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Jes Frellsen

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20 papers

2 author rows

TMLR Journal 2026 Journal Article

Learning Energy-Based Models by Self-Normalising the Likelihood

Hugo Henri Joseph Senetaire
Paul Jeha
Jes Frellsen
Pierre-Alexandre Mattei

Training an energy-based model (EBM) with maximum likelihood is challenging due to the intractable normalisation constant. Traditional methods rely on expensive Markov chain Monte Carlo (MCMC) sampling to estimate the gradient of logartihm of the normalisation constant. We propose a novel objective called self-normalised log-likelihood (SNL) that introduces a single additional learnable parameter representing the normalisation constant compared to the regular log-likelihood. SNL is a lower bound of the log-likelihood, and its optimum corresponds to both the maximum likelihood estimate of the model parameters and the normalisation constant. We show that the SNL objective is concave in the model parameters for exponential family distributions. Unlike the regular log-likelihood, the SNL can be directly optimised using stochastic gradient techniques by sampling from a crude proposal distribution. We validate the effectiveness of our proposed method on various density estimation and parameter estimation tasks. Our results show that the proposed method, while simpler to implement and tune, outperforms existing techniques for small to moderate dimensions but degrades for high-dimensional problems. We extend this framework to handle EBM for regression and show the usefulness of our method in this setting, as we outperform existing techniques.

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TMLR Journal 2026 Journal Article

Scalable physical source-to-field inference with hypernetworks

Berian James
Stefan Pollok
Ignacio Peis
Elizabeth Louise Baker
Jes Frellsen
Rasmus Bjørk

We present a generative model that amortises computation for the field and potential around e.g.~gravitational or electromagnetic sources. Exact numerical calculation has either computational complexity $\mathcal{O}(M\times{}N)$ in the number of sources $M$ and evaluation points $N$, or requires a fixed evaluation grid to exploit fast Fourier transforms. Using an architecture where a hypernetwork produces an implicit representation of the field or potential around a source collection, our model instead performs as $\mathcal{O}(M + N)$, achieves relative error of $\sim\!4\%-6\%$, and allows evaluation at arbitrary locations for arbitrary numbers of sources, greatly increasing the speed of e.g.~physics simulations. We compare with existing models and develop two-dimensional examples, including cases where sources overlap or have more complex geometries, to demonstrate its application.

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ICML Conference 2025 Conference Paper

Hyper-Transforming Latent Diffusion Models

Ignacio Peis
Batuhan Koyuncu
Isabel Valera
Jes Frellsen

We introduce a novel generative framework for functions by integrating Implicit Neural Representations (INRs) and Transformer-based hypernetworks into latent variable models. Unlike prior approaches that rely on MLP-based hypernetworks with scalability limitations, our method employs a Transformer-based decoder to generate INR parameters from latent variables, addressing both representation capacity and computational efficiency. Our framework extends latent diffusion models (LDMs) to INR generation by replacing standard decoders with a Transformer-based hypernetwork, which can be trained either from scratch or via hyper-transforming—a strategy that fine-tunes only the decoder while freezing the pre-trained latent space. This enables efficient adaptation of existing generative models to INR-based representations without requiring full retraining. We validate our approach across multiple modalities, demonstrating improved scalability, expressiveness, and generalization over existing INR-based generative models. Our findings establish a unified and flexible framework for learning structured function representations.

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ICML Conference 2025 Conference Paper

Kinetic Langevin Diffusion for Crystalline Materials Generation

François R. J. Cornet
Federico Bergamin
Arghya Bhowmik
Juan Maria Garcia Lastra
Jes Frellsen
Mikkel N. Schmidt

Generative modeling of crystalline materials using diffusion models presents a series of challenges: the data distribution is characterized by inherent symmetries and involves multiple modalities, with some defined on specific manifolds. Notably, the treatment of fractional coordinates representing atomic positions in the unit cell requires careful consideration, as they lie on a hypertorus. In this work, we introduce Kinetic Langevin Diffusion for Materials (KLDM), a novel diffusion model for crystalline materials generation, where the key innovation resides in the modeling of the coordinates. Instead of resorting to Riemannian diffusion on the hypertorus directly, we generalize Trivialized Diffusion Model (TDM) to account for the symmetries inherent to crystals. By coupling coordinates with auxiliary Euclidean variables representing velocities, the diffusion process is now offset to a flat space. This allows us to effectively perform diffusion on the hypertorus while providing a training objective that accounts for the periodic translation symmetry of the true data distribution. We evaluate KLDM on both Crystal Structure Prediction (CSP) and De-novo Generation (DNG) tasks, demonstrating its competitive performance with current state-of-the-art models.

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NeurIPS Conference 2025 Conference Paper

Zero-shot protein stability prediction by inverse folding models: a free energy interpretation

Jes Frellsen
Maher Kassem
Tone Bengtsen
Lars Olsen
Kresten Lindorff-Larsen
Jesper Ferkinghoff-Borg
Wouter Boomsma

Inverse folding models have proven to be highly effective zero-shot predictors of protein stability. Despite this success, the link between the amino acid preferences of an inverse folding model and the free-energy considerations underlying thermodynamic stability remains incompletely understood. A better understanding would be of interest not only from a theoretical perspective, but also potentially provide the basis for stronger zero-shot stability prediction. In this paper, we take steps to clarify the free-energy foundations of inverse folding models. Our derivation reveals the standard practice of likelihood ratios as a simplistic approximation and suggests several paths towards better estimates of the relative stability. We empirically assess these approaches and demonstrate that considerable gains in zero-shot performance can be achieved with fairly simple means.

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TMLR Journal 2024 Journal Article

Internal-Coordinate Density Modelling of Protein Structure: Covariance Matters

Marloes Arts
Jes Frellsen
Wouter Boomsma

After the recent ground-breaking advances in protein structure prediction, one of the remaining challenges in protein machine learning is to reliably predict distributions of structural states. Parametric models of fluctuations are difficult to fit due to complex covariance structures between degrees of freedom in the protein chain, often causing models to either violate local or global structural constraints. In this paper, we present a new strategy for modelling protein densities in internal coordinates, which uses constraints in 3D space to induce covariance structure between the internal degrees of freedom. We illustrate the potential of the procedure by constructing a variational autoencoder with full covariance output induced by the constraints implied by the conditional mean in 3D, and demonstrate that our approach makes it possible to scale density models of internal coordinates to full protein backbones in two settings: 1) a unimodal setting for proteins exhibiting small fluctuations and limited amounts of available data, and 2) a multimodal setting for larger conformational changes in a high data regime.

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ICML Conference 2023 Conference Paper

Explainability as statistical inference

Hugo Henri Joseph Senetaire
Damien Garreau
Jes Frellsen
Pierre-Alexandre Mattei

A wide variety of model explanation approaches have been proposed in recent years, all guided by very different rationales and heuristics. In this paper, we take a new route and cast interpretability as a statistical inference problem. We propose a general deep probabilistic model designed to produce interpretable predictions. The model’s parameters can be learned via maximum likelihood, and the method can be adapted to any predictor network architecture, and any type of prediction problem. Our model is akin to amortized interpretability methods, where a neural network is used as a selector to allow for fast interpretation at inference time. Several popular interpretability methods are shown to be particular cases of regularized maximum likelihood for our general model. Using our framework, we identify imputation as a common issue of these models. We propose new datasets with ground truth selection which allow for the evaluation of the features importance map and show experimentally that multiple imputation provides more reasonable interpretations.

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NeurIPS Conference 2023 Conference Paper

Implicit Variational Inference for High-Dimensional Posteriors

Anshuk Uppal
Kristoffer Stensbo-Smidt
Wouter Boomsma
Jes Frellsen

In variational inference, the benefits of Bayesian models rely on accurately capturing the true posterior distribution. We propose using neural samplers that specify implicit distributions, which are well-suited for approximating complex multimodal and correlated posteriors in high-dimensional spaces. Our approach introduces novel bounds for approximate inference using implicit distributions by locally linearising the neural sampler. This is distinct from existing methods that rely on additional discriminator networks and unstable adversarial objectives. Furthermore, we present a new sampler architecture that, for the first time, enables implicit distributions over tens of millions of latent variables, addressing computational concerns by using differentiable numerical approximations. We empirically show that our method is capable of recovering correlations across layers in large Bayesian neural networks, a property that is crucial for a network's performance but notoriously challenging to achieve. To the best of our knowledge, no other method has been shown to accomplish this task for such large models. Through experiments in downstream tasks, we demonstrate that our expressive posteriors outperform state-of-the-art uncertainty quantification methods, validating the effectiveness of our training algorithm and the quality of the learned implicit approximation.

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JMLR Journal 2023 Journal Article

Kernel-Matrix Determinant Estimates from stopped Cholesky Decomposition

Simon Bartels
Wouter Boomsma
Jes Frellsen
Damien Garreau

Algorithms involving Gaussian processes or determinantal point processes typically require computing the determinant of a kernel matrix. Frequently, the latter is computed from the Cholesky decomposition, an algorithm of cubic complexity in the size of the matrix. We show that, under mild assumptions, it is possible to estimate the determinant from only a sub-matrix, with probabilistic guarantee on the relative error. We present an augmentation of the Cholesky decomposition that stops under certain conditions before processing the whole matrix. Experiments demonstrate that this can save a considerable amount of time while rarely exceeding an overhead of more than 5% when not stopping early. More generally, we present a probabilistic stopping strategy for the approximation of a sum of known length where addends are revealed sequentially. We do not assume independence between addends, only that they are bounded from below and decrease in conditional expectation. [abs] [ pdf ][ bib ] [ code ] &copy JMLR 2023. ( edit, beta )

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TMLR Journal 2023 Journal Article

Prior and Posterior Networks: A Survey on Evidential Deep Learning Methods For Uncertainty Estimation

Dennis Thomas Ulmer
Christian Hardmeier
Jes Frellsen

Popular approaches for quantifying predictive uncertainty in deep neural networks often involve distributions over weights or multiple models, for instance via Markov Chain sampling, ensembling, or Monte Carlo dropout. These techniques usually incur overhead by having to train multiple model instances or do not produce very diverse predictions. This comprehensive and extensive survey aims to familiarize the reader with an alternative class of models based on the concept of Evidential Deep Learning: For unfamiliar data, they admit "what they don't know" and fall back onto a prior belief. Furthermore, they allow uncertainty estimation in a single model and forward pass by parameterizing distributions over distributions. This survey recapitulates existing works, focusing on the implementation in a classification setting, before surveying the application of the same paradigm to regression. We also reflect on the strengths and weaknesses compared to other existing methods and provide the most fundamental derivations using a unified notation to aid future research.

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ICLR Conference 2023 Conference Paper

That Label's got Style: Handling Label Style Bias for Uncertain Image Segmentation

Kilian Zepf
Eike Petersen
Jes Frellsen
Aasa Feragen

Segmentation uncertainty models predict a distribution over plausible segmentations for a given input, which they learn from the annotator variation in the training set. However, in practice these annotations can differ systematically in the way they are generated, for example through the use of different labeling tools. This results in datasets that contain both data variability and differing label styles. In this paper, we demonstrate that applying state-of-the-art segmentation uncertainty models on such datasets can lead to model bias caused by the different label styles. We present an updated modelling objective conditioning on labeling style for aleatoric uncertainty estimation, and modify two state-of-the-art-architectures for segmentation uncertainty accordingly. We show with extensive experiments that this method reduces label style bias, while improving segmentation performance, increasing the applicability of segmentation uncertainty models in the wild. We curate two datasets, with annotations in different label styles, which we will make publicly available along with our code upon publication.

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ICLR Conference 2022 Conference Paper

How to deal with missing data in supervised deep learning?

Niels Bruun Ipsen
Pierre-Alexandre Mattei
Jes Frellsen

The issue of missing data in supervised learning has been largely overlooked, especially in the deep learning community. We investigate strategies to adapt neural architectures for handling missing values. Here, we focus on regression and classification problems where the features are assumed to be missing at random. Of particular interest are schemes that allow reusing as-is a neural discriminative architecture. To address supervised deep learning with missing values, we propose to marginalize over missing values in a joint model of covariates and outcomes. Thereby, we leverage both the flexibility of deep generative models to describe the distribution of the covariates and the power of purely discriminative models to make predictions. More precisely, a deep latent variable model can be learned jointly with the discriminative model, using importance-weighted variational inference, essentially using importance sampling to mimick averaging over multiple imputations. In low-capacity regimes, or when the discriminative model has a strong inductive bias, we find that our hybrid generative/discriminative approach generally outperforms single imputations methods.

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NeurIPS Conference 2021 Conference Paper

Bounds all around: training energy-based models with bidirectional bounds

Cong Geng
Jia Wang
Zhiyong Gao
Jes Frellsen
Søren Hauberg

Energy-based models (EBMs) provide an elegant framework for density estimation, but they are notoriously difficult to train. Recent work has established links to generative adversarial networks, where the EBM is trained through a minimax game with a variational value function. We propose a bidirectional bound on the EBM log-likelihood, such that we maximize a lower bound and minimize an upper bound when solving the minimax game. We link one bound to a gradient penalty that stabilizes training, thereby provide grounding for best engineering practice. To evaluate the bounds we develop a new and efficient estimator of the Jacobi-determinant of the EBM generator. We demonstrate that these developments stabilize training and yield high-quality density estimation and sample generation.

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ICML Conference 2021 Conference Paper

Hierarchical VAEs Know What They Don't Know

Jakob Drachmann Havtorn
Jes Frellsen
Søren Hauberg
Lars Maaløe

Deep generative models have been demonstrated as state-of-the-art density estimators. Yet, recent work has found that they often assign a higher likelihood to data from outside the training distribution. This seemingly paradoxical behavior has caused concerns over the quality of the attained density estimates. In the context of hierarchical variational autoencoders, we provide evidence to explain this behavior by out-of-distribution data having in-distribution low-level features. We argue that this is both expected and desirable behavior. With this insight in hand, we develop a fast, scalable and fully unsupervised likelihood-ratio score for OOD detection that requires data to be in-distribution across all feature-levels. We benchmark the method on a vast set of data and model combinations and achieve state-of-the-art results on out-of-distribution detection.

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ICLR Conference 2021 Conference Paper

not-MIWAE: Deep Generative Modelling with Missing not at Random Data

Niels Bruun Ipsen
Pierre-Alexandre Mattei
Jes Frellsen

When a missing process depends on the missing values themselves, it needs to be explicitly modelled and taken into account while doing likelihood-based inference. We present an approach for building and fitting deep latent variable models (DLVMs) in cases where the missing process is dependent on the missing data. Specifically, a deep neural network enables us to flexibly model the conditional distribution of the missingness pattern given the data. This allows for incorporating prior information about the type of missingness (e.g.~self-censoring) into the model. Our inference technique, based on importance-weighted variational inference, involves maximising a lower bound of the joint likelihood. Stochastic gradients of the bound are obtained by using the reparameterisation trick both in latent space and data space. We show on various kinds of data sets and missingness patterns that explicitly modelling the missing process can be invaluable.

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ICML Conference 2019 Conference Paper

MIWAE: Deep Generative Modelling and Imputation of Incomplete Data Sets

Pierre-Alexandre Mattei
Jes Frellsen

We consider the problem of handling missing data with deep latent variable models (DLVMs). First, we present a simple technique to train DLVMs when the training set contains missing-at-random data. Our approach, called MIWAE, is based on the importance-weighted autoencoder (IWAE), and maximises a potentially tight lower bound of the log-likelihood of the observed data. Compared to the original IWAE, our algorithm does not induce any additional computational overhead due to the missing data. We also develop Monte Carlo techniques for single and multiple imputation using a DLVM trained on an incomplete data set. We illustrate our approach by training a convolutional DLVM on incomplete static binarisations of MNIST. Moreover, on various continuous data sets, we show that MIWAE provides extremely accurate single imputations, and is highly competitive with state-of-the-art methods.

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ICML Conference 2019 Conference Paper

Partially Exchangeable Networks and Architectures for Learning Summary Statistics in Approximate Bayesian Computation

Samuel Wiqvist
Pierre-Alexandre Mattei
Umberto Picchini
Jes Frellsen

We present a novel family of deep neural architectures, named partially exchangeable networks (PENs) that leverage probabilistic symmetries. By design, PENs are invariant to block-switch transformations, which characterize the partial exchangeability properties of conditionally Markovian processes. Moreover, we show that any block-switch invariant function has a PEN-like representation. The DeepSets architecture is a special case of PEN and we can therefore also target fully exchangeable data. We employ PENs to learn summary statistics in approximate Bayesian computation (ABC). When comparing PENs to previous deep learning methods for learning summary statistics, our results are highly competitive, both considering time series and static models. Indeed, PENs provide more reliable posterior samples even when using less training data.

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NeurIPS Conference 2018 Conference Paper

Leveraging the Exact Likelihood of Deep Latent Variable Models

Pierre-Alexandre Mattei
Jes Frellsen

Deep latent variable models (DLVMs) combine the approximation abilities of deep neural networks and the statistical foundations of generative models. Variational methods are commonly used for inference; however, the exact likelihood of these models has been largely overlooked. The purpose of this work is to study the general properties of this quantity and to show how they can be leveraged in practice. We focus on important inferential problems that rely on the likelihood: estimation and missing data imputation. First, we investigate maximum likelihood estimation for DLVMs: in particular, we show that most unconstrained models used for continuous data have an unbounded likelihood function. This problematic behaviour is demonstrated to be a source of mode collapse. We also show how to ensure the existence of maximum likelihood estimates, and draw useful connections with nonparametric mixture models. Finally, we describe an algorithm for missing data imputation using the exact conditional likelihood of a DLVM. On several data sets, our algorithm consistently and significantly outperforms the usual imputation scheme used for DLVMs.

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NeurIPS Conference 2017 Conference Paper

Spherical convolutions and their application in molecular modelling

Wouter Boomsma
Jes Frellsen

Convolutional neural networks are increasingly used outside the domain of image analysis, in particular in various areas of the natural sciences concerned with spatial data. Such networks often work out-of-the box, and in some cases entire model architectures from image analysis can be carried over to other problem domains almost unaltered. Unfortunately, this convenience does not trivially extend to data in non-euclidean spaces, such as spherical data. In this paper, we introduce two strategies for conducting convolutions on the sphere, using either a spherical-polar grid or a grid based on the cubed-sphere representation. We investigate the challenges that arise in this setting, and extend our discussion to include scenarios of spherical volumes, with several strategies for parameterizing the radial dimension. As a proof of concept, we conclude with an assessment of the performance of spherical convolutions in the context of molecular modelling, by considering structural environments within proteins. We show that the models are capable of learning non-trivial functions in these molecular environments, and that our spherical convolutions generally outperform standard 3D convolutions in this setting. In particular, despite the lack of any domain specific feature-engineering, we demonstrate performance comparable to state-of-the-art methods in the field, which build on decades of domain-specific knowledge.

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AAAI Conference 2017 Conference Paper

The Multivariate Generalised von Mises Distribution: Inference and Applications

Alexandre Navarro
Jes Frellsen
Richard Turner

Circular variables arise in a multitude of data-modelling contexts ranging from robotics to the social sciences, but they have been largely overlooked by the machine learning community. This paper partially redresses this imbalance by extending some standard probabilistic modelling tools to the circular domain. First we introduce a new multivariate distribution over circular variables, called the multivariate Generalised von Mises (mGvM) distribution. This distribution can be constructed by restricting and renormalising a general multivariate Gaussian distribution to the unit hyper-torus. Previously proposed multivariate circular distributions are shown to be special cases of this construction. Second, we introduce a new probabilistic model for circular regression inspired by Gaussian Processes, and a method for probabilistic Principal Component Analysis with circular hidden variables. These models can leverage standard modelling tools (e. g. kernel functions and automatic relevance determination). Third, we show that the posterior distribution in these models is a mGvM distribution which enables development of an efﬁcient variational free-energy scheme for performing approximate inference and approximate maximum-likelihood learning.

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