Bert de Vries
Current Organizations / Institutes
The organizations/institutes from the scholar's latest article
Previous Organizations / Institutes
The organizations / institutes from the scholar's other articles in the past ten years
Research Subjects
Bert de Vries has a total of 37 co-authors. Here are the top co-authors by number of shared publications:
- Wouter W. L. Nuijten
Eindhoven University of Technology
6 shared publications - Dmitry Bagaev
BIASlab, Department of Electrical Engineering, Eindhoven University of Technology , 5600 MBEindhoven
5 shared publications - Bart van Erp
Department of Electrical Engineering Eindhoven University of Technology Eindhoven The Netherlands
4 shared publications - Wouter Marco Kouw
Department of Electrical Engineering, Eindhoven University of Technology, 5612 AZ Eindhoven, The Netherlands
4 shared publications - Albert Podusenko
Technical University of Eindhoven
3 shared publications - İsmail Şenöz
Lazy Dynamics BV Eindhoven
3 shared publications
Latest Publications
- Open Access
- 21 May 2026
- Published by Institute of Electrical and Electronics Engineers (IEEE) in IEEE Open Journal of Signal Processing
- Vol. 7, 591-611
A Probabilistic Generative Model for Spectral Speech Enhancement
Speech enhancement in hearing aids remains difficult in nonstationary acoustic environments. This paper introduces AIDA-2, a unified modular framework that formulates signal processing, learning, and personalization as Bayesian inference with explicit uncertainty tracking. The proposed framework replaces ad hoc algorithm design with a single probabilistic generative model that continuously adapts to changing acoustic conditions and user preferences. It extends spectral subtraction with principled mechanisms for in situ personalization and adaptation to acoustic context. The system is implemented as an interconnected probabilistic state-space model, and inference is performed via variational message passing in the RxInfer.jl probabilistic programming environment, enabling real-time Bayesian processing under hearing-aid constraints. We focus the evaluation on the warped-frequency filter bank (WFB) and speech enhancement model (SEM), evaluated on the public VoiceBank+DEMAND corpus. Additionally, an acoustic context model (ACM) and end-user model (EUM) are described architecturally. The evaluated system requires 85 parameters, two orders of magnitude fewer than the tens of thousands to millions of trainable parameters used by contemporary deep-learning baselines. This proof of concept establishes an interpretable, data-efficient foundation for uncertainty-aware hearing-aid processing, pointing toward devices that learn continuously through probabilistic inference.
- 21 May 2026
- Published by Institute of Electrical and Electronics Engineers (IEEE) in IEEE Open Journal of Signal Processing
- Vol. 7, 591-611
Open AccessA Probabilistic Generative Model for Spectral Speech Enhancement
Speech enhancement in hearing aids remains difficult in nonstationary acoustic environments. This paper introduces AIDA-2, a unified modular framework that formulates signal processing, learning, and personalization as Bayesian inference with explicit uncertainty tracking. The proposed framework replaces ad hoc algorithm design with a single probabilistic generative model that continuously adapts to changing acoustic conditions and user preferences. It extends spectral subtraction with principled mechanisms for in situ personalization and adaptation to acoustic context. The system is implemented as an interconnected probabilistic state-space model, and inference is performed via variational message passing in the RxInfer.jl probabilistic programming environment, enabling real-time Bayesian processing under hearing-aid constraints. We focus the evaluation on the warped-frequency filter bank (WFB) and speech enhancement model (SEM), evaluated on the public VoiceBank+DEMAND corpus. Additionally, an acoustic context model (ACM) and end-user model (EUM) are described architecturally. The evaluated system requires 85 parameters, two orders of magnitude fewer than the tens of thousands to millions of trainable parameters used by contemporary deep-learning baselines. This proof of concept establishes an interpretable, data-efficient foundation for uncertainty-aware hearing-aid processing, pointing toward devices that learn continuously through probabilistic inference.
- Open Access
- 18 May 2026
- Published by IOP Publishing in Neuromorphic Computing and Engineering
- Vol. 6 (2)
A spiking neural network implementation of Gaussian belief propagation
Bayesian inference offers a principled account of information processing in natural agents. However, it remains an open question how neural mechanisms perform their abstract operations. We investigate a hypothesis where a distributed form of Bayesian inference, namely message passing on factor graphs, is performed by a simulated network of leaky-integrate-and-fire neurons. Specifically, we perform Gaussian belief propagation by encoding messages that come into factor nodes as spike-based signals, propagating these signals through a spiking neural network and decoding the spike-based signal back to an outgoing message. Three core linear operations, equality (branching), addition, and multiplication, are realized in networks of leaky integrate-and-fire models. Validation against the standard sum-product algorithm shows accurate message updates, while applications to Kalman filtering and Bayesian linear regression demonstrate the framework's potential for both static and dynamic inference tasks. Our results provide a step toward biologically grounded, neuromorphic implementations of probabilistic reasoning.
- 18 May 2026
- Published by IOP Publishing in Neuromorphic Computing and Engineering
- Vol. 6 (2)
Open AccessA spiking neural network implementation of Gaussian belief propagation
Bayesian inference offers a principled account of information processing in natural agents. However, it remains an open question how neural mechanisms perform their abstract operations. We investigate a hypothesis where a distributed form of Bayesian inference, namely message passing on factor graphs, is performed by a simulated network of leaky-integrate-and-fire neurons. Specifically, we perform Gaussian belief propagation by encoding messages that come into factor nodes as spike-based signals, propagating these signals through a spiking neural network and decoding the spike-based signal back to an outgoing message. Three core linear operations, equality (branching), addition, and multiplication, are realized in networks of leaky integrate-and-fire models. Validation against the standard sum-product algorithm shows accurate message updates, while applications to Kalman filtering and Bayesian linear regression demonstrate the framework's potential for both static and dynamic inference tasks. Our results provide a step toward biologically grounded, neuromorphic implementations of probabilistic reasoning.
- Open Access
A Spiking Neural Network Implementation of Gaussian Belief Propagation
Bayesian inference offers a principled account of information processing in natural agents. However, it remains an open question how neural mechanisms perform their abstract operations. We investigate a hypothesis where a distributed form of Bayesian inference, namely message passing on factor graphs, is performed by a simulated network of leaky-integrate-and-fire neurons. Specifically, we perform Gaussian belief propagation by encoding messages that come into factor nodes as spike-based signals, propagating these signals through a spiking neural network (SNN) and decoding the spike-based signal back to an outgoing message. Three core linear operations, equality (branching), addition, and multiplication, are realized in networks of leaky integrate-and-fire models. Validation against the standard sum-product algorithm shows accurate message updates, while applications to Kalman filtering and Bayesian linear regression demonstrate the framework's potential for both static and dynamic inference tasks. Our results provide a step toward biologically grounded, neuromorphic implementations of probabilistic reasoning.
Open AccessA Spiking Neural Network Implementation of Gaussian Belief Propagation
Bayesian inference offers a principled account of information processing in natural agents. However, it remains an open question how neural mechanisms perform their abstract operations. We investigate a hypothesis where a distributed form of Bayesian inference, namely message passing on factor graphs, is performed by a simulated network of leaky-integrate-and-fire neurons. Specifically, we perform Gaussian belief propagation by encoding messages that come into factor nodes as spike-based signals, propagating these signals through a spiking neural network (SNN) and decoding the spike-based signal back to an outgoing message. Three core linear operations, equality (branching), addition, and multiplication, are realized in networks of leaky integrate-and-fire models. Validation against the standard sum-product algorithm shows accurate message updates, while applications to Kalman filtering and Bayesian linear regression demonstrate the framework's potential for both static and dynamic inference tasks. Our results provide a step toward biologically grounded, neuromorphic implementations of probabilistic reasoning.
- Open Access
- 14 April 2025
- Published by The Open Journal in JuliaCon Proceedings
- Vol. 7 (70) , 179
ExponentialFamilyManifolds.jl: Representing exponential families as Riemannian manifolds
ExponentialFamilyManifolds.jl implements exponential family natural parameter spaces as Riemannian manifolds, enabling geometric optimization over probability distributions. The package automatically manages parameter constraints, such as ensuring the positive definiteness of precision matrices for normal distributions. By representing exponential family distributions as manifolds that conform to the ManifoldsBase.jl interface, it allows users to leverage optimization techniques from Manopt.jl for these manifolds. Applications in maximum likelihood estimation and variational inference highlight the package's practical utility.
- 14 April 2025
- Published by The Open Journal in JuliaCon Proceedings
- Vol. 7 (70) , 179
Open AccessExponentialFamilyManifolds.jl: Representing exponential families as Riemannian manifolds
ExponentialFamilyManifolds.jl implements exponential family natural parameter spaces as Riemannian manifolds, enabling geometric optimization over probability distributions. The package automatically manages parameter constraints, such as ensuring the positive definiteness of precision matrices for normal distributions. By representing exponential family distributions as manifolds that conform to the ManifoldsBase.jl interface, it allows users to leverage optimization techniques from Manopt.jl for these manifolds. Applications in maximum likelihood estimation and variational inference highlight the package's practical utility.
- 31 December 2024
- Published by Springer Nature
- p. 147-161
Reactive Environments for Active Inference Agents with RxEnvironments.jl
- 31 December 2024
- Published by Springer Nature
- p. 147-161
Reactive Environments for Active Inference Agents with RxEnvironments.jl
- 31 December 2024
- Published by Springer Nature
- p. 91-104
Online Structure Learning with Dirichlet Processes Through Message Passing
- 31 December 2024
- Published by Springer Nature
- p. 91-104
Online Structure Learning with Dirichlet Processes Through Message Passing
- Open Access
- 13 December 2024
- Published by Association for Computing Machinery (ACM) in ACM Transactions on Probabilistic Machine Learning
- Vol. 1 (1) , 1-28
On the Importance of the Execution Schedule for Bayesian Inference
Bayesian inference is a probabilistic approach to the problem of drawing conclusions from observed data. Its main challenge is computational, which the Bayesian community tends to address through approximation techniques. However, these techniques come with their own set of challenges, including approximation errors, the difficulty of assessing these errors, and the inherited NP-hardness of the inference problem. Concurrently, in an effort to keep up with Moore’s law, the computer engineering community has developed an increasing number of programming techniques for today’s heterogeneous hardware. These techniques aim to optimize the execution schedule , which refers to the order and mapping of computations on the available execution units. In this work, we advocate for the utilization of these techniques to avoid a common pitfall known as premature approximation . Notably, these techniques have the potential to significantly enhance performance, thereby reducing the need for approximation and thus mitigating the challenges that accompany it. We first demonstrate how optimization of the storage strategy, i.e., when and where intermediate results are stored, allows for a trade-off between runtime and peak memory usage . We then investigate various techniques that aim to automatically generate efficient execution schedules. Finally, we focus on a specific, runtime-efficient execution schedule identified through design space exploration and compare its performance with that of two established solvers for probabilistic inference. The results show that our optimized implementation achieves speedups ranging from \(2\times\) to \(316\times\) for the UAI 2014 Promedus benchmark problems compared to the reference solvers. The ideas and methods presented in our study are examined within the framework of exact inference for discrete random variables. However, they are effectively applicable to scenarios involving continuous variables.- 13 December 2024
- Published by Association for Computing Machinery (ACM) in ACM Transactions on Probabilistic Machine Learning
- Vol. 1 (1) , 1-28
Open AccessOn the Importance of the Execution Schedule for Bayesian Inference
Bayesian inference is a probabilistic approach to the problem of drawing conclusions from observed data. Its main challenge is computational, which the Bayesian community tends to address through approximation techniques. However, these techniques come with their own set of challenges, including approximation errors, the difficulty of assessing these errors, and the inherited NP-hardness of the inference problem. Concurrently, in an effort to keep up with Moore’s law, the computer engineering community has developed an increasing number of programming techniques for today’s heterogeneous hardware. These techniques aim to optimize the execution schedule , which refers to the order and mapping of computations on the available execution units. In this work, we advocate for the utilization of these techniques to avoid a common pitfall known as premature approximation . Notably, these techniques have the potential to significantly enhance performance, thereby reducing the need for approximation and thus mitigating the challenges that accompany it. We first demonstrate how optimization of the storage strategy, i.e., when and where intermediate results are stored, allows for a trade-off between runtime and peak memory usage . We then investigate various techniques that aim to automatically generate efficient execution schedules. Finally, we focus on a specific, runtime-efficient execution schedule identified through design space exploration and compare its performance with that of two established solvers for probabilistic inference. The results show that our optimized implementation achieves speedups ranging from \(2\times\) to \(316\times\) for the UAI 2014 Promedus benchmark problems compared to the reference solvers. The ideas and methods presented in our study are examined within the framework of exact inference for discrete random variables. However, they are effectively applicable to scenarios involving continuous variables. - Open Access
GraphPPL.jl: A Probabilistic Programming Language for Graphical Models
This paper presents GraphPPL.jl, a novel probabilistic programming language designed for graphical models. GraphPPL.jl uniquely represents probabilistic models as factor graphs. A notable feature of GraphPPL.jl is its model nesting capability, which facilitates the creation of modular graphical models and significantly simplifies the development of large (hierarchical) graphical models. Furthermore, GraphPPL.jl offers a plugin system to incorporate inference-specific information into the graph, allowing integration with various well-known inference engines. To demonstrate this, GraphPPL.jl includes a flexible plugin to define a Constrained Bethe Free Energy minimization process, also known as variational inference. In particular, the Constrained Bethe Free Energy defined by GraphPPL.jl serves as a potential inference framework for numerous well-known inference backends, making it a versatile tool for diverse applications. This paper details the design and implementation of GraphPPL.jl, highlighting its power, expressiveness, and user-friendliness. It also emphasizes the clear separation between model definition and inference while providing developers with extensibility and customization options. This establishes GraphPPL.jl as a high-level user interface language that allows users to create complex graphical models without being burdened with the complexity of inference while allowing backend developers to easily adopt GraphPPL.jl as their frontend language.
Open AccessGraphPPL.jl: A Probabilistic Programming Language for Graphical Models
This paper presents GraphPPL.jl, a novel probabilistic programming language designed for graphical models. GraphPPL.jl uniquely represents probabilistic models as factor graphs. A notable feature of GraphPPL.jl is its model nesting capability, which facilitates the creation of modular graphical models and significantly simplifies the development of large (hierarchical) graphical models. Furthermore, GraphPPL.jl offers a plugin system to incorporate inference-specific information into the graph, allowing integration with various well-known inference engines. To demonstrate this, GraphPPL.jl includes a flexible plugin to define a Constrained Bethe Free Energy minimization process, also known as variational inference. In particular, the Constrained Bethe Free Energy defined by GraphPPL.jl serves as a potential inference framework for numerous well-known inference backends, making it a versatile tool for diverse applications. This paper details the design and implementation of GraphPPL.jl, highlighting its power, expressiveness, and user-friendliness. It also emphasizes the clear separation between model definition and inference while providing developers with extensibility and customization options. This establishes GraphPPL.jl as a high-level user interface language that allows users to create complex graphical models without being burdened with the complexity of inference while allowing backend developers to easily adopt GraphPPL.jl as their frontend language.
- Open Access
Reactive Environments for Active Inference Agents with RxEnvironments.jl
Active Inference is a framework that emphasizes the interaction between agents and their environment. While the framework has seen significant advancements in the development of agents, the environmental models are often borrowed from reinforcement learning problems, which may not fully capture the complexity of multi-agent interactions or allow complex, conditional communication. This paper introduces Reactive Environments, a comprehensive paradigm that facilitates complex multi-agent communication. In this paradigm, both agents and environments are defined as entities encapsulated by boundaries with interfaces. This setup facilitates a robust framework for communication in nonequilibrium-Steady-State systems, allowing for complex interactions and information exchange. We present a Julia package RxEnvironments.jl, which is a specific implementation of Reactive Environments, where we utilize a Reactive Programming style for efficient implementation. The flexibility of this paradigm is demonstrated through its application to several complex, multi-agent environments. These case studies highlight the potential of Reactive Environments in modeling sophisticated systems of interacting agents.
Open AccessReactive Environments for Active Inference Agents with RxEnvironments.jl
Active Inference is a framework that emphasizes the interaction between agents and their environment. While the framework has seen significant advancements in the development of agents, the environmental models are often borrowed from reinforcement learning problems, which may not fully capture the complexity of multi-agent interactions or allow complex, conditional communication. This paper introduces Reactive Environments, a comprehensive paradigm that facilitates complex multi-agent communication. In this paradigm, both agents and environments are defined as entities encapsulated by boundaries with interfaces. This setup facilitates a robust framework for communication in nonequilibrium-Steady-State systems, allowing for complex interactions and information exchange. We present a Julia package RxEnvironments.jl, which is a specific implementation of Reactive Environments, where we utilize a Reactive Programming style for efficient implementation. The flexibility of this paradigm is demonstrated through its application to several complex, multi-agent environments. These case studies highlight the potential of Reactive Environments in modeling sophisticated systems of interacting agents.
- Open Access
- 29 November 2023
- Published by Institute of Electrical and Electronics Engineers (IEEE) in IEEE Open Journal of Signal Processing
- Vol. PP, 1-9
Principled Pruning of Bayesian Neural Networks through Variational Free Energy Minimization
Bayesian model reduction provides an efficient approach for comparing the performance of all nested sub-models of a model, without re-evaluating any of these sub-models. Until now, Bayesian model reduction has been applied mainly in the computational neuroscience community on simple models. In this paper, we formulate and apply Bayesian model reduction to perform principled pruning of Bayesian neural networks, based on variational free energy minimization. Direct application of Bayesian model reduction, however, gives rise to approximation errors. Therefore, a novel iterative pruning algorithm is presented to alleviate the problems arising with naive Bayesian model reduction, as supported experimentally on the publicly available UCI datasets for different inference algorithms. This novel parameter pruning scheme solves the shortcomings of current state-of-the-art pruning methods that are used by the signal processing community. The proposed approach has a clear stopping criterion and minimizes the same objective that is used during training. Next to these benefits, our experiments indicate better model performance in comparison to state-of-the-art pruning schemes.
- 29 November 2023
- Published by Institute of Electrical and Electronics Engineers (IEEE) in IEEE Open Journal of Signal Processing
- Vol. PP, 1-9
Open AccessPrincipled Pruning of Bayesian Neural Networks through Variational Free Energy Minimization
Bayesian model reduction provides an efficient approach for comparing the performance of all nested sub-models of a model, without re-evaluating any of these sub-models. Until now, Bayesian model reduction has been applied mainly in the computational neuroscience community on simple models. In this paper, we formulate and apply Bayesian model reduction to perform principled pruning of Bayesian neural networks, based on variational free energy minimization. Direct application of Bayesian model reduction, however, gives rise to approximation errors. Therefore, a novel iterative pruning algorithm is presented to alleviate the problems arising with naive Bayesian model reduction, as supported experimentally on the publicly available UCI datasets for different inference algorithms. This novel parameter pruning scheme solves the shortcomings of current state-of-the-art pruning methods that are used by the signal processing community. The proposed approach has a clear stopping criterion and minimizes the same objective that is used during training. Next to these benefits, our experiments indicate better model performance in comparison to state-of-the-art pruning schemes.