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Barbara Rakitsch

Publications and source records attributed to Barbara Rakitsch.

17 recordsLinked to original sources
arXiv2025

Amortized Safe Active Learning for Real-Time Data Acquisition: Pretrained Neural Policies From Simulated Nonparametric Functions

Safe active learning (AL) is a sequential scheme for learning unknown systems while respecting safety constraints during data acquisition. Existing methods often rely on Gaussian processes (GPs) to model the task and safety constraints, requiring repeated GP updates and constrained acquisition optimization--incurring significant computations which are challenging for real-time decision-making. We propose amortized AL for regression and amortized safe AL, replacing expensive online computations with a pretrained neural policy. Inspired by recent advances in amortized Bayesian experimental design, we leverage GPs as pretraining simulators. We train our policy prior to the AL deployment on simulated nonparametric functions, using Fourier feature-based GP sampling and a differentiable acquisition objective that is safety-aware in the safe AL setting. At deployment, our policy selects informative and (if desired) safe queries via a single forward pass, eliminating GP inference and acquisition optimization. This leads to magnitudes of speed improvements while preserving learning quality. Our framework is modular and, without the safety component, yields fast unconstrained AL for time-sensitive tasks.

cs.LG↗
arXiv2024

Amortized Active Learning for Nonparametric Functions

Active learning (AL) is a sequential learning scheme aiming to select the most informative data. AL reduces data consumption and avoids the cost of labeling large amounts of data. However, AL trains the model and solves an acquisition optimization for each selection. It becomes expensive when the model training or acquisition optimization is challenging. In this paper, we focus on active nonparametric function learning, where the gold standard Gaussian process (GP) approaches suffer from cubic time complexity. We propose an amortized AL method, where new data are suggested by a neural network which is trained up-front without any real data (Figure 1). Our method avoids repeated model training and requires no acquisition optimization during the AL deployment. We (i) utilize GPs as function priors to construct an AL simulator, (ii) train an AL policy that can zero-shot generalize from simulation to real learning problems of nonparametric functions and (iii) achieve real-time data selection and comparable learning performances to time-consuming baseline methods.

cs.LG↗
arXiv2024

Global Safe Sequential Learning via Efficient Knowledge Transfer

Sequential learning methods, such as active learning and Bayesian optimization, aim to select the most informative data for task learning. In many applications, however, data selection is constrained by unknown safety conditions, motivating the development of safe learning approaches. A promising line of safe learning methods uses Gaussian processes to model safety conditions, restricting data selection to areas with high safety confidence. However, these methods are limited to local exploration around an initial seed dataset, as safety confidence centers around observed data points. As a consequence, task exploration is slowed down and safe regions disconnected from the initial seed dataset remain unexplored. In this paper, we propose safe transfer sequential learning to accelerate task learning and to expand the explorable safe region. By leveraging abundant offline data from a related source task, our approach guides exploration in the target task more effectively. We also provide a theoretical analysis to explain why single-task method cannot cope with disconnected regions. Finally, we introduce a computationally efficient approximation of our method that reduces runtime through pre-computations. Our experiments demonstrate that this approach, compared to state-of-the-art methods, learns tasks with lower data consumption and enhances global exploration across multiple disjoint safe regions, while maintaining comparable computational efficiency.

cs.LG↗
arXiv2023

Hybrid Modeling Design Patterns

Design patterns provide a systematic way to convey solutions to recurring modeling challenges. This paper introduces design patterns for hybrid modeling, an approach that combines modeling based on first principles with data-driven modeling techniques. While both approaches have complementary advantages there are often multiple ways to combine them into a hybrid model, and the appropriate solution will depend on the problem at hand. In this paper, we provide four base patterns that can serve as blueprints for combining data-driven components with domain knowledge into a hybrid approach. In addition, we also present two composition patterns that govern the combination of the base patterns into more complex hybrid models. Each design pattern is illustrated by typical use cases from application areas such as climate modeling, engineering, and physics.

cs.AI↗
arXiv2023

Sampling-Free Probabilistic Deep State-Space Models

Many real-world dynamical systems can be described as State-Space Models (SSMs). In this formulation, each observation is emitted by a latent state, which follows first-order Markovian dynamics. A Probabilistic Deep SSM (ProDSSM) generalizes this framework to dynamical systems of unknown parametric form, where the transition and emission models are described by neural networks with uncertain weights. In this work, we propose the first deterministic inference algorithm for models of this type. Our framework allows efficient approximations for training and testing. We demonstrate in our experiments that our new method can be employed for a variety of tasks and enjoys a superior balance between predictive performance and computational budget.

cs.LG↗
arXiv2023

Can you text what is happening? Integrating pre-trained language encoders into trajectory prediction models for autonomous driving

In autonomous driving tasks, scene understanding is the first step towards predicting the future behavior of the surrounding traffic participants. Yet, how to represent a given scene and extract its features are still open research questions. In this study, we propose a novel text-based representation of traffic scenes and process it with a pre-trained language encoder. First, we show that text-based representations, combined with classical rasterized image representations, lead to descriptive scene embeddings. Second, we benchmark our predictions on the nuScenes dataset and show significant improvements compared to baselines. Third, we show in an ablation study that a joint encoder of text and rasterized images outperforms the individual encoders confirming that both representations have their complementary strengths.

cs.CV↗
arXiv2023

Cheap and Deterministic Inference for Deep State-Space Models of Interacting Dynamical Systems

Graph neural networks are often used to model interacting dynamical systems since they gracefully scale to systems with a varying and high number of agents. While there has been much progress made for deterministic interacting systems, modeling is much more challenging for stochastic systems in which one is interested in obtaining a predictive distribution over future trajectories. Existing methods are either computationally slow since they rely on Monte Carlo sampling or make simplifying assumptions such that the predictive distribution is unimodal. In this work, we present a deep state-space model which employs graph neural networks in order to model the underlying interacting dynamical system. The predictive distribution is multimodal and has the form of a Gaussian mixture model, where the moments of the Gaussian components can be computed via deterministic moment matching rules. Our moment matching scheme can be exploited for sample-free inference, leading to more efficient and stable training compared to Monte Carlo alternatives. Furthermore, we propose structured approximations to the covariance matrices of the Gaussian components in order to scale up to systems with many agents. We benchmark our novel framework on two challenging autonomous driving datasets. Both confirm the benefits of our method compared to state-of-the-art methods. We further demonstrate the usefulness of our individual contributions in a carefully designed ablation study and provide a detailed runtime analysis of our proposed covariance approximations. Finally, we empirically demonstrate the generalization ability of our method by evaluating its performance on unseen scenarios.

cs.LG↗
arXiv2023

Combining Slow and Fast: Complementary Filtering for Dynamics Learning

Modeling an unknown dynamical system is crucial in order to predict the future behavior of the system. A standard approach is training recurrent models on measurement data. While these models typically provide exact short-term predictions, accumulating errors yield deteriorated long-term behavior. In contrast, models with reliable long-term predictions can often be obtained, either by training a robust but less detailed model, or by leveraging physics-based simulations. In both cases, inaccuracies in the models yield a lack of short-time details. Thus, different models with contrastive properties on different time horizons are available. This observation immediately raises the question: Can we obtain predictions that combine the best of both worlds? Inspired by sensor fusion tasks, we interpret the problem in the frequency domain and leverage classical methods from signal processing, in particular complementary filters. This filtering technique combines two signals by applying a high-pass filter to one signal, and low-pass filtering the other. Essentially, the high-pass filter extracts high-frequencies, whereas the low-pass filter extracts low frequencies. Applying this concept to dynamics model learning enables the construction of models that yield accurate long- and short-term predictions. Here, we propose two methods, one being purely learning-based and the other one being a hybrid model that requires an additional physics-based simulator.

cs.LG↗
arXiv2022

Learning Interacting Dynamical Systems with Latent Gaussian Process ODEs

We study time uncertainty-aware modeling of continuous-time dynamics of interacting objects. We introduce a new model that decomposes independent dynamics of single objects accurately from their interactions. By employing latent Gaussian process ordinary differential equations, our model infers both independent dynamics and their interactions with reliable uncertainty estimates. In our formulation, each object is represented as a graph node and interactions are modeled by accumulating the messages coming from neighboring objects. We show that efficient inference of such a complex network of variables is possible with modern variational sparse Gaussian process inference techniques. We empirically demonstrate that our model improves the reliability of long-term predictions over neural network based alternatives and it successfully handles missing dynamic or static information. Furthermore, we observe that only our model can successfully encapsulate independent dynamics and interaction information in distinct functions and show the benefit from this disentanglement in extrapolation scenarios.

cs.LG↗
arXiv2022

Safe Active Learning for Multi-Output Gaussian Processes

Multi-output regression problems are commonly encountered in science and engineering. In particular, multi-output Gaussian processes have been emerged as a promising tool for modeling these complex systems since they can exploit the inherent correlations and provide reliable uncertainty estimates. In many applications, however, acquiring the data is expensive and safety concerns might arise (e.g. robotics, engineering). We propose a safe active learning approach for multi-output Gaussian process regression. This approach queries the most informative data or output taking the relatedness between the regressors and safety constraints into account. We prove the effectiveness of our approach by providing theoretical analysis and by demonstrating empirical results on simulated datasets and on a real-world engineering dataset. On all datasets, our approach shows improved convergence compared to its competitors.

cs.LG↗
arXiv2021

Traversing Time with Multi-Resolution Gaussian Process State-Space Models

Gaussian Process state-space models capture complex temporal dependencies in a principled manner by placing a Gaussian Process prior on the transition function. These models have a natural interpretation as discretized stochastic differential equations, but inference for long sequences with fast and slow transitions is difficult. Fast transitions need tight discretizations whereas slow transitions require backpropagating the gradients over long subtrajectories. We propose a novel Gaussian process state-space architecture composed of multiple components, each trained on a different resolution, to model effects on different timescales. The combined model allows traversing time on adaptive scales, providing efficient inference for arbitrarily long sequences with complex dynamics. We benchmark our novel method on semi-synthetic data and on an engine modeling task. In both experiments, our approach compares favorably against its state-of-the-art alternatives that operate on a single time-scale only.

cs.LG↗
arXiv2020

Learning Partially Known Stochastic Dynamics with Empirical PAC Bayes

Neural Stochastic Differential Equations model a dynamical environment with neural nets assigned to their drift and diffusion terms. The high expressive power of their nonlinearity comes at the expense of instability in the identification of the large set of free parameters. This paper presents a recipe to improve the prediction accuracy of such models in three steps: i) accounting for epistemic uncertainty by assuming probabilistic weights, ii) incorporation of partial knowledge on the state dynamics, and iii) training the resultant hybrid model by an objective derived from a PAC-Bayesian generalization bound. We observe in our experiments that this recipe effectively translates partial and noisy prior knowledge into an improved model fit.

cs.LG↗
arXiv2020

A Deterministic Approximation to Neural SDEs

Neural Stochastic Differential Equations (NSDEs) model the drift and diffusion functions of a stochastic process as neural networks. While NSDEs are known to make accurate predictions, their uncertainty quantification properties have been remained unexplored so far. We report the empirical finding that obtaining well-calibrated uncertainty estimations from NSDEs is computationally prohibitive. As a remedy, we develop a computationally affordable deterministic scheme which accurately approximates the transition kernel, when dynamics is governed by a NSDE. Our method introduces a bidimensional moment matching algorithm: vertical along the neural net layers and horizontal along the time direction, which benefits from an original combination of effective approximations. Our deterministic approximation of the transition kernel is applicable to both training and prediction. We observe in multiple experiments that the uncertainty calibration quality of our method can be matched by Monte Carlo sampling only after introducing high computational cost. Thanks to the numerical stability of deterministic training, our method also improves prediction accuracy.

cs.LG↗
arXiv2020

Beyond the Mean-Field: Structured Deep Gaussian Processes Improve the Predictive Uncertainties

Deep Gaussian Processes learn probabilistic data representations for supervised learning by cascading multiple Gaussian Processes. While this model family promises flexible predictive distributions, exact inference is not tractable. Approximate inference techniques trade off the ability to closely resemble the posterior distribution against speed of convergence and computational efficiency. We propose a novel Gaussian variational family that allows for retaining covariances between latent processes while achieving fast convergence by marginalising out all global latent variables. After providing a proof of how this marginalisation can be done for general covariances, we restrict them to the ones we empirically found to be most important in order to also achieve computational efficiency. We provide an efficient implementation of our new approach and apply it to several benchmark datasets. It yields excellent results and strikes a better balance between accuracy and calibrated uncertainty estimates than its state-of-the-art alternatives.

stat.ML↗
arXiv2018

Learning Gaussian Processes by Minimizing PAC-Bayesian Generalization Bounds

Gaussian Processes (GPs) are a generic modelling tool for supervised learning. While they have been successfully applied on large datasets, their use in safety-critical applications is hindered by the lack of good performance guarantees. To this end, we propose a method to learn GPs and their sparse approximations by directly optimizing a PAC-Bayesian bound on their generalization performance, instead of maximizing the marginal likelihood. Besides its theoretical appeal, we find in our evaluation that our learning method is robust and yields significantly better generalization guarantees than other common GP approaches on several regression benchmark datasets.

stat.ML↗
arXiv2012

A mixed model approach for joint genetic analysis of alternatively spliced transcript isoforms using RNA-Seq data

RNA-Seq technology allows for studying the transcriptional state of the cell at an unprecedented level of detail. Beyond quantification of whole-gene expression, it is now possible to disentangle the abundance of individual alternatively spliced transcript isoforms of a gene. A central question is to understand the regulatory processes that lead to differences in relative abundance variation due to external and genetic factors. Here, we present a mixed model approach that allows for (i) joint analysis and genetic mapping of multiple transcript isoforms and (ii) mapping of isoform-specific effects. Central to our approach is to comprehensively model the causes of variation and correlation between transcript isoforms, including the genomic background and technical quantification uncertainty. As a result, our method allows to accurately test for shared as well as transcript-specific genetic regulation of transcript isoforms and achieves substantially improved calibration of these statistical tests. Experiments on genotype and RNA-Seq data from 126 human HapMap individuals demonstrate that our model can help to obtain a more fine-grained picture of the genetic basis of gene expression variation.

q-bio.GN↗
arXiv2012

LMM-Lasso: A Lasso Multi-Marker Mixed Model for Association Mapping with Population Structure Correction

Exploring the genetic basis of heritable traits remains one of the central challenges in biomedical research. In simple cases, single polymorphic loci explain a significant fraction of the phenotype variability. However, many traits of interest appear to be subject to multifactorial control by groups of genetic loci instead. Accurate detection of such multivariate associations is nontrivial and often hindered by limited power. At the same time, confounding influences such as population structure cause spurious association signals that result in false positive findings if they are not accounted for in the model. Here, we propose LMM-Lasso, a mixed model that allows for both, multi-locus mapping and correction for confounding effects. Our approach is simple and free of tuning parameters, effectively controls for population structure and scales to genome-wide datasets. We show practical use in genome-wide association studies and linkage mapping through retrospective analyses. In data from Arabidopsis thaliana and mouse, our method is able to find a genetic cause for significantly greater fractions of phenotype variation in 91% of the phenotypes considered. At the same time, our model dissects this variability into components that result from individual SNP effects and population structure. In addition to this increase of genetic heritability, enrichment of known candidate genes suggests that the associations retrieved by LMM-Lasso are more likely to be genuine.

q-bio.PE↗