Markus Heinonen

Quentin Bouniot, Ievgen Redko, Anton Mallasto et al.

In the last decade, we have witnessed the introduction of several novel deep neural network (DNN) architectures exhibiting ever-increasing performance across diverse tasks. Explaining the upward trend of their performance, however, remains difficult as different DNN architectures of comparable depth and width -- common factors associated with their expressive power -- may exhibit a drastically different performance even when trained on the same dataset. In this paper, we introduce the concept of the non-linearity signature of DNN, the first theoretically sound solution for approximately measuring the non-linearity of deep neural networks. Built upon a score derived from closed-form optimal transport mappings, this signature provides a better understanding of the inner workings of a wide range of DNN architectures and learning paradigms, with a particular emphasis on the computer vision task. We provide extensive experimental results that highlight the practical usefulness of the proposed non-linearity signature and its potential for long-reaching implications. The code for our work is available at https://github.com/qbouniot/AffScoreDeep

Severi Rissanen, Markus Heinonen, Arno Solin

While diffusion models have shown great success in image generation, their noise-inverting generative process does not explicitly consider the structure of images, such as their inherent multi-scale nature. Inspired by diffusion models and the empirical success of coarse-to-fine modelling, we propose a new diffusion-like model that generates images through stochastically reversing the heat equation, a PDE that locally erases fine-scale information when run over the 2D plane of the image. We interpret the solution of the forward heat equation with constant additive noise as a variational approximation in the diffusion latent variable model. Our new model shows emergent qualitative properties not seen in standard diffusion models, such as disentanglement of overall colour and shape in images. Spectral analysis on natural images highlights connections to diffusion models and reveals an implicit coarse-to-fine inductive bias in them.

Yogesh Verma, Samuel Kaski, Markus Heinonen et al.

Generating new molecules is fundamental to advancing critical applications such as drug discovery and material synthesis. Flows can generate molecules effectively by inverting the encoding process, however, existing flow models either require artifactual dequantization or specific node/edge orderings, lack desiderata such as permutation invariance, or induce discrepancy between the encoding and the decoding steps that necessitates post hoc validity correction. We circumvent these issues with novel continuous normalizing E(3)-equivariant flows, based on a system of node ODEs coupled as a graph PDE, that repeatedly reconcile locally toward globally aligned densities. Our models can be cast as message-passing temporal networks, and result in superlative performance on the tasks of density estimation and molecular generation. In particular, our generated samples achieve state-of-the-art on both the standard QM9 and ZINC250K benchmarks.

Trung Trinh, Markus Heinonen, Luigi Acerbi et al.

Bayesian neural networks (BNNs) promise improved generalization under covariate shift by providing principled probabilistic representations of epistemic uncertainty. However, weight-based BNNs often struggle with high computational complexity of large-scale architectures and datasets. Node-based BNNs have recently been introduced as scalable alternatives, which induce epistemic uncertainty by multiplying each hidden node with latent random variables, while learning a point-estimate of the weights. In this paper, we interpret these latent noise variables as implicit representations of simple and domain-agnostic data perturbations during training, producing BNNs that perform well under covariate shift due to input corruptions. We observe that the diversity of the implicit corruptions depends on the entropy of the latent variables, and propose a straightforward approach to increase the entropy of these variables during training. We evaluate the method on out-of-distribution image classification benchmarks, and show improved uncertainty estimation of node-based BNNs under covariate shift due to input perturbations. As a side effect, the method also provides robustness against noisy training labels.

Valerii Iakovlev, Cagatay Yildiz, Markus Heinonen et al.

Training dynamic models, such as neural ODEs, on long trajectories is a hard problem that requires using various tricks, such as trajectory splitting, to make model training work in practice. These methods are often heuristics with poor theoretical justifications, and require iterative manual tuning. We propose a principled multiple shooting technique for neural ODEs that splits the trajectories into manageable short segments, which are optimised in parallel, while ensuring probabilistic control on continuity over consecutive segments. We derive variational inference for our shooting-based latent neural ODE models and propose amortized encodings of irregularly sampled trajectories with a transformer-based recognition network with temporal attention and relative positional encoding. We demonstrate efficient and stable training, and state-of-the-art performance on multiple large-scale benchmark datasets.

Giulio Franzese, Giulio Corallo, Simone Rossi et al.

We introduce Functional Diffusion Processes (FDPs), which generalize score-based diffusion models to infinite-dimensional function spaces. FDPs require a new mathematical framework to describe the forward and backward dynamics, and several extensions to derive practical training objectives. These include infinite-dimensional versions of Girsanov theorem, in order to be able to compute an ELBO, and of the sampling theorem, in order to guarantee that functional evaluations in a countable set of points are equivalent to infinite-dimensional functions. We use FDPs to build a new breed of generative models in function spaces, which do not require specialized network architectures, and that can work with any kind of continuous data. Our results on real data show that FDPs achieve high-quality image generation, using a simple MLP architecture with orders of magnitude fewer parameters than existing diffusion models.

Aarne Talman, Hande Celikkanat, Sami Virpioja et al.

This paper introduces Bayesian uncertainty modeling using Stochastic Weight Averaging-Gaussian (SWAG) in Natural Language Understanding (NLU) tasks. We apply the approach to standard tasks in natural language inference (NLI) and demonstrate the effectiveness of the method in terms of prediction accuracy and correlation with human annotation disagreements. We argue that the uncertainty representations in SWAG better reflect subjective interpretation and the natural variation that is also present in human language understanding. The results reveal the importance of uncertainty modeling, an often neglected aspect of neural language modeling, in NLU tasks.

Trung Trinh, Markus Heinonen, Luigi Acerbi et al.

Deep Ensembles (DEs) demonstrate improved accuracy, calibration and robustness to perturbations over single neural networks partly due to their functional diversity. Particle-based variational inference (ParVI) methods enhance diversity by formalizing a repulsion term based on a network similarity kernel. However, weight-space repulsion is inefficient due to over-parameterization, while direct function-space repulsion has been found to produce little improvement over DEs. To sidestep these difficulties, we propose First-order Repulsive Deep Ensemble (FoRDE), an ensemble learning method based on ParVI, which performs repulsion in the space of first-order input gradients. As input gradients uniquely characterize a function up to translation and are much smaller in dimension than the weights, this method guarantees that ensemble members are functionally different. Intuitively, diversifying the input gradients encourages each network to learn different features, which is expected to improve the robustness of an ensemble. Experiments on image classification datasets and transfer learning tasks show that FoRDE significantly outperforms the gold-standard DEs and other ensemble methods in accuracy and calibration under covariate shift due to input perturbations.

Valerii Iakovlev, Markus Heinonen, Harri Lähdesmäki

We introduce a novel grid-independent model for learning partial differential equations (PDEs) from noisy and partial observations on irregular spatiotemporal grids. We propose a space-time continuous latent neural PDE model with an efficient probabilistic framework and a novel encoder design for improved data efficiency and grid independence. The latent state dynamics are governed by a PDE model that combines the collocation method and the method of lines. We employ amortized variational inference for approximate posterior estimation and utilize a multiple shooting technique for enhanced training speed and stability. Our model demonstrates state-of-the-art performance on complex synthetic and real-world datasets, overcoming limitations of previous approaches and effectively handling partially-observed data. The proposed model outperforms recent methods, showing its potential to advance data-driven PDE modeling and enabling robust, grid-independent modeling of complex partially-observed dynamic processes.

Magnus Ross, Markus Heinonen

Hamiltonian mechanics is one of the cornerstones of natural sciences. Recently there has been significant interest in learning Hamiltonian systems in a free-form way directly from trajectory data. Previous methods have tackled the problem of learning from many short, low-noise trajectories, but learning from a small number of long, noisy trajectories, whilst accounting for model uncertainty has not been addressed. In this work, we present a Gaussian process model for Hamiltonian systems with efficient decoupled parameterisation, and introduce an energy-conserving shooting method that allows robust inference from both short and long trajectories. We demonstrate the method's success in learning Hamiltonian systems in various data settings.

Rafał Karczewski, Samuel Kaski, Markus Heinonen et al.

Several generative models with elaborate training and sampling procedures have been proposed to accelerate structure-based drug design (SBDD); however, their empirical performance turns out to be suboptimal. We seek to better understand this phenomenon from both theoretical and empirical perspectives. Since most of these models apply graph neural networks (GNNs), one may suspect that they inherit the representational limitations of GNNs. We analyze this aspect, establishing the first such results for protein-ligand complexes. A plausible counterview may attribute the underperformance of these models to their excessive parameterizations, inducing expressivity at the expense of generalization. We investigate this possibility with a simple metric-aware approach that learns an economical surrogate for affinity to infer an unlabelled molecular graph and optimizes for labels conditioned on this graph and molecular properties. The resulting model achieves state-of-the-art results using 100x fewer trainable parameters and affords up to 1000x speedup. Collectively, our findings underscore the need to reassess and redirect the existing paradigm and efforts for SBDD. Code is available at https://github.com/rafalkarczewski/SimpleSBDD.

Vishnu Raj, Tianyu Cui, Markus Heinonen et al.

Bayesian neural networks (BNNs) can account for both aleatoric and epistemic uncertainty. However, in BNNs the priors are often specified over the weights which rarely reflects true prior knowledge in large and complex neural network architectures. We present a simple approach to incorporate prior knowledge in BNNs based on external summary information about the predicted classification probabilities for a given dataset. The available summary information is incorporated as augmented data and modeled with a Dirichlet process, and we derive the corresponding \emph{Summary Evidence Lower BOund}. The approach is founded on Bayesian principles, and all hyperparameters have a proper probabilistic interpretation. We show how the method can inform the model about task difficulty and class imbalance. Extensive experiments show that, with negligible computational overhead, our method parallels and in many cases outperforms popular alternatives in accuracy, uncertainty calibration, and robustness against corruptions with both balanced and imbalanced data.

Rafał Karczewski, Markus Heinonen, Vikas Garg

We investigate what kind of images lie in the high-density regions of diffusion models. We introduce a theoretical mode-tracking process capable of pinpointing the exact mode of the denoising distribution, and we propose a practical high-density sampler that consistently generates images of higher likelihood than usual samplers. Our empirical findings reveal the existence of significantly higher likelihood samples that typical samplers do not produce, often manifesting as cartoon-like drawings or blurry images depending on the noise level. Curiously, these patterns emerge in datasets devoid of such examples. We also present a novel approach to track sample likelihoods in diffusion SDEs, which remarkably incurs no additional computational cost. Code is available at https://github.com/Aalto-QuML/high-density-diffusion.

Rafał Karczewski, Markus Heinonen, Vikas Garg

Diffusion models have emerged as a powerful class of generative models, capable of producing high-quality images by mapping noise to a data distribution. However, recent findings suggest that image likelihood does not align with perceptual quality: high-likelihood samples tend to be smooth, while lower-likelihood ones are more detailed. Controlling sample density is thus crucial for balancing realism and detail. In this paper, we analyze an existing technique, Prior Guidance, which scales the latent code to influence image detail. We introduce score alignment, a condition that explains why this method works and show that it can be tractably checked for any continuous normalizing flow model. We then propose Density Guidance, a principled modification of the generative ODE that enables exact log-density control during sampling. Finally, we extend Density Guidance to stochastic sampling, ensuring precise log-density control while allowing controlled variation in structure or fine details. Our experiments demonstrate that these techniques provide fine-grained control over image detail without compromising sample quality. Code is available at https://github.com/Aalto-QuML/density-guidance.

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

Oliver Struckmeier, Ievgen Redko, Anton Mallasto et al.

Optimal transport (OT) is a powerful geometric tool used to compare and align probability measures following the least effort principle. Despite its widespread use in machine learning (ML), OT problem still bears its computational burden, while at the same time suffering from the curse of dimensionality for measures supported on general high-dimensional spaces. In this paper, we propose to tackle these challenges using representation learning. In particular, we seek to learn an embedding space such that the samples of the two input measures become alignable in it with a simple affine mapping that can be calculated efficiently in closed-form. We then show that such approach leads to results that are comparable to solving the original OT problem when applied to the transfer learning task on which many OT baselines where previously evaluated in both homogeneous and heterogeneous DA settings. The code for our contribution is available at \url{https://github.com/Oleffa/LaOT}.

Markus Heinonen, Maria Osmala, Henrik Mannerström et al.

Metabolic flux balance analyses are a standard tool in analysing metabolic reaction rates compatible with measurements, steady-state and the metabolic reaction network stoichiometry. Flux analysis methods commonly place unrealistic assumptions on fluxes due to the convenience of formulating the problem as a linear programming model, and most methods ignore the notable uncertainty in flux estimates. We introduce a novel paradigm of Bayesian metabolic flux analysis that models the reactions of the whole genome-scale cellular system in probabilistic terms, and can infer the full flux vector distribution of genome-scale metabolic systems based on exchange and intracellular (e.g. 13C) flux measurements, steady-state assumptions, and target function assumptions. The Bayesian model couples all fluxes jointly together in a simple truncated multivariate posterior distribution, which reveals informative flux couplings. Our model is a plug-in replacement to conventional metabolic balance methods, such as flux balance analysis (FBA). Our experiments indicate that we can characterise the genome-scale flux covariances, reveal flux couplings, and determine more intracellular unobserved fluxes in C. acetobutylicum from 13C data than flux variability analysis. The COBRA compatible software is available at github.com/markusheinonen/bamfa

Yogesh Verma, Markus Heinonen, Vikas Garg

Climate and weather prediction traditionally relies on complex numerical simulations of atmospheric physics. Deep learning approaches, such as transformers, have recently challenged the simulation paradigm with complex network forecasts. However, they often act as data-driven black-box models that neglect the underlying physics and lack uncertainty quantification. We address these limitations with ClimODE, a spatiotemporal continuous-time process that implements a key principle of advection from statistical mechanics, namely, weather changes due to a spatial movement of quantities over time. ClimODE models precise weather evolution with value-conserving dynamics, learning global weather transport as a neural flow, which also enables estimating the uncertainty in predictions. Our approach outperforms existing data-driven methods in global and regional forecasting with an order of magnitude smaller parameterization, establishing a new state of the art.

Severi Rissanen, RuiKang OuYang, Jiajun He et al. · cambridge

Recent research has focused on designing neural samplers that amortize the process of sampling from unnormalized densities. However, despite significant advancements, they still fall short of the state-of-the-art MCMC approach, Parallel Tempering (PT), when it comes to the efficiency of target evaluations. On the other hand, unlike a well-trained neural sampler, PT yields only dependent samples and needs to be rerun -- at considerable computational cost -- whenever new samples are required. To address these weaknesses, we propose the Progressive Tempering Sampler with Diffusion (PTSD), which trains diffusion models sequentially across temperatures, leveraging the advantages of PT to improve the training of neural samplers. We also introduce a novel method to combine high-temperature diffusion models to generate approximate lower-temperature samples, which are minimally refined using MCMC and used to train the next diffusion model. PTSD enables efficient reuse of sample information across temperature levels while generating well-mixed, uncorrelated samples. Our method significantly improves target evaluation efficiency, outperforming diffusion-based neural samplers.

Severi Rissanen, Markus Heinonen, Arno Solin

The covariance for clean data given a noisy observation is an important quantity in many training-free guided generation methods for diffusion models. Current methods require heavy test-time computation, altering the standard diffusion training process or denoiser architecture, or making heavy approximations. We propose a new framework that sidesteps these issues by using covariance information that is available for free from training data and the curvature of the generative trajectory, which is linked to the covariance through the second-order Tweedie's formula. We integrate these sources of information using (i) a novel method to transfer covariance estimates across noise levels and (ii) low-rank updates in a given noise level. We validate the method on linear inverse problems, where it outperforms recent baselines, especially with fewer diffusion steps.

Alexandru Dumitrescu, Dani Korpela, Markus Heinonen et al.

Obtaining the desired effect of drugs is highly dependent on their molecular geometries. Thus, the current prevailing paradigm focuses on 3D point-cloud atom representations, utilizing graph neural network (GNN) parametrizations, with rotational symmetries baked in via E(3) invariant layers. We prove that such models must necessarily disregard chirality, a geometric property of the molecules that cannot be superimposed on their mirror image by rotation and translation. Chirality plays a key role in determining drug safety and potency. To address this glaring issue, we introduce a novel field-based representation, proposing reference rotations that replace rotational symmetry constraints. The proposed model captures all molecular geometries including chirality, while still achieving highly competitive performance with E(3)-based methods across standard benchmarking metrics.

Madi Matymov, Ba-Hien Tran, Michael Kampffmeyer et al.

Data Augmentation (DA) has become an essential tool to improve robustness and generalization of modern machine learning. However, when deciding on DA strategies it is critical to choose parameters carefully, and this can be a daunting task which is traditionally left to trial-and-error or expensive optimization based on validation performance. In this paper, we counter these limitations by proposing a novel framework for optimizing DA. In particular, we take a probabilistic view of DA, which leads to the interpretation of augmentation parameters as model (hyper)-parameters, and the optimization of the marginal likelihood with respect to these parameters as a Bayesian model selection problem. Due to its intractability, we derive a tractable Evidence Lower BOund (ELBO), which allows us to optimize augmentation parameters jointly with model parameters. We provide extensive theoretical results on variational approximation quality, generalization guarantees, invariance properties, and connections to empirical Bayes. Through experiments on computer vision tasks, we show that our approach improves calibration and yields robust performance over fixed or no augmentation. Our work provides a rigorous foundation for optimizing DA through Bayesian principles with significant potential for robust machine learning.

Yang Yang, Severi Rissanen, Paul E. Chang et al.

Amortized simulator-based inference offers a powerful framework for tackling Bayesian inference in computational fields such as engineering or neuroscience, increasingly leveraging modern generative methods like diffusion models to map observed data to model parameters or future predictions. These approaches yield posterior or posterior-predictive samples for new datasets without requiring further simulator calls after training on simulated parameter-data pairs. However, their applicability is often limited by the prior distribution(s) used to generate model parameters during this training phase. To overcome this constraint, we introduce PriorGuide, a technique specifically designed for diffusion-based amortized inference methods. PriorGuide leverages a novel guidance approximation that enables flexible adaptation of the trained diffusion model to new priors at test time, crucially without costly retraining. This allows users to readily incorporate updated information or expert knowledge post-training, enhancing the versatility of pre-trained inference models.

Yogesh Verma, Markus Heinonen, Vikas Garg

Protein structure prediction and folding are fundamental to understanding biology, with recent deep learning advances reshaping the field. Diffusion-based generative models have revolutionized protein design, enabling the creation of novel proteins. However, these methods often neglect the intrinsic physical realism of proteins, driven by noising dynamics that lack grounding in physical principles. To address this, we first introduce a physically motivated non-linear noising process, grounded in classical physics, that unfolds proteins into secondary structures (e.g., alpha helices, linear beta sheets) while preserving topological integrity--maintaining bonds, and preventing collisions. We then integrate this process with the flow-matching paradigm on SE(3) to model the invariant distribution of protein backbones with high fidelity, incorporating sequence information to enable sequence-conditioned folding and expand the generative capabilities of our model. Experimental results demonstrate that the proposed method achieves state-of-the-art performance in unconditional protein generation, producing more designable and novel protein structures while accurately folding monomer sequences into precise protein conformations.

Mattia Rosso, Simone Rossi, Giulio Franzese et al.

Deep learning has recently revealed the existence of scaling laws, demonstrating that model performance follows predictable trends based on dataset and model sizes. Inspired by these findings and fascinating phenomena emerging in the over-parameterized regime, we examine a parallel direction: do similar scaling laws govern predictive uncertainties in deep learning? In identifiable parametric models, such scaling laws can be derived in a straightforward manner by treating model parameters in a Bayesian way. In this case, for example, we obtain $O(1/N)$ contraction rates for epistemic uncertainty with respect to the number of data $N$. However, in over-parameterized models, these guarantees do not hold, leading to largely unexplored behaviors. In this work, we empirically show the existence of scaling laws associated with various measures of predictive uncertainty with respect to dataset and model sizes. Through experiments on vision and language tasks, we observe such scaling laws for in- and out-of-distribution predictive uncertainty estimated through popular approximate Bayesian inference and ensemble methods. Besides the elegance of scaling laws and the practical utility of extrapolating uncertainties to larger data or models, this work provides strong evidence to dispel recurring skepticism against Bayesian approaches: "In many applications of deep learning we have so much data available: what do we need Bayes for?". Our findings show that "so much data" is typically not enough to make epistemic uncertainty negligible.

Philipp Pilar, Markus Heinonen, Niklas Wahlström

Physics-informed neural networks (PINNs) have proven an effective tool for solving differential equations, in particular when considering non-standard or ill-posed settings. When inferring solutions and parameters of the differential equation from data, uncertainty estimates are preferable to point estimates, as they give an idea about the accuracy of the solution. In this work, we consider the inverse problem and employ repulsive ensembles of PINNs (RE-PINN) for obtaining such estimates. The repulsion is implemented by adding a particular repulsive term to the loss function, which has the property that the ensemble predictions correspond to the true Bayesian posterior in the limit of infinite ensemble members. Where possible, we compare the ensemble predictions to Monte Carlo baselines. Whereas the standard ensemble tends to collapse to maximum-a-posteriori solutions, the repulsive ensemble produces significantly more accurate uncertainty estimates and exhibits higher sample diversity.

Trung Trinh, Markus Heinonen, Luigi Acerbi et al.

Deep neural networks (DNNs) excel on clean images but struggle with corrupted ones. Incorporating specific corruptions into the data augmentation pipeline can improve robustness to those corruptions but may harm performance on clean images and other types of distortion. In this paper, we introduce an alternative approach that improves the robustness of DNNs to a wide range of corruptions without compromising accuracy on clean images. We first demonstrate that input perturbations can be mimicked by multiplicative perturbations in the weight space. Leveraging this, we propose Data Augmentation via Multiplicative Perturbation (DAMP), a training method that optimizes DNNs under random multiplicative weight perturbations. We also examine the recently proposed Adaptive Sharpness-Aware Minimization (ASAM) and show that it optimizes DNNs under adversarial multiplicative weight perturbations. Experiments on image classification datasets (CIFAR-10/100, TinyImageNet and ImageNet) and neural network architectures (ResNet50, ViT-S/16, ViT-B/16) show that DAMP enhances model generalization performance in the presence of corruptions across different settings. Notably, DAMP is able to train a ViT-S/16 on ImageNet from scratch, reaching the top-1 error of 23.7% which is comparable to ResNet50 without extensive data augmentations.

Markus Heinonen, Ba-Hien Tran, Michael Kampffmeyer et al.

Introducing training-time augmentations is a key technique to enhance generalization and prepare deep neural networks against test-time corruptions. Inspired by the success of generative diffusion models, we propose a novel approach of coupling data mollification, in the form of image noising and blurring, with label smoothing to align predicted label confidences with image degradation. The method is simple to implement, introduces negligible overheads, and can be combined with existing augmentations. We demonstrate improved robustness and uncertainty quantification on the corrupted image benchmarks of CIFAR, TinyImageNet and ImageNet datasets.

Yogesh Verma, Markus Heinonen, Vikas Garg

Antibodies are Y-shaped proteins that neutralize pathogens and constitute the core of our adaptive immune system. De novo generation of new antibodies that target specific antigens holds the key to accelerating vaccine discovery. However, this co-design of the amino acid sequence and the 3D structure subsumes and accentuates some central challenges from multiple tasks, including protein folding (sequence to structure), inverse folding (structure to sequence), and docking (binding). We strive to surmount these challenges with a new generative model AbODE that extends graph PDEs to accommodate both contextual information and external interactions. Unlike existing approaches, AbODE uses a single round of full-shot decoding and elicits continuous differential attention that encapsulates and evolves with latent interactions within the antibody as well as those involving the antigen. We unravel fundamental connections between AbODE and temporal networks as well as graph-matching networks. The proposed model significantly outperforms existing methods on standard metrics across benchmarks.

Zheyang Shen, Markus Heinonen, Samuel Kaski

Approximate Bayesian inference estimates descriptors of an intractable target distribution - in essence, an optimization problem within a family of distributions. For example, Langevin dynamics (LD) extracts asymptotically exact samples from a diffusion process because the time evolution of its marginal distributions constitutes a curve that minimizes the KL-divergence via steepest descent in the Wasserstein space. Parallel to LD, Stein variational gradient descent (SVGD) similarly minimizes the KL, albeit endowed with a novel Stein-Wasserstein distance, by deterministically transporting a set of particle samples, thus de-randomizes the stochastic diffusion process. We propose de-randomized kernel-based particle samplers to all diffusion-based samplers known as MCMC dynamics. Following previous work in interpreting MCMC dynamics, we equip the Stein-Wasserstein space with a fiber-Riemannian Poisson structure, with the capacity of characterizing a fiber-gradient Hamiltonian flow that simulates MCMC dynamics. Such dynamics discretizes into generalized SVGD (GSVGD), a Stein-type deterministic particle sampler, with particle updates coinciding with applying the diffusion Stein operator to a kernel function. We demonstrate empirically that GSVGD can de-randomize complex MCMC dynamics, which combine the advantages of auxiliary momentum variables and Riemannian structure, while maintaining the high sample quality from an interacting particle system.

David Blanco-Mulero, Markus Heinonen, Ville Kyrki

Graph Gaussian Processes (GGPs) provide a data-efficient solution on graph structured domains. Existing approaches have focused on static structures, whereas many real graph data represent a dynamic structure, limiting the applications of GGPs. To overcome this we propose evolving-Graph Gaussian Processes (e-GGPs). The proposed method is capable of learning the transition function of graph vertices over time with a neighbourhood kernel to model the connectivity and interaction changes between vertices. We assess the performance of our method on time-series regression problems where graphs evolve over time. We demonstrate the benefits of e-GGPs over static graph Gaussian Process approaches.

Pashupati Hegde, Çağatay Yıldız, Harri Lähdesmäki et al.

Recent machine learning advances have proposed black-box estimation of unknown continuous-time system dynamics directly from data. However, earlier works are based on approximative ODE solutions or point estimates. We propose a novel Bayesian nonparametric model that uses Gaussian processes to infer posteriors of unknown ODE systems directly from data. We derive sparse variational inference with decoupled functional sampling to represent vector field posteriors. We also introduce a probabilistic shooting augmentation to enable efficient inference from arbitrarily long trajectories. The method demonstrates the benefit of computing vector field posteriors, with predictive uncertainty scores outperforming alternative methods on multiple ODE learning tasks.

Anton Mallasto, Karol Arndt, Markus Heinonen et al.

Sample-efficient domain adaptation is an open problem in robotics. In this paper, we present affine transport -- a variant of optimal transport, which models the mapping between state transition distributions between the source and target domains with an affine transformation. First, we derive the affine transport framework; then, we extend the basic framework with Procrustes alignment to model arbitrary affine transformations. We evaluate the method in a number of OpenAI Gym sim-to-sim experiments with simulation environments, as well as on a sim-to-real domain adaptation task of a robot hitting a hockeypuck such that it slides and stops at a target position. In each experiment, we evaluate the results when transferring between each pair of dynamics domains. The results show that affine transport can significantly reduce the model adaptation error in comparison to using the original, non-adapted dynamics model.

Çağatay Yıldız, Markus Heinonen, Harri Lähdesmäki

Model-based reinforcement learning (MBRL) approaches rely on discrete-time state transition models whereas physical systems and the vast majority of control tasks operate in continuous-time. To avoid time-discretization approximation of the underlying process, we propose a continuous-time MBRL framework based on a novel actor-critic method. Our approach also infers the unknown state evolution differentials with Bayesian neural ordinary differential equations (ODE) to account for epistemic uncertainty. We implement and test our method on a new ODE-RL suite that explicitly solves continuous-time control systems. Our experiments illustrate that the model is robust against irregular and noisy data, is sample-efficient, and can solve control problems which pose challenges to discrete-time MBRL methods.

Charles Gadd, Markus Heinonen, Harri Lähdesmäki et al.

Reinforcement learning provides a framework for learning to control which actions to take towards completing a task through trial-and-error. In many applications observing interactions is costly, necessitating sample-efficient learning. In model-based reinforcement learning efficiency is improved by learning to simulate the world dynamics. The challenge is that model inaccuracies rapidly accumulate over planned trajectories. We introduce deep Gaussian processes where the depth of the compositions introduces model complexity while incorporating prior knowledge on the dynamics brings smoothness and structure. Our approach is able to sample a Bayesian posterior over trajectories. We demonstrate highly improved early sample-efficiency over competing methods. This is shown across a number of continuous control tasks, including the half-cheetah whose contact dynamics have previously posed an insurmountable problem for earlier sample-efficient Gaussian process based models.

Trung Trinh, Samuel Kaski, Markus Heinonen

We introduce implicit Bayesian neural networks, a simple and scalable approach for uncertainty representation in deep learning. Standard Bayesian approach to deep learning requires the impractical inference of the posterior distribution over millions of parameters. Instead, we propose to induce a distribution that captures the uncertainty over neural networks by augmenting each layer's inputs with latent variables. We present appropriate input distributions and demonstrate state-of-the-art performance in terms of calibration, robustness and uncertainty characterisation over large-scale, multi-million parameter image classification tasks.

Anton Mallasto, Markus Heinonen, Samuel Kaski

In machine learning and computer vision, optimal transport has had significant success in learning generative models and defining metric distances between structured and stochastic data objects, that can be cast as probability measures. The key element of optimal transport is the so called lifting of an \emph{exact} cost (distance) function, defined on the sample space, to a cost (distance) between probability measures over the sample space. However, in many real life applications the cost is \emph{stochastic}: e.g., the unpredictable traffic flow affects the cost of transportation between a factory and an outlet. To take this stochasticity into account, we introduce a Bayesian framework for inferring the optimal transport plan distribution induced by the stochastic cost, allowing for a principled way to include prior information and to model the induced stochasticity on the transport plans. Additionally, we tailor an HMC method to sample from the resulting transport plan posterior distribution.

Alexander Aushev, Henri Pesonen, Markus Heinonen et al.

In recent years, surrogate models have been successfully used in likelihood-free inference to decrease the number of simulator evaluations. The current state-of-the-art performance for this task has been achieved by Bayesian Optimization with Gaussian Processes (GPs). While this combination works well for unimodal target distributions, it is restricting the flexibility and applicability of Bayesian Optimization for accelerating likelihood-free inference more generally. We address this problem by proposing a Deep Gaussian Process (DGP) surrogate model that can handle more irregularly behaved target distributions. Our experiments show how DGPs can outperform GPs on objective functions with multimodal distributions and maintain a comparable performance in unimodal cases. This confirms that DGPs as surrogate models can extend the applicability of Bayesian Optimization for likelihood-free inference (BOLFI), while adding computational overhead that remains negligible for computationally intensive simulators.

Valerii Iakovlev, Markus Heinonen, Harri Lähdesmäki

The behavior of many dynamical systems follow complex, yet still unknown partial differential equations (PDEs). While several machine learning methods have been proposed to learn PDEs directly from data, previous methods are limited to discrete-time approximations or make the limiting assumption of the observations arriving at regular grids. We propose a general continuous-time differential model for dynamical systems whose governing equations are parameterized by message passing graph neural networks. The model admits arbitrary space and time discretizations, which removes constraints on the locations of observation points and time intervals between the observations. The model is trained with continuous-time adjoint method enabling efficient neural PDE inference. We demonstrate the model's ability to work with unstructured grids, arbitrary time steps, and noisy observations. We compare our method with existing approaches on several well-known physical systems that involve first and higher-order PDEs with state-of-the-art predictive performance.

Simone Rossi, Markus Heinonen, Edwin V. Bonilla et al.

Variational inference techniques based on inducing variables provide an elegant framework for scalable posterior estimation in Gaussian process (GP) models. Besides enabling scalability, one of their main advantages over sparse approximations using direct marginal likelihood maximization is that they provide a robust alternative for point estimation of the inducing inputs, i.e. the location of the inducing variables. In this work we challenge the common wisdom that optimizing the inducing inputs in the variational framework yields optimal performance. We show that, by revisiting old model approximations such as the fully-independent training conditionals endowed with powerful sampling-based inference methods, treating both inducing locations and GP hyper-parameters in a Bayesian way can improve performance significantly. Based on stochastic gradient Hamiltonian Monte Carlo, we develop a fully Bayesian approach to scalable GP and deep GP models, and demonstrate its state-of-the-art performance through an extensive experimental campaign across several regression and classification problems.

Çağatay Yıldız, Markus Heinonen, Harri Lähdesmäki

We present Ordinary Differential Equation Variational Auto-Encoder (ODE$^2$VAE), a latent second order ODE model for high-dimensional sequential data. Leveraging the advances in deep generative models, ODE$^2$VAE can simultaneously learn the embedding of high dimensional trajectories and infer arbitrarily complex continuous-time latent dynamics. Our model explicitly decomposes the latent space into momentum and position components and solves a second order ODE system, which is in contrast to recurrent neural network (RNN) based time series models and recently proposed black-box ODE techniques. In order to account for uncertainty, we propose probabilistic latent ODE dynamics parameterized by deep Bayesian neural networks. We demonstrate our approach on motion capture, image rotation and bouncing balls datasets. We achieve state-of-the-art performance in long term motion prediction and imputation tasks.

Zheyang Shen, Markus Heinonen, Samuel Kaski

We introduce the convolutional spectral kernel (CSK), a novel family of non-stationary, nonparametric covariance kernels for Gaussian process (GP) models, derived from the convolution between two imaginary radial basis functions. We present a principled framework to interpret CSK, as well as other deep probabilistic models, using approximated Fourier transform, yielding a concise representation of input-frequency spectrogram. Observing through the lens of the spectrogram, we provide insight on the interpretability of deep models. We then infer the functional hyperparameters using scalable variational and MCMC methods. On small- and medium-sized spatiotemporal datasets, we demonstrate improved generalization of GP models when equipped with CSK, and their capability to extract non-stationary periodic patterns.

Sami Remes, Markus Heinonen, Samuel Kaski

Standard kernels such as Matérn or RBF kernels only encode simple monotonic dependencies within the input space. Spectral mixture kernels have been proposed as general-purpose, flexible kernels for learning and discovering more complicated patterns in the data. Spectral mixture kernels have recently been generalized into non-stationary kernels by replacing the mixture weights, frequency means and variances by input-dependent functions. These functions have also been modelled as Gaussian processes on their own. In this paper we propose modelling the hyperparameter functions with neural networks, and provide an experimental comparison between the stationary spectral mixture and the two non-stationary spectral mixtures. Scalable Gaussian process inference is implemented within the sparse variational framework for all the kernels considered. We show that the neural variant of the kernel is able to achieve the best performance, among alternatives, on several benchmark datasets.

Zheyang Shen, Markus Heinonen, Samuel Kaski

The expressive power of Gaussian processes depends heavily on the choice of kernel. In this work we propose the novel harmonizable mixture kernel (HMK), a family of expressive, interpretable, non-stationary kernels derived from mixture models on the generalized spectral representation. As a theoretically sound treatment of non-stationary kernels, HMK supports harmonizable covariances, a wide subset of kernels including all stationary and many non-stationary covariances. We also propose variational Fourier features, an inter-domain sparse GP inference framework that offers a representative set of 'inducing frequencies'. We show that harmonizable mixture kernels interpolate between local patterns, and that variational Fourier features offers a robust kernel learning framework for the new kernel family.

Pashupati Hegde, Markus Heinonen, Harri Lähdesmäki et al.

We propose a novel deep learning paradigm of differential flows that learn a stochastic differential equation transformations of inputs prior to a standard classification or regression function. The key property of differential Gaussian processes is the warping of inputs through infinitely deep, but infinitesimal, differential fields, that generalise discrete layers into a dynamical system. We demonstrate state-of-the-art results that exceed the performance of deep Gaussian processes and neural networks

Kenneth Blomqvist, Samuel Kaski, Markus Heinonen

We propose deep convolutional Gaussian processes, a deep Gaussian process architecture with convolutional structure. The model is a principled Bayesian framework for detecting hierarchical combinations of local features for image classification. We demonstrate greatly improved image classification performance compared to current Gaussian process approaches on the MNIST and CIFAR-10 datasets. In particular, we improve CIFAR-10 accuracy by over 10 percentage points.

Cagatay Yildiz, Markus Heinonen, Jukka Intosalmi et al.

We introduce a novel paradigm for learning non-parametric drift and diffusion functions for stochastic differential equation (SDE). The proposed model learns to simulate path distributions that match observations with non-uniform time increments and arbitrary sparseness, which is in contrast with gradient matching that does not optimize simulated responses. We formulate sensitivity equations for learning and demonstrate that our general stochastic distribution optimisation leads to robust and efficient learning of SDE systems.

Pashupati Hegde, Markus Heinonen, Samuel Kaski

Zero-inflated datasets, which have an excess of zero outputs, are commonly encountered in problems such as climate or rare event modelling. Conventional machine learning approaches tend to overestimate the non-zeros leading to poor performance. We propose a novel model family of zero-inflated Gaussian processes (ZiGP) for such zero-inflated datasets, produced by sparse kernels through learning a latent probit Gaussian process that can zero out kernel rows and columns whenever the signal is absent. The ZiGPs are particularly useful for making the powerful Gaussian process networks more interpretable. We introduce sparse GP networks where variable-order latent modelling is achieved through sparse mixing signals. We derive the non-trivial stochastic variational inference tractably for scalable learning of the sparse kernels in both models. The novel output-sparse approach improves both prediction of zero-inflated data and interpretability of latent mixing models.

Markus Heinonen, Cagatay Yildiz, Henrik Mannerström et al.

In conventional ODE modelling coefficients of an equation driving the system state forward in time are estimated. However, for many complex systems it is practically impossible to determine the equations or interactions governing the underlying dynamics. In these settings, parametric ODE model cannot be formulated. Here, we overcome this issue by introducing a novel paradigm of nonparametric ODE modelling that can learn the underlying dynamics of arbitrary continuous-time systems without prior knowledge. We propose to learn non-linear, unknown differential functions from state observations using Gaussian process vector fields within the exact ODE formalism. We demonstrate the model's capabilities to infer dynamics from sparse data and to simulate the system forward into future.

Emmi Jokinen, Markus Heinonen, Harri Lähdesmäki

Proteins are commonly used by biochemical industry for numerous processes. Refining these proteins' properties via mutations causes stability effects as well. Accurate computational method to predict how mutations affect protein stability are necessary to facilitate efficient protein design. However, accuracy of predictive models is ultimately constrained by the limited availability of experimental data. We have developed mGPfusion, a novel Gaussian process (GP) method for predicting protein's stability changes upon single and multiple mutations. This method complements the limited experimental data with large amounts of molecular simulation data. We introduce a Bayesian data fusion model that re-calibrates the experimental and in silico data sources and then learns a predictive GP model from the combined data. Our protein-specific model requires experimental data only regarding the protein of interest and performs well even with few experimental measurements. The mGPfusion models proteins by contact maps and infers the stability effects caused by mutations with a mixture of graph kernels. Our results show that mGPfusion outperforms state-of-the-art methods in predicting protein stability on a dataset of 15 different proteins and that incorporating molecular simulation data improves the model learning and prediction accuracy.