Stefan Bauer

Nico Gürtler, Sebastian Blaes, Pavel Kolev et al.

Learning policies from previously recorded data is a promising direction for real-world robotics tasks, as online learning is often infeasible. Dexterous manipulation in particular remains an open problem in its general form. The combination of offline reinforcement learning with large diverse datasets, however, has the potential to lead to a breakthrough in this challenging domain analogously to the rapid progress made in supervised learning in recent years. To coordinate the efforts of the research community toward tackling this problem, we propose a benchmark including: i) a large collection of data for offline learning from a dexterous manipulation platform on two tasks, obtained with capable RL agents trained in simulation; ii) the option to execute learned policies on a real-world robotic system and a simulation for efficient debugging. We evaluate prominent open-sourced offline reinforcement learning algorithms on the datasets and provide a reproducible experimental setup for offline reinforcement learning on real systems.

Yashas Annadani, Panagiotis Tigas, Desi R. Ivanova et al. · microsoft-research

We introduce a gradient-based approach for the problem of Bayesian optimal experimental design to learn causal models in a batch setting -- a critical component for causal discovery from finite data where interventions can be costly or risky. Existing methods rely on greedy approximations to construct a batch of experiments while using black-box methods to optimize over a single target-state pair to intervene with. In this work, we completely dispose of the black-box optimization techniques and greedy heuristics and instead propose a conceptually simple end-to-end gradient-based optimization procedure to acquire a set of optimal intervention target-state pairs. Such a procedure enables parameterization of the design space to efficiently optimize over a batch of multi-target-state interventions, a setting which has hitherto not been explored due to its complexity. We demonstrate that our proposed method outperforms baselines and existing acquisition strategies in both single-target and multi-target settings across a number of synthetic datasets.

Nico Gürtler, Felix Widmaier, Cansu Sancaktar et al. · deepmind

Experimentation on real robots is demanding in terms of time and costs. For this reason, a large part of the reinforcement learning (RL) community uses simulators to develop and benchmark algorithms. However, insights gained in simulation do not necessarily translate to real robots, in particular for tasks involving complex interactions with the environment. The Real Robot Challenge 2022 therefore served as a bridge between the RL and robotics communities by allowing participants to experiment remotely with a real robot - as easily as in simulation. In the last years, offline reinforcement learning has matured into a promising paradigm for learning from pre-collected datasets, alleviating the reliance on expensive online interactions. We therefore asked the participants to learn two dexterous manipulation tasks involving pushing, grasping, and in-hand orientation from provided real-robot datasets. An extensive software documentation and an initial stage based on a simulation of the real set-up made the competition particularly accessible. By giving each team plenty of access budget to evaluate their offline-learned policies on a cluster of seven identical real TriFinger platforms, we organized an exciting competition for machine learners and roboticists alike. In this work we state the rules of the competition, present the methods used by the winning teams and compare their results with a benchmark of state-of-the-art offline RL algorithms on the challenge datasets.

Panagiotis Tigas, Yashas Annadani, Andrew Jesson et al.

Causal discovery from observational and interventional data is challenging due to limited data and non-identifiability: factors that introduce uncertainty in estimating the underlying structural causal model (SCM). Selecting experiments (interventions) based on the uncertainty arising from both factors can expedite the identification of the SCM. Existing methods in experimental design for causal discovery from limited data either rely on linear assumptions for the SCM or select only the intervention target. This work incorporates recent advances in Bayesian causal discovery into the Bayesian optimal experimental design framework, allowing for active causal discovery of large, nonlinear SCMs while selecting both the interventional target and the value. We demonstrate the performance of the proposed method on synthetic graphs (Erdos-Rènyi, Scale Free) for both linear and nonlinear SCMs as well as on the \emph{in-silico} single-cell gene regulatory network dataset, DREAM.

Nino Scherrer, Anirudh Goyal, Stefan Bauer et al. · mila

Learning models that offer robust out-of-distribution generalization and fast adaptation is a key challenge in modern machine learning. Modelling causal structure into neural networks holds the promise to accomplish robust zero and few-shot adaptation. Recent advances in differentiable causal discovery have proposed to factorize the data generating process into a set of modules, i.e. one module for the conditional distribution of every variable where only causal parents are used as predictors. Such a modular decomposition of knowledge enables adaptation to distributions shifts by only updating a subset of parameters. In this work, we systematically study the generalization and adaption performance of such modular neural causal models by comparing it to monolithic models and structured models where the set of predictors is not constrained to causal parents. Our analysis shows that the modular neural causal models outperform other models on both zero and few-shot adaptation in low data regimes and offer robust generalization. We also found that the effects are more significant for sparser graphs as compared to denser graphs.

Tobias Höppe, Arash Mehrjou, Stefan Bauer et al.

Predicting and anticipating future outcomes or reasoning about missing information in a sequence are critical skills for agents to be able to make intelligent decisions. This requires strong, temporally coherent generative capabilities. Diffusion models have shown remarkable success in several generative tasks, but have not been extensively explored in the video domain. We present Random-Mask Video Diffusion (RaMViD), which extends image diffusion models to videos using 3D convolutions, and introduces a new conditioning technique during training. By varying the mask we condition on, the model is able to perform video prediction, infilling, and upsampling. Due to our simple conditioning scheme, we can utilize the same architecture as used for unconditional training, which allows us to train the model in a conditional and unconditional fashion at the same time. We evaluate RaMViD on two benchmark datasets for video prediction, on which we achieve state-of-the-art results, and one for video generation. High-resolution videos are provided at https://sites.google.com/view/video-diffusion-prediction.

Cheng Zhang, Stefan Bauer, Paul Bennett et al.

We assess the ability of large language models (LLMs) to answer causal questions by analyzing their strengths and weaknesses against three types of causal question. We believe that current LLMs can answer causal questions with existing causal knowledge as combined domain experts. However, they are not yet able to provide satisfactory answers for discovering new knowledge or for high-stakes decision-making tasks with high precision. We discuss possible future directions and opportunities, such as enabling explicit and implicit causal modules as well as deep causal-aware LLMs. These will not only enable LLMs to answer many different types of causal questions for greater impact but also enable LLMs to be more trustworthy and efficient in general.

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.

Mathieu Chevalley, Charlotte Bunne, Andreas Krause et al.

Learning representations that capture the underlying data generating process is a key problem for data efficient and robust use of neural networks. One key property for robustness which the learned representation should capture and which recently received a lot of attention is described by the notion of invariance. In this work we provide a causal perspective and new algorithm for learning invariant representations. Empirically we show that this algorithm works well on a diverse set of tasks and in particular we observe state-of-the-art performance on domain generalization, where we are able to significantly boost the score of existing models.

Yashas Annadani, Nick Pawlowski, Joel Jennings et al.

Bayesian causal discovery aims to infer the posterior distribution over causal models from observed data, quantifying epistemic uncertainty and benefiting downstream tasks. However, computational challenges arise due to joint inference over combinatorial space of Directed Acyclic Graphs (DAGs) and nonlinear functions. Despite recent progress towards efficient posterior inference over DAGs, existing methods are either limited to variational inference on node permutation matrices for linear causal models, leading to compromised inference accuracy, or continuous relaxation of adjacency matrices constrained by a DAG regularizer, which cannot ensure resulting graphs are DAGs. In this work, we introduce a scalable Bayesian causal discovery framework based on a combination of stochastic gradient Markov Chain Monte Carlo (SG-MCMC) and Variational Inference (VI) that overcomes these limitations. Our approach directly samples DAGs from the posterior without requiring any DAG regularization, simultaneously draws function parameter samples and is applicable to both linear and nonlinear causal models. To enable our approach, we derive a novel equivalence to the permutation-based DAG learning, which opens up possibilities of using any relaxed gradient estimator defined over permutations. To our knowledge, this is the first framework applying gradient-based MCMC sampling for causal discovery. Empirical evaluation on synthetic and real-world datasets demonstrate our approach's effectiveness compared to state-of-the-art baselines.

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

Amin Abyaneh, Nino Scherrer, Patrick Schwab et al.

Causal discovery serves a pivotal role in mitigating model uncertainty through recovering the underlying causal mechanisms among variables. In many practical domains, such as healthcare, access to the data gathered by individual entities is limited, primarily for privacy and regulatory constraints. However, the majority of existing causal discovery methods require the data to be available in a centralized location. In response, researchers have introduced federated causal discovery. While previous federated methods consider distributed observational data, the integration of interventional data remains largely unexplored. We propose FedCDI, a federated framework for inferring causal structures from distributed data containing interventional samples. In line with the federated learning framework, FedCDI improves privacy by exchanging belief updates rather than raw samples. Additionally, it introduces a novel intervention-aware method for aggregating individual updates. We analyze scenarios with shared or disjoint intervened covariates, and mitigate the adverse effects of interventional data heterogeneity. The performance and scalability of FedCDI is rigorously tested across a variety of synthetic and real-world graphs.

Qiang Wang, Francisco Roldan Sanchez, Robert McCarthy et al.

This paper describes a deep reinforcement learning (DRL) approach that won Phase 1 of the Real Robot Challenge (RRC) 2021, and then extends this method to a more difficult manipulation task. The RRC consisted of using a TriFinger robot to manipulate a cube along a specified positional trajectory, but with no requirement for the cube to have any specific orientation. We used a relatively simple reward function, a combination of goal-based sparse reward and distance reward, in conjunction with Hindsight Experience Replay (HER) to guide the learning of the DRL agent (Deep Deterministic Policy Gradient (DDPG)). Our approach allowed our agents to acquire dexterous robotic manipulation strategies in simulation. These strategies were then applied to the real robot and outperformed all other competition submissions, including those using more traditional robotic control techniques, in the final evaluation stage of the RRC. Here we extend this method, by modifying the task of Phase 1 of the RRC to require the robot to maintain the cube in a particular orientation, while the cube is moved along the required positional trajectory. The requirement to also orient the cube makes the agent unable to learn the task through blind exploration due to increased problem complexity. To circumvent this issue, we make novel use of a Knowledge Transfer (KT) technique that allows the strategies learned by the agent in the original task (which was agnostic to cube orientation) to be transferred to this task (where orientation matters). KT allowed the agent to learn and perform the extended task in the simulator, which improved the average positional deviation from 0.134 m to 0.02 m, and average orientation deviation from 142° to 76° during evaluation. This KT concept shows good generalisation properties and could be applied to any actor-critic learning algorithm.

Francesco Quinzan, Ashkan Soleymani, Patrick Jaillet et al.

Knowing the features of a complex system that are highly relevant to a particular target variable is of fundamental interest in many areas of science. Existing approaches are often limited to linear settings, sometimes lack guarantees, and in most cases, do not scale to the problem at hand, in particular to images. We propose DRCFS, a doubly robust feature selection method for identifying the causal features even in nonlinear and high dimensional settings. We provide theoretical guarantees, illustrate necessary conditions for our assumptions, and perform extensive experiments across a wide range of simulated and semi-synthetic datasets. DRCFS significantly outperforms existing state-of-the-art methods, selecting robust features even in challenging highly non-linear and high-dimensional problems.

Yaosen Min, Ye Wei, Peizhuo Wang et al.

Accurate prediction of protein-ligand binding affinities is an essential challenge in structure-based drug design. Despite recent advances in data-driven methods for affinity prediction, their accuracy is still limited, partially because they only take advantage of static crystal structures while the actual binding affinities are generally determined by the thermodynamic ensembles between proteins and ligands. One effective way to approximate such a thermodynamic ensemble is to use molecular dynamics (MD) simulation. Here, an MD dataset containing 3,218 different protein-ligand complexes is curated, and Dynaformer, a graph-based deep learning model is further developed to predict the binding affinities by learning the geometric characteristics of the protein-ligand interactions from the MD trajectories. In silico experiments demonstrated that the model exhibits state-of-the-art scoring and ranking power on the CASF-2016 benchmark dataset, outperforming the methods hitherto reported. Moreover, in a virtual screening on heat shock protein 90 (HSP90) using Dynaformer, 20 candidates are identified and their binding affinities are further experimentally validated. Dynaformer displayed promising results in virtual drug screening, revealing 12 hit compounds (two are in the submicromolar range), including several novel scaffolds. Overall, these results demonstrated that the approach offer a promising avenue for accelerating the early drug discovery process.

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.

Jithendaraa Subramanian, Yashas Annadani, Ivaxi Sheth et al.

Causal learning has long concerned itself with the accurate recovery of underlying causal mechanisms. Such causal modelling enables better explanations of out-of-distribution data. Prior works on causal learning assume that the high-level causal variables are given. However, in machine learning tasks, one often operates on low-level data like image pixels or high-dimensional vectors. In such settings, the entire Structural Causal Model (SCM) -- structure, parameters, \textit{and} high-level causal variables -- is unobserved and needs to be learnt from low-level data. We treat this problem as Bayesian inference of the latent SCM, given low-level data. For linear Gaussian additive noise SCMs, we present a tractable approximate inference method which performs joint inference over the causal variables, structure and parameters of the latent SCM from random, known interventions. Experiments are performed on synthetic datasets and a causally generated image dataset to demonstrate the efficacy of our approach. We also perform image generation from unseen interventions, thereby verifying out of distribution generalization for the proposed causal model.

Yichen Zhou, Jonathan Golob, Amir Karimi et al.

Protein language models (pLMs) have shown strong potential for zero-shot prediction of missense variant effects, yet systematic benchmarking on viral proteins remains limited, a critical gap given the need for proactive tools that can anticipate emerging mutations ahead of experimental validation. Here we introduce ViroGym, a comprehensive benchmark evaluating pLMs across three tasks: 79 deep mutational scanning (DMS) assays covering eukaryotic viruses with 552,065 mutated sequences across 7 phenotypic readouts, 21 influenza neutralisation tasks, and a real-world pandemic prediction task for SARS-CoV-2. We benchmark well-established pLMs on fitness landscapes, antigenic diversity, and pandemic forecasting, and find that the ProGen2 family consistently achieves the strongest performance across all three tasks. Crucially, DMS and neutralisation performance reliably identifies models that generalise to real-world emergence, even though the mutation sets they surface barely overlap, revealing that complementary in vitro benchmarks capture the evolutionary constraints needed for real-world mutation forecasting.

Arash Mehrjou, Ashkan Soleymani, Annika Buchholz et al.

Federated learning (FL) has been proposed as a method to train a model on different units without exchanging data. This offers great opportunities in the healthcare sector, where large datasets are available but cannot be shared to ensure patient privacy. We systematically investigate the effectiveness of FL on the publicly available eICU dataset for predicting the survival of each ICU stay. We employ Federated Averaging as the main practical algorithm for FL and show how its performance changes by altering three key hyper-parameters, taking into account that clients can significantly vary in size. We find that in many settings, a large number of local training epochs improves the performance while at the same time reducing communication costs. Furthermore, we outline in which settings it is possible to have only a low number of hospitals participating in each federated update round. When many hospitals with low patient counts are involved, the effect of overfitting can be avoided by decreasing the batchsize. This study thus contributes toward identifying suitable settings for running distributed algorithms such as FL on clinical datasets.

Sarthak Mittal, Guillaume Lajoie, Stefan Bauer et al.

Diffusion-based generative models learn to iteratively transfer unstructured noise to a complex target distribution as opposed to Generative Adversarial Networks (GANs) or the decoder of Variational Autoencoders (VAEs) which produce samples from the target distribution in a single step. Thus, in diffusion models every sample is naturally connected to a random trajectory which is a solution to a learned stochastic differential equation (SDE). Generative models are only concerned with the final state of this trajectory that delivers samples from the desired distribution. Abstreiter et. al showed that these stochastic trajectories can be seen as continuous filters that wash out information along the way. Consequently, it is reasonable to ask if there is an intermediate time step at which the preserved information is optimal for a given downstream task. In this work, we show that a combination of information content from different time steps gives a strictly better representation for the downstream task. We introduce an attention and recurrence based modules that ``learn to mix'' information content of various time-steps such that the resultant representation leads to superior performance in downstream tasks.

Mateusz Olko, Michał Zając, Aleksandra Nowak et al.

Inferring causal structure from data is a challenging task of fundamental importance in science. Observational data are often insufficient to identify a system's causal structure uniquely. While conducting interventions (i.e., experiments) can improve the identifiability, such samples are usually challenging and expensive to obtain. Hence, experimental design approaches for causal discovery aim to minimize the number of interventions by estimating the most informative intervention target. In this work, we propose a novel Gradient-based Intervention Targeting method, abbreviated GIT, that 'trusts' the gradient estimator of a gradient-based causal discovery framework to provide signals for the intervention acquisition function. We provide extensive experiments in simulated and real-world datasets and demonstrate that GIT performs on par with competitive baselines, surpassing them in the low-data regime.

Jithendaraa Subramanian, Yashas Annadani, Ivaxi Sheth et al.

Learning predictors that do not rely on spurious correlations involves building causal representations. However, learning such a representation is very challenging. We, therefore, formulate the problem of learning a causal representation from high dimensional data and study causal recovery with synthetic data. This work introduces a latent variable decoder model, Decoder BCD, for Bayesian causal discovery and performs experiments in mildly supervised and unsupervised settings. We present a series of synthetic experiments to characterize important factors for causal discovery and show that using known intervention targets as labels helps in unsupervised Bayesian inference over structure and parameters of linear Gaussian additive noise latent structural causal models.

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.

Aleena Siji, Amir Mohammad Karimi Mamaghan, Ferdinand Kapl et al.

Protein language models (PLMs) have become widely adopted as general-purpose models, demonstrating strong performance in protein engineering and de novo design. Like large language models (LLMs), they are typically trained as deep transformers with next-token or masked-token prediction objectives on massive sequence corpora and are scaled by increasing model depth. Recent work on autoregressive LLMs has identified the Curse of Depth: later layers contribute little to the final output predictions. These findings naturally raise the question of whether a similar depth inefficiency also appears in PLMs, where many widely used models are not autoregressive, and some are multimodal, accepting both protein sequence and structure as input. In this work, we present a depth analysis of six popular PLMs across model families and scales, spanning three training objectives, namely autoregressive, masked, and diffusion, and quantify how layer contributions evolve with depth using a unified set of probing- and perturbation-based measurements. Across all models, we observe consistent depth-dependent patterns that extend prior findings on LLMs: later layers depend less on earlier computations and mainly refine the final output distribution, and these effects are increasingly pronounced in deeper models. Taken together, our results suggest that PLMs exhibit a form of depth inefficiency, motivating future work on more depth-efficient architectures and training methods.

Ferdinand Kapl, Emmanouil Angelis, Tobias Höppe et al.

Gradually growing the depth of Transformers during training can not only reduce training cost but also lead to improved reasoning performance, as shown by MIDAS (Saunshi et al., 2024). Thus far, however, a mechanistic understanding of these gains has been missing. In this work, we establish a connection to recent work showing that layers in the second half of non-grown, pre-layernorm Transformers contribute much less to the final output distribution than those in the first half - also known as the Curse of Depth (Sun et al., 2025, Csordás et al., 2025). Using depth-wise analyses, we demonstrate that growth via gradual middle stacking yields more effective utilization of model depth, alters the residual stream structure, and facilitates the formation of permutable computational blocks. In addition, we propose a lightweight modification of MIDAS that yields further improvements in downstream reasoning benchmarks. Overall, this work highlights how the gradual growth of model depth can lead to the formation of distinct computational circuits and overcome the limited depth utilization seen in standard non-grown models.

Vincent Pauline, Tobias Höppe, Kirill Neklyudov et al.

Although diffusion models now occupy a central place in generative modeling, introductory treatments commonly assume Euclidean data and seldom clarify their connection to discrete-state analogues. This article is a self-contained primer on diffusion over general state spaces, unifying continuous domains and discrete/categorical structures under one lens. We develop the discrete-time view (forward noising via Markov kernels and learned reverse dynamics) alongside its continuous-time limits -- stochastic differential equations (SDEs) in $\mathbb{R}^d$ and continuous-time Markov chains (CTMCs) on finite alphabets -- and derive the associated Fokker--Planck and master equations. A common variational treatment yields the ELBO that underpins standard training losses. We make explicit how forward corruption choices -- Gaussian processes in continuous spaces and structured categorical transition kernels (uniform, masking/absorbing and more) in discrete spaces -- shape reverse dynamics and the ELBO. The presentation is layered for three audiences: newcomers seeking a self-contained intuitive introduction; diffusion practitioners wanting a global theoretical synthesis; and continuous-diffusion experts looking for an analogy-first path into discrete diffusion. The result is a unified roadmap to modern diffusion methodology across continuous domains and discrete sequences, highlighting a compact set of reusable proofs, identities, and core theoretical principles.

Ferdinand Kapl, Amir Mohammad Karimi Mamaghan, Maximilian Seitzer et al.

Compositional generalization, the ability to reason about novel combinations of familiar concepts, is fundamental to human cognition and a critical challenge for machine learning. Object-centric (OC) representations, which encode a scene as a set of objects, are often argued to support such generalization, but systematic evidence in visually rich settings is limited. We introduce a Visual Question Answering benchmark across three controlled visual worlds (CLEVRTex, Super-CLEVR, and MOVi-C) to measure how well vision encoders, with and without object-centric biases, generalize to unseen combinations of object properties. To ensure a fair and comprehensive comparison, we carefully account for training data diversity, sample size, representation size, downstream model capacity, and compute. We use DINOv2 and SigLIP2, two widely used vision encoders, as the foundation models and their OC counterparts. Our key findings reveal that (1) OC approaches are superior in harder compositional generalization settings; (2) original dense representations surpass OC only on easier settings and typically require substantially more downstream compute; and (3) OC models are more sample efficient, achieving stronger generalization with fewer images, whereas dense encoders catch up or surpass them only with sufficient data and diversity. Overall, object-centric representations offer stronger compositional generalization when any one of dataset size, training data diversity, or downstream compute is constrained.

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.

Ferdinand Kapl, Emmanouil Angelis, Kaitlin Maile et al.

Looping, reusing a block of layers across depth, and depth growing, training shallow-to-deep models by duplicating middle layers, have both been linked to stronger reasoning, but their relationship remains unclear. We provide a mechanistic unification: looped and depth-grown models exhibit convergent depth-wise signatures, including increased reliance on late layers and recurring patterns aligned with the looped or grown block. These shared signatures support the view that their gains stem from a common form of iterative computation. Building on this connection, we show that the two techniques are adaptable and composable: applying inference-time looping to the middle blocks of a depth-grown model improves accuracy on some reasoning primitives by up to $2\times$, despite the model never being trained to loop. Both approaches also adapt better than the baseline when given more in-context examples or additional supervised fine-tuning data. Additionally, depth-grown models achieve the largest reasoning gains when using higher-quality, math-heavy cooldown mixtures, which can be further boosted by adapting a middle block to loop. Overall, our results position depth growth and looping as complementary, practical methods for inducing and scaling iterative computation to improve reasoning.

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.

August DuMont Schütte, Jürgen Hetzel, Sergios Gatidis et al.

Privacy concerns around sharing personally identifiable information are a major practical barrier to data sharing in medical research. However, in many cases, researchers have no interest in a particular individual's information but rather aim to derive insights at the level of cohorts. Here, we utilize Generative Adversarial Networks (GANs) to create derived medical imaging datasets consisting entirely of synthetic patient data. The synthetic images ideally have, in aggregate, similar statistical properties to those of a source dataset but do not contain sensitive personal information. We assess the quality of synthetic data generated by two GAN models for chest radiographs with 14 different radiology findings and brain computed tomography (CT) scans with six types of intracranial hemorrhages. We measure the synthetic image quality by the performance difference of predictive models trained on either the synthetic or the real dataset. We find that synthetic data performance disproportionately benefits from a reduced number of unique label combinations. Our open-source benchmark also indicates that at low number of samples per class, label overfitting effects start to dominate GAN training. We additionally conducted a reader study in which trained radiologists do not perform better than random on discriminating between synthetic and real medical images for intermediate levels of resolutions. In accordance with our benchmark results, the classification accuracy of radiologists increases at higher spatial resolution levels. Our study offers valuable guidelines and outlines practical conditions under which insights derived from synthetic medical images are similar to those that would have been derived from real imaging data. Our results indicate that synthetic data sharing may be an attractive and privacy-preserving alternative to sharing real patient-level data in the right settings.

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.

Clare Lyle, Arash Mehrjou, Pascal Notin et al. · deepmind

The discovery of therapeutics to treat genetically-driven pathologies relies on identifying genes involved in the underlying disease mechanisms. Existing approaches search over the billions of potential interventions to maximize the expected influence on the target phenotype. However, to reduce the risk of failure in future stages of trials, practical experiment design aims to find a set of interventions that maximally change a target phenotype via diverse mechanisms. We propose DiscoBAX, a sample-efficient method for maximizing the rate of significant discoveries per experiment while simultaneously probing for a wide range of diverse mechanisms during a genomic experiment campaign. We provide theoretical guarantees of approximate optimality under standard assumptions, and conduct a comprehensive experimental evaluation covering both synthetic as well as real-world experimental design tasks. DiscoBAX outperforms existing state-of-the-art methods for experimental design, selecting effective and diverse perturbations in biological systems.

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.

Ricardo Vinuesa, Paola Cinnella, Jean Rabault et al. · uw

As modern scientific instruments generate vast amounts of data and the volume of information in the scientific literature continues to grow, machine learning (ML) has become an essential tool for organising, analysing, and interpreting these complex datasets. This paper explores the transformative role of ML in accelerating breakthroughs across a range of scientific disciplines. By presenting key examples -- such as brain mapping and exoplanet detection -- we demonstrate how ML is reshaping scientific research. We also explore different scenarios where different levels of knowledge of the underlying phenomenon are available, identifying strategies to overcome limitations and unlock the full potential of ML. Despite its advances, the growing reliance on ML poses challenges for research applications and rigorous validation of discoveries. We argue that even with these challenges, ML is poised to disrupt traditional methodologies and advance the boundaries of knowledge by enabling researchers to tackle increasingly complex problems. Thus, the scientific community can move beyond the necessary traditional oversimplifications to embrace the full complexity of natural systems, ultimately paving the way for interdisciplinary breakthroughs and innovative solutions to humanity's most pressing challenges.

Yasin Esfandiari, Stefan Bauer, Sebastian U. Stich et al.

Diffusion models for image generation often exhibit a trade-off between perceptual sample quality and data likelihood: training objectives emphasizing high-noise denoising steps yield realistic images but poor likelihoods, whereas likelihood-oriented training overweights low-noise steps and harms visual fidelity. We introduce a simple plug-and-play sampling method that combines two pretrained diffusion experts by switching between them along the denoising trajectory. Specifically, we apply an image-quality expert at high noise levels to shape global structure, then switch to a likelihood expert at low noise levels to refine pixel statistics. The approach requires no retraining or fine-tuning -- only the choice of an intermediate switching step. On CIFAR-10 and ImageNet32, the merged model consistently matches or outperforms its base components, improving or preserving both likelihood and sample quality relative to each expert alone. These results demonstrate that expert switching across noise levels is an effective way to break the likelihood-quality trade-off in image diffusion models.

Christopher Kolloff, Tobias Höppe, Emmanouil Angelis et al.

We propose a regularization framework inspired by thermodynamic work for guiding pre-trained probability flow generative models (e.g., continuous normalizing flows or diffusion models) by minimizing excess work, a concept rooted in statistical mechanics and with strong conceptual connections to optimal transport. Our approach enables efficient guidance in sparse-data regimes common to scientific applications, where only limited target samples or partial density constraints are available. We introduce two strategies: Path Guidance for sampling rare transition states by concentrating probability mass on user-defined subsets, and Observable Guidance for aligning generated distributions with experimental observables while preserving entropy. We demonstrate the framework's versatility on a coarse-grained protein model, guiding it to sample transition configurations between folded/unfolded states and correct systematic biases using experimental data. The method bridges thermodynamic principles with modern generative architectures, offering a principled, efficient, and physics-inspired alternative to standard fine-tuning in data-scarce domains. Empirical results highlight improved sample efficiency and bias reduction, underscoring its applicability to molecular simulations and beyond.

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.

Jean Durand, Yashas Annadani, Stefan Bauer et al.

Causal Bayesian Optimization (CBO) is a methodology designed to optimize an outcome variable by leveraging known causal relationships through targeted interventions. Traditional CBO methods require a fully and accurately specified causal graph, which is a limitation in many real-world scenarios where such graphs are unknown. To address this, we propose a new method for the CBO framework that operates without prior knowledge of the causal graph. Consistent with causal bandit theory, we demonstrate through theoretical analysis and that focusing on the direct causal parents of the target variable is sufficient for optimization, and provide empirical validation in the context of CBO. Furthermore we introduce a new method that learns a Bayesian posterior over the direct parents of the target variable. This allows us to optimize the outcome variable while simultaneously learning the causal structure. Our contributions include a derivation of the closed-form posterior distribution for the linear case. In the nonlinear case where the posterior is not tractable, we present a Gaussian Process (GP) approximation that still enables CBO by inferring the parents of the outcome variable. The proposed method performs competitively with existing benchmarks and scales well to larger graphs, making it a practical tool for real-world applications where causal information is incomplete.

Mohammed Mahfoud, Ghait Boukachab, Michał Koziarski et al.

Building predictive models for tabular data presents fundamental challenges, notably in scaling consistently, i.e., more resources translating to better performance, and generalizing systematically beyond the training data distribution. Designing decision tree models remains especially challenging given the intractably large search space, and most existing methods rely on greedy heuristics, while deep learning inductive biases expect a temporal or spatial structure not naturally present in tabular data. We propose a hybrid amortized structure inference approach to learn predictive decision tree ensembles given data, formulating decision tree construction as a sequential planning problem. We train a deep reinforcement learning (GFlowNet) policy to solve this problem, yielding a generative model that samples decision trees from the Bayesian posterior. We show that our approach, DT-GFN, outperforms state-of-the-art decision tree and deep learning methods on standard classification benchmarks derived from real-world data, robustness to distribution shifts, and anomaly detection, all while yielding interpretable models with shorter description lengths. Samples from the trained DT-GFN model can be ensembled to construct a random forest, and we further show that the performance of scales consistently in ensemble size, yielding ensembles of predictors that continue to generalize systematically.

Amir Mohammad Karimi Mamaghan, Panagiotis Tigas, Karl Henrik Johansson et al.

Representing uncertainty in causal discovery is a crucial component for experimental design, and more broadly, for safe and reliable causal decision making. Bayesian Causal Discovery (BCD) offers a principled approach to encapsulating this uncertainty. Unlike non-Bayesian causal discovery, which relies on a single estimated causal graph and model parameters for assessment, evaluating BCD presents challenges due to the nature of its inferred quantity - the posterior distribution. As a result, the research community has proposed various metrics to assess the quality of the approximate posterior. However, there is, to date, no consensus on the most suitable metric(s) for evaluation. In this work, we reexamine this question by dissecting various metrics and understanding their limitations. Through extensive empirical evaluation, we find that many existing metrics fail to exhibit a strong correlation with the quality of approximation to the true posterior, especially in scenarios with low sample sizes where BCD is most desirable. We highlight the suitability (or lack thereof) of these metrics under two distinct factors: the identifiability of the underlying causal model and the quantity of available data. Both factors affect the entropy of the true posterior, indicating that the current metrics are less fitting in settings of higher entropy. Our findings underline the importance of a more nuanced evaluation of new methods by taking into account the nature of the true posterior, as well as guide and motivate the development of new evaluation procedures for this challenge.