arXiv subjects

Petr Ryšavý

Publications and source records attributed to Petr Ryšavý.

4 recordsLinked to original sources

arXiv2026

ExMAG: Learning of Maximally Ancestral Graphs

In mixed graphs, there are both directed and bidirected edges. An extension of acyclicity to this mixed-graph setting is known as maximally ancestral graphs. This extension is of considerable interest in causal learning in the presence of confounders. There, directed edges represent a clear direction of causality, while bidirected edges represent confounding. We propose a branch-and-cut algorithm for learning maximally ancestral graphs using a formulation as a mixed-integer quadratic program. Empirically, our method achieves comparable or improved reconstruction quality while requiring an order of magnitude fewer samples than state-of-the-art approaches.

cs.LG↗

arXiv2026

Causal Learning in Biomedical Applications: Krebs Cycle as a Benchmark

Learning causal relationships from time series data is an important but challenging problem. Existing synthetic datasets often contain hidden artifacts that can be exploited by causal discovery methods, reducing their usefulness for benchmarking. We present a new benchmark dataset based on simulations of the Krebs cycle, a key biochemical pathway. The data are generated using a particle-based simulator that models molecular interactions in a controlled environment. Four distinct scenarios are provided, varying in time series length, number of samples, and intervention settings. The benchmark includes ground-truth causal graphs for evaluation. It supports quantitative comparisons using metrics such as Structural Hamming Distance, Structural Intervention Distance, and F1-score. A comprehensive evaluation of 14 causal discovery methods from different modelling paradigms is presented. Performance is compared across datasets using multiple accuracy and efficiency measures. The dataset provides a reproducible, interpretable, and non-trivial benchmark for testing causal learning methods on time series data. It avoids common pitfalls such as residual structural patterns and supports interventions and evaluation with known causal ground truth. This makes it a useful tool for the development and comparison of causal discovery algorithms.

cs.LG↗

arXiv2025

Joint Problems in Learning Multiple Dynamical Systems

Clustering of time series is a well-studied problem, with applications ranging from quantitative, personalized models of metabolism obtained from metabolite concentrations to state discrimination in quantum information theory. We consider a variant, where given a set of trajectories and a number of parts, we jointly partition the set of trajectories and learn linear dynamical system (LDS) models for each part, so as to minimize the maximum error across all the models. We present globally convergent methods and EM heuristics, accompanied by promising computational results. The key highlight of this method is that it does not require a predefined hidden state dimension but instead provides an upper bound. Additionally, it offers guidance for determining regularization in the system identification.

math.OC↗

arXiv2017

Estimating Sequence Similarity from Read Sets for Clustering Next-Generation Sequencing data

To cluster sequences given only their read-set representations, one may try to reconstruct each one from the corresponding read set, and then employ conventional (dis)similarity measures such as the edit distance on the assembled sequences. This approach is however problematic and we propose instead to estimate the similarities directly from the read sets. Our approach is based on an adaptation of the Monge-Elkan similarity known from the field of databases. It avoids the NP-hard problem of sequence assembly. For low coverage data it results in a better approximation of the true sequence similarities and consequently in better clustering, in comparison to the first-assemble-then-cluster approach.

cs.DS↗