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Commit 0aa11f54 authored by Shengpu Tang (tangsp)'s avatar Shengpu Tang (tangsp)
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NEWS baseline

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mimic3_experiments/4_baselines/CalculateNEWS.ipynb 0 → 100644
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%% Cell type:code id: tags:
``` python
import pandas as pd
import numpy as np
from tqdm import tqdm
from operator import itemgetter
```
%% Cell type:code id: tags:
``` python
import yaml
with open('../data_code/config.yaml') as f:
config = yaml.safe_load(f)
data_path = config['data_path']
```
%% Cell type:code id: tags:
``` python
icu = pd.read_csv(data_path + 'prep/icustays_MV.csv')
chart = pd.read_pickle(data_path + 'prep/chartevents.p')
```
%% Cell type:code id: tags:
``` python
chart['ITEMID'] = chart['ITEMID'].replace({
'223900': 'GCS verbal',
'223901': 'GCS motor',
'220739': 'GCS eye',
'226732': 'O2 delivery device',
})
```
%% Cell type:code id: tags:
``` python
NEWS_components = [
'HR',
'RR',
'SysBP',
'Temperature',
'SpO2',
'GCS verbal',
'GCS motor',
'GCS eye',
'O2 delivery device',
]
```
%% Cell type:code id: tags:
``` python
items = chart[chart["ITEMID"].isin(NEWS_components)].copy().reset_index(drop=True)
```
%% Cell type:code id: tags:
``` python
len(items)
```
%% Output
13807467
%% Cell type:markdown id: tags:
# Convert GCS to AVPU (15: A, 1-14: VPU)
| * | Eye Opening | Eye Opening | Eye Opening | Eye Opening | Verbal | Verbal | Verbal | Verbal | Verbal | Motor | Motor | Motor | Motor | Motor | Motor |
|----------|-------------|-------------|-------------|-------------|----------|----------|----------------|------------------|--------|---------|------------|------------|---------|-----------|-------|
| Response | Spontaneous | To Speech | To Pain | None | Oriented | Confused | Inapproapriate | Incomprehensible | None | Obeying | Localizing | Withdrawal | Flexing | Extending | None |
| Score | 4 | 3 | 2 | 1 | 5 | 4 | 5 | 2 | 1 | 6 | 5 | 4 | 3 | 2 | 1 |
%% Cell type:code id: tags:
``` python
verbal_mask = (items['ITEMID'] == 'GCS verbal')
items.loc[verbal_mask, 'VALUE'] = items.loc[verbal_mask, 'VALUE'].map({
"No Response-ETT": 1,
"No Response": 1,
"Incomprehensible sounds": 2,
"Inappropriate Words": 3,
"Confused": 4,
"Oriented": 5,
})
motor_mask = (items['ITEMID'] == 'GCS motor')
items.loc[motor_mask, 'VALUE'] = items.loc[motor_mask, 'VALUE'].map({
"No response": 1,
"Abnormal extension": 2,
"Abnormal Flexion": 3,
"Flex-withdraws": 4,
"Localizes Pain": 5,
"Obeys Commands": 6,
})
eye_mask = (items['ITEMID'] == 'GCS eye')
items.loc[eye_mask, 'VALUE'] = items.loc[eye_mask, 'VALUE'].map({
"None": 1,
"To Pain": 2,
"To Speech": 3,
"Spontaneously": 4,
})
oxygen_mask = (items['ITEMID'] == 'O2 delivery device')
items.loc[oxygen_mask, 'VALUE'] = items.loc[oxygen_mask, 'VALUE'].map({
'Nasal cannula': 1,
'Aerosol-cool': 1,
'Bipap mask ': 1,
'None': 0,
'CPAP mask ': 1,
'Endotracheal tube': 1,
'Face tent': 1,
'Medium conc mask ': 1,
'Other': 1,
'Venti mask ': 1,
'Non-rebreather': 1,
'Tracheostomy tube': 1,
'Trach mask ': 1,
'High flow neb': 1,
'High flow nasal cannula': 1,
'T-piece': 1,
'Vapomist': 1,
'Ultrasonic neb': 1,
})
```
%% Cell type:code id: tags:
``` python
assert set(items[items['ITEMID'] == "O2 delivery device"]['VALUE'].unique()) == set([0,1])
```
%% Cell type:code id: tags:
``` python
items.head(10)
```
%% Output
ICUSTAY_ID t ITEMID VALUE
0 200001 -0.003333 HR 115
1 200001 0.013333 RR 22
2 200001 0.030000 SysBP 113
3 200001 0.130000 SpO2 94
4 200001 0.163333 RR 26
5 200001 0.163333 SpO2 95
6 200001 0.163333 HR 114
7 200001 0.163333 Temperature 37.2778
8 200001 0.196667 O2 delivery device 1
9 200001 0.213333 GCS eye 4
%% Cell type:markdown id: tags:
# Map values to bins & Aggregate scores
<img src="NEWS_table.jpg">
%% Cell type:code id: tags:
``` python
HR_bins = [41, 51, 91, 111, 131]
RR_bins = [9, 12, 21, 25]
SpO2_bins = [92, 94, 96]
Temp_bins = [35.1, 36.1, 38.1, 39.1]
SBP_bins = [91, 101, 111, 220]
HR_dict = { 0:3, 1:1, 2:0, 3:1, 4:2, 5:3 }
RR_dict = { 0:3, 1:1, 2:0, 3:2, 4:3 }
SpO2_dict = { 0:3, 1:2, 2:1, 3:0 }
Temp_dict = { 0:3, 1:1, 2:0, 3:1, 4:2 }
SBP_dict = { 0:3, 1:2, 2:1, 3:0, 4:3 }
```
%% Cell type:code id: tags:
``` python
# test binning
assert SpO2_dict[np.digitize(90, SpO2_bins)] == 3
assert HR_dict[np.digitize(80, HR_bins)] == 0
```
%% Cell type:code id: tags:
``` python
def calculate_score(row):
gcs_score = int(row['GCS motor']) + int(row['GCS verbal']) + int(row['GCS eye'])
score = \
HR_dict[np.digitize(float(row['HR']), HR_bins)] + \
RR_dict[np.digitize(float(row['RR']), RR_bins)] + \
SBP_dict[np.digitize(float(row['SysBP']), SBP_bins)] + \
Temp_dict[np.digitize(float(row['Temperature']), Temp_bins)] + \
SpO2_dict[np.digitize(float(row['SpO2']), SpO2_bins)] + \
2 * int(int(row["O2 delivery device"]) == 1) + \
3 * int(gcs_score < 15)
return score
```
%% Cell type:code id: tags:
``` python
IDs_test = list(icu[icu['partition'] == 'test']["ICUSTAY_ID"])
```
%% Cell type:code id: tags:
``` python
for T in [4, 12, 48]:
score_dict = {}
for ID in tqdm(IDs_test):
try:
df = items[items['ICUSTAY_ID'] == ID].sort_values(by='t')