arXiv subjects

Martin Bøgsted

Publications and source records attributed to Martin Bøgsted.

11 recordsLinked to original sources

arXiv2026

Bounds on the Posterior-to-Prior Ratios for Inclusion Belief under Bounded Differential Privacy

Differential privacy has become the standard for generating privacy-protected data releases. However, differential privacy does not translate intuitively to disclosure risk. In particular, it remains unclear how much an adversary's belief about an individual's inclusion in a dataset can change after observing a protected release. To address this question, we derive upper and lower bounds on the posterior-to-prior ratios of inclusion beliefs under bounded probabilistic and approximate differential privacy. By assuming a worst-case adversary with all-but-one auxiliary information, i.e., knowledge of all except for one of the participants in a dataset, we obtain bounds that apply to any adversary. Because these bounds may fail with non-zero probability, we study the corresponding failure probability for the Gaussian mechanism. We derive a theoretical upper limit on this probability and compare it with Monte Carlo estimates across a wide range of parameter settings. The observed failure rate is several orders of magnitude smaller than its theoretical upper limit, indicating that the latter is highly conservative. These findings suggest that the inferential privacy guarantees provided by differentially private mechanisms may be substantially stronger in practice than what is implied by the theoretical upper limit.

math.ST↗

arXiv2026

A normal-inverse-Wishart (NIW) Bayesian synthesizer for multivariate normal data with application to polygenic risk scores

Bayesian synthesis, which generates synthetic data by sampling from the posterior predictive distribution, is a popular approach for privatizing sensitive personal data. However, how attribute disclosure risk is affected by feature dimensionality, the number of individuals in the original dataset, and the amount of released synthetic information remains poorly understood. We propose a mathematically tractable Bayesian synthesizer for multivariate normal data based on a conjugate normal-inverse-Wishart prior for the mean vector and covariance matrix. The conjugate structure yields closed-form posteriors and enables direct investigation of an adversary's ability to infer records under different data and release settings. We then demonstrate several intuitive properties of synthetic data generation through several simulations. Specifically, we show that disclosure risk decreases with the size of the original dataset, but increases with the dimensionality of the feature space and the amount of synthetic information released, whether through the release of larger synthetic datasets or multiple generator realizations. Finally, the proposed synthesizer was used to generate synthetic versions of a polygenic risk score dataset, with the synthetic data exhibiting distributional properties comparable to those of the original data.

stat.ME↗

arXiv2026

VAE-MS: An Asymmetric Variational Autoencoder for Mutational Signature Extraction

Mutational signature analysis has emerged as a powerful method for uncovering the underlying biological processes driving cancer development. However, the signature extraction process, typically performed using non-negative matrix factorization (NMF), often lacks reliability and clinical applicability. To address these limitations, several solutions have been introduced, including the use of neural networks to achieve more accurate estimates and probabilistic methods to better capture natural variation in the data. In this work, we introduce a Variational Autoencoder for Mutational Signatures (VAE-MS), a novel model that leverages both an asymmetric architecture and probabilistic methods for the extraction of mutational signatures. VAE-MS is compared to with three state-of-the-art models for mutational signature extraction: SigProfilerExtractor, the NMF-based gold standard; MUSE-XAE, an autoencoder that employs an asymmetric design without probabilistic components; and SigneR, a Bayesian NMF model, to illustrate the strength in combining a nonlinear extraction with a probabilistic model. In the ability to reconstruct input data and generalize to unseen data, models with probabilistic components (VAE-MS, SigneR) dramatically outperformed models without (SigProfilerExtractor, MUSE-XAE). The NMF-baed models (SigneR, SigProfilerExtractor) had the most accurate reconstructions in simulated data, while VAE-MS reconstructed more accurately on real cancer data. Upon evaluating the ability to extract signatures consistently, no model exhibited a clear advantage over the others. Software for VAE-MS is available at https://github.com/CLINDA-AAU/VAE-MS.

stat.AP↗

arXiv2025

A statistical note on extending Christensen's limits of agreement with the mean

Limits of agreement with the mean (LOAM) can be used for assessing agreement of continuous measurements made by different observers. Definitions of a LOAM for measuring reproducibility has been introduced under a two-way random effects model without interaction between subject and observer. Here we extend that model framework to include a subject-observer interaction, allowing the separation of residual measurement error and systematic variation in how individual observers measure specific objects. Further, our framework extends the LOAM concept to two metrics: one quantifying reproducibility and the other repeatability. We supply estimates and confidence intervals for the reproducibility and repeatibility LOAM and discuss sample size calculations and a test to compare LOAMs between two groups. To make the text self-contained for a complete agreement analysis, we additionally provide estimates and confidence intervals for the variance components.

stat.ME↗

arXiv2025

A Review of Privacy Metrics for Privacy-Preserving Synthetic Data Generation

Privacy Preserving Synthetic Data Generation (PP-SDG) has emerged to produce synthetic datasets from personal data while maintaining privacy and utility. Differential privacy (DP) is the property of a PP-SDG mechanism that establishes how protected individuals are when sharing their sensitive data. It is however difficult to interpret the privacy budget ($\varepsilon$) expressed by DP. To make the actual risk associated with the privacy budget more transparent, multiple privacy metrics (PMs) have been proposed to assess the privacy risk of the data. These PMs are utilized in separate studies to assess newly introduced PP-SDG mechanisms. Consequently, these PMs embody the same assumptions as the PP-SDG mechanism they were made to assess. Therefore, a thorough definition of how these are calculated is necessary. In this work, we present the assumptions and mathematical formulations of 17 distinct privacy metrics.

cs.CR↗

arXiv2024

A primer on synthetic health data

Recent advances in deep generative models have greatly expanded the potential to create realistic synthetic health datasets. These synthetic datasets aim to preserve the characteristics, patterns, and overall scientific conclusions derived from sensitive health datasets without disclosing patient identity or sensitive information. Thus, synthetic data can facilitate safe data sharing that supports a range of initiatives including the development of new predictive models, advanced health IT platforms, and general project ideation and hypothesis development. However, many questions and challenges remain, including how to consistently evaluate a synthetic dataset's similarity and predictive utility in comparison to the original real dataset and risk to privacy when shared. Additional regulatory and governance issues have not been widely addressed. In this primer, we map the state of synthetic health data, including generation and evaluation methods and tools, existing examples of deployment, the regulatory and ethical landscape, access and governance options, and opportunities for further development.

cs.LG↗

arXiv2024

On the Relation Between Autoencoders and Non-negative Matrix Factorization, and Their Application for Mutational Signature Extraction

The aim of this study is to provide a foundation to understand the relationship between non-negative matrix factorization (NMF) and non-negative autoencoders enabling proper interpretation and understanding of autoencoder-based alternatives to NMF. Since its introduction, NMF has been a popular tool for extracting interpretable, low-dimensional representations of high-dimensional data. However, recently, several studies have proposed to replace NMF with autoencoders. This increasing popularity of autoencoders warrants an investigation on whether this replacement is in general valid and reasonable. Moreover, the exact relationship between non-negative autoencoders and NMF has not been thoroughly explored. Thus, a main aim of this study is to investigate in detail the relationship between non-negative autoencoders and NMF. We find that the connection between the two models can be established through convex NMF, which is a restricted case of NMF. In particular, convex NMF is a special case of an autoencoder. The performance of NMF and autoencoders is compared within the context of extraction of mutational signatures from cancer genomics data. We find that the reconstructions based on NMF are more accurate compared to autoencoders, while the signatures extracted using both methods show comparable consistencies and values when externally validated. These findings suggest that the non-negative autoencoders investigated in this article do not provide an improvement of NMF in the field of mutational signature extraction.

stat.AP↗

arXiv2020

Targeted Fused Ridge Estimation of Inverse Covariance Matrices from Multiple High-Dimensional Data Classes

We consider the problem of jointly estimating multiple inverse covariance matrices from high-dimensional data consisting of distinct classes. An $\ell_2$-penalized maximum likelihood approach is employed. The suggested approach is flexible and generic, incorporating several other $\ell_2$-penalized estimators as special cases. In addition, the approach allows specification of target matrices through which prior knowledge may be incorporated and which can stabilize the estimation procedure in high-dimensional settings. The result is a targeted fused ridge estimator that is of use when the precision matrices of the constituent classes are believed to chiefly share the same structure while potentially differing in a number of locations of interest. It has many applications in (multi)factorial study designs. We focus on the graphical interpretation of precision matrices with the proposed estimator then serving as a basis for integrative or meta-analytic Gaussian graphical modeling. Situations are considered in which the classes are defined by data sets and subtypes of diseases. The performance of the proposed estimator in the graphical modeling setting is assessed through extensive simulation experiments. Its practical usability is illustrated by the differential network modeling of 12 large-scale gene expression data sets of diffuse large B-cell lymphoma subtypes. The estimator and its related procedures are incorporated into the R-package rags2ridges.

stat.ME↗

arXiv2019

Regression on imperfect class labels derived by unsupervised clustering

Outcome regressed on class labels identified by unsupervised clustering is custom in many applications. However, it is common to ignore the misclassification of class labels caused by the learning algorithm, which potentially leads to serious bias of the estimated effect parameters. Due to its generality we suggest to redress the situation by use of the simulation and extrapolation method. Performance is illustrated by simulated data from Gaussian mixture models. Finally, we apply our method to a study which regressed overall survival on class labels derived from unsupervised clustering of gene expression data from bone marrow samples of multiple myeloma patients.

stat.ML↗

arXiv2017

Estimating a common covariance matrix for network meta-analysis of gene expression datasets in diffuse large B-cell lymphoma

The estimation of covariance matrices of gene expressions has many applications in cancer systems biology. Many gene expression studies, however, are hampered by low sample size and it has therefore become popular to increase sample size by collecting gene expression data across studies. Motivated by the traditional meta-analysis using random effects models, we present a hierarchical random covariance model and use it for the meta-analysis of gene correlation networks across 11 large-scale gene expression studies of diffuse large B-cell lymphoma (DLBCL). We suggest to use a maximum likelihood estimator for the underlying common covariance matrix and introduce an EM algorithm for estimation. By simulation experiments comparing the estimated covariance matrices by cophenetic correlation and Kullback-Leibler divergence the suggested estimator showed to perform better or not worse than a simple pooled estimator. In a posthoc analysis of the estimated common covariance matrix for the DLBCL data we were able to identify novel biologically meaningful gene correlation networks with eigengenes of prognostic value. In conclusion, the method seems to provide a generally applicable framework for meta-analysis, when multiple features are measured and believed to share a common covariance matrix obscured by study dependent noise.

stat.ML↗

arXiv2013

Reproducible probe-level analysis of the Affymetrix Exon 1.0 ST array with R/Bioconductor

The presence of different transcripts of a gene across samples can be analysed by whole-transcriptome microarrays. Reproducing results from published microarray data represents a challenge due to the vast amounts of data and the large variety of pre-processing and filtering steps employed before the actual analysis is carried out. To guarantee a firm basis for methodological development where results with new methods are compared with previous results it is crucial to ensure that all analyses are completely reproducible for other researchers. We here give a detailed workflow on how to perform reproducible analysis of the GeneChip Human Exon 1.0 ST Array at probe and probeset level solely in R/Bioconductor, choosing packages based on their simplicity of use. To exemplify the use of the proposed workflow we analyse differential splicing and differential gene expression in a publicly available dataset using various statistical methods. We believe this study will provide other researchers with an easy way of accessing gene expression data at different annotation levels and with the sufficient details needed for developing their own tools for reproducible analysis of the GeneChip Human Exon 1.0 ST Array.

stat.AP↗