DOI: 10.5281/zenodo.18320574
title: Benchmark Datasets for IPD Reconstruction: Real IPD, Published KM, and Synthetic KM

description: Overview

This repository contains three benchmarking datasets (Real IPD, Published KM, and Synthetic KM) developed to enable standardized evaluation of Individual Patient Data (IPD) reconstruction methods.

These datasets support the manuscript titled: "A Kaplan–Meier point picker with genetic optimization enables constraint-rich individual patient data reconstruction for multicenter meta-analysis", which is currently under preparation/review.

Dataset Structure

The repository is organized into three main archives:

1. Real IPD Dataset (RealIPD.zip)

Designed for single-curve reconstruction tasks. It integrates participant-level data from TCGA (21 cancer types) and GEO (210 analyses).



RIPD_subGroup.csv: Metadata containing summary-statistic constraints (N, E, R) and identifiers.

RIPD_markerInfo.csv: Comprehensive annotation file recording raw pixel coordinates, axis calibration, and mapped survival data.

km_curve_images/: Directory containing the generated KM curve images (indexed by km_curve_id).

IPD/: Directory containing the ground-truth IPD CSV files (Columns: id, time, status).


2. Published KM Dataset (PublishedKM.zip)

Derived from 280 studies (RCTs, meta-analyses) containing paired curves (Treatment vs. Control).



Note: Due to copyright restrictions, original KM images are NOT included. Instead, we provide extracted numerical data and metadata.

RA_KM.csv: Study-level metadata (Article titles, reported HRs, 95% CIs).

RA_subGroup.csv: Cohort-specific statistics (N, E, R, median survival times, 1-5 year survival rates).

RA_markerInfo.csv: Annotation data extracted from KM images. Uses 'km_curve_id' to identify individual curves within a KM image.


3. Synthetic KM Dataset (SyntheticKM.zip)

A fully controlled benchmarking environment generated via Monte Carlo simulations.



SA_KM.csv & SA_subGroup.csv: Follows the same schema as the Published KM dataset.

SA_markerInfo.csv: Ground-truth coordinates for synthetic curves.

km_paired_images/: Composite KM images (paired arms).

km_curve_images/: Separated single-arm images.


Data Dictionary and Variable Specifications

Variable definitions for RIPD_subGroup.csv




Variable
Label
Description




km_curve_id
KM curve ID
Unique identifier for the KM curve image, where each image contains a single KM curve. This ID corresponds to the source image file in the km_curve_images/ directory.


group
Group label
Identifier for the specific study cohort or dataset series (e.g., TCGA-LUAD or GSE10300_RFS) from which the KM curve and its corresponding IPD were obtained.


sample_size
Sample size ($N$)
Total number of patients in the KM curve.


number_of_events
Number of events ($E$)
Total number of patients with observed events.


at_risk_table
At-risk table ($R$)
JSON-formatted string of time points and corresponding number at risk (format: [[time, number], ...]).




Variable definitions for RIPD_markerInfo.csv




Variable
Label
Description




annotation_id
Annotation ID
Unique identifier for the annotation record of a KM curve.


key_point_coordinates
Marked curve coordinates
Array of $(x, y)$ pixel coordinates representing the marked breakpoints and the end point of the KM curve, mapped onto a standard $1600 \times 800$ canvas.


censoring_time_coordinates
Censoring time coordinates
Array of $(x, y)$ pixel coordinates representing the ticks of marked censoring times, normalized to a $1600 \times 800$ canvas.


survival_probabilities
Survival probability
Array of survival probabilities ($\boldsymbol{p}$) corresponding to the starting point and breakpoints, mapped to the data coordinate system (range $[0, 1]$).


time_values
Time array
Array of time values corresponding to the starting point and breakpoints, mapped to the data coordinate system (actual time units).


end_time
End time
The time value corresponding to the end point ($t_M$) of the KM curve.


min_censoring_counts
Censoring counts ($\boldsymbol{c}^{min}$)
Array of counts of user-marked censoring times within each interval defined by the successive start, break, and end points.


coordinate_origin
Coordinate origin
Pixel coordinates in the normalized image coordinate system representing the axes origin $(0, 0)$ of the data coordinate system.


axis_limit_coordinates
Axis limit coordinate
Pixel coordinates representing the point $(time\_axis\_max\_scale, 1.0)$ in the data coordinate system, used to establish the mapping.


origin_data_values
Origin data values
The numerical values in the data coordinate system corresponding to the origin of the data plot axes $(0, 0)$.


axis_limit_data_values
Axis limit data values
The numerical values corresponding to the maximum identifiable Time axis tick and the maximum Survival probability axis tick ($1.0$).


km_image_id
KM image ID
Unique identifier linking this annotation record to the metadata in RIPD_subGroup.csv and the source image in the km_img directory.




Variable definitions for RA_KM.csv




Variable
Label
Description




km_image_id
KM image ID
Unique identifier for the source KM image, where each image contains a pair of KM curves.


source_study_title
Source study title
Full title of the source study from which the KM image was extracted.


hr
Hazard ratio (HR)
The hazard ratio (HR) reported in the source study specifically corresponding to this KM curve image.


hr_ci_lower
HR lower CI
Reported lower bound of the 95% confidence interval for the hazard ratio, specifically corresponding to this KM curve image.


hr_ci_upper
HR upper CI
Reported upper bound of the 95% confidence interval for the hazard ratio, specifically corresponding to this KM curve image.


reference_group
Reference group
Label of the reference group (exactly matches the group column in RA_subGroup.csv), serving as the denominator in the calculation of the hazard ratio (HR).


experimental_group
Experimental group
Label of the experimental group (exactly matches the group column in RA_subGroup.csv), serving as the numerator in the calculation of the hazard ratio (HR).


event_available
Availability of number of events ($E$)
Binary indicator (1 = available; 0 = unavailable) representing whether the total number of events ($E$) is reported in the source study.


at_risk_available
Availability of at-risk table ($R$)
Binary indicator (1 = available; 0 = unavailable) representing whether the at-risk table ($R$) is reported in the source study.


censoring_available
Availability of censoring times ($C$)
Binary indicator (1 = available; 0 = unavailable) representing whether censoring times ($C$) are marked on the KM curve image.




Variable definitions for RA_subGroup.csv




Variable
Label
Description




km_curve_id
KM curve ID
Unique identifier for each KM curve within a KM image, used to distinguish between the pair of curves present in the image.


km_image_id
KM image ID
Identifier linking to the source KM image record in RA_KM.csv.


group
Group label
Identifier for the specific treatment arm, matching either the reference_group or experimental_group field in the corresponding RA_KM.csv file.


sample_size
Sample size ($N$)
Total number of patients in the group.


number_of_events
Number of events ($E$)
Total number of patients with observed events in the group. Recorded as NULL if unavailable.


at_risk_table
At-risk table ($R$)
JSON-formatted string of time points and corresponding number at risk (format: [[time, number], ...]). Recorded as NULL if unavailable.


median_survival_time
Median survival time
String containing reported median survival time and 95% CI. Recorded as NULL if unavailable.


one_year_survival_rate ... five_year_survival_rate
1-year to 5-year survival rates
Five separate variables recording the survival probability ($S(t)$) at years 1, 2, 3, 4, and 5. Recorded as NULL if unavailable.




Citation

Since the associated manuscript is currently unpublished, please cite this dataset using the Zenodo DOI provided on this page.

LicenseCreative Commons Attribution 4.0 International (CC-BY 4.0)