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Gabriele Schweikert

Publications and source records attributed to Gabriele Schweikert.

2 recordsLinked to original sources

Causal Discovery from Conditionally Stationary Time Series

Causal discovery, i.e., inferring underlying causal relationships from observational data, is highly challenging for AI systems. In a time series modeling context, traditional causal discovery methods mainly consider constrained scenarios with fully observed variables and/or data from stationary time-series. We develop a causal discovery approach to handle a wide class of nonstationary time series that are conditionally stationary, where the nonstationary behaviour is modeled as stationarity conditioned on a set of latent state variables. Named State-Dependent Causal Inference (SDCI), our approach is able to recover the underlying causal dependencies, with provable identifiablity for the state-dependent causal structures. Empirical experiments on nonlinear particle interaction data and gene regulatory networks demonstrate SDCI's superior performance over baseline causal discovery methods. Improved results over non-causal RNNs on modeling NBA player movements demonstrate the potential of our method and motivate the use of causality-driven methods for forecasting.

cs.LG

M3D: a kernel-based test for shape changes in methylation profiles

DNA methylation is an intensely studied epigenetic mark implicated in many biological processes of direct clinical relevance. While sequencing based technologies are increasingly allowing high resolution measurements of DNA methylation, statistical modelling of such data is still challenging. In particular, statistical identification of differentially methylated regions across different conditions poses unresolved challenges in accounting for spatial correlations within the statistical testing procedure. We propose a non-parametric, kernel-based method, M3D, to detect higher-order changes in methylation profiles, such as shape, across pre-defined regions. The test statistic explicitly accounts for differences in coverage levels between samples, thus handling in a principled way a major confounder in the analysis of methylation data. Empirical tests on real and simulated data sets show an increased power compared to established methods, as well as considerable robustness with respect to coverage and replication levels. Code is implemented in R, and is freely available via Bioconductor package M3D.

q-bio.QM