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Vlado Menkovski

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7 papers
2 author rows

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7

ICML Conference 2025 Conference Paper

Deep Neural Cellular Potts Models

  • Koen Minartz
  • Tim D'Hondt
  • Leon Hillmann
  • Jörn Starruß
  • Lutz Brusch
  • Vlado Menkovski

The cellular Potts model (CPM) is a powerful computational method for simulating collective spatiotemporal dynamics of biological cells. To drive the dynamics, CPMs rely on physics-inspired Hamiltonians. However, as first principles remain elusive in biology, these Hamiltonians only approximate the full complexity of real multicellular systems. To address this limitation, we propose NeuralCPM, a more expressive cellular Potts model that can be trained directly on observational data. At the core of NeuralCPM lies the Neural Hamiltonian, a neural network architecture that respects universal symmetries in collective cellular dynamics. Moreover, this approach enables seamless integration of domain knowledge by combining known biological mechanisms and the expressive Neural Hamiltonian into a hybrid model. Our evaluation with synthetic and real-world multicellular systems demonstrates that NeuralCPM is able to model cellular dynamics that cannot be accounted for by traditional analytical Hamiltonians.

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NeurIPS Conference 2023 Conference Paper

Dynamic Sparsity Is Channel-Level Sparsity Learner

  • Lu Yin
  • Gen Li
  • Meng Fang
  • Li Shen
  • Tianjin Huang
  • Zhangyang "Atlas" Wang
  • Vlado Menkovski
  • Xiaolong Ma

Sparse training has received an upsurging interest in machine learning due to its tantalizing saving potential for both the entire training process as well as the inference. Dynamic sparse training (DST) as a leading approach can train deep neural networks at high sparsity from scratch to match the performance of their dense counterparts. However, most if not all DST prior arts demonstrate their effectiveness on unstructured sparsity with highly irregular sparse patterns, which receives limited support in common hardware. This limitation hinders the usage of DST in practice. In this paper, we propose Channel-aware dynamic sparse (Chase), that for the first time seamlessly translates the promise of unstructured dynamic sparsity to GPU-friendly channel-level sparsity (not fine-grained N: M or group sparsity) during one end-to-end training process, without any ad-hoc operations. The resulting small sparse networks can be directly accelerated by commodity hardware, without using any particularly sparsity-aware hardware accelerators. This appealing outcome is partially motivated by a hidden phenomenon of dynamic sparsity: off-the-shelf unstructured DST implicitly involves biased parameter reallocation across channels, with a large fraction of channels (up to 60%) being sparser than others. By progressively identifying and removing these channels during training, our approach transfers unstructured sparsity to channel-wise sparsity. Our experimental results demonstrate that Chase achieves 1. 7x inference throughput speedup on common GPU devices without compromising accuracy with ResNet-50 on ImageNet. We release our code in https: //github. com/luuyin/chase.

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NeurIPS Conference 2023 Conference Paper

Equivariant Neural Simulators for Stochastic Spatiotemporal Dynamics

  • Koen Minartz
  • Yoeri Poels
  • Simon Koop
  • Vlado Menkovski

Neural networks are emerging as a tool for scalable data-driven simulation of high-dimensional dynamical systems, especially in settings where numerical methods are infeasible or computationally expensive. Notably, it has been shown that incorporating domain symmetries in deterministic neural simulators can substantially improve their accuracy, sample efficiency, and parameter efficiency. However, to incorporate symmetries in probabilistic neural simulators that can simulate stochastic phenomena, we need a model that produces equivariant distributions over trajectories, rather than equivariant function approximations. In this paper, we propose Equivariant Probabilistic Neural Simulation (EPNS), a framework for autoregressive probabilistic modeling of equivariant distributions over system evolutions. We use EPNS to design models for a stochastic n-body system and stochastic cellular dynamics. Our results show that EPNS considerably outperforms existing neural network-based methods for probabilistic simulation. More specifically, we demonstrate that incorporating equivariance in EPNS improves simulation quality, data efficiency, rollout stability, and uncertainty quantification. We conclude that EPNS is a promising method for efficient and effective data-driven probabilistic simulation in a diverse range of domains.

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AAAI Conference 2023 Conference Paper

Lottery Pools: Winning More by Interpolating Tickets without Increasing Training or Inference Cost

  • Lu Yin
  • Shiwei Liu
  • Meng Fang
  • Tianjin Huang
  • Vlado Menkovski
  • Mykola Pechenizkiy

Lottery tickets (LTs) is able to discover accurate and sparse subnetworks that could be trained in isolation to match the performance of dense networks. Ensemble, in parallel, is one of the oldest time-proven tricks in machine learning to improve performance by combining the output of multiple independent models. However, the benefits of ensemble in the context of LTs will be diluted since ensemble does not directly lead to stronger sparse subnetworks, but leverages their predictions for a better decision. In this work, we first observe that directly averaging the weights of the adjacent learned subnetworks significantly boosts the performance of LTs. Encouraged by this observation, we further propose an alternative way to perform an "ensemble'' over the subnetworks identified by iterative magnitude pruning via a simple interpolating strategy. We call our method Lottery Pools. In contrast to the naive ensemble which brings no performance gains to each single subnetwork, Lottery Pools yields much stronger sparse subnetworks than the original LTs without requiring any extra training or inference cost. Across various modern architectures on CIFAR-10/100 and ImageNet, we show that our method achieves significant performance gains in both, in-distribution and out-of-distribution scenarios. Impressively, evaluated with VGG-16 and ResNet-18, the produced sparse subnetworks outperform the original LTs by up to 1.88% on CIFAR-100 and 2.36% on CIFAR-100-C; the resulting dense network surpasses the pre-trained dense-model up to 2.22% on CIFAR-100 and 2.38% on CIFAR-100-C. Our source code can be found at https://github.com/luuyin/Lottery-pools.

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ICML Conference 2022 Conference Paper

Quantifying and Learning Linear Symmetry-Based Disentanglement

  • Loek Tonnaer
  • Luis Armando Pérez Rey
  • Vlado Menkovski
  • Mike Holenderski
  • Jim Portegies

The definition of Linear Symmetry-Based Disentanglement (LSBD) formalizes the notion of linearly disentangled representations, but there is currently no metric to quantify LSBD. Such a metric is crucial to evaluate LSBD methods and to compare them to previous understandings of disentanglement. We propose D_LSBD, a mathematically sound metric to quantify LSBD, and provide a practical implementation for SO(2) groups. Furthermore, from this metric we derive LSBD-VAE, a semi-supervised method to learn LSBD representations. We demonstrate the utility of our metric by showing that (1) common VAE-based disentanglement methods don’t learn LSBD representations, (2) LSBD-VAE, as well as other recent methods, can learn LSBD representations needing only limited supervision on transformations, and (3) various desirable properties expressed by existing disentanglement metrics are also achieved by LSBD representations.

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UAI Conference 2022 Conference Paper

Superposing many tickets into one: A performance booster for sparse neural network training

  • Lu Yin 0006
  • Vlado Menkovski
  • Meng Fang
  • Tianjin Huang
  • Yulong Pei
  • Mykola Pechenizkiy

Recent works on sparse neural network training have shown that a compelling trade-off between performance and efficiency can be achieved. Existing sparse training methods usually strive to find the best sparse subnetwork possible in one single run, without involving any expensive dense or pre-training steps. For instance, dynamic sparse training (DST), as one of the most prominent directions, is capable of reaching a competitive performance of dense training by iteratively evolving the sparse topology during the course of training. In this paper, we argue that it is better to allocate the limited resources to create multiple low-loss sparse subnetworks and superpose them into a stronger one, instead of allocating all resources entirely to find an individual subnetwork. To achieve this, two desiderata are required: (1) efficiently producing many low-loss subnetworks, the so-called cheap tickets, within one training process limited to the standard training time used in dense training; (2) effectively superposing these cheap tickets into one stronger subnetwork without going over the constrained parameter budget. To corroborate our conjecture, we present a novel sparse training approach, termed \textbf{Sup-tickets}, which can satisfy the above two desiderata concurrently in a single sparse-to-sparse training process. Across various models on CIFAR-10/100 and ImageNet, we show that Sup-tickets integrates seamlessly with the existing sparse training methods and demonstrates consistent performance improvement.

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IJCAI Conference 2020 Conference Paper

Diffusion Variational Autoencoders

  • Luis A. Perez Rey
  • Vlado Menkovski
  • Jim Portegies

A standard Variational Autoencoder, with a Euclidean latent space, is structurally incapable of capturing topological properties of certain datasets. To remove topological obstructions, we introduce Diffusion Variational Autoencoders (DeltaVAE) with arbitrary (closed) manifolds as a latent space. A Diffusion Variational Autoencoder uses transition kernels of Brownian motion on the manifold. In particular, it uses properties of the Brownian motion to implement the reparametrization trick and fast approximations to the KL divergence. We show that the DeltaVAE is indeed capable of capturing topological properties for datasets with a known underlying latent structure derived from generative processes such as rotations and translations.

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v2026.09.13