arXiv subjects

Vlado Menkovski

Publications and source records attributed to Vlado Menkovski.

At least 19 recordsLinked to original sources

arXiv2026

A Dataset of Equilibrium State Configurations of Adsorption in Zeolites

Zeolites are crystalline nanoporous materials widely used in adsorption, separation, and catalytic processes. Molecular simulations are commonly used to predict adsorption properties, but most high-throughput adsorption datasets report only ensemble-averaged quantities such as loadings or isotherms, rather than the molecular configurations from which these averages are obtained. Here, we present AdsZeo, a coordinate-resolved dataset of equilibrium methane adsorption configurations in aluminium-substituted, sodium-containing zeolite frameworks. The processed release contains 4,775 framework realisations derived from 191 zeolite topologies. Each framework realisation was simulated at 13 methane pressures between 0.1 and 100 bar at 298 K using grand canonical Monte Carlo simulations, giving 62,075 production simulations in total. In addition to scalar adsorption records, the dataset stores production-frame methane pseudo-atom coordinates, mobile Na$^+$ cation coordinates, framework atomic coordinates, per-frame loading and energy statistics, and simulation metadata in a processed DuckDB database. The release contains 12,415,000 saved production-frame records and 1,245,376,215 saved particle-coordinate records. AdsZeo provides coordinate-resolved adsorption data across variations in framework topology, aluminium content and distribution, sodium cation arrangement, pressure, and methane loading, enabling reuse for adsorption analysis, spatial statistics, density estimation, and machine-learning models for molecular configuration generation in charged zeolite pores.

cond-mat.mtrl-sci↗

arXiv2026

BubbleSH: A Dataset of Rising Bubbles with Deformable Interfaces

Bubbly flows exhibit complex multiscale dynamics, with deformable bubbles interacting through the surrounding liquid and giving rise to strongly coupled kinematic and morphological behavior. We present BubbleSH, a bubbly flows dataset consisting of transient, three-dimensional bubble-swarm dynamics obtained from high-fidelity direct numerical simulations of bubbles rising in a periodic domain. The dataset provides time-resolved bubble trajectories, velocities, and shape evolution, with bubble morphology compactly represented using spherical harmonics. Designed to be lightweight yet physically expressive, the dataset enables data-driven modeling of bubbly flow simulators where shape deformation and bubble-bubble interactions play a central role. We characterize the dataset with bubble kinematics, morphology, and interaction patterns, and introduce evaluation metrics for both trajectory and shape prediction. The sensitivity of bubble-swarm dynamics to local perturbations makes BubbleSH particularly well suited to generative models that learn distributions over possible future trajectories. We evaluate a permutationally and translationally equivariant probabilistic emulator on BubbleSH given the proposed metrics. Therefore, we establish a compact, high-fidelity dataset and a benchmark for developing and evaluating data-driven models of deformable, chaotic multiphase systems.

cs.LG↗

arXiv2026

LOREN: Low Rank-Based Code-Rate Adaptation in Neural Receivers

Neural network based receivers have recently demonstrated superior system-level performance compared to traditional receivers. However, their practicality is limited by high memory and power requirements, as separate weight sets must be stored for each code rate. To address this challenge, we propose LOREN, a Low Rank-Based Code-Rate Adaptation Neural Receiver that achieves adaptability with minimal overhead. LOREN integrates lightweight low rank adaptation adapters (LOREN adapters) into convolutional layers, freezing a shared base network while training only small adapters per code rate. An end-to-end training framework over 3GPP CDL channels ensures robustness across realistic wireless environments. LOREN achieves comparable or superior performance relative to fully retrained base neural receivers. The hardware implementation of LOREN in 22nm technology shows more than 65% savings in silicon area and up to 15% power reduction when supporting three code rates.

cs.LG↗

arXiv2025

Towards Fully Automated Molecular Simulations: Multi-Agent Framework for Simulation Setup and Force Field Extraction

Automated characterization of porous materials has the potential to accelerate materials discovery, but it remains limited by the complexity of simulation setup and force field selection. We propose a multi-agent framework in which LLM-based agents can autonomously understand a characterization task, plan appropriate simulations, assemble relevant force fields, execute them and interpret their results to guide subsequent steps. As a first step toward this vision, we present a multi-agent system for literature-informed force field extraction and automated RASPA simulation setup. Initial evaluations demonstrate high correctness and reproducibility, highlighting this approach's potential to enable fully autonomous, scalable materials characterization.

cs.AI↗

arXiv2025

Equivariant Flow Matching for Symmetry-Breaking Bifurcation Problems

Bifurcation phenomena in nonlinear dynamical systems often lead to multiple coexisting stable solutions, particularly in the presence of symmetry breaking. Deterministic machine learning models are unable to capture this multiplicity, averaging over solutions and failing to represent lower-symmetry outcomes. In this work, we formalize the use of generative AI, specifically flow matching, as a principled way to model the full probability distribution over bifurcation outcomes. Our approach builds on existing techniques by combining flow matching with equivariant architectures and an optimal-transport-based coupling mechanism. We generalize equivariant flow matching to a symmetric coupling strategy that aligns predicted and target outputs under group actions, allowing accurate learning in equivariant settings. We validate our approach on a range of systems, from simple conceptual systems to physical problems such as buckling beams and the Allen--Cahn equation. The results demonstrate that the approach accurately captures multimodal distributions and symmetry-breaking bifurcations. Moreover, our results demonstrate that flow matching significantly outperforms non-probabilistic and variational methods. This offers a principled and scalable solution for modeling multistability in high-dimensional systems.

cs.LG↗

arXiv2025

Score Matching on Large Geometric Graphs for Cosmology Generation

Generative models are a promising tool to produce cosmological simulations but face significant challenges in scalability, physical consistency, and adherence to domain symmetries, limiting their utility as alternatives to $N$-body simulations. To address these limitations, we introduce a score-based generative model with an equivariant graph neural network that simulates gravitational clustering of galaxies across cosmologies starting from an informed prior, respects periodic boundaries, and scales to full galaxy counts in simulations. A novel topology-aware noise schedule, crucial for large geometric graphs, is introduced. The proposed equivariant score-based model successfully generates full-scale cosmological point clouds of up to 600,000 halos, respects periodicity and a uniform prior, and outperforms existing diffusion models in capturing clustering statistics while offering significant computational advantages. This work advances cosmology by introducing a generative model designed to closely resemble the underlying gravitational clustering of structure formation, moving closer to physically realistic and efficient simulators for the evolution of large-scale structures in the universe.

astro-ph.CO↗

arXiv2025

Wallpaper Group-Based Mechanical Metamaterials: Dataset Including Mechanical Responses

Mechanical metamaterials often exhibit pattern transformations through instabilities, enabling applications in, e.g., soft robotics, sound reduction, and biomedicine. These transformations and their resulting mechanical properties are closely tied to the symmetries in these metamaterials' microstructures, which remain under-explored. Designing such materials is challenging due to the unbounded design space, and while machine learning offers promising tools, they require extensive training data. Here, we present a large dataset of 2D microstructures and their macroscopic mechanical responses in the hyperelastic, finite-strain regime, including buckling. The microstructures are generated using a novel method, which covers all 17 wallpaper symmetry groups and employs B\'ezier curves for a rich parametric space. Mechanical responses are obtained through finite element-based computational homogenization. The dataset includes 1,020 distinct geometries, each subjected to 12 loading trajectories, totaling 12,240 trajectories. Our dataset supports the development and benchmarking of surrogate models, facilitates the study of symmetry-property relationships, and enables investigations into symmetry-breaking during pattern transformations, potentially revealing emergent behavior in mechanical metamaterials.

cond-mat.soft↗

arXiv2025

STFlow: Data-Coupled Flow Matching for Geometric Trajectory Simulation

Simulating trajectories of dynamical systems is a fundamental problem in a wide range of fields such as molecular dynamics, biochemistry, and pedestrian dynamics. Machine learning has become an invaluable tool for scaling physics-based simulators and developing models directly from experimental data. In particular, recent advances in deep generative modeling and geometric deep learning enable probabilistic simulation by learning complex trajectory distributions while respecting intrinsic permutation and time-shift symmetries. However, trajectories of N-body systems are commonly characterized by high sensitivity to perturbations leading to bifurcations, as well as multi-scale temporal and spatial correlations. To address these challenges, we introduce STFlow (Spatio-Temporal Flow), a generative model based on graph neural networks and hierarchical convolutions. By incorporating data-dependent couplings within the Flow Matching framework, STFlow denoises starting from conditioned random-walks instead of Gaussian noise. This novel informed prior simplifies the learning task by reducing transport cost, increasing training and inference efficiency. We validate our approach on N-body systems, molecular dynamics, and human trajectory forecasting. Across these benchmarks, STFlow achieves the lowest prediction errors with fewer simulation steps and improved scalability.

cs.LG↗

arXiv2025

Plasma State Monitoring and Disruption Characterization using Multimodal VAEs

When a plasma disrupts in a tokamak, significant heat and electromagnetic loads are deposited onto the surrounding device components. These forces scale with plasma current and magnetic field strength, making disruptions one of the key challenges for future devices. Unfortunately, disruptions are not fully understood, with many different underlying causes that are difficult to anticipate. Data-driven models have shown success in predicting them, but they only provide limited interpretability. On the other hand, large-scale statistical analyses have been a great asset to understanding disruptive patterns. In this paper, we leverage data-driven methods to find an interpretable representation of the plasma state for disruption characterization. Specifically, we use a latent variable model to represent diagnostic measurements as a low-dimensional, latent representation. We build upon the Variational Autoencoder (VAE) framework, and extend it for (1) continuous projections of plasma trajectories; (2) a multimodal structure to separate operating regimes; and (3) separation with respect to disruptive regimes. Subsequently, we can identify continuous indicators for the disruption rate and the disruptivity based on statistical properties of measurement data. The proposed method is demonstrated using a dataset of approximately 1600 TCV discharges, selecting for flat-top disruptions or regular terminations. We evaluate the method with respect to (1) the identified disruption risk and its correlation with other plasma properties; (2) the ability to distinguish different types of disruptions; and (3) downstream analyses. For the latter, we conduct a demonstrative study on identifying parameters connected to disruptions using counterfactual-like analysis. Overall, the method can adequately identify distinct operating regimes characterized by varying proximity to disruptions in an interpretable manner.

physics.plasm-ph↗

arXiv2025

Symmetry-Informed Graph Neural Networks for Carbon Dioxide Isotherm and Adsorption Prediction in Aluminum-Substituted Zeolites

Accurately predicting adsorption properties in nanoporous materials using Deep Learning models remains a challenging task. This challenge becomes even more pronounced when attempting to generalize to structures that were not part of the training data.. In this work, we introduce SymGNN, a graph neural network architecture that leverages material symmetries to improve adsorption property prediction. By incorporating symmetry operations into the message-passing mechanism, our model enhances parameter sharing across different zeolite topologies, leading to improved generalization. We evaluate SymGNN on both interpolation and generalization tasks, demonstrating that it successfully captures key adsorption trends, including the influence of both the framework and aluminium distribution on CO$_2$ adsorption. Furthermore, we apply our model to the characterization of experimental adsorption isotherms, using a genetic algorithm to infer likely aluminium distributions. Our results highlight the effectiveness of machine learning models trained on simulations for studying real materials and suggest promising directions for fine-tuning with experimental data and generative approaches for the inverse design of multifunctional nanomaterials.

cond-mat.mtrl-sci↗

arXiv2025

Robust Confinement State Classification with Uncertainty Quantification through Ensembled Data-Driven Methods

Maximizing fusion performance in tokamaks relies on high energy confinement, often achieved through distinct operating regimes. The automated labeling of these confinement states is crucial to enable large-scale analyses or for real-time control applications. While this task becomes difficult to automate near state transitions or in marginal scenarios, much success has been achieved with data-driven models. However, these methods generally provide predictions as point estimates, and cannot adequately deal with missing and/or broken input signals. To enable wide-range applicability, we develop methods for confinement state classification with uncertainty quantification and model robustness. We focus on off-line analysis for TCV discharges, distinguishing L-mode, H-mode, and an in-between dithering phase (D). We propose ensembling data-driven methods on two axes: model formulations and feature sets. The former considers a dynamic formulation based on a recurrent Fourier Neural Operator-architecture and a static formulation based on gradient-boosted decision trees. These models are trained using multiple feature groupings categorized by diagnostic system or physical quantity. A dataset of 302 TCV discharges is fully labeled, and will be publicly released. We evaluate our method quantitatively using Cohen's kappa coefficient for predictive performance and the Expected Calibration Error for the uncertainty calibration. Furthermore, we discuss performance using a variety of common and alternative scenarios, the performance of individual components, out-of-distribution performance, cases of broken or missing signals, and evaluate conditionally-averaged behavior around different state transitions. Overall, the proposed method can distinguish L, D and H-mode with high performance, can cope with missing or broken signals, and provides meaningful uncertainty estimates.

physics.plasm-ph↗

arXiv2025

Deep Neural Cellular Potts Models

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.

cs.LG↗

arXiv2024

Aspect-Based Few-Shot Learning

We generalize the formulation of few-shot learning by introducing the concept of an aspect. In the traditional formulation of few-shot learning, there is an underlying assumption that a single "true" label defines the content of each data point. This label serves as a basis for the comparison between the query object and the objects in the support set. However, when a human expert is asked to execute the same task without a predefined set of labels, they typically consider the rest of the data points in the support set as context. This context specifies the level of abstraction and the aspect from which the comparison can be made. In this work, we introduce a novel architecture and training procedure that develops a context given the query and support set and implements aspect-based few-shot learning that is not limited to a predetermined set of classes. We demonstrate that our method is capable of forming and using an aspect for few-shot learning on the Geometric Shapes and Sprites dataset. The results validate the feasibility of our approach compared to traditional few-shot learning.

cs.CV↗

arXiv2024

Understanding complex crowd dynamics with generative neural simulators

Understanding the dynamics of pedestrian crowds is an outstanding challenge crucial for designing efficient urban infrastructure and ensuring safe crowd management. To this end, both small-scale laboratory and large-scale real-world measurements have been used. However, these approaches respectively lack statistical resolution and parametric controllability, both essential to discovering physical relationships underlying the complex stochastic dynamics of crowds. Here, we establish an investigation paradigm that offers laboratory-like controllability, while ensuring the statistical resolution of large-scale real-world datasets. Using our data-driven Neural Crowd Simulator (NeCS), which we train on large-scale data and validate against key statistical features of crowd dynamics, we show that we can perform effective surrogate crowd dynamics experiments without training on specific scenarios. We not only reproduce known experimental results on pairwise avoidance, but also uncover the vision-guided and topological nature of N-body interactions. These findings show how virtual experiments based on neural simulation enable data-driven scientific discovery.

physics.soc-ph↗

arXiv2024

Equivariant Neural Simulators for Stochastic Spatiotemporal Dynamics

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.

cs.LG↗

arXiv2024

Topological degree as a discrete diagnostic for disentanglement, with applications to the $Δ$VAE

We investigate the ability of Diffusion Variational Autoencoder ($Δ$VAE) with unit sphere $\mathcal{S}^2$ as latent space to capture topological and geometrical structure and disentangle latent factors in datasets. For this, we introduce a new diagnostic of disentanglement: namely the topological degree of the encoder, which is a map from the data manifold to the latent space. By using tools from homology theory, we derive and implement an algorithm that computes this degree. We use the algorithm to compute the degree of the encoder of models that result from the training procedure. Our experimental results show that the $Δ$VAE achieves relatively small LSBD scores, and that regardless of the degree after initialization, the degree of the encoder after training becomes $-1$ or $+1$, which implies that the resulting encoder is at least homotopic to a homeomorphism.

cs.LG↗

arXiv2024

Accelerating Simulation of Two-Phase Flows with Neural PDE Surrogates

Simulation is a powerful tool to better understand physical systems, but generally requires computationally expensive numerical methods. Downstream applications of such simulations can become computationally infeasible if they require many forward solves, for example in the case of inverse design with many degrees of freedom. In this work, we investigate and extend neural PDE solvers as a tool to aid in scaling simulations for two-phase flow problems, and simulations of oil expulsion from a pore specifically. We extend existing numerical methods for this problem to a more complex setting involving varying geometries of the domain to generate a challenging dataset. Further, we investigate three prominent neural PDE solver methods, namely the UNet, DRN, and U-FNO, and extend them for characteristics of the oil-expulsion problem: (1) spatial conditioning on the geometry; (2) periodicity in the boundary; (3) approximate mass conservation. We scale all methods and benchmark their speed-accuracy trade-off, evaluate qualitative properties, and perform an ablation study. We find that the investigated methods can accurately model the droplet dynamics with up to three orders of magnitude speed-up, that our extensions improve performance over the baselines, and that the introduced varying geometries constitute a significantly more challenging setting over the previously considered oil expulsion problem.

cs.LG↗

arXiv2024

VADA: a Data-Driven Simulator for Nanopore Sequencing

Nanopore sequencing offers the ability for real-time analysis of long DNA sequences at a low cost, enabling new applications such as early detection of cancer. Due to the complex nature of nanopore measurements and the high cost of obtaining ground truth datasets, there is a need for nanopore simulators. Existing simulators rely on handcrafted rules and parameters and do not learn an internal representation that would allow for analysing underlying biological factors of interest. Instead, we propose VADA, a purely data-driven method for simulating nanopores based on an autoregressive latent variable model. We embed subsequences of DNA and introduce a conditional prior to address the challenge of a collapsing conditioning. We introduce an auxiliary regressor on the latent variable to encourage our model to learn an informative latent representation. We empirically demonstrate that our model achieves competitive simulation performance on experimental nanopore data. Moreover, we show we have learned an informative latent representation that is predictive of the DNA labels. We hypothesize that other biological factors of interest, beyond the DNA labels, can potentially be extracted from such a learned latent representation.

q-bio.QM↗