45 joss submission

.github/workflows/draft-pdf.yml

@@ -0,0 +1,24 @@
+name: Draft PDF
+on: [push]
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          # This should be the path to the paper within your repo.
+          paper-path: paper/paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v4
+        with:
+          name: paper
+          # This is the output path where Pandoc will write the compiled
+          # PDF. Note, this should be the same directory as the input
+          # paper.md
+          path: paper.pdf

paper/paper.bib

@@ -0,0 +1,364 @@
+@article{davidson2019lifelines,
+  title={lifelines: survival analysis in Python},
+  author={Davidson-Pilon, Cameron},
+  journal={Journal of Open Source Software},
+  volume={4},
+  number={40},
+  pages={1317},
+  year={2019}
+}
+
+@article{therneau2015survival,
+  title={Package ‘survival’},
+  author={Therneau, Terry M and Lumley, Thomas},
+  journal={R Top Doc},
+  volume={128},
+  number={10},
+  pages={28--33},
+  year={2015}
+}
+
+@article{paszke2019pytorch,
+  title={Pytorch: An imperative style, high-performance deep learning library},
+  author={Paszke, Adam and Gross, Sam and Massa, Francisco and Lerer, Adam and Bradbury, James and Chanan, Gregory and Killeen, Trevor and Lin, Zeming and Gimelshein, Natalia and Antiga, Luca and others},
+  journal={Advances in neural information processing systems},
+  volume={32},
+  year={2019}
+}
+
+@article{polsterl2020scikit,
+  title={scikit-survival: A Library for Time-to-Event Analysis Built on Top of scikit-learn},
+  author={P{\"o}lsterl, Sebastian},
+  journal={The Journal of Machine Learning Research},
+  volume={21},
+  number={1},
+  pages={8747--8752},
+  year={2020},
+  publisher={JMLRORG}
+}
+
+@article{potapov2023packagesurvAUC,
+  title={Package ‘survAUC’},
+  author={Potapov, Sergej and Adler, Werner and Schmid, Matthias and Potapov, Maintainer Sergej},
+  journal={Statistics in Medicine},
+  volume={25},
+  pages={3474--3486},
+  year={2023}
+}
+
+@inproceedings{he2020momentum,
+  title={Momentum contrast for unsupervised visual representation learning},
+  author={He, Kaiming and Fan, Haoqi and Wu, Yuxin and Xie, Saining and Girshick, Ross},
+  booktitle={Proceedings of the IEEE/CVF conference on computer vision and pattern recognition},
+  pages={9729--9738},
+  year={2020}
+}
+
+@article{katzman2018deepsurv,
+  title={DeepSurv: personalized treatment recommender system using a Cox proportional hazards deep neural network},
+  author={Katzman, Jared L and Shaham, Uri and Cloninger, Alexander and Bates, Jonathan and Jiang, Tingting and Kluger, Yuval},
+  journal={BMC medical research methodology},
+  volume={18},
+  number={1},
+  pages={1--12},
+  year={2018},
+  publisher={BioMed Central}
+}
+
+@article{Kvamme2019pycox,
+  author  = {H{{\aa}}vard Kvamme and {{\O}}rnulf Borgan and Ida Scheel},
+  title   = {Time-to-Event Prediction with Neural Networks and Cox Regression},
+  journal = {Journal of Machine Learning Research},
+  year    = {2019},
+  volume  = {20},
+  number  = {129},
+  pages   = {1--30},
+  url     = {http://jmlr.org/papers/v20/18-424.html}
+}
+
+@inproceedings{nagpal2022auton,
+  title={auton-survival: An open-source package for regression, counterfactual estimation, evaluation and phenotyping with censored time-to-event data},
+  author={Nagpal, Chirag and Potosnak, Willa and Dubrawski, Artur},
+  booktitle={Machine Learning for Healthcare Conference},
+  pages={585--608},
+  year={2022},
+  organization={PMLR}
+}
+
+@article{Cox1972,
+  title = {Regression Models and Life‐Tables},
+  volume = {34},
+  ISSN = {2517-6161},
+  number = {2},
+  journal = {Journal of the Royal Statistical Society: Series B (Methodological)},
+  publisher = {Wiley},
+  author = {Cox,  D. R.},
+  year = {1972},
+  month = jan,
+  pages = {187–202}
+}
+
+@article{Kzlers2018,
+  title = {The Weibull Distribution},
+  volume = {15},
+  ISSN = {1740-9713},
+  number = {2},
+  journal = {Significance},
+  publisher = {Oxford University Press (OUP)},
+  author = {Kızılers\"{u},  Ayşe and Kreer,  Markus and Thomas,  Anthony W.},
+  year = {2018},
+  month = apr,
+  pages = {10–11}
+}
+
+@article{Carroll2003,
+  title = {On the use and utility of the Weibull model in the analysis of survival data},
+  volume = {24},
+  ISSN = {0197-2456},
+  url = {http://dx.doi.org/10.1016/S0197-2456(03)00072-2},
+  DOI = {10.1016/s0197-2456(03)00072-2},
+  number = {6},
+  journal = {Controlled Clinical Trials},
+  publisher = {Elsevier BV},
+  author = {Carroll,  Kevin J.},
+  year = {2003},
+  month = dec,
+  pages = {682–701}
+}
+
+@Manual{survivalpackage,
+    title = {A Package for Survival Analysis in R},
+    author = {Terry M Therneau},
+    year = {2024},
+    note = {R package version 3.5-8},
+    url = {https://CRAN.R-project.org/package=survival},
+  }
+
+@Manual{torchlifeAbeywardana,
+    title = {torchlife: Survival Analysis using pytorch},
+    author = {Sachinthaka Abeywardana},
+    year = {2021},
+    url = {https://sachinruk.github.io/torchlife//index.html},
+  }
+
+@Manual{survAUCpackage,
+    title = {Estimators of prediction accuracy for time-to-event data},
+    author = {Sergej Potapov and Werner Adler and Matthias Schmid},
+    year = {2023},
+    note = {R package version 1.2-0},
+    url = {https://CRAN.R-project.org/package=survAUC},
+  }
+
+@Manual{timeROCpackage,
+    title = {Time-Dependent ROC Curve and AUC for Censored Survival Data},
+    author = {Paul Blanche},
+    year = {2019},
+    note = {R package version 0.4},
+    url = {https://CRAN.R-project.org/package=timeROC},
+  }
+
+@Manual{risksetROCpackage,
+    title = {Riskset ROC Curve Estimation from Censored Survival Data},
+    author = {Patrick J. Heagerty},
+    year = {2022},
+    note = {R package version 1.0.4.1},
+    url = {https://CRAN.R-project.org/package=risksetROC},
+  }
+
+@Manual{survivalROCpackage,
+    title = {Time-Dependent ROC Curve Estimation from Censored Survival Data},
+    author = {Patrick J. Heagerty},
+    year = {2022},
+    note = {R package version 1.0.3.1},
+    url = {https://CRAN.R-project.org/package=survivalROC},
+  }
+
+@article{survcomppackage,
+  title = {survcomp: an R/Bioconductor package for performance assessment and comparison of survival models},
+  volume = {27},
+  ISSN = {1367-4803},
+  url = {http://dx.doi.org/10.1093/bioinformatics/btr511},
+  DOI = {10.1093/bioinformatics/btr511},
+  number = {22},
+  journal = {Bioinformatics},
+  publisher = {Oxford University Press (OUP)},
+  author = {Schr\"{o}der,  Markus S. and Culhane,  Aedín C. and Quackenbush,  John and Haibe-Kains,  Benjamin},
+  year = {2011},
+  month = sep,
+  pages = {3206–3208}
+}
+
+@Manual{riskRegressionpackage,
+    title = {Risk Regression Models and Prediction Scores for Survival Analysis with Competing Risks},
+    author = {Thomas Alexander Gerds and Johan Sebastian Ohlendorff and Paul Blanche and Rikke Mortensen and Marvin Wright and Nikolaj Tollenaar and John Muschelli and Ulla Brasch Mogensen and Brice Ozenne},
+    year = {2023},
+    note = {R package version 2023.12.21},
+    url = {https://CRAN.R-project.org/package=riskRegression},
+  }
+
+@Manual{SurvMetricspackage,
+    title = {Predictive Evaluation Metrics in Survival Analysis},
+    author = {Hanpu Zhou and Xuewei Cheng and Sizheng Wang and Yi Zou and Hong Wang},
+    year = {2022},
+    note = {R package version 0.5.0},
+    url = {https://CRAN.R-project.org/package=SurvMetrics},
+  }
+
+@Manual{pecpackage,
+    title = {Prediction Error Curves for Risk Prediction Models in Survival Analysis},
+    author = {Thomas A. Gerds},
+    year = {2023},
+    note = {R package version 2023.04.12},
+    url = {https://CRAN.R-project.org/package=pec},
+  }
+
+@article{Heagerty2000,
+  title = {Time‐Dependent ROC Curves for Censored Survival Data and a Diagnostic Marker},
+  volume = {56},
+  ISSN = {1541-0420},
+  url = {http://dx.doi.org/10.1111/j.0006-341x.2000.00337.x},
+  DOI = {10.1111/j.0006-341x.2000.00337.x},
+  number = {2},
+  journal = {Biometrics},
+  publisher = {Oxford University Press (OUP)},
+  author = {Heagerty,  Patrick J. and Lumley,  Thomas and Pepe,  Margaret S.},
+  year = {2000},
+  month = jun,
+  pages = {337–344}
+}
+
+@article{Heagerty2005,
+ author = {Heagerty, Patrick J. and Zheng, Yingye},
+ doi = {10.1111/j.0006-341x.2005.030814.x},
+ issn = {1541-0420},
+ journal = {Biometrics},
+ month = {February},
+ number = {1},
+ pages = {92–105},
+ publisher = {Oxford University Press (OUP)},
+ title = {Survival Model Predictive Accuracy and ROC Curves},
+ url = {http://dx.doi.org/10.1111/j.0006-341x.2005.030814.x},
+ volume = {61},
+ year = {2005}
+}
+
+
+@article{Blanche2013,
+  title = {Review and comparison of ROC curve estimators for a time‐dependent outcome with marker‐dependent censoring},
+  volume = {55},
+  ISSN = {1521-4036},
+  url = {http://dx.doi.org/10.1002/bimj.201200045},
+  DOI = {10.1002/bimj.201200045},
+  number = {5},
+  journal = {Biometrical Journal},
+  publisher = {Wiley},
+  author = {Blanche,  Paul and Dartigues,  Jean‐Fran\c{c}ois and Jacqmin‐Gadda,  Hélène},
+  year = {2013},
+  month = jun,
+  pages = {687–704}
+}
+
+@article{Uno2007,
+  title = {Evaluating Prediction Rules fort-Year Survivors With Censored Regression Models},
+  volume = {102},
+  ISSN = {1537-274X},
+  url = {http://dx.doi.org/10.1198/016214507000000149},
+  DOI = {10.1198/016214507000000149},
+  number = {478},
+  journal = {Journal of the American Statistical Association},
+  publisher = {Informa UK Limited},
+  author = {Uno,  Hajime and Cai,  Tianxi and Tian,  Lu and Wei,  L. J},
+  year = {2007},
+  month = jun,
+  pages = {527–537}
+}
+
+@article{Blanche2018,
+ author = {Blanche, Paul and Kattan, Michael W and Gerds, Thomas A},
+ doi = {10.1093/biostatistics/kxy006},
+ issn = {1468-4357},
+ journal = {Biostatistics},
+ month = {February},
+ number = {2},
+ pages = {347–357},
+ publisher = {Oxford University Press (OUP)},
+ title = {The c-index is not proper for the evaluation of $t$-year predicted risks},
+ url = {http://dx.doi.org/10.1093/biostatistics/kxy006},
+ volume = {20},
+ year = {2018}
+}
+
+@article{Uno_2011,
+ author = {Uno, Hajime and Cai, Tianxi and Pencina, Michael J. and D’Agostino, Ralph B. and Wei, L. J.},
+ doi = {10.1002/sim.4154},
+ issn = {1097-0258},
+ journal = {Statistics in Medicine},
+ month = {January},
+ number = {10},
+ pages = {1105–1117},
+ publisher = {Wiley},
+ title = {On the C‐statistics for evaluating overall adequacy of risk prediction procedures with censored survival data},
+ url = {http://dx.doi.org/10.1002/sim.4154},
+ volume = {30},
+ year = {2011}
+}
+
+@article{Harrell1996,
+ author = {Harrell, Frank E. and Lee, Kerry L. and Mark, Daniel B.},
+ doi = {10.1002/(sici)1097-0258(19960229)15:4<361::aid-sim168>3.0.co;2-4},
+ issn = {1097-0258},
+ journal = {Statistics in Medicine},
+ month = {February},
+ number = {4},
+ pages = {361–387},
+ publisher = {Wiley},
+ title = {Multivariate Prognostic Models: Issues in Developing models, Evaluating Assumptions and Adequacy, and Measuring and Reducing Errors},
+ url = {http://dx.doi.org/10.1002/(SICI)1097-0258(19960229)15:4<361::AID-SIM168>3.0.CO;2-4},
+ volume = {15},
+ year = {1996}
+}
+
+@article{Graf_1999,
+ author = {Graf, Erika and Schmoor, Claudia and Sauerbrei, Willi and Schumacher, Martin},
+ doi = {10.1002/(sici)1097-0258(19990915/30)18:17/18<2529::aid-sim274>3.0.co;2-5},
+ issn = {1097-0258},
+ journal = {Statistics in Medicine},
+ month = {September},
+ number = {17–18},
+ pages = {2529–2545},
+ publisher = {Wiley},
+ title = {Assessment and comparison of prognostic classification schemes for survival data},
+ url = {http://dx.doi.org/10.1002/(SICI)1097-0258(19990915/30)18:17/18<2529::AID-SIM274>3.0.CO;2-5},
+ volume = {18},
+ year = {1999}
+}
+
+@article{Efron1977,
+  title = {The Efficiency of Cox’s Likelihood Function for Censored Data},
+  volume = {72},
+  ISSN = {1537-274X},
+  url = {http://dx.doi.org/10.1080/01621459.1977.10480613},
+  DOI = {10.1080/01621459.1977.10480613},
+  number = {359},
+  journal = {Journal of the American Statistical Association},
+  publisher = {Informa UK Limited},
+  author = {Efron,  Bradley},
+  year = {1977},
+  month = sep,
+  pages = {557–565}
+}
+
+@article{Breslow1975,
+  title = {Analysis of Survival Data under the Proportional Hazards Model},
+  volume = {43},
+  ISSN = {0306-7734},
+  url = {http://dx.doi.org/10.2307/1402659},
+  DOI = {10.2307/1402659},
+  number = {1},
+  journal = {International Statistical Review / Revue Internationale de Statistique},
+  publisher = {JSTOR},
+  author = {Breslow,  N. E.},
+  year = {1975},
+  month = apr,
+  pages = {45}
+}