Search arXiv⌕ Search
Home/Archive/arXiv

arXiv · 1905.07438

A Fast and Scalable Implementation Method for Competing Risks Data with the R Package fastcmprsk

Eric S Kawaguchi·Jenny I Shen·Gang Li·Marc A Suchard
View original source ↗Read source document ↗Export metadata ↓

Abstract

Advancements in medical informatics tools and high-throughput biological experimentation make large-scale biomedical data routinely accessible to researchers. Competing risks data are typical in biomedical studies where individuals are at risk to more than one cause (type of event) which can preclude the others from happening. The Fine-Gray model is a popular and well-appreciated model for competing risks data and is currently implemented in a number of statistical software packages. However, current implementations are not computationally scalable for large-scale competing risks data. We have developed an R package, fastcmprsk, that uses a novel forward-backward scan algorithm to significantly reduce the computational complexity for parameter estimation by exploiting the structure of the subject-specific risk sets. Numerical studies compare the speed and scalability of our implementation to current methods for unpenalized and penalized Fine-Gray regression and show impressive gains in computational efficiency.

Explore related subjects

stat.CO

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Eric S Kawaguchi, Jenny I Shen, Gang Li, Marc A Suchard. 2021-11-28. A Fast and Scalable Implementation Method for Competing Risks Data with the R Package fastcmprsk. https://doi.org/10.32614/rj-2021-010

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

arXiv2026

Fast inversion of the generalized Fisher transformation of correlation matrices

The generalized Fisher transformation maps a non-singular correlation matrix to an unconstrained real vector through the off-diagonal elements of its matrix logarithm. Evaluating its inverse is a computational bottleneck in dynamic correlation and multivariate volatility models. We develop a fast inversion algorithm by characterizing the unknown diagonal as the minimizer of a smooth, strictly convex, and coercive objective. An explicit Hessian and global spectral bounds identify the standard fixed-point iteration as a quasi-Newton method and explain why it can converge slowly near singularity. Every fixed-point step decreases the objective, and the iteration converges from every starting point. These results motivate GFT-FP+N, a hybrid of fixed-point and matrix-free Newton steps that never forms the Jacobian. In benchmarks with up to 1,000 replications per design and dimensions up to 800, GFT-FP+N reduces computation time by up to a factor of forty-five relative to the fixed-point iteration and converged in every replication, including on designs where Broyden's method almost always fails. Julia and R packages are provided.

stat.CO↗
arXiv2026

Exact Simulation of Diffusions via Brownian Bridge Range Reconstruction

We develop an exact simulation algorithm for scalar diffusion paths and diffusion bridges when the Poisson potential is unbounded in both tails. The method reconstructs the realized range of a Brownian bridge proposal by sampling its maximum and location, together with the maxima and locations of the two adjacent restricted Brownian meanders. Conditional on this finite information, the remaining path decomposes into four conditionally independent interval-constrained Brownian bridges, which can be sampled exactly at the Poisson times required by the rejection test. In contrast to constructions based on an enclosing range layer, the proposed representation retains the exact extrema and their locations. Our algorithm returns an exact finite-dimensional skeleton without time-discretization error and permits exact post-acceptance refinement at arbitrary finite collections of times. Numerical experiments validate the resulting finite-dimensional laws and identify the restricted-meander extremum simulation as the principal computational cost in the nonlinear example.

stat.CO↗
arXiv2026

Wasserstein mixing of a systematic-scan random rotation sampler

We study the mixing time of a systematic-scan analogue of Kac's walk that was proposed as a fast surrogate for Haar-distributed orthogonal matrices in randomized high-dimensional algorithms and was conjectured to approach Haar measure after only logarithmically many sweeps. We show that this conjectured speed-up does not occur for convergence of the full matrix law to Haar measure in Frobenius Wasserstein distance. At fixed normalized accuracy, the mixing time lies between order $n/\log n$ and order $n$ sweeps; at fixed absolute Frobenius accuracy, the corresponding bounds are between order $n$ and order $n\log n$. More strongly, below the scale $n/\log n$, the normalized Wasserstein distance remains asymptotically at its extremal value. We also show that the output law is singular with respect to Haar measure for fewer than $n/2$ sweeps. Thus the sampler may provide effective application-specific randomization without exhibiting the much faster full-Haar mixing.

stat.CO↗