arXiv subjects

Tejs Vegge

Publications and source records attributed to Tejs Vegge.

At least 19 recordsLinked to original sources

arXiv2026

How Molecular Generative Models Organize Molecular Identity

Generative models for matter are often evaluated as samplers over output representations, and their latent spaces are commonly used as proxies for navigating chemical space. Much less is known about how these models internally arrange discrete chemical identities within those representations. We study this arrangement by making molecular identity explicit and pulling it back through the generative process. Through these pullbacks we probe the regions that generate the same object, exposing the trained model's internal repertoire: a fixed partition that determines which objects (novel or not) the model can produce. Across three molecular generative architectures, we find that this repertoire is arranged into piecewise-constant regions separated by recurring coarse-to-fine boundaries. Its organization depends on the representation probed, the identity convention, decoder stochasticity, and the metric used to compare coordinates. During training, local chemical organization stabilizes while the number of distinct molecular identities represented within each neighborhood continues to change. Internal organization must therefore be characterized, rather than assumed, before a generative space can be treated as chemically navigable.

cs.LG↗

arXiv2026

AtomComposer: Discovering Chemical Space from First Principles with Reinforcement Learning

Discovering novel stable molecules without training data remains a grand scientific challenge. Current molecular generative models are trained on large, pre-curated datasets, which introduce biases and limit exploration of novel chemistry. In contrast, we propose a new paradigm: autonomous, generalized agents capable of mapping vast, unknown chemical spaces without any pretraining. For the first time, we present AtomComposer, a self-guided agent that autonomously constructs valid 3D isomers under stoichiometric constraints and is trained exclusively online using reinforcement learning. Unlike existing approaches that generally overfit to a specific chemical formula, we establish a multi-composition training scheme that enables a broad generalization across diverse chemistry, guided by energy- and validity-based rewards. Our agent can discover up to an order of magnitude more valid isomers on unseen test formulas than existing single-composition reinforcement-learning baselines trained with per-step energy rewards. These results fulfill the promise of online reinforcement learning as a powerful paradigm for scalable, from-scratch exploration of chemical configuration space.

cs.LG↗

arXiv2026

A large scale multi-modal workflow for battery characterization: from concept to implementation

The development of material acceleration platforms in battery research requires integrating complementary techniques and correlating heterogeneous experimental datasets. Here, this challenge is tackled in a large-scale multimodal program involving fifteen laboratories and facilities across Europe. Coordinated multi-site experiments are performed on state-of-the-art graphite / LiNiO2 Li-ion full cells to address two archetypal scientific questions: is the electrolyte composition impacting electrode properties, and how do electrode materials evolve when cells are cycled to their end-of-life? A fully standardized and centralized workflow is demonstrated, from sample production and delivery, to metadata and data handling, generating seventy-five concatenated datasets shared among all partners. Their integrated analysis shows that scientific conclusions depend critically on both the observable chosen to describe electrode properties, and the measurement technique employed. Individual experiments provide detailed information into specific aspects, such as crystal structures, redox activity, surface processes, morphology, etc., but can also function as binary diagnostic tool. Two-dimensional observable-technique patterns are introduced, in which each pixel encodes a yes, no or uncertain answer to a given scientific question. These patterns serve as multi-property metaviews, e.g. visual genotypes, enabling to classify material behavior and technique suitability according to predefined user demand and criteria, highlighting the interdependencies between measurement choices, extracted parameters and scientific interpretation. This multimodal workflow establishes a proof-of-concept for correlative analysis and underscores challenges toward fully integrated, automated and holistic approaches in energy material science.

physics.app-ph↗

arXiv2026

Global Plane Waves From Local Gaussians: Periodic Charge Densities in a Blink

We introduce ELECTRAFI, a fast, end-to-end differentiable model for predicting periodic charge densities in crystalline materials. ELECTRAFI constructs anisotropic Gaussians in real space and exploits their closed-form Fourier transforms to analytically evaluate plane-wave coefficients via the Poisson summation formula. This formulation delegates non-local and periodic behavior to analytic transforms, enabling reconstruction of the full periodic charge density with a single inverse FFT. By avoiding explicit real-space grid probing, periodic image summation, and spherical harmonic expansions, ELECTRAFI matches or exceeds state-of-the-art accuracy across periodic benchmarks while being up to $633 \times$ faster than the strongest competing method, reconstructing crystal charge densities in a fraction of a second. When used to initialize DFT calculations, ELECTRAFI reduces total DFT compute cost by up to ~20%, whereas slower charge density models negate savings due to high inference times. Our results show that accuracy and inference cost jointly determine end-to-end DFT speedups, and motivate our focus on efficiency.

cond-mat.mtrl-sci↗

arXiv2025

Implementing a Scalable, Redeployable and Multitiered Repository for FAIR and Secure Scientific Data Sharing: The BIG-MAP Archive

Data sharing in large consortia, such as research collaborations or industry partnerships, requires addressing both organizational and technical challenges. A common platform is essential to promote collaboration, facilitate exchange of findings, and ensure secure access to sensitive data. Key technical challenges include creating a scalable architecture, a user-friendly interface, and robust security and access control. The BIG-MAP Archive is a cloud-based, disciplinary, private repository designed to address these challenges. Built on InvenioRDM, it leverages platform functionalities to meet consortium-specific needs, providing a tailored solution compared to general repositories. Access can be restricted to members of specific communities or open to the entire consortium, such as the BATTERY 2030+, a consortium accelerating advanced battery technologies. Uploaded data and metadata are controlled via fine grained permissions, allowing access to individual project members or the full initiative. The formalized upload process ensures data are formatted and ready for publication in open repositories when needed. This paper reviews the repository's key features, showing how the BIG-MAP Archive enables secure, controlled data sharing within large consortia. It ensures data confidentiality while supporting flexible, permissions-based access and can be easily redeployed for other consortia, including MaterialsCommons4.eu and RAISE (Resource for AI Science in Europe).

cs.DB↗

arXiv2025

GO-Diff: Data-free and amortized global structure optimization

We introduce GO-Diff, a diffusion-based method for global structure optimization that learns to directly sample low-energy atomic configurations without requiring prior data or explicit relaxation. GO-Diff is trained from scratch using a Boltzmann-weighted score-matching loss, leveraging only the known energy function to guide generation toward thermodynamically favorable regions. The method operates in a two-stage loop of self-sampling and model refinement, progressively improving its ability to target low-energy structures. Compared to traditional optimization pipelines, GO-Diff achieves competitive results with significantly fewer energy evaluations. Moreover, by reusing pretrained models across related systems, GO-Diff supports amortized optimization - enabling faster convergence on new tasks without retraining from scratch.

physics.comp-ph↗

arXiv2025

HIP: Hessian Interatomic Potentials without derivatives

Molecular Hessians, the second derivatives of the potential energy, are fundamental to many workflows in computational chemistry. Usually, accurate Hessians are computationally expensive to calculate and scale poorly with system size, whether computed using quantum chemistry methods or machine-learning interatomic potentials (MLIPs). In this work, we introduce Hessian interatomic potentials (HIPs), a deep learning model that directly predicts Hessians without relying on automatic differentiation or finite differences. To do so, we construct SE(3)-equivariant, symmetric Hessians from irreducible representation (irrep) features up to degree $l$=2, computed by a graph neural network. HIP Hessians are one to two orders of magnitude faster, more accurate, more memory efficient, easier to train, and exhibit more favourable scaling with system size. We validate our predictions across a wide range of downstream tasks, demonstrating consistently superior performance in transition state search, geometry optimization, zero-point energy corrections, and vibrational analysis. We open-source the HIP code and model weights.

cs.LG↗

arXiv2025

A Perspective on Quantum Computing Applications in Quantum Chemistry using 25--100 Logical Qubits

The intersection of quantum computing and quantum chemistry represents a promising frontier for achieving quantum utility in domains of both scientific and societal relevance. Owing to the exponential growth of classical resource requirements for simulating quantum systems, quantum chemistry has long been recognized as a natural candidate for quantum computation. This perspective focuses on identifying scientifically meaningful use cases where early fault-tolerant quantum computers, which are considered to be equipped with approximately 25--100 logical qubits, could deliver tangible impact. While recent advances in classical computing have pushed the boundaries of tractable simulations to unprecedented scales, this logical-qubit regime represents the first window where quantum devices can pursue qualitatively distinct strategies, such as polynomial-scaling phase estimation, direct simulation of quantum dynamics, and active-space embedding, that remain challenging for classical solvers, for instance, multireference charge-transfer and conical-intersection states central to photochemistry and materials design. We highlight near-term opportunities in algorithm and software design, discuss representative chemical problems suited for quantum acceleration, and propose strategic roadmaps and collaborative pathways for advancing practical quantum utility in quantum chemistry.

quant-ph↗

arXiv2025

Acoustic Classification of Maritime Vessels using Learnable Filterbanks

Reliably monitoring and recognizing maritime vessels based on acoustic signatures is complicated by the variability of different recording scenarios. A robust classification framework must be able to generalize across diverse acoustic environments and variable source-sensor distances. To this end, we present a deep learning model with robust performance across different recording scenarios. Using a trainable spectral front-end and temporal feature encoder to learn a Gabor filterbank, the model can dynamically emphasize different frequency components. Trained on the VTUAD hydrophone recordings from the Strait of Georgia, our model, CATFISH, achieves a state-of-the-art 96.63 % percent test accuracy across varying source-sensor distances, surpassing the previous benchmark by over 12 percentage points. We present the model, justify our architectural choices, analyze the learned Gabor filters, and perform ablation studies on sensor data fusion and attention-based pooling.

cs.SD↗

arXiv2025

Autonomous nanoparticle synthesis by design

Controlled synthesis of materials with specified atomic structures underpins technological advances yet remains reliant on iterative, trial-and-error approaches. Nanoparticles (NPs), whose atomic arrangement dictates their emergent properties, are particularly challenging to synthesise due to numerous tunable parameters. Here, we introduce an autonomous approach explicitly targeting synthesis of atomic-scale structures. Our method autonomously designs synthesis protocols by matching real time experimental total scattering (TS) and pair distribution function (PDF) data to simulated target patterns, without requiring prior synthesis knowledge. We demonstrate this capability at a synchrotron, successfully synthesising two structurally distinct gold NPs: 5 nm decahedral and 10 nm face-centred cubic structures. Ultimately, specifying a simulated target scattering pattern, thus representing a bespoke atomic structure, and obtaining both the synthesised material and its reproducible synthesis protocol on demand may revolutionise materials design. Thus, ScatterLab provides a generalisable blueprint for autonomous, atomic structure-targeted synthesis across diverse systems and applications.

cond-mat.mtrl-sci↗

arXiv2025

ELECTRA: A Cartesian Network for 3D Charge Density Prediction with Floating Orbitals

We present the Electronic Tensor Reconstruction Algorithm (ELECTRA) - an equivariant model for predicting electronic charge densities using floating orbitals. Floating orbitals are a long-standing concept in the quantum chemistry community that promises more compact and accurate representations by placing orbitals freely in space, as opposed to centering all orbitals at the position of atoms. Finding the ideal placement of these orbitals requires extensive domain knowledge, though, which thus far has prevented widespread adoption. We solve this in a data-driven manner by training a Cartesian tensor network to predict the orbital positions along with orbital coefficients. This is made possible through a symmetry-breaking mechanism that is used to learn position displacements with lower symmetry than the input molecule while preserving the rotation equivariance of the charge density itself. Inspired by recent successes of Gaussian Splatting in representing densities in space, we are using Gaussian orbitals and predicting their weights and covariance matrices. Our method achieves a state-of-the-art balance between computational efficiency and predictive accuracy on established benchmarks. Furthermore, ELECTRA is able to lower the compute time required to arrive at converged DFT solutions - initializing calculations using our predicted densities yields an average 50.72 % reduction in self-consistent field (SCF) iterations on unseen molecules.

cs.LG↗

arXiv2025

A tomographic interpretation of structure-property relations for materials discovery

Recent advancements in machine learning (ML) for materials have demonstrated that "simple" materials representations (e.g., the chemical formula alone without structural information) can sometimes achieve competitive property prediction performance in common-tasks. Our physics-based intuition would suggest that such representations are "incomplete", which indicates a gap in our understanding. This work proposes a tomographic interpretation of structure-property relations of materials to bridge that gap by defining what is a material representation, material properties, the material and the relationships between these three concepts using ideas from information theory. We verify this framework performing an exhaustive comparison of property-augmented representations on a range of material's property prediction objectives, providing insight into how different properties can encode complementary information.

cond-mat.mtrl-sci↗

arXiv2024

MolMiner: Toward Controllable, 3D-Aware, Fragment-Based Molecular Design

We introduce MolMiner, a fragment-based, geometry-aware, and order-agnostic autoregressive model for molecular design. MolMiner supports high-dimensional conditional control over twelve physicochemical and structural properties from partial specifications, constructs molecules via symmetry-aware fragment attachments, and conditions each generation step on force-field-relaxed three-dimensional geometry of the partial structure. Conditional control emerges without auxiliary property losses. On targeted property windows, conditioning lifts hit rates by up to 5.25x over unconditional generation and 3.5x over the training distribution itself -- overriding the model's intrinsic biases -- at the cost of a small reduction in unconditional distributional fidelity. MolMiner unifies dynamic geometry, symmetry handling, order-agnostic generation, and scalable multi-property conditioning within a single framework.

cs.LG↗

arXiv2023

A foundation model for atomistic materials chemistry

Atomistic simulations of matter, especially those that leverage first-principles (ab initio) electronic structure theory, provide a microscopic view of the world, underpinning much of our understanding of chemistry and materials science. Over the last decade or so, machine-learned force fields have transformed atomistic modeling by enabling simulations of ab initio quality over unprecedented time and length scales. However, early ML force fields have largely been limited by: (i) the substantial computational and human effort of developing and validating potentials for each particular system of interest; and (ii) a general lack of transferability from one chemical system to the next. Here we show that it is possible to create a general-purpose atomistic ML model, trained on a public dataset of moderate size, that is capable of running stable molecular dynamics for a wide range of molecules and materials. We demonstrate the power of the MACE-MP-0 model - and its qualitative and at times quantitative accuracy - on a diverse set of problems in the physical sciences, including properties of solids, liquids, gases, chemical reactions, interfaces and even the dynamics of a small protein. The model can be applied out of the box as a starting or "foundation" model for any atomistic system of interest and, when desired, can be fine-tuned on just a handful of application-specific data points to reach ab initio accuracy. Establishing that a stable force-field model can cover almost all materials changes atomistic modeling in a fundamental way: experienced users get reliable results much faster, and beginners face a lower barrier to entry. Foundation models thus represent a step towards democratising the revolution in atomic-scale modeling that has been brought about by ML force fields.

physics.chem-ph↗

arXiv2023

Graph Neural Network Interatomic Potential Ensembles with Calibrated Aleatoric and Epistemic Uncertainty on Energy and Forces

Inexpensive machine learning potentials are increasingly being used to speed up structural optimization and molecular dynamics simulations of materials by iteratively predicting and applying interatomic forces. In these settings, it is crucial to detect when predictions are unreliable to avoid wrong or misleading results. Here, we present a complete framework for training and recalibrating graph neural network ensemble models to produce accurate predictions of energy and forces with calibrated uncertainty estimates. The proposed method considers both epistemic and aleatoric uncertainty and the total uncertainties are recalibrated post hoc using a nonlinear scaling function to achieve good calibration on previously unseen data, without loss of predictive accuracy. The method is demonstrated and evaluated on two challenging, publicly available datasets, ANI-1x (Smith et al.) and Transition1x (Schreiner et al.), both containing diverse conformations far from equilibrium. A detailed analysis of the predictive performance and uncertainty calibration is provided. In all experiments, the proposed method achieved low prediction error and good uncertainty calibration, with predicted uncertainty correlating with expected error, on energy and forces. To the best of our knowledge, the method presented in this paper is the first to consider a complete framework for obtaining calibrated epistemic and aleatoric uncertainty predictions on both energy and forces in ML potentials.

physics.chem-ph↗

arXiv2023

Wave function Ansatz (but Periodic) Networks and the Homogeneous Electron Gas

We design a neural network Ansatz for variationally finding the ground-state wave function of the Homogeneous Electron Gas, a fundamental model in the physics of extended systems of interacting fermions. We study the spin-polarised and paramagnetic phases with 7, 14 and 19 electrons over a broad range of densities from $r_s=1$ to $r_s=100$, obtaining similar or higher accuracy compared to a state-of-the-art iterative backflow baseline even in the challenging regime of very strong correlation. Our work extends previous applications of neural network Ansätze to molecular systems with methods for handling periodic boundary conditions, and makes two notable changes to improve performance: splitting the pairwise streams by spin alignment and generating backflow coordinates for the orbitals from the network. We illustrate the advantage of our high quality wave functions in computing the reduced single particle density matrix. This contribution establishes neural network models as flexible and high precision Ansätze for periodic electronic systems, an important step towards applications to crystalline solids.

physics.chem-ph↗

arXiv2022

NeuralNEB -- Neural Networks can find Reaction Paths Fast

Quantum mechanical methods like Density Functional Theory (DFT) are used with great success alongside efficient search algorithms for studying kinetics of reactive systems. However, DFT is prohibitively expensive for large scale exploration. Machine Learning (ML) models have turned out to be excellent emulators of small molecule DFT calculations and could possibly replace DFT in such tasks. For kinetics, success relies primarily on the models capability to accurately predict the Potential Energy Surface (PES) around transition-states and Minimal Energy Paths (MEPs). Previously this has not been possible due to scarcity of relevant data in the literature. In this paper we train state of the art equivariant Graph Neural Network (GNN)-based models on around 10.000 elementary reactions from the Transition1x dataset. We apply the models as potentials for the Nudged Elastic Band (NEB) algorithm and achieve a Mean Average Error (MAE) of 0.13+/-0.03 eV on barrier energies on unseen reactions. We compare the results against equivalent models trained on QM9 and ANI1x. We also compare with and outperform Density Functional based Tight Binding (DFTB) on both accuracy and computational resource. The implication is that ML models, given relevant data, are now at a level where they can be applied for downstream tasks in quantum chemistry transcending prediction of simple molecular features.

physics.comp-ph↗

arXiv2022

Transition1x -- a Dataset for Building Generalizable Reactive Machine Learning Potentials

Machine Learning (ML) models have, in contrast to their usefulness in molecular dynamics studies, had limited success as surrogate potentials for reaction barrier search. It is due to the scarcity of training data in relevant transition state regions of chemical space. Currently, available datasets for training ML models on small molecular systems almost exclusively contain configurations at or near equilibrium. In this work, we present the dataset Transition1x containing 9.6 million Density Functional Theory (DFT) calculations of forces and energies of molecular configurations on and around reaction pathways at the wB97x/6-31G(d) level of theory. The data was generated by running Nudged Elastic Band (NEB) calculations with DFT on 10k reactions while saving intermediate calculations. We train state-of-the-art equivariant graph message-passing neural network models on Transition1x and cross-validate on the popular ANI1x and QM9 datasets. We show that ML models cannot learn features in transition-state regions solely by training on hitherto popular benchmark datasets. Transition1x is a new challenging benchmark that will provide an important step towards developing next-generation ML force fields that also work far away from equilibrium configurations and reactive systems.

physics.chem-ph↗