arXiv subjects

Jörn-Henrik Jacobsen

Publications and source records attributed to Jörn-Henrik Jacobsen.

At least 19 recordsLinked to original sources

arXiv2025

Inferring Optical Tissue Properties from Photoplethysmography using Hybrid Amortized Inference

Smart wearables enable continuous tracking of established biomarkers such as heart rate, heart rate variability, and blood oxygen saturation via photoplethysmography (PPG). Beyond these metrics, PPG waveforms contain richer physiological information, as recent deep learning (DL) studies demonstrate. However, DL models often rely on features with unclear physiological meaning, creating a tension between predictive power, clinical interpretability, and sensor design. We address this gap by introducing PPGen, a biophysical model that relates PPG signals to interpretable physiological and optical parameters. Building on PPGen, we propose hybrid amortized inference (HAI), enabling fast, robust, and scalable estimation of relevant physiological parameters from PPG signals while correcting for model misspecification. In extensive in-silico experiments, we show that HAI can accurately infer physiological parameters under diverse noise and sensor conditions. Our results illustrate a path toward PPG models that retain the fidelity needed for DL-based features while supporting clinical interpretation and informed hardware design.

cs.LG↗

arXiv2025

Addressing Misspecification in Simulation-based Inference through Data-driven Calibration

Driven by steady progress in deep generative modeling, simulation-based inference (SBI) has emerged as the workhorse for inferring the parameters of stochastic simulators. However, recent work has demonstrated that model misspecification can compromise the reliability of SBI, preventing its adoption in important applications where only misspecified simulators are available. This work introduces robust posterior estimation~(RoPE), a framework that overcomes model misspecification with a small real-world calibration set of ground-truth parameter measurements. We formalize the misspecification gap as the solution of an optimal transport~(OT) problem between learned representations of real-world and simulated observations, allowing RoPE to learn a model of the misspecification without placing additional assumptions on its nature. RoPE demonstrates how OT and a calibration set provide a controllable balance between calibrated uncertainty and informative inference, even under severely misspecified simulators. Results on four synthetic tasks and two real-world problems with ground-truth labels demonstrate that RoPE outperforms baselines and consistently returns informative and calibrated credible intervals.

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arXiv2024

Simulation-based Inference for Cardiovascular Models

Over the past decades, hemodynamics simulators have steadily evolved and have become tools of choice for studying cardiovascular systems in-silico. While such tools are routinely used to simulate whole-body hemodynamics from physiological parameters, solving the corresponding inverse problem of mapping waveforms back to plausible physiological parameters remains both promising and challenging. Motivated by advances in simulation-based inference (SBI), we cast this inverse problem as statistical inference. In contrast to alternative approaches, SBI provides \textit{posterior distributions} for the parameters of interest, providing a \textit{multi-dimensional} representation of uncertainty for \textit{individual} measurements. We showcase this ability by performing an in-silico uncertainty analysis of five biomarkers of clinical interest comparing several measurement modalities. Beyond the corroboration of known facts, such as the feasibility of estimating heart rate, our study highlights the potential of estimating new biomarkers from standard-of-care measurements. SBI reveals practically relevant findings that cannot be captured by standard sensitivity analyses, such as the existence of sub-populations for which parameter estimation exhibits distinct uncertainty regimes. Finally, we study the gap between in-vivo and in-silico with the MIMIC-III waveform database and critically discuss how cardiovascular simulations can inform real-world data analysis.

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arXiv2024

Leveraging Cardiovascular Simulations for In-Vivo Prediction of Cardiac Biomarkers

Whole-body hemodynamics simulators, which model blood flow and pressure waveforms as functions of physiological parameters, are now essential tools for studying cardiovascular systems. However, solving the corresponding inverse problem of mapping observations (e.g., arterial pressure waveforms at specific locations in the arterial network) back to plausible physiological parameters remains challenging. Leveraging recent advances in simulation-based inference, we cast this problem as statistical inference by training an amortized neural posterior estimator on a newly built large dataset of cardiac simulations that we publicly release. To better align simulated data with real-world measurements, we incorporate stochastic elements modeling exogenous effects. The proposed framework can further integrate in-vivo data sources to refine its predictive capabilities on real-world data. In silico, we demonstrate that the proposed framework enables finely quantifying uncertainty associated with individual measurements, allowing trustworthy prediction of four biomarkers of clinical interest--namely Heart Rate, Cardiac Output, Systemic Vascular Resistance, and Left Ventricular Ejection Time--from arterial pressure waveforms and photoplethysmograms. Furthermore, we validate the framework in vivo, where our method accurately captures temporal trends in CO and SVR monitoring on the VitalDB dataset. Finally, the predictive error made by the model monotonically increases with the predicted uncertainty, thereby directly supporting the automatic rejection of unusable measurements.

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arXiv2024

Considerations for Distribution Shift Robustness of Diagnostic Models in Healthcare

We consider robustness to distribution shifts in the context of diagnostic models in healthcare, where the prediction target $Y$, e.g., the presence of a disease, is causally upstream of the observations $X$, e.g., a biomarker. Distribution shifts may occur, for instance, when the training data is collected in a domain with patients having particular demographic characteristics while the model is deployed on patients from a different demographic group. In the domain of applied ML for health, it is common to predict $Y$ from $X$ without considering further information about the patient. However, beyond the direct influence of the disease $Y$ on biomarker $X$, a predictive model may learn to exploit confounding dependencies (or shortcuts) between $X$ and $Y$ that are unstable under certain distribution shifts. In this work, we highlight a data generating mechanism common to healthcare settings and discuss how recent theoretical results from the causality literature can be applied to build robust predictive models. We theoretically show why ignoring covariates as well as common invariant learning approaches will in general not yield robust predictors in the studied setting, while including certain covariates into the prediction model will. In an extensive simulation study, we showcase the robustness (or lack thereof) of different predictors under various data generating processes. Lastly, we analyze the performance of the different approaches using the PTB-XL dataset, a public dataset of annotated ECG recordings.

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arXiv2023

Shortcut Learning in Deep Neural Networks

Deep learning has triggered the current rise of artificial intelligence and is the workhorse of today's machine intelligence. Numerous success stories have rapidly spread all over science, industry and society, but its limitations have only recently come into focus. In this perspective we seek to distill how many of deep learning's problems can be seen as different symptoms of the same underlying problem: shortcut learning. Shortcuts are decision rules that perform well on standard benchmarks but fail to transfer to more challenging testing conditions, such as real-world scenarios. Related issues are known in Comparative Psychology, Education and Linguistics, suggesting that shortcut learning may be a common characteristic of learning systems, biological and artificial alike. Based on these observations, we develop a set of recommendations for model interpretation and benchmarking, highlighting recent advances in machine learning to improve robustness and transferability from the lab to real-world applications.

cs.CV↗

arXiv2023

Robust Hybrid Learning With Expert Augmentation

Hybrid modelling reduces the misspecification of expert models by combining them with machine learning (ML) components learned from data. Similarly to many ML algorithms, hybrid model performance guarantees are limited to the training distribution. Leveraging the insight that the expert model is usually valid even outside the training domain, we overcome this limitation by introducing a hybrid data augmentation strategy termed \textit{expert augmentation}. Based on a probabilistic formalization of hybrid modelling, we demonstrate that expert augmentation, which can be incorporated into existing hybrid systems, improves generalization. We empirically validate the expert augmentation on three controlled experiments modelling dynamical systems with ordinary and partial differential equations. Finally, we assess the potential real-world applicability of expert augmentation on a dataset of a real double pendulum.

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arXiv2022

Learning Invariant Representations with Missing Data

Spurious correlations allow flexible models to predict well during training but poorly on related test distributions. Recent work has shown that models that satisfy particular independencies involving correlation-inducing \textit{nuisance} variables have guarantees on their test performance. Enforcing such independencies requires nuisances to be observed during training. However, nuisances, such as demographics or image background labels, are often missing. Enforcing independence on just the observed data does not imply independence on the entire population. Here we derive \acrshort{mmd} estimators used for invariance objectives under missing nuisances. On simulations and clinical data, optimizing through these estimates achieves test performance similar to using estimators that make use of the full data.

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arXiv2021

Understanding and Mitigating Exploding Inverses in Invertible Neural Networks

Invertible neural networks (INNs) have been used to design generative models, implement memory-saving gradient computation, and solve inverse problems. In this work, we show that commonly-used INN architectures suffer from exploding inverses and are thus prone to becoming numerically non-invertible. Across a wide range of INN use-cases, we reveal failures including the non-applicability of the change-of-variables formula on in- and out-of-distribution (OOD) data, incorrect gradients for memory-saving backprop, and the inability to sample from normalizing flow models. We further derive bi-Lipschitz properties of atomic building blocks of common architectures. These insights into the stability of INNs then provide ways forward to remedy these failures. For tasks where local invertibility is sufficient, like memory-saving backprop, we propose a flexible and efficient regularizer. For problems where global invertibility is necessary, such as applying normalizing flows on OOD data, we show the importance of designing stable INN building blocks.

cs.LG↗

arXiv2021

Environment Inference for Invariant Learning

Learning models that gracefully handle distribution shifts is central to research on domain generalization, robust optimization, and fairness. A promising formulation is domain-invariant learning, which identifies the key issue of learning which features are domain-specific versus domain-invariant. An important assumption in this area is that the training examples are partitioned into "domains" or "environments". Our focus is on the more common setting where such partitions are not provided. We propose EIIL, a general framework for domain-invariant learning that incorporates Environment Inference to directly infer partitions that are maximally informative for downstream Invariant Learning. We show that EIIL outperforms invariant learning methods on the CMNIST benchmark without using environment labels, and significantly outperforms ERM on worst-group performance in the Waterbirds and CivilComments datasets. Finally, we establish connections between EIIL and algorithmic fairness, which enables EIIL to improve accuracy and calibration in a fair prediction problem.

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arXiv2020

Your Classifier is Secretly an Energy Based Model and You Should Treat it Like One

We propose to reinterpret a standard discriminative classifier of p(y|x) as an energy based model for the joint distribution p(x,y). In this setting, the standard class probabilities can be easily computed as well as unnormalized values of p(x) and p(x|y). Within this framework, standard discriminative architectures may beused and the model can also be trained on unlabeled data. We demonstrate that energy based training of the joint distribution improves calibration, robustness, andout-of-distribution detection while also enabling our models to generate samplesrivaling the quality of recent GAN approaches. We improve upon recently proposed techniques for scaling up the training of energy based models and presentan approach which adds little overhead compared to standard classification training. Our approach is the first to achieve performance rivaling the state-of-the-artin both generative and discriminative learning within one hybrid model.

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arXiv2020

Fundamental Tradeoffs between Invariance and Sensitivity to Adversarial Perturbations

Adversarial examples are malicious inputs crafted to induce misclassification. Commonly studied sensitivity-based adversarial examples introduce semantically-small changes to an input that result in a different model prediction. This paper studies a complementary failure mode, invariance-based adversarial examples, that introduce minimal semantic changes that modify an input's true label yet preserve the model's prediction. We demonstrate fundamental tradeoffs between these two types of adversarial examples. We show that defenses against sensitivity-based attacks actively harm a model's accuracy on invariance-based attacks, and that new approaches are needed to resist both attack types. In particular, we break state-of-the-art adversarially-trained and certifiably-robust models by generating small perturbations that the models are (provably) robust to, yet that change an input's class according to human labelers. Finally, we formally show that the existence of excessively invariant classifiers arises from the presence of overly-robust predictive features in standard datasets.

cs.LG↗

arXiv2020

Residual Flows for Invertible Generative Modeling

Flow-based generative models parameterize probability distributions through an invertible transformation and can be trained by maximum likelihood. Invertible residual networks provide a flexible family of transformations where only Lipschitz conditions rather than strict architectural constraints are needed for enforcing invertibility. However, prior work trained invertible residual networks for density estimation by relying on biased log-density estimates whose bias increased with the network's expressiveness. We give a tractable unbiased estimate of the log density using a "Russian roulette" estimator, and reduce the memory required during training by using an alternative infinite series for the gradient. Furthermore, we improve invertible residual blocks by proposing the use of activation functions that avoid derivative saturation and generalizing the Lipschitz condition to induced mixed norms. The resulting approach, called Residual Flows, achieves state-of-the-art performance on density estimation amongst flow-based models, and outperforms networks that use coupling blocks at joint generative and discriminative modeling.

stat.ML↗

arXiv2020

Excessive Invariance Causes Adversarial Vulnerability

Despite their impressive performance, deep neural networks exhibit striking failures on out-of-distribution inputs. One core idea of adversarial example research is to reveal neural network errors under such distribution shifts. We decompose these errors into two complementary sources: sensitivity and invariance. We show deep networks are not only too sensitive to task-irrelevant changes of their input, as is well-known from epsilon-adversarial examples, but are also too invariant to a wide range of task-relevant changes, thus making vast regions in input space vulnerable to adversarial attacks. We show such excessive invariance occurs across various tasks and architecture types. On MNIST and ImageNet one can manipulate the class-specific content of almost any image without changing the hidden activations. We identify an insufficiency of the standard cross-entropy loss as a reason for these failures. Further, we extend this objective based on an information-theoretic analysis so it encourages the model to consider all task-dependent features in its decision. This provides the first approach tailored explicitly to overcome excessive invariance and resulting vulnerabilities.

cs.LG↗

arXiv2020

How to train your neural ODE: the world of Jacobian and kinetic regularization

Training neural ODEs on large datasets has not been tractable due to the necessity of allowing the adaptive numerical ODE solver to refine its step size to very small values. In practice this leads to dynamics equivalent to many hundreds or even thousands of layers. In this paper, we overcome this apparent difficulty by introducing a theoretically-grounded combination of both optimal transport and stability regularizations which encourage neural ODEs to prefer simpler dynamics out of all the dynamics that solve a problem well. Simpler dynamics lead to faster convergence and to fewer discretizations of the solver, considerably decreasing wall-clock time without loss in performance. Our approach allows us to train neural ODE-based generative models to the same performance as the unregularized dynamics, with significant reductions in training time. This brings neural ODEs closer to practical relevance in large-scale applications.

stat.ML↗

arXiv2020

Understanding the Limitations of Conditional Generative Models

Class-conditional generative models hold promise to overcome the shortcomings of their discriminative counterparts. They are a natural choice to solve discriminative tasks in a robust manner as they jointly optimize for predictive performance and accurate modeling of the input distribution. In this work, we investigate robust classification with likelihood-based generative models from a theoretical and practical perspective to investigate if they can deliver on their promises. Our analysis focuses on a spectrum of robustness properties: (1) Detection of worst-case outliers in the form of adversarial examples; (2) Detection of average-case outliers in the form of ambiguous inputs and (3) Detection of incorrectly labeled in-distribution inputs. Our theoretical result reveals that it is impossible to guarantee detectability of adversarially-perturbed inputs even for near-optimal generative classifiers. Experimentally, we find that while we are able to train robust models for MNIST, robustness completely breaks down on CIFAR10. We relate this failure to various undesirable model properties that can be traced to the maximum likelihood training objective. Despite being a common choice in the literature, our results indicate that likelihood-based conditional generative models may are surprisingly ineffective for robust classification.

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arXiv2019

Preventing Gradient Attenuation in Lipschitz Constrained Convolutional Networks

Lipschitz constraints under L2 norm on deep neural networks are useful for provable adversarial robustness bounds, stable training, and Wasserstein distance estimation. While heuristic approaches such as the gradient penalty have seen much practical success, it is challenging to achieve similar practical performance while provably enforcing a Lipschitz constraint. In principle, one can design Lipschitz constrained architectures using the composition property of Lipschitz functions, but Anil et al. recently identified a key obstacle to this approach: gradient norm attenuation. They showed how to circumvent this problem in the case of fully connected networks by designing each layer to be gradient norm preserving. We extend their approach to train scalable, expressive, provably Lipschitz convolutional networks. In particular, we present the Block Convolution Orthogonal Parameterization (BCOP), an expressive parameterization of orthogonal convolution operations. We show that even though the space of orthogonal convolutions is disconnected, the largest connected component of BCOP with 2n channels can represent arbitrary BCOP convolutions over n channels. Our BCOP parameterization allows us to train large convolutional networks with provable Lipschitz bounds. Empirically, we find that it is competitive with existing approaches to provable adversarial robustness and Wasserstein distance estimation.

cs.LG↗

arXiv2019

Flexibly Fair Representation Learning by Disentanglement

We consider the problem of learning representations that achieve group and subgroup fairness with respect to multiple sensitive attributes. Taking inspiration from the disentangled representation learning literature, we propose an algorithm for learning compact representations of datasets that are useful for reconstruction and prediction, but are also \emph{flexibly fair}, meaning they can be easily modified at test time to achieve subgroup demographic parity with respect to multiple sensitive attributes and their conjunctions. We show empirically that the resulting encoder---which does not require the sensitive attributes for inference---enables the adaptation of a single representation to a variety of fair classification tasks with new target labels and subgroup definitions.

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