings as needed neurosurgery recommendations dilantin was discontinued do not need to restart if no seizure activity is seen coumadin is fine for the right foot please see dr weeks from discharge with a head ct w o contrast please call paresa to make this appointment vascular surgery recommendations please follow up with dr in weeks for further evaluation please call his office for an appointment followup instructions general surgery please follow up with dr in weeks please call for an appointment neurosurgery please follow up with dr weeks from discharge with a head ct w o contrast please call paresa to make this appointment vascular surgery please follow up with dr in month please call his office for an appointment neurosurgery f u with dr weeks from discharge with a head ct w o contrast please call paresa to make this md completed by addendum on the day of discharge the patient was started on lovenox and his coumadin was stopped the baa flakes were discontinued from his tube feeds to prevent clogging of the dobhoff he was discharged to the extended care facility in improved condition with a picc and flexiseal in place", 
                "Sample summary 2": "date of birth:               sex:   m service medicine allergies percocet erythromycin base a c e inhibitors nsaids attending chief complaint fevers rigors major surgical or invasive procedure dialysis bilateral hematoma and right lower quadrant hematoma incision and drainage left arm picc placement history of present illness year old male with a history of end stage renal disease of unknown etiology on hd htn prior history of hodgkin s disease gout peptic ulcer disease hypothyroidism depression presenting with fevers after right subclavian hd line was placed by transplant surgery days prior to admission mr went for his first hd treatment after new line placement day prior to admission with temps to he also developed rigors this morning and presented to his fever climbed to and was given vancomycin blood cultures from his hd line and was given fluid boluses and was then transferred to given that his nephrologist and transplant team are here in the ed his heart rates were in the 130s with a rectal temperature of he was visibly in rigors and not endorsing any pain otherwise he received tylenol and ativan for his rigors zosyn was added on to his vancomycin transplant team pulled his hd line and tip was sent for culture an ekg done in the ed showed st elevations in avf and lead iii with st depressions in v1 and v2 however these resolved on repeat ekg set of troponins was elevated to with no prior troponins to compare to ck mb was of normal fraction cards was consulted and they felt the troponin elevation was in the setting of chronic renal failure and demand ischemia in setting of tachycardia aspirin was given they did not recommend anticoagulation in setting of demand iv vancomycin was redosed and l of iv fluids were given vitals in the ed were hr bp rr satting ra past medical history chronic renal failure cr baseline followed by dr at no kidney biopsy hypertension hodgkin s disease s p chemotherapy with and radiation reportedly as a result of chemo treatment left him with numbness below the waist depression with one prior psych hospitalization h o suicidal attempt with narcotics overdose left eye blindness evaluated in ed on with functional overlay back pain right flank pain requiring chronic narcotics as per pt unknown etiology hypothyroidism gout tear post radiation pancreatitis chronic anemia social history pt lives with his wife and his children he is on disability used to work as emt pt denies tobacco alcohol or illicit drug use family history father s p renal transplant hypertensive nephropathy mother depression and alcohol dependence two sons ages and with renal dysplasia no history of deafness or cystic kidney disease physical exam admission physical exam vs hr 120s bp ra rr temp gen in nad lying in bed heent anicteric oropharynx clear cardiac tachycardic no murmurs appreciable chest old suture evident from prior line placement pulm clear in anterior fields abd soft and nontender ext no edema noted discharge physical exam vs tm tc bp hr rr s02 ra gen lying in bed comfortable apparing cardiac muffled s1 and s2 rrr systolic murmur at the apex as well as llsb cardiac friction rub present lungs crackles at the bases but otherwise clear abdomen mod firm and distended two incision sites in rlq and llq show staples in place without drainage minimal tenderness around rlq incision ue significant erythema and swelling in lue le dp radial pulses trace swelling in bilat le pertinent results admission results cbc wbc rbc hgb hct mcv mch mchc rdw plt ct neuts lymphs monos eos baso coags pt ptt inr pt chem glucose urean creat na k cl hco3 angap lfts alt ast ck cpk alkphos totbili lytes calcium phos mg abx vanco lactate cardiac markers 58pm blood ctropnt 42am blood ck mb mb indx ctropnt 37am blood ck mb ctropnt 00pm blood ck mb ctropnt 55am blood ck mb ctropnt 01pm blood ck mb ctropnt 51pm blood ck mb ctropnt 12am blood ck mb ctropnt 27am blood ck mb ctropnt 36am blood ck mb ctropnt 40am blood ck mb ctropnt 59am blood ck mb ctropnt relevant results 55am blood esr 55am blood crp 15pm blood aca igg aca igm 30am blood aca igg aca igm 30am blood lupus pos 58pm blood lipase 55am blood lipase 20am blood lipase 30am blood hapto 55am blood hba1c eag 55am blood triglyc hdl chol hd ldlcalc 27am blood hbsag negative hbsab positive hav ab positive 27am blood hcv ab negative micro pm blood culture final report blood culture routine final staph aureus coag consultations with id are recommended for all blood cultures positive for staphylococcus aureus and species final sensitivities staphylococcus species may develop resistance during prolonged therapy with quinolones therefore isolates that are initially susceptible may become resistant within three to four days after initiation of therapy testing of repeat isolates may be warranted sensitivities mic expressed in mcg ml staph aureus coag clindamycin s erythromycin s gentamicin s levofloxacin s oxacillin s trimethoprim sulfa s aerobic bottle gram stain final reported by phone to at 35pm on gram positive cocci in clusters anaerobic bottle gram stain final gram positive cocci in clusters pm catheter tip iv aerobic anaerobic final report wound culture final staph aureus coag colonies staphylococcus species may develop resistance during prolonged therapy with quinolones therefore isolates that are initially susceptible may become resistant within three to four days after initiation of therapy testing of repeat isolates may be warranted sensitivities mic expressed in mcg ml staph aureus coag clindamycin s erythromycin s gentamicin s levofloxacin s oxacillin s trimethoprim sulfa s cardiology tte the left atrium is elongated the right atrium is moderately dilated no atrial septal defect is seen by 2d or color doppler left ventricular wall thicknesses are normal the left ventricular cavity is moderately dilated lv systolic function appears depressed ejection fraction percent secondary to severe hypokinesis of the inferior septum inferior free wall and posterior wall there is no ventricular septal defect right ventricular chamber size is normal with depressed free wall contractility the aortic valve leaflets appear structurally normal with good leaflet excursion and no aortic stenosis no masses or vegetations are seen on the aortic valve but cannot be fully excluded due to suboptimal image quality mild aortic regurgitation is seen the mitral valve appears structurally normal with trivial mitral regurgitation there is no mitral valve prolapse no masses or vegetations are seen on the mitral valve but cannot be fully excluded due to suboptimal image quality no masses or vegetations are seen on the tricuspid valve but cannot be fully excluded due to suboptimal image quality no masses or vegetations are seen on the pulmonic valve but cannot be fully excluded due to suboptimal image quality there is no pericardial effusion impression no obvious vegetation but suboptimal study tee no atrial septal defect is seen by 2d or color doppler left ventricular wall thickness cavity size and global systolic function are normal lvef right ventricular chamber size and free wall motion are normal the aortic valve leaflets appear structurally normal with good leaflet excursion no masses or vegetations are seen on the aortic valve no aortic regurgitation is seen the mitral valve leaflets are structurally normal no mass or vegetation is seen on the mitral valve mild mitral regurgitation is seen no vegetations or abscess normal biventricular systolic function mild mitral regurgitation radiology u s r hd graft patent right upper extremity av graft with no stenosis no evidence of abscess u s rue and r ij nonocclusive thrombus seen in the mid right internal jugular vein no evidence of perigraft abscess of hd graft u s bilateral hips no hip joint effusion on the left or right side slight asymmetry of psoas muscle on the right suspicious for a psoas paraspinal process mri bilateral thighs bilateral heterogeneous fluid collections in the iliacus muscles most consistent with abscesses right greater than left fluid fluid levels with areas of t1 hyperintensity suggest the presence of internal hemorrhage and or proteinaceous debris collection on the right extends into the iliopsoas bursa with associated myositis and small area of focal fluid near the rectus femoris origin no evidence of hip effusions ct of pelvis large right and small left iliac muscle abscess with percutaneous drain in place on the right right iliac abscess extends inferiorly distal to the inguinal ligament but does not reach the iliopsoas insertion site at the lesser trochanter left iliac muscle abscess ends about cm distal to the inguinal ligament ct of pelvis right iliopsoas pigtail catheter removal and subsequent washout now with packing surgicell gauze in place and a skin staple closure over it this was confirmed with the description in the operative note as well as with at on right subcutaneous fat fluid collection with air fluid level and hematocrit suggestive of hematoma extensive subcutaneous gas likely postoperative although gas producing infection cannot be ruled out pelvic arteriogram pelvic arteriograms without signs of active bleeding no embolization was performed l groin u s there is a x x cm collection with a fluid fluid level within the left groin suggestive of a hematoma there is no internal vascularity there is no connection with the underlying vessels the underlying left common femoral artery and vein demonstrate normal waveforms and are patent abd u s multiple superficial hypoechoic fluid collections in the right lower quadrant adjacent to the incision one of which measures cm with complex features located above the right inguinal fold raising question of abscess this site has been marked for possible aspiration although not definitely amenable to drainage given internal echoes abd ct two fluid collections in the right anterior abdominal wall one may be residual hematoma the other may be fluid infection is not excluded multiple locules of air within the right iliacus muscle some of which may be post operative the remaining may be related to surgical packing with surgicel a small amount of air may be intraperitoneal persistent large amount of air in the anterior abdominal wall fascititis is not excluded heterogeneous attenuation of the left iliacus muscle may reflect residual hematoma at the site but no locules of air within the left iliacus small amount of free fluid within the pelvis mrv chest without contrast no findings of svc thrombosis no contrast was administered due to diminished gfr reidentification of nonocclusive chronic appearing thrombosis in the mid right jugular vein better appreciated on the previously performed ultrasound moderate left pleural effusion and pericardial effusion abdominal ultrasound a cm fluid collection in the subcutaneous fat of the right lower quadrant tte the left atrium is normal in size the estimated right atrial pressure is 15mmhg left ventricular wall thicknesses and cavity size are normal there is moderate regional left ventricular systolic dysfunction with basal to mid akinesis of the inferior wall there is mild hypokinesis of the remaining segments lvef the estimated cardiac index is normal 5l min m2 right ventricular chamber size is normal with mild global free wall hypokinesis the diameters of aorta at the sinus ascending and arch levels are normal the aortic valve leaflets appear structurally normal with good leaflet excursion and no aortic regurgitation the mitral valve leaflets are structurally normal mild mitral regurgitation is seen the pulmonary artery systolic pressure could not be determined there is a moderate sized pericardial effusion no right ventricular diastolic collapse is seen there is brief right atrial diastolic collapse there is significant accentuated respiratory variation in mitral tricuspid valve inflows consistent with impaired ventricular filling compared with the prior study images reviewed of there is a moderate sized pericardial effusion without frank tamponade ekg sinus tachycardia left bundle branch block since the previous tracing of there is probably no significant change tte the left atrium is mildly dilated the estimated right atrial pressure is 20mmhg left ventricular wall thicknesses are normal the left ventricular cavity size is normal there is moderate to severe global left ventricular hypokinesis lvef right ventricular chamber size is normal with depressed free wall contractility the aortic valve leaflets are mildly thickened but aortic stenosis is not present no aortic regurgitation is seen the mitral valve leaflets are mildly thickened there is no mitral valve prolapse the estimated pulmonary artery systolic pressure is normal there is a moderate sized pericardial effusion there are no echocardiographic signs of tamponade no right ventricular diastolic collapse is seen there is brief right atrial diastolic invagination compared with the findings of the prior study images reviewed of the pericardial effusion is slightly smaller tte the estimated right atrial pressure is 10mmhg there is mild regional left ventricular systolic dysfunction with basal to mid inferoseptal inferior and inferolateral hypokinesis overall left ventricular systolic function is mildly depressed lvef right ventricular chamber size is normal with borderline normal free wall function there is a moderate sized pericardial effusion no right ventricular diastolic collapse is seen there is brief right atrial diastolic collapse there is significant accentuated respiratory variation in mitral tricuspid valve inflows consistent with impaired ventricular filling compared with the prior study images reviewed of the pericardial effusion size is similar without tamponade the left ventricular systolic function may be slightly improved upper extremity us with doppler short segment of nonocclusive thrombus along the left basilic picc in the upper arm discharge labs 24am blood wbc rbc hgb hct mcv mch mchc rdw plt ct 24am blood pt ptt inr pt 24am blood glucose urean creat na k cl hco3 angap 24am blood calcium phos mg brief hospital course year old with a complicated medical history including prior hodgkins htn pud hypothyroidism depression hx of lupus anticoagulant requring warfarin use and esrd of unclear etiology on transferred from osh to ed on two days prior to presentation the patient had a right ij tunneled hd line placed placed by dr transplant surgery one day prior to presentation went to hd with fevers had rigors morning of presentation on and went to mssa line sepsis patient was initially admitted directly to the micu for concern of line sepsis in the setting of fevers and rigors transplant surgery was notified and removed newly placed subclavian line osh blood cultures grew staph aureus and patient was started on vancomycin while sensitivities were pending blood cultures at were taken prior to antibiotic administration these cultures also grew gram positive cocci patient continued to spike intermittent fevers surveillance cultures were taken daily while in the micu a tte was completed and did not indicate any valvular abnormalities however it did show focal areas of hypokinesis and a depressed ef as noted below tee was arranged with cardiology and showed no vegetations on day of transfer to floor patient was also started on nafcillin as cultures came back mssa plan was complete a week course of antibiotics for mssa bacteremia with nafcillin being used while in hospital and then transition to cefazolin with hemodialysis once patient was discharged as noted below abx were changed for days to emperic vanco cefepime due to concerns for thigh and abdominal abscess but patient was transitioned back to nafcillin ciprofloxacin and flagyl once the culture data from these thigh abdomen collections was negative the patient was transitioned from nafcillin to cefazolin prior to discharge cefazolin ciprofloxacin and flagyl were to be continued until cefazolin to be given with hd grams on monday and wednesday and g on friday was contact directly regarding the cefazolin as it was left out of his discharge medication list pericardial effusion patient had mrv of chest to evaluate for clot burden which revealed an incidental pericardial effusion pulsus physiology was difficult to detect as patient had av graft in right extremity and a picc line in his left extremity a tte was subsequently perfromed to characterize the effusion more carefully and revealed a cm pericardial effusion without evidence of tamponade though brief right atrial collapse was noted a repeat tte hours later revealed a slightly smaller effusion with only right atrial involution appreciated a third tte was performed on the day of discharge approximately houurs later which again showed a slightly smaller pericardial effusion with noted brief right atrial diastolic collapse a copy of the most recent tte report was sent with the patient at to communicate with him regarding follow up the patient is to have repeat ttes on and a follow up cardiology appointment was made for the patient on troponin leak on admission patient had ekg changes concerning for cardiac ischemia initial troponins were elevated although ck mb was within normal limits cardiology was notified in the ed and said that the troponin level was consistent with esrd and demand ischemia as patient was tachycardic for a prolonged period however tte demonstrated inferior wall hypokinesis with ef of which made it appear that the patient had a cardiac event prior to admission and still had elevated troponins from this event because of no renal clearance pt was started on full strength asa high dose atorvastatin beta blocker and kept on heparin drip which had already been started for below coagulation issues cardiology initially planned to perform cardiac catheterization during his hospitalization but tee done to evaluate for endocarditis a few days after initially tte no longer showed evidence of hypokinetic wall segments and showed and ef bringing back to the forefront the idea that perhaps the patient had not had a cardiac event and had merely spilled troponins in the setting of some coronary disease exacerbated by tachycardia septic physiology and esrd decision was made for no coronary intervention and atorvastatin dose was decreased in setting of elevated lfts troponins continued to slowly trend down although never really resolved during the hospitalization likely secondary to his esrd late in this hospital course the troponins were no longer followed heparin was stopped as patient developed hematomas as per below and it was felt that the risk to bleeding was more significant that risk of clotting ttes were performed per above the last tte on day of discharge revealed an ef of cardiology follow up per above esrd renal was notified upon admission and patient received a line holiday while in the micu receiving abx electrolytes were monitored plan was for patient to restart normal mwf schedule using mature graft of r upper extremity however ptt was on morning of planned graft access and infectious disease was also concerned about the possibility that graft infected in the setting of bacteremia as a result a temporary l subclavian tunneled hd catheter was placed by ir and used for two hd sessions while ptt was brought under better control and u s of r vascular graft was done to r o infection u s showed no evidence of perigraft abscess of fluid collection so graft was used for hd starting on temporary hd line was removed after successful use of the graft pt was continued on mwf hd schedule for throughout his hospitalization antibiotics to be given at hd after discharge as per above coagulopathy at time of admission pt was on therapeutic warfarin with presenting inr of per patient report he was on this medication because of anti phospholipid hypercoag state that had been discovered at hospital as part of a work up to determine why he kept clotting off hd access grafts fistulas pt warfarin was held at presentation to because of need for multiple procedures and pt was placed on heparin gtt this was continued through much of hospitalization but pt still developed multiple thrombotic complications in the icu difficulty threading a l ij line led team to believe there must be a clot in the l ij additionally a non occlusive thrombus in r ij at site of recent central line was found on u s pt later developed significant r hip thigh pain with some swelling ultra sound of the area showed and asymmetry that was suspicious for a psoas paraspinal process as a result f u mri of the r hip thigh was performed and showed bilateral heterogeneous fluid collections in the iliacus muscles most consistent with abscesses right greater than left fluid fluid levels with areas of t1 hyperintensity suggest the presence of internal hemorrhage and or proteinaceous debris collection on the right extends into the iliopsoas bursa with associated myositis and small area of focal fluid near the rectus femoris origin because patient was febrile with significant pain in the area ct guided ir drainage of r thigh abscesses were performed on with drain placed in the r side a follow up ct on showed persistence of fluid and in light of continuing fevers and concern for permanent neurologic damage to nerve structures in the area orthopedic surgery took pt to the or to debride the abscesses during surgery these were found to be hematomas r l from the or pt was transferred to the tsicu due to hypotension sbp down to the s and complications from bleeding which continued to ooze during surgery preventing initial closure of the wound in the tsicu mr was placed on peripheral pressors initially due to access issues and was also transfused blood products due to hct drop and hypotension also he had an elevated white count and fevers left femoral line was placed on additionally was switched from nafcillin to vancomycin cefepime on with suggestion of a day course switch made at id s suggestion due to concern of possible infected hematomas at sites of abscesses these abx continued until slightly longer than initially planned because concern for a wound infection had developed in the interim as noted below pressors d c d morning of and the pt s vs remained stable and afebrile had pelvic arteriograms performed to assess for possible bleeds which were negative went back to the or on to have packing removed from washout on cultures ultimately negative from this source and hematomas seemed to have spontaneously formed while on heparin gtt pt was transfered back to the floor but shortly thereafter developed pain in l groin and significant rlq pain with surrounding skin erythema induration and dusky changes ultra sound of l groin showed a small hematoma which had formed at site of femoral line removal the day before there was no vessel aneurysm and the hematoma was not connected to other vascular structures so since small no intervention was undertaken ultra sound of abdomen showed multiple superficial hypoechoic fluid collections in the rightnlower quadrant adjacent to the recent surgical incision one of which measured cm withcomplex features located above the right inguinal fold raising question of abscess a ct of abdomen with contrast showed two fluid collections in r ant abdominal wall one likely hematoma with the other containing fluid that could not have infection excluded because pt has having recurrence of fever spikes there was concern for post surgical abscess orthopedics took pt back to the or on for i d of the wound and found it to be a hematoma not abscess cultures were sent but like previous hematoma cultures remained negatived the heparin gtt was eventually disconinued as the risk of bleeding was considered greater than the risk of clotting hematology was consulted as an inpatient but had low suspicion for a hypercoaguable state the patient was discharged with the contact information to make a follow up appointment so that his possible anti phospholipid syndrome could be evaluated more appropriately as an outpatient pain control pt with significant pain control issues during hospitalization mostly related to pain at sites of various hematoma formations initially pain was controlled with iv morphine but this was ultimately changed to dilaudid because of pt s poor renal function dilaudid pca was initiated when difficulty controlling pain with iv pushes pt then started on long acting oxycontin which was uptitrated in effort to provide more consistent pain control dilaudid pca weaned as long acting pos uptitrated and pt ultimately transitioned over to po dilaudid for breakthrough pain as better control was achieved the patient was eventually transitioned to oxycontin for pain control the patient reported significantly improved pain late in his hospital course left upper extremity thrombosis the day prior to discharge the patient had left upper extremity swelling and mild surround erythema an us was ordered for evaluation of a thrombosis and revealed a short segment of nonocclusive thrombus along the left basilic picc in the upper arm per report good flow was noted around the picc line the picc line was pulled as it was considered the most likely source of the thrombosis no anticoagulation was persued due to above issues and due to its non occlusive nature and thought that it would resolve after the picc line was removed medications on admission albuterol allopurinol mg daily nephrocaps caps daily calcium acetate mg daily citalopram mg daily vicodin levothyroxine mcg daily morphine mg daily pantoprazole mg daily trazodone mg qhs venlafaxine mg daily coumadin alternating colace senna discharge disposition extended care facility discharge diagnosis primary diagnosis mssa methicillin sensitive staphylococcus aureus bacteremia bilateral psoas and right lower quadrant hematomas pericardial effusion myocardial ischemia secondary diagnoses end stage renal disease possible lupus anticoagulant anti phospholipid antibody syndrome discharge condition mental status clear and coherent level of consciousness alert and interactive activity status ambulatory independent discharge instructions mr you were admitted to with a bloodstream infection that was most likely from your tunneled hd line blood cultures revealed a bacteria called staphylococcus aureus that was sensitive to the antibiotic nafcillin you were treated with nafcillin throughout most of your stay but were transitioned to cefazolin prior to discharge you will need to continue cefazolin as instructed below on admission to the hospital you were also on coumadin for a possible diagnosis of anti phospholipid antibody syndrome as you subsequently developed several hematomas during your hospitalization this medication was discontinued and the hematology service was consulted the diagnosis of anti phospholipid antibody syndrome is difficult to make as an inpatient you will need to follow up with the hematology department as an outpatient and the information has been provided below the following changes were made to your medications start cefazolin grams with hemodialysis on mondays and wednesdays and grams with hemodialysis on fridays you will need this antibiotic for a total of two weeks from stop this medication on stop taking vancomycin which you were admitted on from the outside hospital your senna was increased from tablet by mouth twice a day for constipation to tablets twice a day for constipation stop taking the cefazolin that you were admitted on and continue as directed above stop taking morphine sulfate mg intravenously every four hours for pain start taking oxycontin mg by mouth every hours start taking docusate sodium mg by mouth twice a day for constipation start taking atorvastatin mg by mouth once a day for hyperlipidemia start taking ciprofloxacin mg by mouth once a day for days start this medication on and stop on start taking metronidazole mg by mouth every eight hours for days you will need one dose the evening of otherwise you will need to take this medication three times a day from to start taking trazodone mg by mouth at night as needed for insomnia start taking nephrocaps b complex vitamin c folic acid tab by mouth daily start taking calcium acetate mg take two capsules three times a day with meals start taking sevelamer carbonate mg take one tablet by mouth three times a day with meals start taking nitroglycerin mg tablets take one tablet every five minutes as needed for chest pain do not exceed tablets in a minute period given the severity of your renal failure you will also need to receive epoetin alfa with dialysis this medication will not appear on your medication list in the following documents as it was dosed and administered according to protocols no other changes were made to your other medications while in the hospital and you should continue taking all other medications as previously prescribed followup instructions please keep all follow up appointments as below please call the hematology oncology department at to establish a follow up appointment in the hemostasis and clinic for further evaluation of the possible anti phospholipid antibody syndrome please call the orthopedics department at to make a follow up appointment the appointment should be for approximately one month from the date of discharge and should be made with the the nurse practitioner please keep the infectious disease appointment as below department infectious disease when monday at am with md building lm bldg campus west best parking garage below are instructions for the labs that will need to be sent to the infectious disease department prior to your appintment on outpatient antibiotic regimen and projected duration and dose cefazolin 2g with dialysis on mo we 3g with dialysis on friday start date stop date required laboratory monitoring lab tests cbc bun crea lfts esr and crp frequency qweekly all laboratory results should be faxed to infectious disease r ns at patient will need weekly monitoring of his pericardial effusion with a transthoracic echocardiogram please communicate this information to the md completed by ",
                "Sample summary 3": "date of birth:               sex:   f service neurosurgery allergies no known allergies adverse drug reactions attending chief complaint nausea vomiting major surgical or invasive procedure cerebral angiogram with coiling history of present illness 67f fell off step stool days ago and possible loc had laceration on back of head with much bleeding did not seek medical attention at that time has been nauseaous and vomiting since that time daughters brought to osh found diffuse sah and possible r mca distribution loaded with dilantin and transferred to ed and possible r mca distribution loaded with dilantin and transferred to ed past medical history high cholesterol social history married has three children family history parents deceased sister and children alive and well physical exam hunt and grade gcs e v motor o t bp hr r18 o2sats96 gen wd wn comfortable nad heent pupils eoms neck in hard collar extrem warm and well perfused no c c e neuro mental status awake and alert cooperative with exam normal affect orientation oriented to person place and date recall objects at minutes language speech fluent with good comprehension and repetition naming intact no dysarthria or paraphasic errors cranial nerves i not tested ii pupils equally round and reactive to light to mm bilaterally visual fields are full to confrontation iii iv vi extraocular movements intact bilaterally without nystagmus v vii facial strength and sensation intact and symmetric viii hearing intact to finger rub bilaterally ix x palatal elevation symmetrical sternocleidomastoid and trapezius normal bilaterally xii tongue midline without fasciculations motor normal bulk and tone bilaterally no abnormal movements tremors strength full power throughout no pronator drift sensation intact to light touch bilaterally toes downgoing bilaterally on the day of discharge alert and oriented to person place and time patient has full strength and sensation eoms are intact 2mm with brisk reaction bilaterally no pronator drift the patient ambulate with a steady gait and is out of bed to the chair this morning eating breakfast the patient ambulate independently and is out of bed to the pertinent results cta head impression subarachnoid hemorrhage seen on head ct ct angiography of the head demonstrates a x mm aneurysm at the anterior communicating artery with irregular contour study date of pm sinus bradycardia non diagnostic inferior q wave pattern may be a normal variant but cannot exclude prior inferior myocardial infarction left ventricular hypertrophy with marked repolarization abnormalities consistent with left ventricular strain pattern no previous tracing available for comparison read by intervals axes rate pr qrs qt qtc p qrs t ct cspine impression no evidence of acute fracture or dislocation of the cervical spine chest portable ap study date of pm impression mild lingular and bibasilar atelectasis no focal consolidation ct head impression post embolization of the acomm aneurysm sah stable cta head impression interval coiling of anterior communicating artery aneurysm there is no evidence of large vessel occlusion or significant vasospasm the coil pack obscures the aneurysm itself and some adjacent vessels of the anterior circle of persistent moderate hydrocephalus with intraventricular hemorrhage echo the left atrium is elongated no atrial septal defect is seen by 2d or color doppler there is mild symmetric left ventricular hypertrophy the left ventricular cavity size is normal regional left ventricular wall motion is normal left ventricular systolic function is hyperdynamic ef there is a very mild resting left ventricular outflow tract obstruction there is no ventricular septal defect right ventricular chamber size and free wall motion are normal the ascending aorta is mildly dilated the aortic arch is mildly dilated the aortic valve leaflets appear structurally normal with good leaflet excursion there is no valvular aortic stenosis the increased transaortic velocity is likely related to high cardiac output no aortic regurgitation is seen the mitral valve appears structurally normal with trivial mitral regurgitation the pulmonary artery systolic pressure could not be determined there is no pericardial effusion cta head w w o c recons study date of am impression no evidence to suggest vasospasm in the intracranial arterial vasculature further evolution of the subarachnoid and intraventricular hemorrhage 30pm blood wbc rbc hgb hct mcv mch mchc rdw plt ct 45pm blood neuts lymphs monos eos baso 30pm blood plt ct 30pm blood pt ptt inr pt 25am blood glucose urean creat na k cl hco3 angap 30pm blood glucose urean creat na k cl hco3 angap 12am blood glucose urean creat na k cl hco3 angap 43am blood glucose urean creat na k cl hco3 angap 16am blood glucose urean creat na k cl hco3 angap 41am blood glucose urean creat na k cl hco3 angap 01am blood glucose urean creat na k cl hco3 angap 20pm blood glucose urean creat na k cl hco3 angap 51am blood glucose urean creat na k cl hco3 angap 48pm blood glucose urean creat na k cl hco3 angap 45pm blood glucose urean creat na k cl hco3 angap a normal variant but cannot exclude prior inferior myocardial infarction left ventricular hypertrophy with marked repolarization abnormalities consistent with left ventricular strain pattern no previous tracing available for comparison brief hospital course ms is a year old woman who was admitted to the nsicu under the care of dr on after a fall with ct findings of sah and acomm aneurysm she was on dilantin for seizure prophylaxis a ua showed a uti and she was started on cipro seh had some heart block on ekg and some bradycardia in the icu she received a dilantin bolus for a low drug level on she underwent a cerebral angiogram with coiling immediately post angio she was lethargic a head ct was obtained which was stable as patient awoke from sedation her exam was stable on her dilantin level was cardiology consult was called for persistant htn and bradycardia they noted 3sec sinus pauses episodes of sinus arrest with ventricular escape with heart rate to 30s but sbp was stable at ekg showed changes consistent with left ventricular hypertrophy vs cerebral t waves consistent with sah they felt that her bradycardia and htn were consistent with effect from her sah they asked that her calcium channel blocker be stopped which it was on on at she was noted to have a new left facial droop and she was lethargic she had some right deltoid and grasp weakness this strength exam has varied during her admission cta was ordered there was no increase in ventricular size and no concern for vasospasm she was transfered to dr service on her icu course was uneventful she had serial tcds as of which have showed no evidence of vasospasms nimodipine was discontinued secondary to bradycardia and hypotension she completed her course of cipro for urinary tract infection the patients serum sodium was and her serum bun of on patient was transferred to the step down unit in stable condition the patient has a cta consistent with no evidence to suggest vasospasm in the intracranial arterial vasculature and further evolution of the subarachnoid and intraventricular hemorrhage the patient s serum sodium was and her serum bun of on the patients serum sodium was and her serum bun of on routine laboratory blood work was sent and a serum sodium was and her serum bun of sodium chloride tablets grams po bid were initiated for hyponatremia po intake was encouraged her floor course was otherwise uneventful now the day of discharge she is afebrile vital signs were stable and neuro exam stable she is tolerating a good oral diet and her pain is well controlled the patient has had a bowel movement and is voiding without difficulty the patient s serum sodium was and her serum bun of the patient had a point rise in her serum sodium since the day prior while on the sodium chloride tablets the patient will go home on this medication for days at a lower dose of gram with follow up with her primary care this week for follow up of hyponatremia elevated bun and hypertension she is set for discharge home the patient s daughter has concerns about the patients ability to amubulate around the house independently physical therapy assesed the patient prior to discharge the patient was able to ambulate independently but slowly she was able to climb up and down stairs the patient did not need assistance or use of cane or walker but continued to have high level balance and endurance difficulties it was recommended that the patient be discharged home with a course of physical therapy at home for high level balance and endurance the patients daughter was called at home and this was discussed in ma was contact at they will contact the patient either or tuesday medications on admission none discharge medications hydralazine mg tablet sig one tablet po q6h every hours disp tablet s refills acetaminophen mg tablet sig two tablet po q6h every hours as needed for pain do not exceed grams tylenol in hours bisacodyl mg tablet sig two tablet delayed release e c po daily daily as needed for constipation hold for loose stools disp tablet delayed release e c s refills oxycodone mg tablet sig tablets po every six hours as needed for pain do not drive while taking this medication di not take if lethargic disp tablet s refills docusate sodium mg capsule sig one capsule po tid times a day disp capsule s refills senna mg tablet sig one tablet po bid times a day hold for loose stools disp tablet s refills sodium chloride gram tablet sig one tablet po every twelve hours for days please follow up at your primary care physicians to follow your sodium level this week disp tablet s refills outpatient lab work please draw a chem wednesday to monitor bun slightly elevated the day of discharge and serum sodium trending down currently day of discharge while on sodium tablet repleation follow up with your primary care this week please make an appointment with your primary care physcian this week after having your labs drawn on wenesday to follow up your slightly elevated bun and low trending serum sodium and to eveluate further need of sodium chloride tablets po every hours and hypertension and initiation of hydralazine for treatment of high blood pressure during your hospital stay outpatient physical therapy physical therapy at home for high level balance and endurance discharge disposition home discharge diagnosis subarachnoid hemorrhage anterior comunicating artery aneurysm ruptured urinary tract infection bradycardia hyponatremia hypertension discharge condition mental status clear and coherent level of consciousness alert and interactive activity status ambulatory independent activity status ambulatory independent no use of walker or cane able to perform stairs independently continues to have high level balance endurance issues discharge instructions angiogram with embolization coiling ofanterior communicating artery medications continue all other medications you were taking before surgery unless otherwise directed you make take tylenol or prescribed pain medications for any post procedure pain or discomfort what activities you can and cannot do when you go home you may walk and go up and down stairs you may shower let the soapy water run over groin incision rinse and pat dry your incision may be left uncovered unless you have small amounts of drainage from the wound then place a dry dressing or band aid over the area that is draining as needed no heavy lifting pushing or pulling greater than lbs for week to allow groin puncture to heal after week you may resume sexual activity after week gradually increase your activities and distance walked as you can tolerate no driving until you are no longer taking pain medications what to report to office changes in vision loss of vision blurring double vision half vision slurring of speech or difficulty finding correct words to use severe headache or worsening headache not controlled by pain medication a sudden change in the ability to move or use your arm or leg or the ability to feel your arm or leg trouble swallowing breathing or talking numbness coldness or pain in lower extremities temperature greater than 5f for hours new or increased drainage from incision or white yellow or green drainage from incisions bleeding from groin puncture site sudden severe bleeding or swelling groin puncture site lie down keep leg straight and have someone apply firm pressure to area for minutes if bleeding stops call our office if bleeding does not stop call for transfer to closest emergency room angiogram with embolization coiling of anterior communicating followup instructions please follow up with dr in weeks with a mri mra of the brain protocol please call to make this appointment please follow up with you primary care physician this week as your serum bun has been slightly elevated and your serum sodium is has been trending slightly low you will be given a prescription to have your lab studies drawn and please follow up with you primary care by friday to dicuss you were also started on a medication for high blood pressure hydralazine please discuss further management of your hypertension at that time completed by md addendum this entire discharge summary is a duplicate of the discharge summary from earlier today with addendum added to brief hospital course as patient will have physical therapy at home for high level balance and endurance"}

def update_textbox(selected):
    sample_text = sample_texts[selected]
    text_input = (sample_text)
    return text_input
    

with gr.Blocks() as demo:
    gr.Markdown(
    """
    # Improvised Transformer-based approach for ICD 9 code prediction
    Select a model and use a sample Discharge Summary or copy your Discharge summary to predict the relevant ICD 9 codes.
    """)
    
    sample = gr.Dropdown(label="Select Sample Text", choices=sample_texts, info = "Use the selected sample text to Predict relevant ICD9 codes")
    use_sample_btn = gr.Button("Use Sample Text")
    text_input = gr.Textbox(label="Enter Medical summary")
    use_sample_btn.click(fn =update_textbox, inputs=[sample], outputs=text_input)
    
    model = gr.Radio(["HiLAT", "ClinicalLongformer", "Long-LAT", "Long-HiLAT"], label="Model", info="Select the model used for prediction")
    label_count = gr.Radio(["5", "50"],label = "ICD Code Prediction Range", info="Select the number of top ICD codes to predict: either the top 5 or the top 50")
    predict_btn = gr.Button("Predict")
    output = gr.HTML(label="ICD Codes")
    predict_btn.click(fn = predict_icd, inputs=[text_input, model, label_count], outputs=[output])

demo.launch(debug= True, share=True)