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https://github.com/bblodfon/paad-survival-bench

Benchmark survival ML models against a multimodal TCGA dataset

https://github.com/bblodfon/paad-survival-bench

Science Score: 13.0%

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Keywords

benchmark curatedtcgadata mlr3 mlr3proba survival-prediction tcga
Last synced: 5 months ago · JSON representation

Repository

Benchmark survival ML models against a multimodal TCGA dataset

Basic Info
  • Host: GitHub
  • Owner: bblodfon
  • License: mit
  • Language: R
  • Default Branch: main
  • Homepage:
  • Size: 155 MB
Statistics
  • Stars: 3
  • Watchers: 2
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
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benchmark curatedtcgadata mlr3 mlr3proba survival-prediction tcga
Created over 3 years ago · Last pushed almost 3 years ago
Metadata Files
Readme License

README.md

paad-survival-bench

The aim of this repo is to benchmark ML survival models (available via mlr3proba) on the TCGA PAAD dataset from the PanCancer Atlas project.

  • TCGA data download and filter: tcga_paad.R
  • Data preprocessing: preprocessing.R
  • The scripts directory has several benchmarks, with some output results stored and the most important produced plots. The most important scripts/investigations are the following:
    • Benchmark CoxNet, Survival Trees and Survival Forests using nested-CV - script
    • Tuning strategy investigation (Random search vs Bayesian Optimization) using CoxNet and Survival Forests - script
    • XGBoost survival learner performance on mRNA dataset - script
    • CoxPH baseline performance using clinical features and several resampling strategies - script
    • CoxBoost (mRNA only and mRNA + clinical) vs CoxPH (clinical) - script
    • Glmboost survival learner performance on mRNA dataset - script
    • Wrapper-based Ensemble Feature Selection (eFS) per data modality - see script for mRNA data
    • Task powerset benchmark after eFS is applied (using simple CoxPH or multiple learners)

Owner

  • Name: John Zobolas
  • Login: bblodfon
  • Kind: user

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Last synced: over 1 year ago

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  • Total Commits: 220
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john b****n@g****m 219
John Zobolas b****n 1

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Last synced: 11 months ago

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  • RaphaelS1 (1)
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