CODE-AE

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CONTEXT-AWARE DECONFOUNDING AUTOENCODER

• Paper

@article{he2022context,
  title={A context-aware deconfounding autoencoder for robust prediction of personalized clinical drug response from cell-line compound screening},
  author={He, Di and Liu, Qiao and Wu, You and Xie, Lei},
  journal={Nature Machine Intelligence},
  volume={4},
  number={10},
  pages={879--892},
  year={2022},
  publisher={Nature Publishing Group UK London}
}

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1. Introduction

CODE-AE is a Python implementation of Context-aware Deconfounding Autoencoder (CODE-AE) that can extract common biological signals masked by context-specific patterns and confounding factors.

Architecture

3. Installation

CODE-AE depends on Numpy, SciPy, PyTorch (CUDA toolkit if use GPU), scikit-learn, pandas. You must have them installed before using CODE-AE.

The simple way to install them is using Docker: the Dockerfile is given within folder code/

4. Usage

4.1. Data

Benchmark datasets available at Zenodo[http://doi.org/10.5281/zenodo.4776448] (version 2.0)

4.2 Basic Usage

4.2.1 Pre-train encoders

    $ python pretrain_hyper_main.py

Arguments in this script:

• --method: method to be used for encoder pre-training, choose from ['code_adv', 'dsna', 'dsn', 'code_base', 'code_mmd', 'adae', 'coral', 'dae', 'vae','vaen', 'ae']
• --train: retrain the encoders
• --no-train: no re-training
• --norm: use L2 normalization for embedding
• --no-norm: don't use L2 normalization for embedding

4.2.1 Fine-tune encoders for different drug response predictive models

    $ python drug_ft_hyper_main.py

Arguments in this script:

• --method: method to be used for encoder pre-training, choose from ['code_adv', 'dsna', 'dsn', 'code_base', 'code_mmd', 'adae', 'coral', 'dae', 'vae','vaen', 'ae']
• --train: retrain the encoders
• --no-train: no re-training
• --norm: use L2 normalization for embedding
• --no-norm: don't use L2 normalization for embedding
• --metric: metric used in early stopping
• --pdtc: fine-tune PDTC drugs (target therapy agents)
• --no-pdtc: fine-tune chemotherapy drugs

Additional scripts

• adae_hyper_main.py: run ADAE de-confounding experiments
• drug_inference_main.py: generate TCGA sample prediction
• generate_encoded_features.py: generate encoded features by pre-trained encoders
• ml_baseline.py: get benchmark experiments' results using random forest and elastic net
• mlp_main.py: get benchmark experiments' results using simple multi-layer neural network
• tcrp_main.py: get benchmark experiments' results using TCRP
• vaen_main.py: get benchmark experiments' results using VAEN (VAE+elastic net)