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Jakob Runge

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14 papers

2 author rows

CLeaR Conference 2026 Conference Paper

Learning a Spatial Partitioning and its Causal Relations from Temporal Data

Philippe Brouillard
Sebastien Lachapelle
Julia Kaltenborn
Yaniv Gurwicz
Dhanya Sridhar
Alexandre Drouin
Peer Nowack
Jakob Runge

Scientific research often seeks to understand the causal structure underlying high-level variables in a system. For example, climate scientists study how phenomena, such as El Niño, affect other climate processes at remote locations across the globe. However, scientists typically collect low-level measurements, such as geographically distributed temperature readings. From these, one needs to learn both a mapping to causally-relevant latent variables, such as a high-level representation of the El Niño phenomenon and other processes, as well as the causal model over them. The challenge is that this task, called causal representation learning, is highly underdetermined from observational data alone, requiring other constraints during learning to resolve the indeterminacies. In this work, we consider the task of partitioning observed variables into disentangled factors, such as extracting regions from geographically gridded measurement data in climate research or capturing brain regions from neural activity data. We demonstrate the identifiability of the resulting model and propose a differentiable method, Causal Discovery with Single-parent Decoding (CDSD), that simultaneously learns, from temporal data, the underlying latents and a causal graph over them. We assess the validity of our theoretical results using simulated data and showcase the practical validity of our method in an application to real-world data from the climate science field.

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ICML Conference 2025 Conference Paper

Sanity Checking Causal Representation Learning on a Simple Real-World System

Juan L. Gamella
Simon Bing
Jakob Runge

We evaluate methods for causal representation learning (CRL) on a simple, real-world system where these methods are expected to work. The system consists of a controlled optical experiment specifically built for this purpose, which satisfies the core assumptions of CRL and where the underlying causal factors—the inputs to the experiment—are known, providing a ground truth. We select methods representative of different approaches to CRL and find that they all fail to recover the underlying causal factors. To understand the failure modes of the evaluated algorithms, we perform an ablation on the data by substituting the real data-generating process with a simpler synthetic equivalent. The results reveal a reproducibility problem, as most methods already fail on this synthetic ablation despite its simple data-generating process. Additionally, we observe that common assumptions on the mixing function are crucial for the performance of some of the methods but do not hold in the real data. Our efforts highlight the contrast between the theoretical promise of the state of the art and the challenges in its application. We hope the benchmark serves as a simple, real-world sanity check to further develop and validate methodology, bridging the gap towards CRL methods that work in practice. We make all code and datasets publicly available at.

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UAI Conference 2024 Conference Paper

A Global Markov Property for Solutions of Stochastic Difference Equations and the corresponding Full Time Graphs

Tom Hochsprung
Jakob Runge
Andreas Gerhardus

Structural Causal Models (SCMs) are an important tool in causal inference. They induce a graph and if the graph is acyclic, a unique observational distribution. A standard result states that in this acyclic case, the induced observational distribution satisfies a d-separation global Markov property relative to the induced graph. Time series can also be modelled like SCMs: One just interprets the stochastic difference equations that a time series solves as structural equations. However, technical problems arise when time series "start" at minus infinity. In particular, a d-separation global Markov property for time series and the corresponding infinite graphs, the so-called full time graphs, has thus far only been shown for stable vector autoregressive processes with independent finite-second-moment noise. In this paper, we prove a much more general version of this Markov property. We discuss our assumptions and study violations of them. Doing so hints at several pitfalls at the intersection of time series analysis and causal inference. Moreover, we introduce a new projection procedure for these infinite graphs which might be of independent interest.

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NeurIPS Conference 2024 Conference Paper

Causal discovery with endogenous context variables

Wiebke Günther
Oana-Iuliana Popescu
Martin Rabel
Urmi Ninad
Andreas Gerhardus
Jakob Runge

Systems with variations of the underlying generating mechanism between different contexts, i. e. , different environments or internal states in which the system operates, are common in the real world, such as soil moisture regimes in Earth science. Besides understanding the shared properties of the system, in practice, the question of context-specific properties, i. e. , the change in causal relationships between contexts, arises. For real-world data, contexts are often driven by system variables, e. g. , precipitation highly influences soil moisture. Nevertheless, this setup needs to be studied more. To account for such endogenous contexts in causal discovery, our work proposes a constraint-based method that can efficiently discover context-specific causal graphs using an adaptive testing approach. Our approach tests conditional independence on the pooled datasets to infer the dependence between system variables, including the context, to avoid introducing selection bias. To yield context-specific insights, conditional independence is tested on context-specific data. We work out the theoretical framework for this adaptive testing approach and give a detailed discussion of the connection to structural causal models, including sufficiency assumptions, which allow to prove the soundness of our algorithm and to interpret the results causally. A simulation study to evaluate numerical properties shows that our approach behaves as expected, but also leads to a further understanding of current limitations and viable extensions.

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TMLR Journal 2024 Journal Article

Invariance & Causal Representation Learning: Prospects and Limitations

Simon Bing
Tom Hochsprung
Jonas Wahl
Urmi Ninad
Jakob Runge

Learning causal representations without assumptions is known to be fundamentally impossible, thus establishing the need for suitable inductive biases. At the same time, the invariance of causal mechanisms has emerged as a promising principle to address the challenge of out-of-distribution prediction which machine learning models face. In this work, we explore this invariance principle as a candidate assumption to achieve identifiability of causal representations. While invariance has been utilized for inference in settings where the causal variables are observed, theoretical insights of this principle in the context of causal representation learning are largely missing. We assay the connection between invariance and causal representation learning by establishing impossibility results which show that invariance alone is insufficient to identify latent causal variables. Together with practical considerations, we use our results to reflect generally on the commonly used notion of identifiability in causal representation learning and potential adaptations of this goal moving forward.

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UAI Conference 2023 Conference Paper

Causal Discovery for time series from multiple datasets with latent contexts

Wiebke Günther
Urmi Ninad
Jakob Runge

Causal discovery from time series data is a typical problem setting across the sciences. Often, multiple datasets of the same system variables are available, for instance, time series of river runoff from different catchments. The local catchment systems then share certain causal parents, such as time-dependent large-scale weather over all catchments, but differ in other catchment-specific drivers, such as the altitude of the catchment. These drivers can be called temporal and spatial contexts, respectively, and are often partially unobserved. Pooling the datasets and considering the joint causal graph among system, context, and certain auxiliary variables enables us to overcome such latent confounding of system variables. In this work, we present a non-parametric time series causal discovery method, J(oint)-PCMCI$^+$, that efficiently learns such joint causal time series graphs when both observed and latent contexts are present, including time lags. We present asymptotic consistency results and numerical experiments demonstrating the utility and limitations of the method.

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NeurIPS Conference 2023 Conference Paper

ClimateSet: A Large-Scale Climate Model Dataset for Machine Learning

Julia Kaltenborn
Charlotte Lange
Venkatesh Ramesh
Philippe Brouillard
Yaniv Gurwicz
Chandni Nagda
Jakob Runge
Peer Nowack

Climate models have been key for assessing the impact of climate change and simulating future climate scenarios. The machine learning (ML) community has taken an increased interest in supporting climate scientists’ efforts on various tasks such as climate model emulation, downscaling, and prediction tasks. Many of those tasks have been addressed on datasets created with single climate models. However, both the climate science and ML communities have suggested that to address those tasks at scale, we need large, consistent, and ML-ready climate model datasets. Here, we introduce ClimateSet, a dataset containing the inputs and outputs of 36 climate models from the Input4MIPs and CMIP6 archives. In addition, we provide a modular dataset pipeline for retrieving and preprocessing additional climate models and scenarios. We showcase the potential of our dataset by using it as a benchmark for ML-based climate model emulation. We gain new insights about the performance and generalization capabilities of the different ML models by analyzing their performance across different climate models. Furthermore, the dataset can be used to train an ML emulator on several climate models instead of just one. Such a “super emulator” can quickly project new climate change scenarios, complementing existing scenarios already provided to policymakers. We believe ClimateSet will create the basis needed for the ML community to tackle climate-related tasks at scale.

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JMLR Journal 2023 Journal Article

Distinguishing Cause and Effect in Bivariate Structural Causal Models: A Systematic Investigation

Christoph Käding
Jakob Runge

Distinguishing cause and effect from purely observational data is a fundamental problem in science. Even the atomic bivariate case, seemingly the simplest, is challenging and re- quires further assumptions to be identifiable at all. In recent years a variety of approaches to address this problem has been developed, each with its own assumptions, strengths, and weaknesses. In machine learning common benchmarks with real and synthetic data have been a main driver of innovation. Synthetic benchmarks can explicitly model data characteristics such as the underlying functional relations and distributions to assess how methods deal with these. However, a systematic assessment of the state-of-the-art of meth- ods is currently missing. We provide a detailed and systematic comparison of a range of methods on a novel collection of datasets that systematically models individual data challenges. Further, we evaluate more recent methods missing in previous benchmarks. The novel suite of datasets will be contributed to the causeme.net benchmark platform to provide a continuously updated and searchable causal discovery method intercomparison database. Our aim is to assist users in finding the most suitable methods for their problem setting and for method developers to improve current and develop new methods. [abs] [ pdf ][ bib ] &copy JMLR 2023. ( edit, beta )

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UAI Conference 2023 Conference Paper

Increasing effect sizes of pairwise conditional independence tests between random vectors

Tom Hochsprung
Jonas Wahl
Andreas Gerhardus
Urmi Ninad
Jakob Runge

A simple approach to test for conditional independence of two random vectors given a third random vector is to simultaneously test for conditional independence of every pair of components of the two random vectors given the third random vector. In this work, we show that conditioning on additional components of the two random vectors that are independent given the third one increases the tests’ effect sizes while leaving the validity of the overall approach unchanged. We leverage this result to derive a practical pairwise testing algorithm that first chooses tests with a relatively large effect size and then does the actual testing. We show both numerically and theoretically that our algorithm outperforms standard pairwise independence testing and other existing methods if the dependence within the two random vectors is sufficiently high.

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AAAI Conference 2023 Conference Paper

Vector Causal Inference between Two Groups of Variables

Jonas Wahl
Urmi Ninad
Jakob Runge

Methods to identify cause-effect relationships currently mostly assume the variables to be scalar random variables. However, in many fields the objects of interest are vectors or groups of scalar variables. We present a new constraint-based non-parametric approach for inferring the causal relationship between two vector-valued random variables from observational data. Our method employs sparsity estimates of directed and undirected graphs and is based on two new principles for groupwise causal reasoning that we justify theoretically in Pearl's graphical model-based causality framework. Our theoretical considerations are complemented by two new causal discovery algorithms for causal interactions between two random vectors which find the correct causal direction reliably in simulations even if interactions are nonlinear. We evaluate our methods empirically and compare them to other state-of-the-art techniques.

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NeurIPS Conference 2022 Conference Paper

Conditional Independence Testing with Heteroskedastic Data and Applications to Causal Discovery

Wiebke Günther
Urmi Ninad
Jonas Wahl
Jakob Runge

Conditional independence (CI) testing is frequently used in data analysis and machine learning for various scientific fields and it forms the basis of constraint-based causal discovery. Oftentimes, CI testing relies on strong, rather unrealistic assumptions. One of these assumptions is homoskedasticity, in other words, a constant conditional variance is assumed. We frame heteroskedasticity in a structural causal model framework and present an adaptation of the partial correlation CI test that works well in the presence of heteroskedastic noise, given that expert knowledge about the heteroskedastic relationships is available. Further, we provide theoretical consistency results for the proposed CI test which carry over to causal discovery under certain assumptions. Numerical causal discovery experiments demonstrate that the adapted partial correlation CI test outperforms the standard test in the presence of heteroskedasticity and is on par for the homoskedastic case. Finally, we discuss the general challenges and limits as to how expert knowledge about heteroskedasticity can be accounted for in causal discovery.

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NeurIPS Conference 2021 Conference Paper

Necessary and sufficient graphical conditions for optimal adjustment sets in causal graphical models with hidden variables

Jakob Runge

The problem of selecting optimal backdoor adjustment sets to estimate causal effects in graphical models with hidden and conditioned variables is addressed. Previous work has defined optimality as achieving the smallest asymptotic estimation variance and derived an optimal set for the case without hidden variables. For the case with hidden variables there can be settings where no optimal set exists and currently only a sufficient graphical optimality criterion of limited applicability has been derived. In the present work optimality is characterized as maximizing a certain adjustment information which allows to derive a necessary and sufficient graphical criterion for the existence of an optimal adjustment set and a definition and algorithm to construct it. Further, the optimal set is valid if and only if a valid adjustment set exists and has higher (or equal) adjustment information than the Adjust-set proposed in Perkovi{\'c} et~al. [Journal of Machine Learning Research, 18: 1--62, 2018] for any graph. The results translate to minimal asymptotic estimation variance for a class of estimators whose asymptotic variance follows a certain information-theoretic relation. Numerical experiments indicate that the asymptotic results also hold for relatively small sample sizes and that the optimal adjustment set or minimized variants thereof often yield better variance also beyond that estimator class. Surprisingly, among the randomly created setups more than 90\% fulfill the optimality conditions indicating that also in many real-world scenarios graphical optimality may hold.

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UAI Conference 2020 Conference Paper

Discovering contemporaneous and lagged causal relations in autocorrelated nonlinear time series datasets

Jakob Runge

The paper introduces a novel conditional independence (CI) based method for linear and nonlinear, lagged and contemporaneous causal discovery from observational time series in the causally sufficient case. Existing CI-based methods such as the PC algorithm and also common methods from other frameworks suffer from low recall and partially inflated false positives for strong autocorrelation which is an ubiquitous challenge in time series. The novel method, PCMCI$^+$, extends PCMCI [Runge et al. , 2019b] to include discovery of contemporaneous links. PCMCI$^+$ improves the reliability of CI tests by optimizing the choice of conditioning sets and even benefits from autocorrelation. The method is order-independent and consistent in the oracle case. A broad range of numerical experiments demonstrates that PCMCI$^+$ has higher adjacency detection power and especially more contemporaneous orientation recall compared to other methods while better controlling false positives. Optimized conditioning sets also lead to much shorter runtimes than the PC algorithm. PCMCI$^+$ can be of considerable use in many real world application scenarios where often time resolutions are too coarse to resolve time delays and strong autocorrelation is present.

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NeurIPS Conference 2020 Conference Paper

High-recall causal discovery for autocorrelated time series with latent confounders

Andreas Gerhardus
Jakob Runge

We present a new method for linear and nonlinear, lagged and contemporaneous constraint-based causal discovery from observational time series in the presence of latent confounders. We show that existing causal discovery methods such as FCI and variants suffer from low recall in the autocorrelated time series case and identify low effect size of conditional independence tests as the main reason. Information-theoretical arguments show that effect size can often be increased if causal parents are included in the conditioning sets. To identify parents early on, we suggest an iterative procedure that utilizes novel orientation rules to determine ancestral relationships already during the edge removal phase. We prove that the method is order-independent, and sound and complete in the oracle case. Extensive simulation studies for different numbers of variables, time lags, sample sizes, and further cases demonstrate that our method indeed achieves much higher recall than existing methods for the case of autocorrelated continuous variables while keeping false positives at the desired level. This performance gain grows with stronger autocorrelation. At github. com/jakobrunge/tigramite we provide Python code for all methods involved in the simulation studies.

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