Søren Hauberg

Hadi Beik-Mohammadi, Søren Hauberg, Georgios Arvanitidis et al.

In recent decades, advancements in motion learning have enabled robots to acquire new skills and adapt to unseen conditions in both structured and unstructured environments. In practice, motion learning methods capture relevant patterns and adjust them to new conditions such as dynamic obstacle avoidance or variable targets. In this paper, we investigate the robot motion learning paradigm from a Riemannian manifold perspective. We argue that Riemannian manifolds may be learned via human demonstrations in which geodesics are natural motion skills. The geodesics are generated using a learned Riemannian metric produced by our novel variational autoencoder (VAE), which is especially intended to recover full-pose end-effector states and joint space configurations. In addition, we propose a technique for facilitating on-the-fly end-effector/multiple-limb obstacle avoidance by reshaping the learned manifold using an obstacle-aware ambient metric. The motion generated using these geodesics may naturally result in multiple-solution tasks that have not been explicitly demonstrated previously. We extensively tested our approach in task space and joint space scenarios using a 7-DoF robotic manipulator. We demonstrate that our method is capable of learning and generating motion skills based on complicated motion patterns demonstrated by a human operator. Additionally, we assess several obstacle avoidance strategies and generate trajectories in multiple-mode settings.

Federico Bergamin, Pierre-Alexandre Mattei, Jakob D. Havtorn et al.

We present simple methods for out-of-distribution detection using a trained generative model. These techniques, based on classical statistical tests, are model-agnostic in the sense that they can be applied to any differentiable generative model. The idea is to combine a classical parametric test (Rao's score test) with the recently introduced typicality test. These two test statistics are both theoretically well-founded and exploit different sources of information based on the likelihood for the typicality test and its gradient for the score test. We show that combining them using Fisher's method overall leads to a more accurate out-of-distribution test. We also discuss the benefits of casting out-of-distribution detection as a statistical testing problem, noting in particular that false positive rate control can be valuable for practical out-of-distribution detection. Despite their simplicity and generality, these methods can be competitive with model-specific out-of-distribution detection algorithms without any assumptions on the out-distribution.

Federico Bergamin, Pablo Moreno-Muñoz, Søren Hauberg et al.

Bayesian neural networks often approximate the weight-posterior with a Gaussian distribution. However, practical posteriors are often, even locally, highly non-Gaussian, and empirical performance deteriorates. We propose a simple parametric approximate posterior that adapts to the shape of the true posterior through a Riemannian metric that is determined by the log-posterior gradient. We develop a Riemannian Laplace approximation where samples naturally fall into weight-regions with low negative log-posterior. We show that these samples can be drawn by solving a system of ordinary differential equations, which can be done efficiently by leveraging the structure of the Riemannian metric and automatic differentiation. Empirically, we demonstrate that our approach consistently improves over the conventional Laplace approximation across tasks. We further show that, unlike the conventional Laplace approximation, our method is not overly sensitive to the choice of prior, which alleviates a practical pitfall of current approaches.

Miguel González-Duque, Rasmus Berg Palm, Søren Hauberg et al.

Deep generative models can automatically create content of diverse types. However, there are no guarantees that such content will satisfy the criteria necessary to present it to end-users and be functional, e.g. the generated levels could be unsolvable or incoherent. In this paper we study this problem from a geometric perspective, and provide a method for reliable interpolation and random walks in the latent spaces of Categorical VAEs based on Riemannian geometry. We test our method with "Super Mario Bros" and "The Legend of Zelda" levels, and against simpler baselines inspired by current practice. Results show that the geometry we propose is better able to interpolate and sample, reliably staying closer to parts of the latent space that decode to playable content.

Andri Bergsson, Søren Hauberg

Faithful visualizations of data residing on manifolds must take the underlying geometry into account when producing a flat planar view of the data. In this paper, we extend the classic stochastic neighbor embedding (SNE) algorithm to data on general Riemannian manifolds. We replace standard Gaussian assumptions with Riemannian diffusion counterparts and propose an efficient approximation that only requires access to calculations of Riemannian distances and volumes. We demonstrate that the approach also allows for mapping data from one manifold to another, e.g. from a high-dimensional sphere to a low-dimensional one.

Thoranna Bender, Simon Moe Sørensen, Alireza Kashani et al.

We present WineSensed, a large multimodal wine dataset for studying the relations between visual perception, language, and flavor. The dataset encompasses 897k images of wine labels and 824k reviews of wines curated from the Vivino platform. It has over 350k unique bottlings, annotated with year, region, rating, alcohol percentage, price, and grape composition. We obtained fine-grained flavor annotations on a subset by conducting a wine-tasting experiment with 256 participants who were asked to rank wines based on their similarity in flavor, resulting in more than 5k pairwise flavor distances. We propose a low-dimensional concept embedding algorithm that combines human experience with automatic machine similarity kernels. We demonstrate that this shared concept embedding space improves upon separate embedding spaces for coarse flavor classification (alcohol percentage, country, grape, price, rating) and aligns with the intricate human perception of flavor.

Kilian Zepf, Selma Wanna, Marco Miani et al.

Image segmentation relies heavily on neural networks which are known to be overconfident, especially when making predictions on out-of-distribution (OOD) images. This is a common scenario in the medical domain due to variations in equipment, acquisition sites, or image corruptions. This work addresses the challenge of OOD detection by proposing Laplacian Segmentation Networks (LSN): methods which jointly model epistemic (model) and aleatoric (data) uncertainty for OOD detection. In doing so, we propose the first Laplace approximation of the weight posterior that scales to large neural networks with skip connections that have high-dimensional outputs. We demonstrate on three datasets that the LSN-modeled parameter distributions, in combination with suitable uncertainty measures, gives superior OOD detection.

Johan Ziruo Ye, Thomas Ørkild, Peter Lempel Søndergaard et al.

Digital dentistry has made significant advancements, yet numerous challenges remain. This paper introduces the FDI 16 dataset, an extensive collection of tooth meshes and point clouds. Additionally, we present a novel approach: Variational FoldingNet (VF-Net), a fully probabilistic variational autoencoder for point clouds. Notably, prior latent variable models for point clouds lack a one-to-one correspondence between input and output points. Instead, they rely on optimizing Chamfer distances, a metric that lacks a normalized distributional counterpart, rendering it unsuitable for probabilistic modeling. We replace the explicit minimization of Chamfer distances with a suitable encoder, increasing computational efficiency while simplifying the probabilistic extension. This allows for straightforward application in various tasks, including mesh generation, shape completion, and representation learning. Empirically, we provide evidence of lower reconstruction error in dental reconstruction and interpolation, showcasing state-of-the-art performance in dental sample generation while identifying valuable latent representations

Alison Pouplin, David Eklund, Carl Henrik Ek et al.

Riemannian geometry provides us with powerful tools to explore the latent space of generative models while preserving the underlying structure of the data. The latent space can be equipped it with a Riemannian metric, pulled back from the data manifold. With this metric, we can systematically navigate the space relying on geodesics defined as the shortest curves between two points. Generative models are often stochastic, causing the data space, the Riemannian metric, and the geodesics, to be stochastic as well. Stochastic objects are at best impractical, and at worst impossible, to manipulate. A common solution is to approximate the stochastic pullback metric by its expectation. But the geodesics derived from this expected Riemannian metric do not correspond to the expected length-minimising curves. In this work, we propose another metric whose geodesics explicitly minimise the expected length of the pullback metric. We show this metric defines a Finsler metric, and we compare it with the expected Riemannian metric. In high dimensions, we prove that both metrics converge to each other at a rate of $O\left(\frac{1}{D}\right)$. This convergence implies that the established expected Riemannian metric is an accurate approximation of the theoretically more grounded Finsler metric. This provides justification for using the expected Riemannian metric for practical implementations.

Helene Hauschultz, Rasmus Berg Palm. Pablo Moreno-Muños, Nicki Skafte Detlefsen et al.

The encoder network of an autoencoder is an approximation of the nearest point projection onto the manifold spanned by the decoder. A concern with this approximation is that, while the output of the encoder is always unique, the projection can possibly have infinitely many values. This implies that the latent representations learned by the autoencoder can be misleading. Borrowing from geometric measure theory, we introduce the idea of using the reach of the manifold spanned by the decoder to determine if an optimal encoder exists for a given dataset and decoder. We develop a local generalization of this reach and propose a numerical estimator thereof. We demonstrate that this allows us to determine which observations can be expected to have a unique, and thereby trustworthy, latent representation. As our local reach estimator is differentiable, we investigate its usage as a regularizer and show that this leads to learned manifolds for which projections are more often unique than without regularization.

Marco Miani, Frederik Warburg, Pablo Moreno-Muñoz et al.

Established methods for unsupervised representation learning such as variational autoencoders produce none or poorly calibrated uncertainty estimates making it difficult to evaluate if learned representations are stable and reliable. In this work, we present a Bayesian autoencoder for unsupervised representation learning, which is trained using a novel variational lower-bound of the autoencoder evidence. This is maximized using Monte Carlo EM with a variational distribution that takes the shape of a Laplace approximation. We develop a new Hessian approximation that scales linearly with data size allowing us to model high-dimensional data. Empirically, we show that our Laplacian autoencoder estimates well-calibrated uncertainties in both latent and output space. We demonstrate that this results in improved performance across a multitude of downstream tasks.

Yevgen Zainchkovskyy, Jesper Ferkinghoff-Borg, Anja Bennett et al.

Pre-trained protein language models have demonstrated significant applicability in different protein engineering task. A general usage of these pre-trained transformer models latent representation is to use a mean pool across residue positions to reduce the feature dimensions to further downstream tasks such as predicting bio-physics properties or other functional behaviours. In this paper we provide a two-fold contribution to machine learning (ML) driven drug design. Firstly, we demonstrate the power of sparsity by promoting penalization of pre-trained transformer models to secure more robust and accurate melting temperature (Tm) prediction of single-chain variable fragments with a mean absolute error of 0.23C. Secondly, we demonstrate the power of framing our prediction problem in a probabilistic framework. Specifically, we advocate for the need of adopting probabilistic frameworks especially in the context of ML driven drug design.

Stas Syrota, Pablo Moreno-Muñoz, Søren Hauberg

Latent space geometry provides a rigorous and empirically valuable framework for interacting with the latent variables of deep generative models. This approach reinterprets Euclidean latent spaces as Riemannian through a pull-back metric, allowing for a standard differential geometric analysis of the latent space. Unfortunately, data manifolds are generally compact and easily disconnected or filled with holes, suggesting a topological mismatch to the Euclidean latent space. The most established solution to this mismatch is to let uncertainty be a proxy for topology, but in neural network models, this is often realized through crude heuristics that lack principle and generally do not scale to high-dimensional representations. We propose using ensembles of decoders to capture model uncertainty and show how to easily compute geodesics on the associated expected manifold. Empirically, we find this simple and reliable, thereby coming one step closer to easy-to-use latent geometries.

Pablo Moreno-Muñoz, Pol G. Recasens, Søren Hauberg

Masked pre-training removes random input dimensions and learns a model that can predict the missing values. Empirical results indicate that this intuitive form of self-supervised learning yields models that generalize very well to new domains. A theoretical understanding is, however, lacking. This paper shows that masked pre-training with a suitable cumulative scoring function corresponds to maximizing the model's marginal likelihood, which is de facto the Bayesian model selection measure of generalization. Beyond shedding light on the success of masked pre-training, this insight also suggests that Bayesian models can be trained with appropriately designed self-supervision. Empirically, we confirm the developed theory and explore the main learning principles of masked pre-training in large language models.

Pablo Moreno-Muñoz, Cilie W Feldager, Søren Hauberg

Decoders built on Gaussian processes (GPs) are enticing due to the marginalisation over the non-linear function space. Such models (also known as GP-LVMs) are often expensive and notoriously difficult to train in practice, but can be scaled using variational inference and inducing points. In this paper, we revisit active set approximations. We develop a new stochastic estimate of the log-marginal likelihood based on recently discovered links to cross-validation, and propose a computationally efficient approximation thereof. We demonstrate that the resulting stochastic active sets (SAS) approximation significantly improves the robustness of GP decoder training while reducing computational cost. The SAS-GP obtains more structure in the latent space, scales to many datapoints and learns better representations than variational autoencoders, which is rarely the case for GP decoders.

Andrea Testa, Søren Hauberg, Tamim Asfour et al.

The Schrödinger Bridge provides a principled framework for modeling stochastic processes between distributions; however, existing methods are limited by energy-conservation assumptions, which constrains the bridge's shape preventing it from model varying-energy phenomena. To overcome this, we introduce the non-conservative generalized Schrödinger bridge (NCGSB), a novel, energy-varying reformulation based on contact Hamiltonian mechanics. By allowing energy to change over time, the NCGSB provides a broader class of real-world stochastic processes, capturing richer and more faithful intermediate dynamics. By parameterizing the Wasserstein manifold, we lift the bridge problem to a tractable geodesic computation in a finite-dimensional space. Unlike computationally expensive iterative solutions, our contact Wasserstein geodesic (CWG) is naturally implemented via a ResNet architecture and relies on a non-iterative solver with near-linear complexity. Furthermore, CWG supports guided generation by modulating a task-specific distance metric. We validate our framework on tasks including manifold navigation, molecular dynamics predictions, and image generation, demonstrating its practical benefits and versatility.

Andreas Bjerregaard, Søren Hauberg, Anders Krogh

Riemannian representation learning typically relies on an encoder to estimate densities on chosen manifolds. This involves optimizing numerically brittle objectives, potentially harming model training and quality. To completely circumvent this issue, we introduce the Riemannian generative decoder, a unifying approach for finding manifold-valued latents on any Riemannian manifold. Latents are learned with a Riemannian optimizer while jointly training a decoder network. By discarding the encoder, we vastly simplify the manifold constraint compared to current approaches which often only handle few specific manifolds. We validate our approach on three case studies -- a synthetic branching diffusion process, human migrations inferred from mitochondrial DNA, and cells undergoing a cell division cycle -- each showing that learned representations respect the prescribed geometry and capture intrinsic non-Euclidean structure. Our method requires only a decoder, is compatible with existing architectures, and yields interpretable latent spaces aligned with data geometry. Code available on https://github.com/yhsure/riemannian-generative-decoder.

Rafał Karczewski, Markus Heinonen, Alison Pouplin et al.

We present a novel geometric perspective on the latent space of diffusion models. We first show that the standard pullback approach, utilizing the deterministic probability flow ODE decoder, is fundamentally flawed. It provably forces geodesics to decode as straight segments in data space, effectively ignoring any intrinsic data geometry beyond the ambient Euclidean space. Complementing this view, diffusion also admits a stochastic decoder via the reverse SDE, which enables an information geometric treatment with the Fisher-Rao metric. However, a choice of $x_T$ as the latent representation collapses this metric due to memorylessness. We address this by introducing a latent spacetime $z=(x_t,t)$ that indexes the family of denoising distributions $p(x_0 | x_t)$ across all noise scales, yielding a nontrivial geometric structure. We prove these distributions form an exponential family and derive simulation-free estimators for curve lengths, enabling efficient geodesic computation. The resulting structure induces a principled Diffusion Edit Distance, where geodesics trace minimal sequences of noise and denoise edits between data. We also demonstrate benefits for transition path sampling in molecular systems, including constrained variants such as low-variance transitions and region avoidance. Code is available at: https://github.com/rafalkarczewski/spacetime-geometry

Frederik Möbius Rygaard, Shen Zhu, Yinzhu Jin et al.

Interpolation in generative models allows for controlled generation, model inspection, and more. Unfortunately, most generative models lack a principal notion of interpolants without restrictive assumptions on either the model or data dimension. In this paper, we develop a general interpolation scheme that targets likely transition paths compatible with different metrics and probability distributions. We consider interpolants analogous to a geodesic constrained to a suitable data distribution and derive a novel algorithm for computing these curves, which requires no additional training. Theoretically, we show that our method locally can be considered as a geodesic under a suitable Riemannian metric. We quantitatively show that our interpolation scheme traverses higher density regions than baselines across a range of models and datasets.

Hadi Beik-Mohammadi, Søren Hauberg, Georgios Arvanitidis et al.

Stability guarantees are crucial when ensuring a fully autonomous robot does not take undesirable or potentially harmful actions. Unfortunately, global stability guarantees are hard to provide in dynamical systems learned from data, especially when the learned dynamics are governed by neural networks. We propose a novel methodology to learn neural contractive dynamical systems, where our neural architecture ensures contraction, and hence, global stability. To efficiently scale the method to high-dimensional dynamical systems, we develop a variant of the variational autoencoder that learns dynamics in a low-dimensional latent representation space while retaining contractive stability after decoding. We further extend our approach to learning contractive systems on the Lie group of rotations to account for full-pose end-effector dynamic motions. The result is the first highly flexible learning architecture that provides contractive stability guarantees with capability to perform obstacle avoidance. Empirically, we demonstrate that our approach encodes the desired dynamics more accurately than the current state-of-the-art, which provides less strong stability guarantees.

Miguel López-Pérez, Søren Hauberg, Aasa Feragen

Racial bias in medicine, such as in dermatology, presents significant ethical and clinical challenges. This is likely to happen because there is a significant underrepresentation of darker skin tones in training datasets for machine learning models. While efforts to address bias in dermatology have focused on improving dataset diversity and mitigating disparities in discriminative models, the impact of racial bias on generative models remains underexplored. Generative models, such as Variational Autoencoders (VAEs), are increasingly used in healthcare applications, yet their fairness across diverse skin tones is currently not well understood. In this study, we evaluate the fairness of generative models in clinical dermatology with respect to racial bias. For this purpose, we first train a VAE with a perceptual loss to generate and reconstruct high-quality skin images across different skin tones. We utilize the Fitzpatrick17k dataset to examine how racial bias influences the representation and performance of these models. Our findings indicate that VAE performance is, as expected, influenced by representation, i.e. increased skin tone representation comes with increased performance on the given skin tone. However, we also observe, even independently of representation, that the VAE performs better for lighter skin tones. Additionally, the uncertainty estimates produced by the VAE are ineffective in assessing the model's fairness. These results highlight the need for more representative dermatological datasets, but also a need for better understanding the sources of bias in such model, as well as improved uncertainty quantification mechanisms to detect and address racial bias in generative models for trustworthy healthcare technologies.

Richard Michael, Simon Bartels, Miguel González-Duque et al.

To optimize efficiently over discrete data and with only few available target observations is a challenge in Bayesian optimization. We propose a continuous relaxation of the objective function and show that inference and optimization can be computationally tractable. We consider in particular the optimization domain where very few observations and strict budgets exist; motivated by optimizing protein sequences for expensive to evaluate bio-chemical properties. The advantages of our approach are two-fold: the problem is treated in the continuous setting, and available prior knowledge over sequences can be incorporated directly. More specifically, we utilize available and learned distributions over the problem domain for a weighting of the Hellinger distance which yields a covariance function. We show that the resulting acquisition function can be optimized with both continuous or discrete optimization algorithms and empirically assess our method on two bio-chemical sequence optimization tasks.

Cong Geng, Tian Han, Peng-Tao Jiang et al.

Generative models have shown strong generation ability while efficient likelihood estimation is less explored. Energy-based models~(EBMs) define a flexible energy function to parameterize unnormalized densities efficiently but are notorious for being difficult to train. Adversarial EBMs introduce a generator to form a minimax training game to avoid expensive MCMC sampling used in traditional EBMs, but a noticeable gap between adversarial EBMs and other strong generative models still exists. Inspired by diffusion-based models, we embedded EBMs into each denoising step to split a long-generated process into several smaller steps. Besides, we employ a symmetric Jeffrey divergence and introduce a variational posterior distribution for the generator's training to address the main challenges that exist in adversarial EBMs. Our experiments show significant improvement in generation compared to existing adversarial EBMs, while also providing a useful energy function for efficient density estimation.

Andrea Testa, Søren Hauberg, Tamim Asfour et al.

Accurately modeling and predicting complex dynamical systems, particularly those involving force exchange and dissipation, is crucial for applications ranging from fluid dynamics to robotics, but presents significant challenges due to the intricate interplay of geometric constraints and energy transfer. This paper introduces Geometric Contact Flows (GFC), a novel framework leveraging Riemannian and Contact geometry as inductive biases to learn such systems. GCF constructs a latent contact Hamiltonian model encoding desirable properties like stability or energy conservation. An ensemble of contactomorphisms then adapts this model to the target dynamics while preserving these properties. This ensemble allows for uncertainty-aware geodesics that attract the system's behavior toward the data support, enabling robust generalization and adaptation to unseen scenarios. Experiments on learning dynamics for physical systems and for controlling robots on interaction tasks demonstrate the effectiveness of our approach.

Leonel Rozo, Miguel González-Duque, Noémie Jaquier et al.

Latent variable models are powerful tools for learning low-dimensional manifolds from high-dimensional data. However, when dealing with constrained data such as unit-norm vectors or symmetric positive-definite matrices, existing approaches ignore the underlying geometric constraints or fail to provide meaningful metrics in the latent space. To address these limitations, we propose to learn Riemannian latent representations of such geometric data. To do so, we estimate the pullback metric induced by a Wrapped Gaussian Process Latent Variable Model, which explicitly accounts for the data geometry. This enables us to define geometry-aware notions of distance and shortest paths in the latent space, while ensuring that our model only assigns probability mass to the data manifold. This generalizes previous work and allows us to handle complex tasks in various domains, including robot motion synthesis and analysis of brain connectomes.

Marco Miani, Hrittik Roy, Søren Hauberg

Bayesian deep learning all too often underfits so that the Bayesian prediction is less accurate than a simple point estimate. Uncertainty quantification then comes at the cost of accuracy. For linearized models, the null space of the generalized Gauss-Newton matrix corresponds to parameters that preserve the training predictions of the point estimate. We propose to build Bayesian approximations in this null space, thereby guaranteeing that the Bayesian predictive does not underfit. We suggest a matrix-free algorithm for projecting onto this null space, which scales linearly with the number of parameters and quadratically with the number of output dimensions. We further propose an approximation that only scales linearly with parameters to make the method applicable to generative models. An extensive empirical evaluation shows that the approach scales to large models, including vision transformers with 28 million parameters.

Hrittik Roy, Søren Hauberg, Nicholas Krämer

This paper argues that the method of least squares has significant unfulfilled potential in modern machine learning, far beyond merely being a tool for fitting linear models. To release its potential, we derive custom gradients that transform the solver into a differentiable operator, like a neural network layer, enabling many diverse applications. Empirically, we demonstrate: (i) scalability by enforcing weight sparsity on a 50 million parameter model; (ii) imposing conservativeness constraints in score-based generative models; and (iii) hyperparameter tuning of Gaussian processes based on predictive performance. By doing this, our work represents the next iteration in developing differentiable linear-algebra tools and making them widely accessible to machine learning practitioners.

Hanlin Yu, Søren Hauberg, Marcelo Hartmann et al.

Real world data often lie on low-dimensional Riemannian manifolds embedded in high-dimensional spaces. This motivates learning degenerate normalizing flows that map between the ambient space and a low-dimensional latent space. However, if the manifold has a non-trivial topology, it can never be correctly learned using a single flow. Instead multiple flows must be `glued together'. In this paper, we first propose the general training scheme for learning such a collection of flows, and secondly we develop the first numerical algorithms for computing geodesics on such manifolds. Empirically, we demonstrate that this leads to highly significant improvements in topology estimation.

Stas Syrota, Yevgen Zainchkovskyy, Johnny Xi et al.

Deep latent variable models learn condensed representations of data that, hopefully, reflect the inner workings of the studied phenomena. Unfortunately, these latent representations are not statistically identifiable, meaning they cannot be uniquely determined. Domain experts, therefore, need to tread carefully when interpreting these. Current solutions limit the lack of identifiability through additional constraints on the latent variable model, e.g. by requiring labeled training data, or by restricting the expressivity of the model. We change the goal: instead of identifying the latent variables, we identify relationships between them such as meaningful distances, angles, and volumes. We prove this is feasible under very mild model conditions and without additional labeled data. We empirically demonstrate that our theory results in more reliable latent distances, offering a principled path forward in extracting trustworthy conclusions from deep latent variable models.

Hadi Beik Mohammadi, Søren Hauberg, Georgios Arvanitidis et al.

Stability guarantees are crucial when ensuring that a fully autonomous robot does not take undesirable or potentially harmful actions. We recently proposed the Neural Contractive Dynamical Systems (NCDS), which is a neural network architecture that guarantees contractive stability. With this, learning-from-demonstrations approaches can trivially provide stability guarantees. However, our early work left several unanswered questions, which we here address. Beyond providing an in-depth explanation of NCDS, this paper extends the framework with more careful regularization, a conditional variant of the framework for handling multiple tasks, and an uncertainty-driven approach to latent obstacle avoidance. Experiments verify that the developed system has the flexibility of ordinary neural networks while providing the stability guarantees needed for autonomous robotics.

Samuel G. Fadel, Hrittik Roy, Nicholas Krämer et al.

Variational mean field approximations tend to struggle with contemporary overparametrized deep neural networks. Where a Bayesian treatment is usually associated with high-quality predictions and uncertainties, the practical reality has been the opposite, with unstable training, poor predictive power, and subpar calibration. Building upon recent work on reparametrizations of neural networks, we propose a simple variational family that considers two independent linear subspaces of the parameter space. These represent functional changes inside and outside the support of training data. This allows us to build a fully-correlated approximate posterior reflecting the overparametrization that tunes easy-to-interpret hyperparameters. We develop scalable numerical routines that maximize the associated evidence lower bound (ELBO) and sample from the approximate posterior. Empirically, we observe state-of-the-art performance across tasks, models, and datasets compared to a wide array of baseline methods. Our results show that approximate Bayesian inference applied to deep neural networks is far from a lost cause when constructing inference mechanisms that reflect the geometry of reparametrizations.

Cong Geng, Jia Wang, Li Chen et al.

Energy-based models (EBMs) estimate unnormalized densities in an elegant framework, but they are generally difficult to train. Recent work has linked EBMs to generative adversarial networks, by noting that they can be trained through a minimax game using a variational lower bound. To avoid the instabilities caused by minimizing a lower bound, we propose to instead work with bidirectional bounds, meaning that we maximize a lower bound and minimize an upper bound when training the EBM. We investigate four different bounds on the log-likelihood derived from different perspectives. We derive lower bounds based on the singular values of the generator Jacobian and on mutual information. To upper bound the negative log-likelihood, we consider a gradient penalty-like bound, as well as one based on diffusion processes. In all cases, we provide algorithms for evaluating the bounds. We compare the different bounds to investigate, the pros and cons of the different approaches. Finally, we demonstrate that the use of bidirectional bounds stabilizes EBM training and yields high-quality density estimation and sample generation.

Miguel López-Pérez, Marco Miani, Valery Naranjo et al.

Generative models are popular for medical imaging tasks such as anomaly detection, feature extraction, data visualization, or image generation. Since they are parameterized by deep learning models, they are often sensitive to distribution shifts and unreliable when applied to out-of-distribution data, creating a risk of, e.g. underrepresentation bias. This behavior can be flagged using uncertainty quantification methods for generative models, but their availability remains limited. We propose SLUG: A new UQ method for VAEs that combines recent advances in Laplace approximations with stochastic trace estimators to scale gracefully with image dimensionality. We show that our UQ score -- unlike the VAE's encoder variances -- correlates strongly with reconstruction error and racial underrepresentation bias for dermatological images. We also show how pixel-wise uncertainty can detect out-of-distribution image content such as ink, rulers, and patches, which is known to induce learning shortcuts in predictive models.

Miguel González-Duque, Richard Michael, Simon Bartels et al.

Optimizing discrete black-box functions is key in several domains, e.g. protein engineering and drug design. Due to the lack of gradient information and the need for sample efficiency, Bayesian optimization is an ideal candidate for these tasks. Several methods for high-dimensional continuous and categorical Bayesian optimization have been proposed recently. However, our survey of the field reveals highly heterogeneous experimental set-ups across methods and technical barriers for the replicability and application of published algorithms to real-world tasks. To address these issues, we develop a unified framework to test a vast array of high-dimensional Bayesian optimization methods and a collection of standardized black-box functions representing real-world application domains in chemistry and biology. These two components of the benchmark are each supported by flexible, scalable, and easily extendable software libraries (poli and poli-baselines), allowing practitioners to readily incorporate new optimization objectives or discrete optimizers. Project website: https://machinelearninglifescience.github.io/hdbo_benchmark

Hrittik Roy, Marco Miani, Carl Henrik Ek et al.

Current approximate posteriors in Bayesian neural networks (BNNs) exhibit a crucial limitation: they fail to maintain invariance under reparameterization, i.e. BNNs assign different posterior densities to different parametrizations of identical functions. This creates a fundamental flaw in the application of Bayesian principles as it breaks the correspondence between uncertainty over the parameters with uncertainty over the parametrized function. In this paper, we investigate this issue in the context of the increasingly popular linearized Laplace approximation. Specifically, it has been observed that linearized predictives alleviate the common underfitting problems of the Laplace approximation. We develop a new geometric view of reparametrizations from which we explain the success of linearization. Moreover, we demonstrate that these reparameterization invariance properties can be extended to the original neural network predictive using a Riemannian diffusion process giving a straightforward algorithm for approximate posterior sampling, which empirically improves posterior fit.

Jakob D. Havtorn, Lasse Borgholt, Søren Hauberg et al.

Stochastic latent variable models (LVMs) achieve state-of-the-art performance on natural image generation but are still inferior to deterministic models on speech. In this paper, we develop a speech benchmark of popular temporal LVMs and compare them against state-of-the-art deterministic models. We report the likelihood, which is a much used metric in the image domain, but rarely, or incomparably, reported for speech models. To assess the quality of the learned representations, we also compare their usefulness for phoneme recognition. Finally, we adapt the Clockwork VAE, a state-of-the-art temporal LVM for video generation, to the speech domain. Despite being autoregressive only in latent space, we find that the Clockwork VAE can outperform previous LVMs and reduce the gap to deterministic models by using a hierarchy of latent variables.

Simon Bartels, Kristoffer Stensbo-Smidt, Pablo Moreno-Muñoz et al.

We present a method to approximate Gaussian process regression models for large datasets by considering only a subset of the data. Our approach is novel in that the size of the subset is selected on the fly during exact inference with little computational overhead. From an empirical observation that the log-marginal likelihood often exhibits a linear trend once a sufficient subset of a dataset has been observed, we conclude that many large datasets contain redundant information that only slightly affects the posterior. Based on this, we provide probabilistic bounds on the full model evidence that can identify such subsets. Remarkably, these bounds are largely composed of terms that appear in intermediate steps of the standard Cholesky decomposition, allowing us to modify the algorithm to adaptively stop the decomposition once enough data have been observed.

Andrea Vallone, Frederik Warburg, Hans Hansen et al.

Place recognition and visual localization are particularly challenging in wide baseline configurations. In this paper, we contribute with the \emph{Danish Airs and Grounds} (DAG) dataset, a large collection of street-level and aerial images targeting such cases. Its main challenge lies in the extreme viewing-angle difference between query and reference images with consequent changes in illumination and perspective. The dataset is larger and more diverse than current publicly available data, including more than 50 km of road in urban, suburban and rural areas. All images are associated with accurate 6-DoF metadata that allows the benchmarking of visual localization methods. We also propose a map-to-image re-localization pipeline, that first estimates a dense 3D reconstruction from the aerial images and then matches query street-level images to street-level renderings of the 3D model. The dataset can be downloaded at: https://frederikwarburg.github.io/DAG

Pierre Segonne, Yevgen Zainchkovskyy, Søren Hauberg

Probabilistic models often use neural networks to control their predictive uncertainty. However, when making out-of-distribution (OOD)} predictions, the often-uncontrollable extrapolation properties of neural networks yield poor uncertainty predictions. Such models then don't know what they don't know, which directly limits their robustness w.r.t unexpected inputs. To counter this, we propose to explicitly train the uncertainty predictor where we are not given data to make it reliable. As one cannot train without data, we provide mechanisms for generating pseudo-inputs in informative low-density regions of the input space, and show how to leverage these in a practical Bayesian framework that casts a prior distribution over the model uncertainty. With a holistic evaluation, we demonstrate that this yields robust and interpretable predictions of uncertainty while retaining state-of-the-art performance on diverse tasks such as regression and generative modelling

Cong Geng, Jia Wang, Zhiyong Gao et al.

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 providing 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 significantly stabilize training and yield high-quality density estimation and sample generation.

Georgios Arvanitidis, Miguel González-Duque, Alison Pouplin et al.

Latent space geometry has shown itself to provide a rich and rigorous framework for interacting with the latent variables of deep generative models. The existing theory, however, relies on the decoder being a Gaussian distribution as its simple reparametrization allows us to interpret the generating process as a random projection of a deterministic manifold. Consequently, this approach breaks down when applied to decoders that are not as easily reparametrized. We here propose to use the Fisher-Rao metric associated with the space of decoder distributions as a reference metric, which we pull back to the latent space. We show that we can achieve meaningful latent geometries for a wide range of decoder distributions for which the previous theory was not applicable, opening the door to `black box' latent geometries.

Hadi Beik-Mohammadi, Søren Hauberg, Georgios Arvanitidis et al.

For robots to work alongside humans and perform in unstructured environments, they must learn new motion skills and adapt them to unseen situations on the fly. This demands learning models that capture relevant motion patterns, while offering enough flexibility to adapt the encoded skills to new requirements, such as dynamic obstacle avoidance. We introduce a Riemannian manifold perspective on this problem, and propose to learn a Riemannian manifold from human demonstrations on which geodesics are natural motion skills. We realize this with a variational autoencoder (VAE) over the space of position and orientations of the robot end-effector. Geodesic motion skills let a robot plan movements from and to arbitrary points on the data manifold. They also provide a straightforward method to avoid obstacles by redefining the ambient metric in an online fashion. Moreover, geodesics naturally exploit the manifold resulting from multiple--mode tasks to design motions that were not explicitly demonstrated previously. We test our learning framework using a 7-DoF robotic manipulator, where the robot satisfactorily learns and reproduces realistic skills featuring elaborated motion patterns, avoids previously unseen obstacles, and generates novel movements in multiple-mode settings.

Dimitris Kalatzis, Johan Ziruo Ye, Alison Pouplin et al.

We present a framework for learning probability distributions on topologically non-trivial manifolds, utilizing normalizing flows. Current methods focus on manifolds that are homeomorphic to Euclidean space, enforce strong structural priors on the learned models or use operations that do not easily scale to high dimensions. In contrast, our method learns distributions on a data manifold by "gluing" together multiple local models, thus defining an open cover of the data manifold. We demonstrate the efficiency of our approach on synthetic data of known manifolds, as well as higher dimensional manifolds of unknown topology, where our method exhibits better sample efficiency and competitive or superior performance against baselines in a number of tasks.

Jakob D. Havtorn, Jes Frellsen, Søren Hauberg et al.

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.

Nicki Skafte Detlefsen, Søren Hauberg, Wouter Boomsma

How we choose to represent our data has a fundamental impact on our ability to subsequently extract information from them. Machine learning promises to automatically determine efficient representations from large unstructured datasets, such as those arising in biology. However, empirical evidence suggests that seemingly minor changes to these machine learning models yield drastically different data representations that result in different biological interpretations of data. This begs the question of what even constitutes the most meaningful representation. Here, we approach this question for representations of protein sequences, which have received considerable attention in the recent literature. We explore two key contexts in which representations naturally arise: transfer learning and interpretable learning. In the first context, we demonstrate that several contemporary practices yield suboptimal performance, and in the latter we demonstrate that taking representation geometry into account significantly improves interpretability and lets the models reveal biological information that is otherwise obscured.

Frederik Warburg, Martin Jørgensen, Javier Civera et al.

Uncertainty quantification in image retrieval is crucial for downstream decisions, yet it remains a challenging and largely unexplored problem. Current methods for estimating uncertainties are poorly calibrated, computationally expensive, or based on heuristics. We present a new method that views image embeddings as stochastic features rather than deterministic features. Our two main contributions are (1) a likelihood that matches the triplet constraint and that evaluates the probability of an anchor being closer to a positive than a negative; and (2) a prior over the feature space that justifies the conventional l2 normalization. To ensure computational efficiency, we derive a variational approximation of the posterior, called the Bayesian triplet loss, that produces state-of-the-art uncertainty estimates and matches the predictive performance of current state-of-the-art methods.

Martin Jørgensen, Søren Hauberg

Causal discovery estimates the underlying physical process that generates the observed data: does X cause Y or does Y cause X? Current methodologies use structural conditions to turn the causal query into a statistical query, when only observational data is available. But what if these statistical queries are sensitive to causal invariants? This study investigates one such invariant: the causal relationship between X and Y is invariant to the marginal distributions of X and Y. We propose an algorithm that uses a non-parametric estimator that is robust to changes in the marginal distributions. This way we may marginalize the marginals, and inspect what relationship is intrinsically there. The resulting causal estimator is competitive with current methodologies and has high emphasis on the uncertainty in the causal query; an aspect just as important as the query itself.

Georgios Arvanitidis, Søren Hauberg, Bernhard Schölkopf

A common assumption in generative models is that the generator immerses the latent space into a Euclidean ambient space. Instead, we consider the ambient space to be a Riemannian manifold, which allows for encoding domain knowledge through the associated Riemannian metric. Shortest paths can then be defined accordingly in the latent space to both follow the learned manifold and respect the ambient geometry. Through careful design of the ambient metric we can ensure that shortest paths are well-behaved even for deterministic generators that otherwise would exhibit a misleading bias. Experimentally we show that our approach improves interpretability of learned representations both using stochastic and deterministic generators.

Martin Jørgensen, Søren Hauberg

We present a probabilistic model where the latent variable respects both the distances and the topology of the modeled data. The model leverages the Riemannian geometry of the generated manifold to endow the latent space with a well-defined stochastic distance measure, which is modeled locally as Nakagami distributions. These stochastic distances are sought to be as similar as possible to observed distances along a neighborhood graph through a censoring process. The model is inferred by variational inference based on observations of pairwise distances. We demonstrate how the new model can encode invariances in the learned manifolds.

Pola Schwöbel, Frederik Warburg, Martin Jørgensen et al.

Spatial Transformer Networks (STNs) estimate image transformations that can improve downstream tasks by `zooming in' on relevant regions in an image. However, STNs are hard to train and sensitive to mis-predictions of transformations. To circumvent these limitations, we propose a probabilistic extension that estimates a stochastic transformation rather than a deterministic one. Marginalizing transformations allows us to consider each image at multiple poses, which makes the localization task easier and the training more robust. As an additional benefit, the stochastic transformations act as a localized, learned data augmentation that improves the downstream tasks. We show across standard imaging benchmarks and on a challenging real-world dataset that these two properties lead to improved classification performance, robustness and model calibration. We further demonstrate that the approach generalizes to non-visual domains by improving model performance on time-series data.