Stefan Bauer

Alejandro Tejada-Lapuerta, Paul Bertin, Stefan Bauer et al.

Advances in single-cell omics allow for unprecedented insights into the transcription profiles of individual cells. When combined with large-scale perturbation screens, through which specific biological mechanisms can be targeted, these technologies allow for measuring the effect of targeted perturbations on the whole transcriptome. These advances provide an opportunity to better understand the causative role of genes in complex biological processes such as gene regulation, disease progression or cellular development. However, the high-dimensional nature of the data, coupled with the intricate complexity of biological systems renders this task nontrivial. Within the machine learning community, there has been a recent increase of interest in causality, with a focus on adapting established causal techniques and algorithms to handle high-dimensional data. In this perspective, we delineate the application of these methodologies within the realm of single-cell genomics and their challenges. We first present the model that underlies most of current causal approaches to single-cell biology and discuss and challenge the assumptions it entails from the biological point of view. We then identify open problems in the application of causal approaches to single-cell data: generalising to unseen environments, learning interpretable models, and learning causal models of dynamics. For each problem, we discuss how various research directions - including the development of computational approaches and the adaptation of experimental protocols - may offer ways forward, or on the contrary pose some difficulties. With the advent of single cell atlases and increasing perturbation data, we expect causal models to become a crucial tool for informed experimental design.

Emmanouil Angelis, Francesco Quinzan, Ashkan Soleymani et al.

Learning the causes of time-series data is a fundamental task in many applications, spanning from finance to earth sciences or bio-medical applications. Common approaches for this task are based on vector auto-regression, and they do not take into account unknown confounding between potential causes. However, in settings with many potential causes and noisy data, these approaches may be substantially biased. Furthermore, potential causes may be correlated in practical applications or even contain cycles. To address these challenges, we propose a new double machine learning based method for structure identification from temporal data (DR-SIT). We provide theoretical guarantees, showing that our method asymptotically recovers the true underlying causal structure. Our analysis extends to cases where the potential causes have cycles, and they may even be confounded. We further perform extensive experiments to showcase the superior performance of our method. Code: https://github.com/sdi1100041/TMLR_submission_DR_SIT

Chris Chinenye Emezue, Alexandre Drouin, Tristan Deleu et al.

The practical utility of causality in decision-making is widespread and brought about by the intertwining of causal discovery and causal inference. Nevertheless, a notable gap exists in the evaluation of causal discovery methods, where insufficient emphasis is placed on downstream inference. To address this gap, we evaluate seven established baseline causal discovery methods including a newly proposed method based on GFlowNets, on the downstream task of treatment effect estimation. Through the implementation of a distribution-level evaluation, we offer valuable and unique insights into the efficacy of these causal discovery methods for treatment effect estimation, considering both synthetic and real-world scenarios, as well as low-data scenarios. The results of our study demonstrate that some of the algorithms studied are able to effectively capture a wide range of useful and diverse ATE modes, while some tend to learn many low-probability modes which impacts the (unrelaxed) recall and precision.

Amir Mohammad Karimi Mamaghan, Samuele Papa, Karl Henrik Johansson et al.

Object-centric (OC) representations, which model visual scenes as compositions of discrete objects, have the potential to be used in various downstream tasks to achieve systematic compositional generalization and facilitate reasoning. However, these claims have yet to be thoroughly validated empirically. Recently, foundation models have demonstrated unparalleled capabilities across diverse domains, from language to computer vision, positioning them as a potential cornerstone of future research for a wide range of computational tasks. In this paper, we conduct an extensive empirical study on representation learning for downstream Visual Question Answering (VQA), which requires an accurate compositional understanding of the scene. We thoroughly investigate the benefits and trade-offs of OC models and alternative approaches including large pre-trained foundation models on both synthetic and real-world data, ultimately identifying a promising path to leverage the strengths of both paradigms. The extensiveness of our study, encompassing over 600 downstream VQA models and 15 different types of upstream representations, also provides several additional insights that we believe will be of interest to the community at large.

Amir Mohammad Karimi Mamaghan, Andrea Dittadi, Stefan Bauer et al.

Causal reasoning can be considered a cornerstone of intelligent systems. Having access to an underlying causal graph comes with the promise of cause-effect estimation and the identification of efficient and safe interventions. However, learning causal representations remains a major challenge, due to the complexity of many real-world systems. Previous works on causal representation learning have mostly focused on Variational Auto-Encoders (VAE). These methods only provide representations from a point estimate, and they are unsuitable to handle high dimensions. To overcome these problems, we proposed a new Diffusion-based Causal Representation Learning (DCRL) algorithm. This algorithm uses diffusion-based representations for causal discovery. DCRL offers access to infinite dimensional latent codes, which encode different levels of information in the latent code. In a first proof of principle, we investigate the use of DCRL for causal representation learning. We further demonstrate experimentally that this approach performs comparably well in identifying the causal structure and causal variables.

Stefan Feuerriegel, Dennis Frauen, Valentyn Melnychuk et al.

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.

Haroui Ma, Francesco Quinzan, Theresa Willem et al.

Machine learning (ML) systems for medical imaging have demonstrated remarkable diagnostic capabilities, but their susceptibility to biases poses significant risks, since biases may negatively impact generalization performance. In this paper, we introduce a novel statistical framework to evaluate the dependency of medical imaging ML models on sensitive attributes, such as demographics. Our method leverages the concept of counterfactual invariance, measuring the extent to which a model's predictions remain unchanged under hypothetical changes to sensitive attributes. We present a practical algorithm that combines conditional latent diffusion models with statistical hypothesis testing to identify and quantify such biases without requiring direct access to counterfactual data. Through experiments on synthetic datasets and large-scale real-world medical imaging datasets, including \textsc{cheXpert} and MIMIC-CXR, we demonstrate that our approach aligns closely with counterfactual fairness principles and outperforms standard baselines. This work provides a robust tool to ensure that ML diagnostic systems generalize well, e.g., across demographic groups, offering a critical step towards AI safety in healthcare. Code: https://github.com/Neferpitou3871/AI-Alignment-Medical-Imaging.

Arash Mehrjou, Ashkan Soleymani, Andrew Jesson et al.

In vitro cellular experimentation with genetic interventions, using for example CRISPR technologies, is an essential step in early-stage drug discovery and target validation that serves to assess initial hypotheses about causal associations between biological mechanisms and disease pathologies. With billions of potential hypotheses to test, the experimental design space for in vitro genetic experiments is extremely vast, and the available experimental capacity - even at the largest research institutions in the world - pales in relation to the size of this biological hypothesis space. Machine learning methods, such as active and reinforcement learning, could aid in optimally exploring the vast biological space by integrating prior knowledge from various information sources as well as extrapolating to yet unexplored areas of the experimental design space based on available data. However, there exist no standardised benchmarks and data sets for this challenging task and little research has been conducted in this area to date. Here, we introduce GeneDisco, a benchmark suite for evaluating active learning algorithms for experimental design in drug discovery. GeneDisco contains a curated set of multiple publicly available experimental data sets as well as open-source implementations of state-of-the-art active learning policies for experimental design and exploration.

Niklas Funk, Charles Schaff, Rishabh Madan et al.

Dexterous manipulation is a challenging and important problem in robotics. While data-driven methods are a promising approach, current benchmarks require simulation or extensive engineering support due to the sample inefficiency of popular methods. We present benchmarks for the TriFinger system, an open-source robotic platform for dexterous manipulation and the focus of the 2020 Real Robot Challenge. The benchmarked methods, which were successful in the challenge, can be generally described as structured policies, as they combine elements of classical robotics and modern policy optimization. This inclusion of inductive biases facilitates sample efficiency, interpretability, reliability and high performance. The key aspects of this benchmarking is validation of the baselines across both simulation and the real system, thorough ablation study over the core features of each solution, and a retrospective analysis of the challenge as a manipulation benchmark. The code and demo videos for this work can be found on our website (https://sites.google.com/view/benchmark-rrc).

Đorđe Miladinović, Aleksandar Stanić, Stefan Bauer et al.

How to improve generative modeling by better exploiting spatial regularities and coherence in images? We introduce a novel neural network for building image generators (decoders) and apply it to variational autoencoders (VAEs). In our spatial dependency networks (SDNs), feature maps at each level of a deep neural net are computed in a spatially coherent way, using a sequential gating-based mechanism that distributes contextual information across 2-D space. We show that augmenting the decoder of a hierarchical VAE by spatial dependency layers considerably improves density estimation over baseline convolutional architectures and the state-of-the-art among the models within the same class. Furthermore, we demonstrate that SDN can be applied to large images by synthesizing samples of high quality and coherence. In a vanilla VAE setting, we find that a powerful SDN decoder also improves learning disentangled representations, indicating that neural architectures play an important role in this task. Our results suggest favoring spatial dependency over convolutional layers in various VAE settings. The accompanying source code is given at https://github.com/djordjemila/sdn.

Ossama Ahmed, Frederik Träuble, Anirudh Goyal et al.

Despite recent successes of reinforcement learning (RL), it remains a challenge for agents to transfer learned skills to related environments. To facilitate research addressing this problem, we propose CausalWorld, a benchmark for causal structure and transfer learning in a robotic manipulation environment. The environment is a simulation of an open-source robotic platform, hence offering the possibility of sim-to-real transfer. Tasks consist of constructing 3D shapes from a given set of blocks - inspired by how children learn to build complex structures. The key strength of CausalWorld is that it provides a combinatorial family of such tasks with common causal structure and underlying factors (including, e.g., robot and object masses, colors, sizes). The user (or the agent) may intervene on all causal variables, which allows for fine-grained control over how similar different tasks (or task distributions) are. One can thus easily define training and evaluation distributions of a desired difficulty level, targeting a specific form of generalization (e.g., only changes in appearance or object mass). Further, this common parametrization facilitates defining curricula by interpolating between an initial and a target task. While users may define their own task distributions, we present eight meaningful distributions as concrete benchmarks, ranging from simple to very challenging, all of which require long-horizon planning as well as precise low-level motor control. Finally, we provide baseline results for a subset of these tasks on distinct training curricula and corresponding evaluation protocols, verifying the feasibility of the tasks in this benchmark.

Manuel Wüthrich, Felix Widmaier, Felix Grimminger et al.

Dexterous object manipulation remains an open problem in robotics, despite the rapid progress in machine learning during the past decade. We argue that a hindrance is the high cost of experimentation on real systems, in terms of both time and money. We address this problem by proposing an open-source robotic platform which can safely operate without human supervision. The hardware is inexpensive (about \SI{5000}[\$]{}) yet highly dynamic, robust, and capable of complex interaction with external objects. The software operates at 1-kilohertz and performs safety checks to prevent the hardware from breaking. The easy-to-use front-end (in C++ and Python) is suitable for real-time control as well as deep reinforcement learning. In addition, the software framework is largely robot-agnostic and can hence be used independently of the hardware proposed herein. Finally, we illustrate the potential of the proposed platform through a number of experiments, including real-time optimal control, deep reinforcement learning from scratch, throwing, and writing.

Tarun Gupta, Wenbo Gong, Chao Ma et al.

Recent advances in foundation models, especially in large multi-modal models and conversational agents, have ignited interest in the potential of generally capable embodied agents. Such agents will require the ability to perform new tasks in many different real-world environments. However, current foundation models fail to accurately model physical interactions and are therefore insufficient for Embodied AI. The study of causality lends itself to the construction of veridical world models, which are crucial for accurately predicting the outcomes of possible interactions. This paper focuses on the prospects of building foundation world models for the upcoming generation of embodied agents and presents a novel viewpoint on the significance of causality within these. We posit that integrating causal considerations is vital to facilitating meaningful physical interactions with the world. Finally, we demystify misconceptions about causality in this context and present our outlook for future research.

Leonard Waldmann, Ando Shah, Yi Wang et al.

Earth observation (EO) data features diverse sensing platforms with varying spectral bands, spatial resolutions, and sensing modalities. While most prior work has constrained inputs to fixed sensors, a new class of any-sensor foundation models able to process arbitrary sensors has recently emerged. Contributing to this line of work, we propose Panopticon, an any-sensor foundation model built on the DINOv2 framework. We extend DINOv2 by (1) treating images of the same geolocation across sensors as natural augmentations, (2) subsampling channels to diversify spectral input, and (3) adding a cross attention over channels as a flexible patch embedding mechanism. By encoding the wavelength and modes of optical and synthetic aperture radar sensors, respectively, Panopticon can effectively process any combination of arbitrary channels. In extensive evaluations, we achieve state-of-the-art performance on GEO-Bench, especially on the widely-used Sentinel-1 and Sentinel-2 sensors, while out-competing other any-sensor models, as well as domain adapted fixed-sensor models on unique sensor configurations. Panopticon enables immediate generalization to both existing and future satellite platforms, advancing sensor-agnostic EO.

Mihir Mahajan, Alfred Nguyen, Franz Srambical et al.

While world models are increasingly positioned as a pathway to overcoming data scarcity in domains such as robotics, open training infrastructure for world modeling remains nascent. We introduce Jasmine, a performant JAX-based world modeling codebase that scales from single hosts to hundreds of accelerators with minimal code changes. Jasmine achieves an order-of-magnitude faster reproduction of the CoinRun case study compared to prior open implementations, enabled by performance optimizations across data loading, training and checkpointing. The codebase guarantees fully reproducible training and supports diverse sharding configurations. By pairing Jasmine with curated large-scale datasets, we establish infrastructure for rigorous benchmarking pipelines across model families and architectural ablations.

Yashas Annadani, Syrine Belakaria, Stefano Ermon et al.

Offline multi-objective optimization aims to identify Pareto-optimal solutions given a dataset of designs and their objective values. In this work, we propose a preference-guided diffusion model that generates Pareto-optimal designs by leveraging a classifier-based guidance mechanism. Our guidance classifier is a preference model trained to predict the probability that one design dominates another, directing the diffusion model toward optimal regions of the design space. Crucially, this preference model generalizes beyond the training distribution, enabling the discovery of Pareto-optimal solutions outside the observed dataset. We introduce a novel diversity-aware preference guidance, augmenting Pareto dominance preference with diversity criteria. This ensures that generated solutions are optimal and well-distributed across the objective space, a capability absent in prior generative methods for offline multi-objective optimization. We evaluate our approach on various continuous offline multi-objective optimization tasks and find that it consistently outperforms other inverse/generative approaches while remaining competitive with forward/surrogate-based optimization methods. Our results highlight the effectiveness of classifier-guided diffusion models in generating diverse and high-quality solutions that approximate the Pareto front well.

R. Patrick Xian, Qiming Cui, Stefan Bauer et al. · berkeley

Temporal progression is an integral part of knowledge accumulation and update. Web search is frequently adopted as grounding for agent knowledge, yet an improper configuration affects the quality of the agent's responses. Here, we assess the agent behavior using distinct date-controlled tools (DCTs) as stress test to measure the knowledge variability of large language model (LLM) agents. We demonstrate the temporal effects of an LLM agent as a writing assistant, which uses web search to complete scientific publication abstracts. We show that the temporality of search engine translates into tool-dependent agent performance but can be alleviated with base model choice and explicit reasoning instructions such as chain-of-thought prompting. Our results indicate that agent design and evaluations should take a dynamical view and implement measures to account for the temporal influence of external resources to ensure reliability.

Paul Bertin, Joseph D. Viviano, Alejandro Tejada-Lapuerta et al.

Single-cell data provide high-dimensional measurements of the transcriptional states of cells, but extracting insights into the regulatory functions of genes, particularly identifying transcriptional mechanisms affected by biological perturbations, remains a challenge. Many perturbations induce compensatory cellular responses, making it difficult to distinguish direct from indirect effects on gene regulation. Modeling how gene regulatory functions shape the temporal dynamics of these responses is key to improving our understanding of biological perturbations. Dynamical models based on differential equations offer a principled way to capture transcriptional dynamics, but their application to single-cell data has been hindered by computational constraints, stochasticity, sparsity, and noise. Existing methods either rely on low-dimensional representations or make strong simplifying assumptions, limiting their ability to model transcriptional dynamics at scale. We introduce a Functional and Learnable model of Cell dynamicS, FLeCS, that incorporates gene network structure into coupled differential equations to model gene regulatory functions. Given (pseudo)time-series single-cell data, FLeCS accurately infers cell dynamics at scale, provides improved functional insights into transcriptional mechanisms perturbed by gene knockouts, both in myeloid differentiation and K562 Perturb-seq experiments, and simulates single-cell trajectories of A549 cells following small-molecule perturbations.

Yukun Chen, Andrea Dittadi, Frederik Träuble et al.

Disentanglement is hypothesized to be beneficial towards a number of downstream tasks. However, a common assumption in learning disentangled representations is that the data generative factors are statistically independent. As current methods are almost solely evaluated on toy datasets where this ideal assumption holds, we investigate their performance in hierarchical settings, a relevant feature of real-world data. In this work, we introduce Boxhead, a dataset with hierarchically structured ground-truth generative factors. We use this novel dataset to evaluate the performance of state-of-the-art autoencoder-based disentanglement models and observe that hierarchical models generally outperform single-layer VAEs in terms of disentanglement of hierarchically arranged factors.

Nino Scherrer, Olexa Bilaniuk, Yashas Annadani et al.

Discovering causal structures from data is a challenging inference problem of fundamental importance in all areas of science. The appealing properties of neural networks have recently led to a surge of interest in differentiable neural network-based methods for learning causal structures from data. So far, differentiable causal discovery has focused on static datasets of observational or fixed interventional origin. In this work, we introduce an active intervention targeting (AIT) method which enables a quick identification of the underlying causal structure of the data-generating process. Our method significantly reduces the required number of interactions compared with random intervention targeting and is applicable for both discrete and continuous optimization formulations of learning the underlying directed acyclic graph (DAG) from data. We examine the proposed method across multiple frameworks in a wide range of settings and demonstrate superior performance on multiple benchmarks from simulated to real-world data.

Arthur Allshire, Mayank Mittal, Varun Lodaya et al.

We present a system for learning a challenging dexterous manipulation task involving moving a cube to an arbitrary 6-DoF pose with only 3-fingers trained with NVIDIA's IsaacGym simulator. We show empirical benefits, both in simulation and sim-to-real transfer, of using keypoints as opposed to position+quaternion representations for the object pose in 6-DoF for policy observations and in reward calculation to train a model-free reinforcement learning agent. By utilizing domain randomization strategies along with the keypoint representation of the pose of the manipulated object, we achieve a high success rate of 83% on a remote TriFinger system maintained by the organizers of the Real Robot Challenge. With the aim of assisting further research in learning in-hand manipulation, we make the codebase of our system, along with trained checkpoints that come with billions of steps of experience available, at https://s2r2-ig.github.io

Nan Rosemary Ke, Aniket Didolkar, Sarthak Mittal et al.

Inducing causal relationships from observations is a classic problem in machine learning. Most work in causality starts from the premise that the causal variables themselves are observed. However, for AI agents such as robots trying to make sense of their environment, the only observables are low-level variables like pixels in images. To generalize well, an agent must induce high-level variables, particularly those which are causal or are affected by causal variables. A central goal for AI and causality is thus the joint discovery of abstract representations and causal structure. However, we note that existing environments for studying causal induction are poorly suited for this objective because they have complicated task-specific causal graphs which are impossible to manipulate parametrically (e.g., number of nodes, sparsity, causal chain length, etc.). In this work, our goal is to facilitate research in learning representations of high-level variables as well as causal structures among them. In order to systematically probe the ability of methods to identify these variables and structures, we design a suite of benchmarking RL environments. We evaluate various representation learning algorithms from the literature and find that explicitly incorporating structure and modularity in models can help causal induction in model-based reinforcement learning.

Yashas Annadani, Jonas Rothfuss, Alexandre Lacoste et al.

Learning the causal structure that underlies data is a crucial step towards robust real-world decision making. The majority of existing work in causal inference focuses on determining a single directed acyclic graph (DAG) or a Markov equivalence class thereof. However, a crucial aspect to acting intelligently upon the knowledge about causal structure which has been inferred from finite data demands reasoning about its uncertainty. For instance, planning interventions to find out more about the causal mechanisms that govern our data requires quantifying epistemic uncertainty over DAGs. While Bayesian causal inference allows to do so, the posterior over DAGs becomes intractable even for a small number of variables. Aiming to overcome this issue, we propose a form of variational inference over the graphs of Structural Causal Models (SCMs). To this end, we introduce a parametric variational family modelled by an autoregressive distribution over the space of discrete DAGs. Its number of parameters does not grow exponentially with the number of variables and can be tractably learned by maximising an Evidence Lower Bound (ELBO). In our experiments, we demonstrate that the proposed variational posterior is able to provide a good approximation of the true posterior.

Sonali Parbhoo, Stefan Bauer, Patrick Schwab

Estimating an individual's potential response to interventions from observational data is of high practical relevance for many domains, such as healthcare, public policy or economics. In this setting, it is often the case that combinations of interventions may be applied simultaneously, for example, multiple prescriptions in healthcare or different fiscal and monetary measures in economics. However, existing methods for counterfactual inference are limited to settings in which actions are not used simultaneously. Here, we present Neural Counterfactual Relation Estimation (NCoRE), a new method for learning counterfactual representations in the combination treatment setting that explicitly models cross-treatment interactions. NCoRE is based on a novel branched conditional neural representation that includes learnt treatment interaction modulators to infer the potential causal generative process underlying the combination of multiple treatments. Our experiments show that NCoRE significantly outperforms existing state-of-the-art methods for counterfactual treatment effect estimation that do not account for the effects of combining multiple treatments across several synthetic, semi-synthetic and real-world benchmarks.

Bernhard Schölkopf, Francesco Locatello, Stefan Bauer et al.

The two fields of machine learning and graphical causality arose and developed separately. However, there is now cross-pollination and increasing interest in both fields to benefit from the advances of the other. In the present paper, we review fundamental concepts of causal inference and relate them to crucial open problems of machine learning, including transfer and generalization, thereby assaying how causality can contribute to modern machine learning research. This also applies in the opposite direction: we note that most work in causality starts from the premise that the causal variables are given. A central problem for AI and causality is, thus, causal representation learning, the discovery of high-level causal variables from low-level observations. Finally, we delineate some implications of causality for machine learning and propose key research areas at the intersection of both communities.

Andrea Dittadi, Frederik Träuble, Francesco Locatello et al.

Learning meaningful representations that disentangle the underlying structure of the data generating process is considered to be of key importance in machine learning. While disentangled representations were found to be useful for diverse tasks such as abstract reasoning and fair classification, their scalability and real-world impact remain questionable. We introduce a new high-resolution dataset with 1M simulated images and over 1,800 annotated real-world images of the same setup. In contrast to previous work, this new dataset exhibits correlations, a complex underlying structure, and allows to evaluate transfer to unseen simulated and real-world settings where the encoder i) remains in distribution or ii) is out of distribution. We propose new architectures in order to scale disentangled representation learning to realistic high-resolution settings and conduct a large-scale empirical study of disentangled representations on this dataset. We observe that disentanglement is a good predictor for out-of-distribution (OOD) task performance.

Muhammad Waleed Gondal, Shruti Joshi, Nasim Rahaman et al.

Meta-learning algorithms adapt quickly to new tasks that are drawn from the same task distribution as the training tasks. The mechanism leading to fast adaptation is the conditioning of a downstream predictive model on the inferred representation of the task's underlying data generative process, or \emph{function}. This \emph{meta-representation}, which is computed from a few observed examples of the underlying function, is learned jointly with the predictive model. In this work, we study the implications of this joint training on the transferability of the meta-representations. Our goal is to learn meta-representations that are robust to noise in the data and facilitate solving a wide range of downstream tasks that share the same underlying functions. To this end, we propose a decoupled encoder-decoder approach to supervised meta-learning, where the encoder is trained with a contrastive objective to find a good representation of the underlying function. In particular, our training scheme is driven by the self-supervision signal indicating whether two sets of examples stem from the same function. Our experiments on a number of synthetic and real-world datasets show that the representations we obtain outperform strong baselines in terms of downstream performance and noise robustness, even when these baselines are trained in an end-to-end manner.

Francesco Locatello, Stefan Bauer, Mario Lucic et al.

The goal of the unsupervised learning of disentangled representations is to separate the independent explanatory factors of variation in the data without access to supervision. In this paper, we summarize the results of Locatello et al., 2019, and focus on their implications for practitioners. We discuss the theoretical result showing that the unsupervised learning of disentangled representations is fundamentally impossible without inductive biases and the practical challenges it entails. Finally, we comment on our experimental findings, highlighting the limitations of state-of-the-art approaches and directions for future research.

Nasim Rahaman, Anirudh Goyal, Muhammad Waleed Gondal et al.

Capturing the structure of a data-generating process by means of appropriate inductive biases can help in learning models that generalize well and are robust to changes in the input distribution. While methods that harness spatial and temporal structures find broad application, recent work has demonstrated the potential of models that leverage sparse and modular structure using an ensemble of sparingly interacting modules. In this work, we take a step towards dynamic models that are capable of simultaneously exploiting both modular and spatiotemporal structures. We accomplish this by abstracting the modeled dynamical system as a collection of autonomous but sparsely interacting sub-systems. The sub-systems interact according to a topology that is learned, but also informed by the spatial structure of the underlying real-world system. This results in a class of models that are well suited for modeling the dynamics of systems that only offer local views into their state, along with corresponding spatial locations of those views. On the tasks of video prediction from cropped frames and multi-agent world modeling from partial observations in the challenging Starcraft2 domain, we find our models to be more robust to the number of available views and better capable of generalization to novel tasks without additional training, even when compared against strong baselines that perform equally well or better on the training distribution.

Frederik Träuble, Elliot Creager, Niki Kilbertus et al.

The focus of disentanglement approaches has been on identifying independent factors of variation in data. However, the causal variables underlying real-world observations are often not statistically independent. In this work, we bridge the gap to real-world scenarios by analyzing the behavior of the most prominent disentanglement approaches on correlated data in a large-scale empirical study (including 4260 models). We show and quantify that systematically induced correlations in the dataset are being learned and reflected in the latent representations, which has implications for downstream applications of disentanglement such as fairness. We also demonstrate how to resolve these latent correlations, either using weak supervision during training or by post-hoc correcting a pre-trained model with a small number of labels.

Felix Leeb, Guilia Lanzillotta, Yashas Annadani et al.

We study the problem of self-supervised structured representation learning using autoencoders for downstream tasks such as generative modeling. Unlike most methods which rely on matching an arbitrary, relatively unstructured, prior distribution for sampling, we propose a sampling technique that relies solely on the independence of latent variables, thereby avoiding the trade-off between reconstruction quality and generative performance typically observed in VAEs. We design a novel autoencoder architecture capable of learning a structured representation without the need for aggressive regularization. Our structural decoders learn a hierarchy of latent variables, thereby ordering the information without any additional regularization or supervision. We demonstrate how these models learn a representation that improves results in a variety of downstream tasks including generation, disentanglement, and extrapolation using several challenging and natural image datasets.

Patrick Schwab, August DuMont Schütte, Benedikt Dietz et al.

Coronavirus Disease 2019 (COVID-19) is a rapidly emerging respiratory disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Due to the rapid human-to-human transmission of SARS-CoV-2, many healthcare systems are at risk of exceeding their healthcare capacities, in particular in terms of SARS-CoV-2 tests, hospital and intensive care unit (ICU) beds and mechanical ventilators. Predictive algorithms could potentially ease the strain on healthcare systems by identifying those who are most likely to receive a positive SARS-CoV-2 test, be hospitalised or admitted to the ICU. Here, we study clinical predictive models that estimate, using machine learning and based on routinely collected clinical data, which patients are likely to receive a positive SARS-CoV-2 test, require hospitalisation or intensive care. To evaluate the predictive performance of our models, we perform a retrospective evaluation on clinical and blood analysis data from a cohort of 5644 patients. Our experimental results indicate that our predictive models identify (i) patients that test positive for SARS-CoV-2 a priori at a sensitivity of 75% (95% CI: 67%, 81%) and a specificity of 49% (95% CI: 46%, 51%), (ii) SARS-CoV-2 positive patients that require hospitalisation with 0.92 AUC (95% CI: 0.81, 0.98), and (iii) SARS-CoV-2 positive patients that require critical care with 0.98 AUC (95% CI: 0.95, 1.00). In addition, we determine which clinical features are predictive to what degree for each of the aforementioned clinical tasks. Our results indicate that predictive models trained on routinely collected clinical data could be used to predict clinical pathways for COVID-19, and therefore help inform care and prioritise resources.

Emmanouil Angelis, Philippe Wenk, Bernhard Schölkopf et al.

Gaussian processes are an important regression tool with excellent analytic properties which allow for direct integration of derivative observations. However, vanilla GP methods scale cubically in the amount of observations. In this work, we propose a novel approach for scaling GP regression with derivatives based on quadrature Fourier features. We then prove deterministic, non-asymptotic and exponentially fast decaying error bounds which apply for both the approximated kernel as well as the approximated posterior. To furthermore illustrate the practical applicability of our method, we then apply it to ODIN, a recently developed algorithm for ODE parameter inference. In an extensive experiments section, all results are empirically validated, demonstrating the speed, accuracy, and practical applicability of this approach.

Muhammad Waleed Gondal, Manuel Wüthrich, Đorđe Miladinović et al.

Learning meaningful and compact representations with disentangled semantic aspects is considered to be of key importance in representation learning. Since real-world data is notoriously costly to collect, many recent state-of-the-art disentanglement models have heavily relied on synthetic toy data-sets. In this paper, we propose a novel data-set which consists of over one million images of physical 3D objects with seven factors of variation, such as object color, shape, size and position. In order to be able to control all the factors of variation precisely, we built an experimental platform where the objects are being moved by a robotic arm. In addition, we provide two more datasets which consist of simulations of the experimental setup. These datasets provide for the first time the possibility to systematically investigate how well different disentanglement methods perform on real data in comparison to simulation, and how simulated data can be leveraged to build better representations of the real world. We provide a first experimental study of these questions and our results indicate that learned models transfer poorly, but that model and hyperparameter selection is an effective means of transferring information to the real world.

Đorđe Miladinović, Muhammad Waleed Gondal, Bernhard Schölkopf et al.

Sequential data often originates from diverse domains across which statistical regularities and domain specifics exist. To specifically learn cross-domain sequence representations, we introduce disentangled state space models (DSSM) -- a class of SSM in which domain-invariant state dynamics is explicitly disentangled from domain-specific information governing that dynamics. We analyze how such separation can improve knowledge transfer to new domains, and enable robust prediction, sequence manipulation and domain characterization. We furthermore propose an unsupervised VAE-based training procedure to implement DSSM in form of Bayesian filters. In our experiments, we applied VAE-DSSM framework to achieve competitive performance in online ODE system identification and regression across experimental settings, and controlled generation and prediction of bouncing ball video sequences across varying gravitational influences.

Francesco Locatello, Gabriele Abbati, Tom Rainforth et al.

Recently there has been a significant interest in learning disentangled representations, as they promise increased interpretability, generalization to unseen scenarios and faster learning on downstream tasks. In this paper, we investigate the usefulness of different notions of disentanglement for improving the fairness of downstream prediction tasks based on representations. We consider the setting where the goal is to predict a target variable based on the learned representation of high-dimensional observations (such as images) that depend on both the target variable and an \emph{unobserved} sensitive variable. We show that in this setting both the optimal and empirical predictions can be unfair, even if the target variable and the sensitive variable are independent. Analyzing the representations of more than \num{12600} trained state-of-the-art disentangled models, we observe that several disentanglement scores are consistently correlated with increased fairness, suggesting that disentanglement may be a useful property to encourage fairness when sensitive variables are not observed.

Francesco Locatello, Michael Tschannen, Stefan Bauer et al.

Learning disentangled representations is considered a cornerstone problem in representation learning. Recently, Locatello et al. (2019) demonstrated that unsupervised disentanglement learning without inductive biases is theoretically impossible and that existing inductive biases and unsupervised methods do not allow to consistently learn disentangled representations. However, in many practical settings, one might have access to a limited amount of supervision, for example through manual labeling of (some) factors of variation in a few training examples. In this paper, we investigate the impact of such supervision on state-of-the-art disentanglement methods and perform a large scale study, training over 52000 models under well-defined and reproducible experimental conditions. We observe that a small number of labeled examples (0.01--0.5\% of the data set), with potentially imprecise and incomplete labels, is sufficient to perform model selection on state-of-the-art unsupervised models. Further, we investigate the benefit of incorporating supervision into the training process. Overall, we empirically validate that with little and imprecise supervision it is possible to reliably learn disentangled representations.

Anant Raj, Luigi Gresele, Michel Besserve et al.

The problem of inferring the direct causal parents of a response variable among a large set of explanatory variables is of high practical importance in many disciplines. Recent work exploits stability of regression coefficients or invariance properties of models across different experimental conditions for reconstructing the full causal graph. These approaches generally do not scale well with the number of the explanatory variables and are difficult to extend to nonlinear relationships. Contrary to existing work, we propose an approach which even works for observational data alone, while still offering theoretical guarantees including the case of partially nonlinear relationships. Our algorithm requires only one estimation for each variable and in our experiments we apply our causal discovery algorithm even to large graphs, demonstrating significant improvements compared to well established approaches.

Gabriele Abbati, Philippe Wenk, Michael A Osborne et al.

Stochastic differential equations are an important modeling class in many disciplines. Consequently, there exist many methods relying on various discretization and numerical integration schemes. In this paper, we propose a novel, probabilistic model for estimating the drift and diffusion given noisy observations of the underlying stochastic system. Using state-of-the-art adversarial and moment matching inference techniques, we avoid the discretization schemes of classical approaches. This leads to significant improvements in parameter accuracy and robustness given random initial guesses. On four established benchmark systems, we compare the performance of our algorithms to state-of-the-art solutions based on extended Kalman filtering and Gaussian processes.

Diego Agudelo-España, Sebastian Gomez-Gonzalez, Stefan Bauer et al.

Online detection of instantaneous changes in the generative process of a data sequence generally focuses on retrospective inference of such change points without considering their future occurrences. We extend the Bayesian Online Change Point Detection algorithm to also infer the number of time steps until the next change point (i.e., the residual time). This enables to handle observation models which depend on the total segment duration, which is useful to model data sequences with temporal scaling. The resulting inference algorithm for segment detection can be deployed in an online fashion, and we illustrate applications to synthetic and to two medical real-world data sets.

Francesco Locatello, Stefan Bauer, Mario Lucic et al.

The key idea behind the unsupervised learning of disentangled representations is that real-world data is generated by a few explanatory factors of variation which can be recovered by unsupervised learning algorithms. In this paper, we provide a sober look at recent progress in the field and challenge some common assumptions. We first theoretically show that the unsupervised learning of disentangled representations is fundamentally impossible without inductive biases on both the models and the data. Then, we train more than 12000 models covering most prominent methods and evaluation metrics in a reproducible large-scale experimental study on seven different data sets. We observe that while the different methods successfully enforce properties ``encouraged'' by the corresponding losses, well-disentangled models seemingly cannot be identified without supervision. Furthermore, increased disentanglement does not seem to lead to a decreased sample complexity of learning for downstream tasks. Our results suggest that future work on disentanglement learning should be explicit about the role of inductive biases and (implicit) supervision, investigate concrete benefits of enforcing disentanglement of the learned representations, and consider a reproducible experimental setup covering several data sets.

Raphael Suter, Đorđe Miladinović, Bernhard Schölkopf et al.

The ability to learn disentangled representations that split underlying sources of variation in high dimensional, unstructured data is important for data efficient and robust use of neural networks. While various approaches aiming towards this goal have been proposed in recent times, a commonly accepted definition and validation procedure is missing. We provide a causal perspective on representation learning which covers disentanglement and domain shift robustness as special cases. Our causal framework allows us to introduce a new metric for the quantitative evaluation of deep latent variable models. We show how this metric can be estimated from labeled observational data and further provide an efficient estimation algorithm that scales linearly in the dataset size.

Niklas Pfister, Stefan Bauer, Jonas Peters

Learning kinetic systems from data is one of the core challenges in many fields. Identifying stable models is essential for the generalization capabilities of data-driven inference. We introduce a computationally efficient framework, called CausalKinetiX, that identifies structure from discrete time, noisy observations, generated from heterogeneous experiments. The algorithm assumes the existence of an underlying, invariant kinetic model, a key criterion for reproducible research. Results on both simulated and real-world examples suggest that learning the structure of kinetic systems benefits from a causal perspective. The identified variables and models allow for a concise description of the dynamics across multiple experimental settings and can be used for prediction in unseen experiments. We observe significant improvements compared to well established approaches focusing solely on predictive performance, especially for out-of-sample generalization.

Alexander Neitz, Giambattista Parascandolo, Stefan Bauer et al.

We introduce a method which enables a recurrent dynamics model to be temporally abstract. Our approach, which we call Adaptive Skip Intervals (ASI), is based on the observation that in many sequential prediction tasks, the exact time at which events occur is irrelevant to the underlying objective. Moreover, in many situations, there exist prediction intervals which result in particularly easy-to-predict transitions. We show that there are prediction tasks for which we gain both computational efficiency and prediction accuracy by allowing the model to make predictions at a sampling rate which it can choose itself.

Nico S. Gorbach, Stefan Bauer, Joachim M. Buhmann

Gradient matching is a promising tool for learning parameters and state dynamics of ordinary differential equations. It is a grid free inference approach, which, for fully observable systems is at times competitive with numerical integration. However, for many real-world applications, only sparse observations are available or even unobserved variables are included in the model description. In these cases most gradient matching methods are difficult to apply or simply do not provide satisfactory results. That is why, despite the high computational cost, numerical integration is still the gold standard in many applications. Using an existing gradient matching approach, we propose a scalable variational inference framework which can infer states and parameters simultaneously, offers computational speedups, improved accuracy and works well even under model misspecifications in a partially observable system.

Nico S. Gorbach, Stefan Bauer, Joachim M. Buhmann

Gradient matching with Gaussian processes is a promising tool for learning parameters of ordinary differential equations (ODE's). The essence of gradient matching is to model the prior over state variables as a Gaussian process which implies that the joint distribution given the ODE's and GP kernels is also Gaussian distributed. The state-derivatives are integrated out analytically since they are modelled as latent variables. However, the state variables themselves are also latent variables because they are contaminated by noise. Previous work sampled the state variables since integrating them out is \textit{not} analytically tractable. In this paper we use mean-field approximation to establish tight variational lower bounds that decouple state variables and are therefore, in contrast to the integral over state variables, analytically tractable and even concave for a restricted family of ODE's, including nonlinear and periodic ODE's. Such variational lower bounds facilitate "hill climbing" to determine the maximum a posteriori estimate of ODE parameters. An additional advantage of our approach over sampling methods is the determination of a proxy to the intractable posterior distribution over state variables given observations and the ODE's.

Benjamin Fischer, Nico Gorbach, Stefan Bauer et al.

Gaussian processes are powerful, yet analytically tractable models for supervised learning. A Gaussian process is characterized by a mean function and a covariance function (kernel), which are determined by a model selection criterion. The functions to be compared do not just differ in their parametrization but in their fundamental structure. It is often not clear which function structure to choose, for instance to decide between a squared exponential and a rational quadratic kernel. Based on the principle of approximation set coding, we develop a framework for model selection to rank kernels for Gaussian process regression. In our experiments approximation set coding shows promise to become a model selection criterion competitive with maximum evidence (also called marginal likelihood) and leave-one-out cross-validation.

Stefan Bauer, Nicolas Carion, Peter Schüffler et al.

Accurate and robust cell nuclei classification is the cornerstone for a wider range of tasks in digital and Computational Pathology. However, most machine learning systems require extensive labeling from expert pathologists for each individual problem at hand, with no or limited abilities for knowledge transfer between datasets and organ sites. In this paper we implement and evaluate a variety of deep neural network models and model ensembles for nuclei classification in renal cell cancer (RCC) and prostate cancer (PCa). We propose a convolutional neural network system based on residual learning which significantly improves over the state-of-the-art in cell nuclei classification. Finally, we show that the combination of tissue types during training increases not only classification accuracy but also overall survival analysis.

Stefan Bauer, Lutz-P. Nolte, Mauricio Reyes

Skull-stripping separates the skull region of the head from the soft brain tissues. In many cases of brain image analysis, this is an essential preprocessing step in order to improve the final result. This is true for both registration and segmentation tasks. In fact, skull-stripping of magnetic resonance images (MRI) is a well-studied problem with numerous publications in recent years. Many different algorithms have been proposed, a summary and comparison of which can be found in [Fennema-Notestine, 2006]. Despite the abundance of approaches, we discovered that the algorithms which had been suggested so far, perform poorly when dealing with tumor-bearing brain images. This is mostly due to additional difficulties in separating the brain from the skull in this case, especially when the lesion is located very close to the skull border. Additionally, images acquired according to standard clinical protocols, often exhibit anisotropic resolution and only partial coverage, which further complicates the task. Therefore, we developed a method which is dedicated to skull-stripping for clinically acquired tumor-bearing brain images.