weicheng113 / dl4h-project

Project for Deep Learning for Healthcare

Paper Reproduction Study - TPC Networks for LoS

In this project we aim to replicate the paper 'Temporal Pointwise Convolutional Networks for Length of Stay Prediction in the Intensive Care Unit' by Emma Rocheteau, Pietro Li `o and Stephanie Hyland. The original repository for the paper can be found here. This repository contains some modifications in order to carry out experiments. The final reproduction study report is here.

Setup New Conda Environment

Use the first command to create new independent environment for the project. Or use the other two commands to remove or update the Conda environment.

# to create conda environment.
conda env create -f environment.yml

# to remove conda environment.
conda remove --name dl4h-project --all

# to update conda environment when some new libraries are added.
conda env update -f environment.yml --prune

Download eICU Data

Download eICU Data from pyhsionet - https://physionet.org/content/eicu-crd/2.0/.

Setup eICU Database Locally

Follow the steps below to set up the database locally.

# 1. Install Postgres http://www.postgresql.org/download/

# 2. Create database
# 2.1 start SQL Shell(psql)
# 2.2 create tables
\i [path to eicu-code]/build-db/postgres/postgres_create_tables.sql
# 2.3 navigate to data directory
\cd [path to eicu-collaborative-research-database-2.0]
# 2.4 load data
\i [path to eicu-code]/build-db/postgres/postgres_load_data_gz.sql
# 2.5 add indices
\i [path to eicu-code]/build-db/postgres/postgres_add_indexes.sql
# 2.6 validate
\i [path to eicu-code]/build-db/postgres/postgres_checks.sql
# 2.7 create views
\cd [path to DL4H-Project/]
\i eICU_preprocessing/create_all_tables.sql

Pre-processing

Follow the steps below to pre-process the data and prepare the data for training.

# 1. activate dl4h-project Conda environment.
conda activate dl4h-project

# 2. run the pre-processing scripts
python -m eICU_preprocessing.run_all_preprocessing

# 3. modify paths.json 
{"eICU_path": "[path to eICU_data folder produced by preprocessing step]"}

# 4. create lmdb databases to supports random data item access.
python csv2lmdb.py

Training

To train the models, run one of following commands.

# a. To train various TPC models. Model choices --model: [tpc, tpc-multitask, tpc-mse, pointwise-only, temp-only, tpc-no-skip, "tpc-mask-skip"]
python train_tpc.py --model tpc

# b. To train channel-wise LSTM model.
python train_lstm.py

# c. To train transformer model.
python train_transformer.py

Evaluation

To test the models, run one of following commands.

# a. To test various TPC models. Model choices --model: [tpc, tpc-multitask, tpc-mse, pointwise-only, temp-only, tpc-no-skip, "tpc-mask-skip"]
python test_tpc.py --model tpc

# b. To test channel-wise LSTM model.
python test_lstm.py

# c. To test transformer model.
python test_transformer.py

Results

Below is the result comparison for TPC model between the original paper and our replication experiment on eICU test data.

Model	MAD	MSE	MAPE	MSLE	R^2	KAPPA
TPC(original paper)	1.78±0.02	21.7±0.5	63.5±4.3	0.70±0.03	0.27±0.02	0.58±0.01
TPC(replication)	1.658	19.539	49.697	0.458	0.443	0.710

Below is the result comparison for TPC model vs other baseline models.

Model	MAD	MSE	MAPE	MSLE	R^2	KAPPA
TPC	1.658	19.539	49.697	0.458	0.443	0.710
Channel-wise LSTM	2.631	31.825	115.745	1.424	0.096	0.324
Transformer	2.592	30.617	126.388	1.437	0.127	0.340

Below is the result comparison for TPC model vs other TPC variant models.

Model	MAD	MSE	MAPE	MSLE	R^2	KAPPA
TPC	1.658	19.539	49.697	0.458	0.443	0.710
TPC(multitask)	1.241	16.058	27.520	0.214	0.542	0.821
TPC(no skip)	1.918	22.929	64.399	0.716	0.346	0.627
Temp. only	1.798	21.437	57.617	0.615	0.389	0.665
Point. only	2.665	31.458	110.025	1.517	0.106	0.336
TPC(MSE)	2.107	20.965	144.790	1.565	0.402	0.639

Below is the result comparison for TPC model vs an additional TPC model with mask field included in skip connection.

Model	MAD	MSE	MAPE	MSLE	R^2	KAPPA
TPC	1.658	19.539	49.697	0.458	0.443	0.710
TPC(mask skip)	1.267	15.385	30.231	0.222	0.561	0.817

Citation

@inproceedings{rocheteau2021,
author = {Rocheteau, Emma and Li\`{o}, Pietro and Hyland, Stephanie},
title = {Temporal Pointwise Convolutional Networks for Length of Stay Prediction in the Intensive Care Unit},
year = {2021},
isbn = {9781450383592},
publisher = {Association for Computing Machinery},
address = {New York, NY, USA},
url = {https://doi.org/10.1145/3450439.3451860},
doi = {10.1145/3450439.3451860},
booktitle = {Proceedings of the Conference on Health, Inference, and Learning},
pages = {58–68},
numpages = {11},
keywords = {intensive care unit, length of stay, temporal convolution, mortality, patient outcome prediction},
location = {Virtual Event, USA},
series = {CHIL '21}
}