Continual Learning of Electronic Health Records (EHR).

Related tags

Deep Learningehrcontinual-learningdphil
Overview

arXiv License: MIT

Continual Learning of Longitudinal Health Records

Repo for reproducing the experiments in Continual Learning of Longitudinal Health Records (2021). Release v0.1 of the project corresponds to published results.

Experiments evaluate various continual learning strategies on standard ICU predictive tasks exhibiting covariate shift. Task outcomes are binary, and input data are multi-modal time-series from patient ICU admissions.

Setup

  1. Clone this repo to your local machine.
  2. Request access to MIMIC-III and eICU-CRD.1
  3. Download the preprocessed datasets to the /data subfolder.
  4. (Recommended) Create and activate a new virtual environment: 
    python3 -m venv .venv --upgrade-deps
  5. Install dependencies: 
    pip install -U wheel buildtools
pip install -r requirements.txt

Results

To reproduce main results:

python3 main.py --train

Figures will be saved to /results/figs. Instructions to reproduce supplementary experiments can be found here. Bespoke experiments can be specified with appropriate flags e.g:

python3 main.py --domain_shift hospital --outcome mortality_48h --models CNN --strategies EWC Replay --validate --train

A complete list of available options can be found here or with python3 main.py --help.

Citation

If you use any of this code in your work, please reference us:

@misc{armstrong2021continual,
      title={Continual learning of longitudinal health records}, 
      author={J. Armstrong and D. Clifton},
      year={2021},
      eprint={2112.11944},
      archivePrefix={arXiv},
      primaryClass={cs.LG}
}

Python versions

Notes

Note that Temporal Domain Incremental learning experiments require linkage with original MIMIC-III dataset. Requires downloading ADMISSIONS.csv from MIMIC-III to the /data/mimic3/ folder.

Stack

For standardisation of ICU predictive task definitions, feature pre-processing, and Continual Learning method implementations, we use the following tools:

Tool Source
ICU Data MIMIC-III
eICU-CRD
Data preprocessing / task definition FIDDLE
Continual Learning strategies Avalanche
Comments
  • Change experience to class balanced replay

    Change experience to class balanced replay

    Have manually edited the replay definition for now. Will need to update avalanche and do change based on training.storage_policy.

    May also need to change memory buffer to n_tasks * buffer (since GEM etc use this number for experience-wise buffer sizes).

    opened by iacobo 1
  • Bump numpy from 1.20.3 to 1.22.0

    Bump numpy from 1.20.3 to 1.22.0

    Bumps numpy from 1.20.3 to 1.22.0.

    Release notes

    Sourced from numpy's releases.

    v1.22.0

    NumPy 1.22.0 Release Notes

    NumPy 1.22.0 is a big release featuring the work of 153 contributors spread over 609 pull requests. There have been many improvements, highlights are:

    • Annotations of the main namespace are essentially complete. Upstream is a moving target, so there will likely be further improvements, but the major work is done. This is probably the most user visible enhancement in this release.
    • A preliminary version of the proposed Array-API is provided. This is a step in creating a standard collection of functions that can be used across application such as CuPy and JAX.
    • NumPy now has a DLPack backend. DLPack provides a common interchange format for array (tensor) data.
    • New methods for quantile, percentile, and related functions. The new methods provide a complete set of the methods commonly found in the literature.
    • A new configurable allocator for use by downstream projects.

    These are in addition to the ongoing work to provide SIMD support for commonly used functions, improvements to F2PY, and better documentation.

    The Python versions supported in this release are 3.8-3.10, Python 3.7 has been dropped. Note that 32 bit wheels are only provided for Python 3.8 and 3.9 on Windows, all other wheels are 64 bits on account of Ubuntu, Fedora, and other Linux distributions dropping 32 bit support. All 64 bit wheels are also linked with 64 bit integer OpenBLAS, which should fix the occasional problems encountered by folks using truly huge arrays.

    Expired deprecations

    Deprecated numeric style dtype strings have been removed

    Using the strings "Bytes0", "Datetime64", "Str0", "Uint32", and "Uint64" as a dtype will now raise a TypeError.

    (gh-19539)

    Expired deprecations for loads, ndfromtxt, and mafromtxt in npyio

    numpy.loads was deprecated in v1.15, with the recommendation that users use pickle.loads instead. ndfromtxt and mafromtxt were both deprecated in v1.17 - users should use numpy.genfromtxt instead with the appropriate value for the usemask parameter.

    (gh-19615)

    ... (truncated)

    Commits

    Dependabot compatibility score

    Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting @dependabot rebase.

    Dependabot commands and options

    You can trigger Dependabot actions by commenting on this PR:

    • @dependabot rebase will rebase this PR
    • @dependabot recreate will recreate this PR, overwriting any edits that have been made to it
    • @dependabot merge will merge this PR after your CI passes on it
    • @dependabot squash and merge will squash and merge this PR after your CI passes on it
    • @dependabot cancel merge will cancel a previously requested merge and block automerging
    • @dependabot reopen will reopen this PR if it is closed
    • @dependabot close will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually
    • @dependabot ignore this major version will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)
    • @dependabot ignore this minor version will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)
    • @dependabot ignore this dependency will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)
    • @dependabot use these labels will set the current labels as the default for future PRs for this repo and language
    • @dependabot use these reviewers will set the current reviewers as the default for future PRs for this repo and language
    • @dependabot use these assignees will set the current assignees as the default for future PRs for this repo and language
    • @dependabot use this milestone will set the current milestone as the default for future PRs for this repo and language

    You can disable automated security fix PRs for this repo from the Security Alerts page.

    dependencies 
    opened by dependabot[bot] 0
  • Add Naive with no regularization?

    Add Naive with no regularization?

    Maybe add naive with no regularization? I.e. no dropout etc, to enable clearer ablation testing of naive fine tuning and inherent regularization mechanisms vs explicit CL strategy.

    opened by iacobo 0
  • CNN fails with kernel_size 5 or 7

    CNN fails with kernel_size 5 or 7

    Getting the following error (on GPU) with CNN runs with kernel_size in [5,7]:

    RuntimeError: CUDA error: CUBLAS_STATUS_INVALID_VALUE when calling `cublasSgemm( handle, opa, opb, m, n, k, &alpha, a, lda, b, ldb, &beta, c, ldc)`

    https://stackoverflow.com/questions/66600362/runtimeerror-cuda-error-cublas-status-execution-failed-when-calling-cublassge?answertab=votes#tab-top

    opened by iacobo 0
  • Add early stopping to avoid over-large number of epochs for diff models

    Add early stopping to avoid over-large number of epochs for diff models

    MLP / LSTM take shorter time to train than CNN / Transformer. Add early stopping to avoid overtraining, saturating.

    Change strategy to base strategy inheriting from strat and earlystopping plugin.

    opened by iacobo 0
  • Correct code for ROC AUC and AUPRC

    Correct code for ROC AUC and AUPRC

    Cannot average metrics over minibatches as is done for other metrics, since they depend on threshold. Need to calculate over all. Check e.g. MeanScore for inspiration on metric definition.

    opened by iacobo 0
  • Need to add code for further experiments

    Need to add code for further experiments 

    plotting.plot_demographics()

# Secondary experiments:
########################
# Sensitivity to sequence length (4hr vs 12hr)
# Sensitivity to replay size Naive -> replay -> Cumulative
# Sensitivity to hyperparams of reg methods (Tune hyperparams over increasing number of tasks?)
# Sensitivity to number of variables (full vs Vitals only e.g.)
# Sensitivity to size of domains - e.g. white ethnicity much larger than all other groups, affect of order of sequence
    opened by iacobo 1
  • Ray Tune warnings

    Ray Tune warnings

    Ray Tune produces the following warnings:

    INFO registry.py:66 -- Detected unknown callable for trainable. Converting to class.
WARNING experiment.py:295 -- No name detected on trainable. Using DEFAULT.

    Non-fatal, but it's annoying to have these messages bloating the console output.

    raytune 
    opened by iacobo 2
Releases(v0.1)
Owner
Jacob
Data Scientist @publichealthengland
Jacob
GitHub Repository
A PyTorch implementation of "Cluster-GCN: An Efficient Algorithm for Training Deep and Large Graph Convolutional Networks" (KDD 2019).

ClusterGCN ⠀⠀ A PyTorch implementation of "Cluster-GCN: An Efficient Algorithm for Training Deep and Large Graph Convolutional Networks" (KDD 2019). A

Benedek Rozemberczki 697 Dec 27, 2022
We utilize deep reinforcement learning to obtain favorable trajectories for visual-inertial system calibration.

Unified Data Collection for Visual-Inertial Calibration via Deep Reinforcement Learning Update: The lastest code will be updated in this branch. Pleas

ETHZ ASL 27 Dec 29, 2022
Deploy tensorflow graphs for fast evaluation and export to tensorflow-less environments running numpy.

Deploy tensorflow graphs for fast evaluation and export to tensorflow-less environments running numpy. Now with tensorflow 1.0 support. Evaluation usa

Marcel R. 349 Aug 06, 2022
PyTorch implementation of Anomaly Transformer: Time Series Anomaly Detection with Association Discrepancy

Anomaly Transformer in PyTorch This is an implementation of Anomaly Transformer: Time Series Anomaly Detection with Association Discrepancy. This pape

spencerbraun 160 Dec 19, 2022
TLXZoo - Pre-trained models based on TensorLayerX

Pre-trained models based on TensorLayerX. TensorLayerX is a multi-backend AI fra

TensorLayer Community 13 Dec 07, 2022
🔥 TensorFlow Code for technical report: "YOLOv3: An Incremental Improvement"

🆕 Are you looking for a new YOLOv3 implemented by TF2.0 ? If you hate the fucking tensorflow1.x very much, no worries! I have implemented a new YOLOv

3.6k Dec 26, 2022
Code for "Adversarial Attack Generation Empowered by Min-Max Optimization", NeurIPS 2021

Min-Max Adversarial Attacks [Paper] [arXiv] [Video] [Slide] Adversarial Attack Generation Empowered by Min-Max Optimization Jingkang Wang, Tianyun Zha

Jingkang Wang 12 Nov 23, 2022
Piotr - IoT firmware emulation instrumentation for training and research

Piotr: Pythonic IoT exploitation and Research Introduction to Piotr Piotr is an emulation helper for Qemu that provides a convenient way to create, sh

Damien Cauquil 51 Nov 09, 2022
Collection of Docker images for ML/DL and video processing projects

Collection of Docker images for ML/DL and video processing projects. Overview of images Three types of images differ by tag postfix: base: Python with

OSAI 87 Nov 22, 2022
LinkNet - This repository contains our Torch7 implementation of the network developed by us at e-Lab.

LinkNet This repository contains our Torch7 implementation of the network developed by us at e-Lab. You can go to our blogpost or read the article Lin

e-Lab 158 Nov 11, 2022
Fuwa-http - The http client implementation for the fuwa eco-system

Fuwa HTTP The HTTP client implementation for the fuwa eco-system Example import

Fuwa 2 Feb 16, 2022
Official PyTorch Implementation for "Recurrent Video Deblurring with Blur-Invariant Motion Estimation and Pixel Volumes"

PVDNet: Recurrent Video Deblurring with Blur-Invariant Motion Estimation and Pixel Volumes This repository contains the official PyTorch implementatio

Junyong Lee 98 Nov 06, 2022
Light-weight network, depth estimation, knowledge distillation, real-time depth estimation, auxiliary data.

light-weight-depth-estimation Boosting Light-Weight Depth Estimation Via Knowledge Distillation, https://arxiv.org/abs/2105.06143 Junjie Hu, Chenyou F

Junjie Hu 13 Dec 10, 2022
Bonnet: An Open-Source Training and Deployment Framework for Semantic Segmentation in Robotics.

Bonnet: An Open-Source Training and Deployment Framework for Semantic Segmentation in Robotics. By Andres Milioto @ University of Bonn. (for the new P

Photogrammetry & Robotics Bonn 314 Dec 30, 2022
Rethinking the Importance of Implementation Tricks in Multi-Agent Reinforcement Learning

RIIT Our open-source code for RIIT: Rethinking the Importance of Implementation Tricks in Multi-AgentReinforcement Learning. We implement and standard

405 Jan 06, 2023
This is the official implementation of the paper "Object Propagation via Inter-Frame Attentions for Temporally Stable Video Instance Segmentation".

[CVPRW 2021] - Object Propagation via Inter-Frame Attentions for Temporally Stable Video Instance Segmentation

Anirudh S Chakravarthy 6 May 03, 2022
PyTorch implementations of Top-N recommendation, collaborative filtering recommenders.

PyTorch implementations of Top-N recommendation, collaborative filtering recommenders.

Yoonki Jeong 129 Dec 22, 2022
[2021 MultiMedia] CONQUER: Contextual Query-aware Ranking for Video Corpus Moment Retrieval

CONQUER: Contexutal Query-aware Ranking for Video Corpus Moment Retreival PyTorch implementation of CONQUER: Contexutal Query-aware Ranking for Video

Hou zhijian 23 Dec 26, 2022
CR-FIQA: Face Image Quality Assessment by Learning Sample Relative Classifiability

This is the official repository of the paper: CR-FIQA: Face Image Quality Assessment by Learning Sample Relative Classifiability A private copy of the

Fadi Boutros 33 Dec 31, 2022
Laplacian Score-regularized Concrete Autoencoders

Laplacian Score-regularized Concrete Autoencoders Requirements: torch = 1.9 scikit-learn = 0.24 omegaconf = 2.0.6 scipy = 1.6.0 matplotlib How to

JS 6 Dec 07, 2022