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Thomas B. Schön

Thomas B. Schön contributes to research discovery and scholarly infrastructure.

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Published work

14 published item(s)

preprint2026arXiv

How Do Electrocardiogram Models Scale?

While scaling laws have established a fundamental framework for foundation models in natural language processing, their applicability to electrocardiogram (ECG) models remains poorly characterized. Indeed, recent studies do not always yield consistent downstream gains as one increases the model size or pre-training dataset size of ECG models, leaving the exact roles of architectural inductive biases, pre-training paradigms, and expected improvements with size largely unanswered. In this work, we systematically investigate neural and loss-to-loss scaling laws within the ECG domain. By pre-training over $120$ models (ranging from $20$K to $200$M parameters) on the large-scale CODE dataset ($2.3$M records), we decouple the effects of model architecture (ResNet vs. Transformer) and pre-training paradigm, namely supervised learning (SL) versus self-supervised learning (SSL). We found that (i) SL models are data-bottlenecked in-distribution, whereas SSL models scale robustly across both model and data sizes; (ii) for out-of-distribution (OOD) generalization, ResNets are $1.3$ to $2.5$ times more parameter-efficient than Transformers, while SSL is up to $16$ times more data-efficient and achieves up to $7.6$ times higher transfer efficiency than SL on unseen clinical tasks; (iii) across the observed scales, ResNet-based models generally achieve the lowest OOD loss, with SSL dominating on unseen clinical tasks and self-supervised Transformers overtaking at very large model sizes. Our results suggest that the path to effective ECG foundation models lies in the strategic alignment of architecture and paradigm rather than brute-force scaling.

preprint2026arXiv

Structure-Preserving Gaussian Processes Via Discrete Euler-Lagrange Equations

In this paper, we propose Lagrangian Gaussian Processes (LGPs) for probabilistic and data-efficient learning of dynamics via discrete forced Euler-Lagrange equations. Importantly, the geometric structure of the Lagrange-d'Alembert principle, which governs the motion of dynamical systems, is preserved by construction in the absence of external forces. This allows learning physically consistent models that overcome erroneous drift in the system's energy, thereby providing stable long-term predictions. At the core of our approach lie linear operators for Gaussian process conditioning, constructed from discrete forced Euler-Lagrange equations and variational discretization schemes. Thereby and unlike prior work, the method enables learning dynamics from discrete position snapshots, i.e., without access to a system's velocities or momenta. This is particularly relevant for a large class of practical scenarios where only position measurements are available, for instance, in motion capture or visual servoing applications. We demonstrate the data-efficiency and generalization capabilities of the LGPs in various synthetic and real-world case studies, including a real-world soft robot with hysteresis. The experimental results underscore that the LGPs learn physically consistent dynamics with uncertainty quantification solely from sparse positional data and enable stable long-term predictions.

preprint2022arXiv

Efficient Learning of the Parameters of Non-Linear Models using Differentiable Resampling in Particle Filters

It has been widely documented that the sampling and resampling steps in particle filters cannot be differentiated. The {\itshape reparameterisation trick} was introduced to allow the sampling step to be reformulated into a differentiable function. We extend the {\itshape reparameterisation trick} to include the stochastic input to resampling therefore limiting the discontinuities in the gradient calculation after this step. Knowing the gradients of the prior and likelihood allows us to run particle Markov Chain Monte Carlo (p-MCMC) and use the No-U-Turn Sampler (NUTS) as the proposal when estimating parameters. We compare the Metropolis-adjusted Langevin algorithm (MALA), Hamiltonian Monte Carlo with different number of steps and NUTS. We consider two state-space models and show that NUTS improves the mixing of the Markov chain and can produce more accurate results in less computational time.

preprint2021arXiv

How Convolutional Neural Networks Deal with Aliasing

The convolutional neural network (CNN) remains an essential tool in solving computer vision problems. Standard convolutional architectures consist of stacked layers of operations that progressively downscale the image. Aliasing is a well-known side-effect of downsampling that may take place: it causes high-frequency components of the original signal to become indistinguishable from its low-frequency components. While downsampling takes place in the max-pooling layers or in the strided-convolutions in these models, there is no explicit mechanism that prevents aliasing from taking place in these layers. Due to the impressive performance of these models, it is natural to suspect that they, somehow, implicitly deal with this distortion. The question we aim to answer in this paper is simply: "how and to what extent do CNNs counteract aliasing?" We explore the question by means of two examples: In the first, we assess the CNNs capability of distinguishing oscillations at the input, showing that the redundancies in the intermediate channels play an important role in succeeding at the task; In the second, we show that an image classifier CNN while, in principle, capable of implementing anti-aliasing filters, does not prevent aliasing from taking place in the intermediate layers.

preprint2021arXiv

Probabilistic programming for birth-death models of evolution using an alive particle filter with delayed sampling

We consider probabilistic programming for birth-death models of evolution and introduce a new widely-applicable inference method that combines an extension of the alive particle filter (APF) with automatic Rao-Blackwellization via delayed sampling. Birth-death models of evolution are an important family of phylogenetic models of the diversification processes that lead to evolutionary trees. Probabilistic programming languages (PPLs) give phylogeneticists a new and exciting tool: their models can be implemented as probabilistic programs with just a basic knowledge of programming. The general inference methods in PPLs reduce the need for external experts, allow quick prototyping and testing, and accelerate the development and deployment of new models. We show how these birth-death models can be implemented as simple programs in existing PPLs, and demonstrate the usefulness of the proposed inference method for such models. For the popular BiSSE model the method yields an increase of the effective sample size and the conditional acceptance rate by a factor of 30 in comparison with a standard bootstrap particle filter. Although concentrating on phylogenetics, the extended APF is a general inference method that shows its strength in situations where particles are often assigned zero weight. In the case when the weights are always positive, the extra cost of using the APF rather than the bootstrap particle filter is negligible, making our method a suitable drop-in replacement for the bootstrap particle filter in probabilistic programming inference.

preprint2020arXiv

Automated learning with a probabilistic programming language: Birch

This work offers a broad perspective on probabilistic modeling and inference in light of recent advances in probabilistic programming, in which models are formally expressed in Turing-complete programming languages. We consider a typical workflow and how probabilistic programming languages can help to automate this workflow, especially in the matching of models with inference methods. We focus on two properties of a model that are critical in this matching: its structure---the conditional dependencies between random variables---and its form---the precise mathematical definition of those dependencies. While the structure and form of a probabilistic model are often fixed a priori, it is a curiosity of probabilistic programming that they need not be, and may instead vary according to random choices made during program execution. We introduce a formal description of models expressed as programs, and discuss some of the ways in which probabilistic programming languages can reveal the structure and form of these, in order to tailor inference methods. We demonstrate the ideas with a new probabilistic programming language called Birch, with a multiple object tracking example.

preprint2020arXiv

Automatic diagnosis of the 12-lead ECG using a deep neural network

The role of automatic electrocardiogram (ECG) analysis in clinical practice is limited by the accuracy of existing models. Deep Neural Networks (DNNs) are models composed of stacked transformations that learn tasks by examples. This technology has recently achieved striking success in a variety of task and there are great expectations on how it might improve clinical practice. Here we present a DNN model trained in a dataset with more than 2 million labeled exams analyzed by the Telehealth Network of Minas Gerais and collected under the scope of the CODE (Clinical Outcomes in Digital Electrocardiology) study. The DNN outperform cardiology resident medical doctors in recognizing 6 types of abnormalities in 12-lead ECG recordings, with F1 scores above 80% and specificity over 99%. These results indicate ECG analysis based on DNNs, previously studied in a single-lead setup, generalizes well to 12-lead exams, taking the technology closer to the standard clinical practice.

preprint2020arXiv

Beyond exploding and vanishing gradients: analysing RNN training using attractors and smoothness

The exploding and vanishing gradient problem has been the major conceptual principle behind most architecture and training improvements in recurrent neural networks (RNNs) during the last decade. In this paper, we argue that this principle, while powerful, might need some refinement to explain recent developments. We refine the concept of exploding gradients by reformulating the problem in terms of the cost function smoothness, which gives insight into higher-order derivatives and the existence of regions with many close local minima. We also clarify the distinction between vanishing gradients and the need for the RNN to learn attractors to fully use its expressive power. Through the lens of these refinements, we shed new light on recent developments in the RNN field, namely stable RNN and unitary (or orthogonal) RNNs.

preprint2020arXiv

Energy-Based Models for Deep Probabilistic Regression

While deep learning-based classification is generally tackled using standardized approaches, a wide variety of techniques are employed for regression. In computer vision, one particularly popular such technique is that of confidence-based regression, which entails predicting a confidence value for each input-target pair (x,y). While this approach has demonstrated impressive results, it requires important task-dependent design choices, and the predicted confidences lack a natural probabilistic meaning. We address these issues by proposing a general and conceptually simple regression method with a clear probabilistic interpretation. In our proposed approach, we create an energy-based model of the conditional target density p(y|x), using a deep neural network to predict the un-normalized density from (x,y). This model of p(y|x) is trained by directly minimizing the associated negative log-likelihood, approximated using Monte Carlo sampling. We perform comprehensive experiments on four computer vision regression tasks. Our approach outperforms direct regression, as well as other probabilistic and confidence-based methods. Notably, our model achieves a 2.2% AP improvement over Faster-RCNN for object detection on the COCO dataset, and sets a new state-of-the-art on visual tracking when applied for bounding box estimation. In contrast to confidence-based methods, our approach is also shown to be directly applicable to more general tasks such as age and head-pose estimation. Code is available at https://github.com/fregu856/ebms_regression.

preprint2020arXiv

Evaluating Scalable Bayesian Deep Learning Methods for Robust Computer Vision

While deep neural networks have become the go-to approach in computer vision, the vast majority of these models fail to properly capture the uncertainty inherent in their predictions. Estimating this predictive uncertainty can be crucial, for example in automotive applications. In Bayesian deep learning, predictive uncertainty is commonly decomposed into the distinct types of aleatoric and epistemic uncertainty. The former can be estimated by letting a neural network output the parameters of a certain probability distribution. Epistemic uncertainty estimation is a more challenging problem, and while different scalable methods recently have emerged, no extensive comparison has been performed in a real-world setting. We therefore accept this task and propose a comprehensive evaluation framework for scalable epistemic uncertainty estimation methods in deep learning. Our proposed framework is specifically designed to test the robustness required in real-world computer vision applications. We also apply this framework to provide the first properly extensive and conclusive comparison of the two current state-of-the-art scalable methods: ensembling and MC-dropout. Our comparison demonstrates that ensembling consistently provides more reliable and practically useful uncertainty estimates. Code is available at https://github.com/fregu856/evaluating_bdl.

preprint2020arXiv

How to Train Your Energy-Based Model for Regression

Energy-based models (EBMs) have become increasingly popular within computer vision in recent years. While they are commonly employed for generative image modeling, recent work has applied EBMs also for regression tasks, achieving state-of-the-art performance on object detection and visual tracking. Training EBMs is however known to be challenging. While a variety of different techniques have been explored for generative modeling, the application of EBMs to regression is not a well-studied problem. How EBMs should be trained for best possible regression performance is thus currently unclear. We therefore accept the task of providing the first detailed study of this problem. To that end, we propose a simple yet highly effective extension of noise contrastive estimation, and carefully compare its performance to six popular methods from literature on the tasks of 1D regression and object detection. The results of this comparison suggest that our training method should be considered the go-to approach. We also apply our method to the visual tracking task, achieving state-of-the-art performance on five datasets. Notably, our tracker achieves 63.7% AUC on LaSOT and 78.7% Success on TrackingNet. Code is available at https://github.com/fregu856/ebms_regression.

preprint2020arXiv

On the smoothness of nonlinear system identification

We shed new light on the \textit{smoothness} of optimization problems arising in prediction error parameter estimation of linear and nonlinear systems. We show that for regions of the parameter space where the model is not contractive, the Lipschitz constant and $β$-smoothness of the objective function might blow up exponentially with the simulation length, making it hard to numerically find minima within those regions or, even, to escape from them. In addition to providing theoretical understanding of this problem, this paper also proposes the use of multiple shooting as a viable solution. The proposed method minimizes the error between a prediction model and the observed values. Rather than running the prediction model over the entire dataset, multiple shooting splits the data into smaller subsets and runs the prediction model over each subset, making the simulation length a design parameter and making it possible to solve problems that would be infeasible using a standard approach. The equivalence to the original problem is obtained by including constraints in the optimization. The new method is illustrated by estimating the parameters of nonlinear systems with chaotic or unstable behavior, as well as neural networks. We also present a comparative analysis of the proposed method with multi-step-ahead prediction error minimization.

preprint2020arXiv

Particle filter with rejection control and unbiased estimator of the marginal likelihood

We consider the combined use of resampling and partial rejection control in sequential Monte Carlo methods, also known as particle filters. While the variance reducing properties of rejection control are known, there has not been (to the best of our knowledge) any work on unbiased estimation of the marginal likelihood (also known as the model evidence or the normalizing constant) in this type of particle filter. Being able to estimate the marginal likelihood without bias is highly relevant for model comparison, computation of interpretable and reliable confidence intervals, and in exact approximation methods, such as particle Markov chain Monte Carlo. In the paper we present a particle filter with rejection control that enables unbiased estimation of the marginal likelihood.

preprint2020arXiv

Registration by tracking for sequential 2D MRI

Our anatomy is in constant motion. With modern MR imaging it is possible to record this motion in real-time during an ongoing radiation therapy session. In this paper we present an image registration method that exploits the sequential nature of 2D MR images to estimate the corresponding displacement field. The method employs several discriminative correlation filters that independently track specific points. Together with a sparse-to-dense interpolation scheme we can then estimate of the displacement field. The discriminative correlation filters are trained online, and our method is modality agnostic. For the interpolation scheme we use a neural network with normalized convolutions that is trained using synthetic diffeomorphic displacement fields. The method is evaluated on a segmented cardiac dataset and when compared to two conventional methods we observe an improved performance. This improvement is especially pronounced when it comes to the detection of larger motions of small objects.