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Research Group Niki Kilbertus

Link to Niki Kilbertus

Niki Kilbertus

Prof. Dr.

Principal Investigator

Ethics in Systems Design and Machine Learning

Niki Kilbertus

is Assistant Professor of Ethics in Systems Design and Machine Learning at TU Munich.

He and his team investigate the interactions between machine learning algorithms and humans with a focus on ethical consequences and trustworthiness. They currently study identification and estimation of causal effects from observational data in automated decision-making and dynamic environments.

Team members @MCML

Link to Elisabeth Ailer

Elisabeth Ailer

Ethics in Systems Design and Machine Learning

Link to Sören Becker

Sören Becker

Ethics in Systems Design and Machine Learning

Link to Cecilia Casolo

Cecilia Casolo

Ethics in Systems Design and Machine Learning

Link to Birgit Kühbacher

Birgit Kühbacher

Ethics in Systems Design and Machine Learning

Link to Zhufeng Li

Zhufeng Li

Ethics in Systems Design and Machine Learning

Link to Jiaqi Lu

Jiaqi Lu

Ethics in Systems Design and Machine Learning

Link to Kirtan Padh

Kirtan Padh

Ethics in Systems Design and Machine Learning

Link to Nora Schneider

Nora Schneider

Ethics in Systems Design and Machine Learning

Publications @MCML

[12]
E. Ailer, N. Dern, J. Hartford and N. Kilbertus.
Targeted Sequential Indirect Experiment Design.
38th Conference on Neural Information Processing Systems (NeurIPS 2024). Vancouver, Canada, Dec 10-15, 2024. To be published. Preprint at arXiv. arXiv.
Abstract

Scientific hypotheses typically concern specific aspects of complex, imperfectly understood or entirely unknown mechanisms, such as the effect of gene expression levels on phenotypes or how microbial communities influence environmental health. Such queries are inherently causal (rather than purely associational), but in many settings, experiments can not be conducted directly on the target variables of interest, but are indirect. Therefore, they perturb the target variable, but do not remove potential confounding factors. If, additionally, the resulting experimental measurements are multi-dimensional and the studied mechanisms nonlinear, the query of interest is generally not identified. We develop an adaptive strategy to design indirect experiments that optimally inform a targeted query about the ground truth mechanism in terms of sequentially narrowing the gap between an upper and lower bound on the query. While the general formulation consists of a bi-level optimization procedure, we derive an efficiently estimable analytical kernel-based estimator of the bounds for the causal effect, a query of key interest, and demonstrate the efficacy of our approach in confounded, multivariate, nonlinear synthetic settings.

MCML Authors
Link to Elisabeth Ailer

Elisabeth Ailer

Ethics in Systems Design and Machine Learning

Link to Niki Kilbertus

Niki Kilbertus

Prof. Dr.

Ethics in Systems Design and Machine Learning


[11]
B. Kühbacher, F. Iglesias-Suarez, N. Kilbertus and V. Eyring.
Towards Physically Consistent Deep Learning For Climate Model Parameterizations.
Preprint at arXiv (Oct. 2024). arXiv.
Abstract

Climate models play a critical role in understanding and projecting climate change. Due to their complexity, their horizontal resolution of about 40-100 km remains too coarse to resolve processes such as clouds and convection, which need to be approximated via parameterizations. These parameterizations are a major source of systematic errors and large uncertainties in climate projections. Deep learning (DL)-based parameterizations, trained on data from computationally expensive short, high-resolution simulations, have shown great promise for improving climate models in that regard. However, their lack of interpretability and tendency to learn spurious non-physical correlations result in reduced trust in the climate simulation. We propose an efficient supervised learning framework for DL-based parameterizations that leads to physically consistent models with improved interpretability and negligible computational overhead compared to standard supervised training. First, key features determining the target physical processes are uncovered. Subsequently, the neural network is fine-tuned using only those relevant features. We show empirically that our method robustly identifies a small subset of the inputs as actual physical drivers, therefore removing spurious non-physical relationships. This results in by design physically consistent and interpretable neural networks while maintaining the predictive performance of unconstrained black-box DL-based parameterizations.

MCML Authors
Link to Birgit Kühbacher

Birgit Kühbacher

Ethics in Systems Design and Machine Learning

Link to Niki Kilbertus

Niki Kilbertus

Prof. Dr.

Ethics in Systems Design and Machine Learning


[10]
G. Manten, C. Casolo, E. Ferrucci, S. Mogensen, C. Salvi and N. Kilbertus.
Signature Kernel Conditional Independence Tests in Causal Discovery for Stochastic Processes.
Preprint at arXiv (Oct. 2024). arXiv.
Abstract

Inferring the causal structure underlying stochastic dynamical systems from observational data holds great promise in domains ranging from science and health to finance. Such processes can often be accurately modeled via stochastic differential equations (SDEs), which naturally imply causal relationships via ‘which variables enter the differential of which other variables’. In this paper, we develop conditional independence (CI) constraints on coordinate processes over selected intervals that are Markov with respect to the acyclic dependence graph (allowing self-loops) induced by a general SDE model. We then provide a sound and complete causal discovery algorithm, capable of handling both fully and partially observed data, and uniquely recovering the underlying or induced ancestral graph by exploiting time directionality assuming a CI oracle. Finally, to make our algorithm practically usable, we also propose a flexible, consistent signature kernel-based CI test to infer these constraints from data. We extensively benchmark the CI test in isolation and as part of our causal discovery algorithms, outperforming existing approaches in SDE models and beyond.

MCML Authors
Link to Cecilia Casolo

Cecilia Casolo

Ethics in Systems Design and Machine Learning

Link to Niki Kilbertus

Niki Kilbertus

Prof. Dr.

Ethics in Systems Design and Machine Learning


[9]
T. Schwarz, C. Casolo and N. Kilbertus.
Uncertainty-Aware Optimal Treatment Selection for Clinical Time Series.
Preprint at arXiv (Oct. 2024). arXiv.
Abstract

In personalized medicine, the ability to predict and optimize treatment outcomes across various time frames is essential. Additionally, the ability to select cost-effective treatments within specific budget constraints is critical. Despite recent advancements in estimating counterfactual trajectories, a direct link to optimal treatment selection based on these estimates is missing. This paper introduces a novel method integrating counterfactual estimation techniques and uncertainty quantification to recommend personalized treatment plans adhering to predefined cost constraints. Our approach is distinctive in its handling of continuous treatment variables and its incorporation of uncertainty quantification to improve prediction reliability. We validate our method using two simulated datasets, one focused on the cardiovascular system and the other on COVID-19. Our findings indicate that our method has robust performance across different counterfactual estimation baselines, showing that introducing uncertainty quantification in these settings helps the current baselines in finding more reliable and accurate treatment selection. The robustness of our method across various settings highlights its potential for broad applicability in personalized healthcare solutions.

MCML Authors
Link to Cecilia Casolo

Cecilia Casolo

Ethics in Systems Design and Machine Learning

Link to Niki Kilbertus

Niki Kilbertus

Prof. Dr.

Ethics in Systems Design and Machine Learning


[8]
J. Schweisthal, D. Frauen, M. Schröder, K. Hess, N. Kilbertus and S. Feuerriegel.
Learning Representations of Instruments for Partial Identification of Treatment Effects.
Preprint at arXiv (Oct. 2024). arXiv.
Abstract

Reliable estimation of treatment effects from observational data is important in many disciplines such as medicine. However, estimation is challenging when unconfoundedness as a standard assumption in the causal inference literature is violated. In this work, we leverage arbitrary (potentially high-dimensional) instruments to estimate bounds on the conditional average treatment effect (CATE). Our contributions are three-fold: (1) We propose a novel approach for partial identification through a mapping of instruments to a discrete representation space so that we yield valid bounds on the CATE. This is crucial for reliable decision-making in real-world applications. (2) We derive a two-step procedure that learns tight bounds using a tailored neural partitioning of the latent instrument space. As a result, we avoid instability issues due to numerical approximations or adversarial training. Furthermore, our procedure aims to reduce the estimation variance in finite-sample settings to yield more reliable estimates. (3) We show theoretically that our procedure obtains valid bounds while reducing estimation variance. We further perform extensive experiments to demonstrate the effectiveness across various settings. Overall, our procedure offers a novel path for practitioners to make use of potentially high-dimensional instruments (e.g., as in Mendelian randomization).

MCML Authors
Link to Jonas Schweisthal

Jonas Schweisthal

Artificial Intelligence in Management

Link to Dennis Frauen

Dennis Frauen

Artificial Intelligence in Management

Link to Maresa Schröder

Maresa Schröder

Artificial Intelligence in Management

Link to Niki Kilbertus

Niki Kilbertus

Prof. Dr.

Ethics in Systems Design and Machine Learning

Link to Stefan Feuerriegel

Stefan Feuerriegel

Prof. Dr.

Artificial Intelligence in Management


[7]
A. White, A. Büttner, M. Gelbrecht, V. Duruisseaux, N. Kilbertus, F. Hellmann and N. Boers.
Projected Neural Differential Equations for Learning Constrained Dynamics.
Preprint at arXiv (Oct. 2024). arXiv.
Abstract

Neural differential equations offer a powerful approach for learning dynamics from data. However, they do not impose known constraints that should be obeyed by the learned model. It is well-known that enforcing constraints in surrogate models can enhance their generalizability and numerical stability. In this paper, we introduce projected neural differential equations (PNDEs), a new method for constraining neural differential equations based on projection of the learned vector field to the tangent space of the constraint manifold. In tests on several challenging examples, including chaotic dynamical systems and state-of-the-art power grid models, PNDEs outperform existing methods while requiring fewer hyperparameters. The proposed approach demonstrates significant potential for enhancing the modeling of constrained dynamical systems, particularly in complex domains where accuracy and reliability are essential.

MCML Authors
Link to Niki Kilbertus

Niki Kilbertus

Prof. Dr.

Ethics in Systems Design and Machine Learning


[6]
F. Quinzan, C. Casolo, K. Muandet, Y. Luo and N. Kilbertus.
Learning Counterfactually Invariant Predictors.
Transactions on Machine Learning Research (Jul. 2024). URL.
Abstract

Notions of counterfactual invariance (CI) have proven essential for predictors that are fair, robust, and generalizable in the real world. We propose graphical criteria that yield a sufficient condition for a predictor to be counterfactually invariant in terms of a conditional independence in the observational distribution. In order to learn such predictors, we propose a model-agnostic framework, called Counterfactually Invariant Prediction (CIP), building on the Hilbert-Schmidt Conditional Independence Criterion (HSCIC), a kernel-based conditional dependence measure. Our experimental results demonstrate the effectiveness of CIP in enforcing counterfactual invariance across various simulated and real-world datasets including scalar and multi-variate settings.

MCML Authors
Link to Cecilia Casolo

Cecilia Casolo

Ethics in Systems Design and Machine Learning

Link to Niki Kilbertus

Niki Kilbertus

Prof. Dr.

Ethics in Systems Design and Machine Learning


[5]
S. d'Ascoli, S. Becker, P. Schwaller, A. Mathis and N. Kilbertus.
ODEFormer: Symbolic Regression of Dynamical Systems with Transformers.
12th International Conference on Learning Representations (ICLR 2024). Vienna, Austria, May 07-11, 2024. URL. GitHub.
Abstract

We introduce ODEFormer, the first transformer able to infer multidimensional ordinary differential equation (ODE) systems in symbolic form from the observation of a single solution trajectory. We perform extensive evaluations on two datasets: (i) the existing ‘Strogatz’ dataset featuring two-dimensional systems; (ii) ODEBench, a collection of one- to four-dimensional systems that we carefully curated from the literature to provide a more holistic benchmark. ODEFormer consistently outperforms existing methods while displaying substantially improved robustness to noisy and irregularly sampled observations, as well as faster inference.

MCML Authors
Link to Sören Becker

Sören Becker

Ethics in Systems Design and Machine Learning

Link to Niki Kilbertus

Niki Kilbertus

Prof. Dr.

Ethics in Systems Design and Machine Learning


[4]
L. Eyring, D. Klein, T. Palla, N. Kilbertus, Z. Akata and F. J. Theis.
Unbalancedness in Neural Monge Maps Improves Unpaired Domain Translation.
12th International Conference on Learning Representations (ICLR 2024). Vienna, Austria, May 07-11, 2024. URL.
Abstract

In optimal transport (OT), a Monge map is known as a mapping that transports a source distribution to a target distribution in the most cost-efficient way. Recently, multiple neural estimators for Monge maps have been developed and applied in diverse unpaired domain translation tasks, e.g. in single-cell biology and computer vision. However, the classic OT framework enforces mass conservation, which makes it prone to outliers and limits its applicability in real-world scenarios. The latter can be particularly harmful in OT domain translation tasks, where the relative position of a sample within a distribution is explicitly taken into account. While unbalanced OT tackles this challenge in the discrete setting, its integration into neural Monge map estimators has received limited attention. We propose a theoretically grounded method to incorporate unbalancedness into any Monge map estimator. We improve existing estimators to model cell trajectories over time and to predict cellular responses to perturbations. Moreover, our approach seamlessly integrates with the OT flow matching (OT-FM) framework. While we show that OT-FM performs competitively in image translation, we further improve performance by incorporating unbalancedness (UOT-FM), which better preserves relevant features. We hence establish UOT-FM as a principled method for unpaired image translation.

MCML Authors
Link to Luca Eyring

Luca Eyring

Interpretable and Reliable Machine Learning

Link to Niki Kilbertus

Niki Kilbertus

Prof. Dr.

Ethics in Systems Design and Machine Learning

Link to Zeynep Akata

Zeynep Akata

Prof. Dr.

Interpretable and Reliable Machine Learning

Link to Fabian Theis

Fabian Theis

Prof. Dr.

Mathematical Modelling of Biological Systems


[3]
Z. Li, S. S. Cranganore, N. Youngblut and N. Kilbertus.
Whole Genome Transformer for Gene Interaction Effects in Microbiome Habitat Specificity.
Preprint at arXiv (May. 2024). arXiv.
Abstract

Leveraging the vast genetic diversity within microbiomes offers unparalleled insights into complex phenotypes, yet the task of accurately predicting and understanding such traits from genomic data remains challenging. We propose a framework taking advantage of existing large models for gene vectorization to predict habitat specificity from entire microbial genome sequences. Based on our model, we develop attribution techniques to elucidate gene interaction effects that drive microbial adaptation to diverse environments. We train and validate our approach on a large dataset of high quality microbiome genomes from different habitats. We not only demonstrate solid predictive performance, but also how sequence-level information of entire genomes allows us to identify gene associations underlying complex phenotypes. Our attribution recovers known important interaction networks and proposes new candidates for experimental follow up.

MCML Authors
Link to Zhufeng Li

Zhufeng Li

Ethics in Systems Design and Machine Learning

Link to Niki Kilbertus

Niki Kilbertus

Prof. Dr.

Ethics in Systems Design and Machine Learning


[2]
S. Feuerriegel, D. Frauen, V. Melnychuk, J. Schweisthal, K. Hess, A. Curth, S. Bauer, N. Kilbertus, I. S. Kohane and M. van der Schaar.
Causal machine learning for predicting treatment outcomes.
Nature Medicine 30 (Apr. 2024). DOI.
Abstract

Causal machine learning (ML) offers flexible, data-driven methods for predicting treatment outcomes including efficacy and toxicity, thereby supporting the assessment and safety of drugs. A key benefit of causal ML is that it allows for estimating individualized treatment effects, so that clinical decision-making can be personalized to individual patient profiles. Causal ML can be used in combination with both clinical trial data and real-world data, such as clinical registries and electronic health records, but caution is needed to avoid biased or incorrect predictions. In this Perspective, we discuss the benefits of causal ML (relative to traditional statistical or ML approaches) and outline the key components and steps. Finally, we provide recommendations for the reliable use of causal ML and effective translation into the clinic.

MCML Authors
Link to Stefan Feuerriegel

Stefan Feuerriegel

Prof. Dr.

Artificial Intelligence in Management

Link to Dennis Frauen

Dennis Frauen

Artificial Intelligence in Management

Link to Valentyn Melnychuk

Valentyn Melnychuk

Artificial Intelligence in Management

Link to Jonas Schweisthal

Jonas Schweisthal

Artificial Intelligence in Management

Link to Stefan Bauer

Stefan Bauer

Prof. Dr.

Algorithmic Machine Learning & Explainable AI

Link to Niki Kilbertus

Niki Kilbertus

Prof. Dr.

Ethics in Systems Design and Machine Learning


[1]
L. Hetzel, S. Boehm, N. Kilbertus, S. Günnemann, M. Lotfollahi and F. J. Theis.
Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution.
36th Conference on Neural Information Processing Systems (NeurIPS 2022). New Orleans, LA, USA, Nov 28-Dec 09, 2022. PDF.
MCML Authors
Link to Leon Hetzel

Leon Hetzel

Mathematical Modelling of Biological Systems

Link to Niki Kilbertus

Niki Kilbertus

Prof. Dr.

Ethics in Systems Design and Machine Learning

Link to Stephan Günnemann

Stephan Günnemann

Prof. Dr.

Data Analytics & Machine Learning

Link to Fabian Theis

Fabian Theis

Prof. Dr.

Mathematical Modelling of Biological Systems