arXiv subjects

Dominik Linzner

Publications and source records attributed to Dominik Linzner.

7 recordsLinked to original sources

arXiv2024

BoFire: Bayesian Optimization Framework Intended for Real Experiments

Our open-source Python package BoFire combines Bayesian Optimization (BO) with other design of experiments (DoE) strategies focusing on developing and optimizing new chemistry. Previous BO implementations, for example as they exist in the literature or software, require substantial adaptation for effective real-world deployment in chemical industry. BoFire provides a rich feature-set with extensive configurability and realizes our vision of fast-tracking research contributions into industrial use via maintainable open-source software. Owing to quality-of-life features like JSON-serializability of problem formulations, BoFire enables seamless integration of BO into RESTful APIs, a common architecture component for both self-driving laboratories and human-in-the-loop setups. This paper discusses the differences between BoFire and other BO implementations and outlines ways that BO research needs to be adapted for real-world use in a chemistry setting.

cs.LG↗

arXiv2021

Active Learning of Continuous-time Bayesian Networks through Interventions

We consider the problem of learning structures and parameters of Continuous-time Bayesian Networks (CTBNs) from time-course data under minimal experimental resources. In practice, the cost of generating experimental data poses a bottleneck, especially in the natural and social sciences. A popular approach to overcome this is Bayesian optimal experimental design (BOED). However, BOED becomes infeasible in high-dimensional settings, as it involves integration over all possible experimental outcomes. We propose a novel criterion for experimental design based on a variational approximation of the expected information gain. We show that for CTBNs, a semi-analytical expression for this criterion can be calculated for structure and parameter learning. By doing so, we can replace sampling over experimental outcomes by solving the CTBNs master-equation, for which scalable approximations exist. This alleviates the computational burden of sampling possible experimental outcomes in high-dimensions. We employ this framework in order to recommend interventional sequences. In this context, we extend the CTBN model to conditional CTBNs in order to incorporate interventions. We demonstrate the performance of our criterion on synthetic and real-world data.

stat.ML↗

arXiv2020

Continuous-Time Bayesian Networks with Clocks

Structured stochastic processes evolving in continuous time present a widely adopted framework to model phenomena occurring in nature and engineering. However, such models are often chosen to satisfy the Markov property to maintain tractability. One of the more popular of such memoryless models are Continuous Time Bayesian Networks (CTBNs). In this work, we lift its restriction to exponential survival times to arbitrary distributions. Current extensions achieve this via auxiliary states, which hinder tractability. To avoid that, we introduce a set of node-wise clocks to construct a collection of graph-coupled semi-Markov chains. We provide algorithms for parameter and structure inference, which make use of local dependencies and conduct experiments on synthetic data and a data-set generated through a benchmark tool for gene regulatory networks. In doing so, we point out advantages compared to current CTBN extensions.

stat.ML↗

arXiv2019

A Variational Perturbative Approach to Planning in Graph-based Markov Decision Processes

Coordinating multiple interacting agents to achieve a common goal is a difficult task with huge applicability. This problem remains hard to solve, even when limiting interactions to be mediated via a static interaction-graph. We present a novel approximate solution method for multi-agent Markov decision problems on graphs, based on variational perturbation theory. We adopt the strategy of planning via inference, which has been explored in various prior works. We employ a non-trivial extension of a novel high-order variational method that allows for approximate inference in large networks and has been shown to surpass the accuracy of existing variational methods. To compare our method to two state-of-the-art methods for multi-agent planning on graphs, we apply the method different standard GMDP problems. We show that in cases, where the goal is encoded as a non-local cost function, our method performs well, while state-of-the-art methods approach the performance of random guess. In a final experiment, we demonstrate that our method brings significant improvement for synchronization tasks.

cs.LG↗

arXiv2019

Scalable Structure Learning of Continuous-Time Bayesian Networks from Incomplete Data

Continuous-time Bayesian Networks (CTBNs) represent a compact yet powerful framework for understanding multivariate time-series data. Given complete data, parameters and structure can be estimated efficiently in closed-form. However, if data is incomplete, the latent states of the CTBN have to be estimated by laboriously simulating the intractable dynamics of the assumed CTBN. This is a problem, especially for structure learning tasks, where this has to be done for each element of a super-exponentially growing set of possible structures. In order to circumvent this notorious bottleneck, we develop a novel gradient-based approach to structure learning. Instead of sampling and scoring all possible structures individually, we assume the generator of the CTBN to be composed as a mixture of generators stemming from different structures. In this framework, structure learning can be performed via a gradient-based optimization of mixture weights. We combine this approach with a new variational method that allows for a closed-form calculation of this mixture marginal likelihood. We show the scalability of our method by learning structures of previously inaccessible sizes from synthetic and real-world data.

stat.ML↗

arXiv2018

Cluster Variational Approximations for Structure Learning of Continuous-Time Bayesian Networks from Incomplete Data

Continuous-time Bayesian networks (CTBNs) constitute a general and powerful framework for modeling continuous-time stochastic processes on networks. This makes them particularly attractive for learning the directed structures among interacting entities. However, if the available data is incomplete, one needs to simulate the prohibitively complex CTBN dynamics. Existing approximation techniques, such as sampling and low-order variational methods, either scale unfavorably in system size, or are unsatisfactory in terms of accuracy. Inspired by recent advances in statistical physics, we present a new approximation scheme based on cluster-variational methods significantly improving upon existing variational approximations. We can analytically marginalize the parameters of the approximate CTBN, as these are of secondary importance for structure learning. This recovers a scalable scheme for direct structure learning from incomplete and noisy time-series data. Our approach outperforms existing methods in terms of scalability.

stat.ML↗

arXiv2016

Reservoir-induced Thouless pumping and symmetry protected topological order in open quantum chains

We introduce a classification scheme for symmetry protected topological phases applicable to stationary states of open systems based on a generalization of the many-body polarization. The polarization can be used to probe the topological properties of non-interacting and interacting closed and open systems as well and remains a meaningful quantity even in the presence of moderate particle-number fluctuations. As examples, we discuss two open-system versions of a topological Thouless pump in the steady state of one-dimensional lattices driven by Markovian reservoirs. In the analogous unitary system, the Rice-Mele model, symmetries enforce topological properties which lead to a non-trivial winding of the geometric Zak phase upon cyclic variations of model parameters. Associated with this is a winding of the many-body polarization, corresponding to a quantized transport in the bulk (Thouless pump). We here show that in the open system, where the Zak phase looses its meaning, the same symmetries enforce a winding of the generalized many- body polarization. This winding is shown to be robust against Hamiltonian perturbations as well as homogeneous dephasing and particle losses..

cond-mat.quant-gas↗