CEliver model

This model is early liver cancer detection model, developed based on automated capillary electrophoresis data of cell-free DNA.

Classes definition

• 0 = Non-cancer
• 1 = Liver cancer

Installation

Docker

Docker >= 28.5.1 with docker compose plugin Docker installation

git clone https://github.com/cmuteam-medcmu/celiver.git
cd celiver
docker compose run --rm celiver

Test with demo dataset

bash celiver-run.sh

Run through python argument

#!/bin/bash

compose_path="docker-compose.yaml" 
output_dir="test"

docker compose -f $compose_path \
    -v $output_dir:/output \
    run --rm \
    celiver \
    --input dataset/test_dataset.csv \
    --prefic celiver \
    --fromraw True \
    --validate dataset/true_label.csv \
    --outdir /output

Run through configuration file

#!/bin/bash

compose_path="docker-compose.yaml" 
output_dir="test"

docker compose -f $compose_path \
    -v $output_dir:/output \
    run --rm \
    celiver \
    -c test/config.yaml

Singularity

Singularity installation

singularity pull celiver-v1.0.0.sif docker://moonipur148/celiver:latest
git clone https://github.com/cmuteam-medcmu/celiver.git
cd celiver

Run through singularity with configulation file

#!/bin/bash

celiver_root="$PWD" # Change to your full path

singularity run --cleanenv \
    --pwd /work \
    -B "test":/output \
    -B $celiver_root:/work \
    celiver.sif \
    -c /work/test/config.yaml 

Citation

If you use CEliver in your research, please cite our paper:

APA: Udomruk, S. et al. (2026). Machine learning–based cfDNA fragmentation profiling using automated capillary electrophoresis for early detection of hepatocellular carcinoma. Communications Medicine, 6(1). https://www.nature.com/articles/s43856-026-01437-5

BibTeX:

@article{Udomruk2026,
  title = {Machine learning–based cfDNA fragmentation profiling using automated capillary electrophoresis for early detection of hepatocellular carcinoma},
  author = {Udomruk, Sasimol et al.},
  journal = {Communications Medicine},
  year = {2026},
  volume = {6},
  number = {1},
  doi = {https://www.nature.com/articles/s43856-026-01437-5}
}

License

CEliver © 2025 by Cancer Research Unit, CMUTEAM, Faculty of Medicine, Chiang Mai University is licensed under CC BY-NC 4.0