Concept-based models are an emerging paradigm in deep learning that constrains the inference process to operate through human-interpretable variables, facilitating explainability and human interaction. However, these architectures, on par with popular opaque neural models, fail to account for the true causal mechanisms underlying the target phenomena represented in the data. This hampers their ability to support causal reasoning tasks, limits out-of-distribution generalization, and hinders the implementation of fairness constraints. To overcome these issues, we propose Causally reliable Concept Bottleneck Models (C2BMs), a class of concept-based architectures that enforce reasoning through a bottleneck of concepts structured according to a model of the real-world causal mechanisms. We also introduce a pipeline to automatically learn this structure from observational data and unstructured background knowledge (e.g., scientific literature). Experimental evidence suggests that C2BMs are more interpretable, causally reliable, and improve responsiveness to interventions w.r.t.

In single-cell perturbation prediction, a central task is to forecast the effects of perturbing a gene unseen in the training data. The efficacy of such predictions depends on two factors: (1) the similarity of the target gene to those covered in the training data, which informs model (epistemic) uncertainty, and (2) the quality of the corresponding training data, which reflects data (aleatoric) uncertainty. Both factors are critical for determining the reliability of a prediction, particularly as gene perturbation is an inherently stochastic biochemical process. In this paper, we propose PRESCRIBE (PREdicting Single-Cell Response wIth Bayesian Estimation), a multivariate deep evidential regression framework designed to measure both sources of uncertainty jointly. Our analysis demonstrates that PRESCRIBE effectively estimates a confidence score for each prediction, which strongly correlates with its empirical accuracy. This capability enables the filtering of untrustworthy results, and in our experiments, it achieves steady accuracy improvements of over 3% compared to comparable baselines.

Variational inference (VI) is a popular approach in Bayesian inference, that looks for the best approximation of the posterior distribution within a parametric family, minimizing a loss that is typically the (reverse) Kullback-Leibler (KL) divergence. In this paper, we focus on the following parametric family: mixtures of isotropic Gaussians (i.e., with diagonal covariance matrices proportional to the identity) and uniform weights. We develop a variational framework and provide efficient algorithms suited for this family. In contrast with mixtures of Gaussian with generic covariance matrices, this choice presents a balance between accurate approximations of multimodal Bayesian posteriors, while being memory and computationally efficient. Our algorithms implement gradient descent on the location of the mixture components (the modes of the Gaussians), and either (an entropic) Mirror or Bures descent on their variance parameters. We illustrate the performance of our algorithms on numerical experiments.

However, deploying these models can be unreliable when significant distribution gaps exist between training and test data, while fine-tuning for diverse scenarios is often costly. This creates a need for methods that can efficiently adapt to new data at test time without expensive retraining. Cache-based test-time adapters serve this purpose by storing representative test samples to guide subsequent classifications. Yet, these methods typically employ naive cache management with limited capacity, leading to severe catastrophic forgetting when samples are inevitably dropped during updates. In this paper, we propose Dota(DistributiOnal Test-time Adaptation), a simple yet effective method addressing this limitation. Crucially, instead of merely memorizing individual test samples, Dotacontinuously estimates the underlying distribution of the test data stream. Test-time posterior probabilities are then computed using these dynamically estimated distributions via Bayes' theorem for adaptation. This distribution-centric approach enables the model to continually learn and adapt to the deployment environment. Extensive experiments validate that Dota significantly mitigates forgetting and achieves state-of-the-art performance compared to existing methods.

Online advertising platforms use automated auctions to connect advertisers with potential customers, requiring effective bidding strategies to maximize profits. Accurate ad impact estimation requires considering three key factors: delayed and long-term effects, cumulative ad impacts such as reinforcement or fatigue, and customer heterogeneity. However, these effects are often not jointly addressed in previous studies. To capture these factors, we model ad bidding as a Contextual Markov Decision Process (CMDP) with delayed Poisson rewards. For efficient estimation, we propose a two-stage maximum likelihood estimator combined with data-splitting strategies, ensuring controlled estimation error based on the first-stage estimator's (in)accuracy. Building on this, we design a reinforcement learning algorithm to derive efficient personalized bidding strategies. This approach achieves a near-optimal regret bound of O(dH2 T), where d is the contextual dimension, H is the number of rounds, and T is the number of customers. Our theoretical findings are validated by simulation experiments.

Emergency traffic control presents an increasingly critical challenge, requiring seamless coordination among emergency vehicles, regular vehicles, and traffic lights to ensure efficient passage for all vehicles. Existing models primarily only focus on traffic light control, leaving emergency and regular vehicles prone to delay due to the lack of navigation strategies. To address this issue, we propose the Role-aware Multi-agent Traffic Control (RMTC) framework, which dynamically assigns appropriate roles to traffic components for better cooperation by considering their relations with emergency vehicles and adaptively adjusting their policies. Specifically, RMTC introduces a Heterogeneous Temporal Traffic Graph (HTTG) to model the spatial and temporal relationships among all traffic components (traffic lights, regular and emergency vehicles) at each time step. Furthermore, we develop a Dynamic Role Learning model to infer the evolving roles of traffic lights and regular vehicles based on HTTG. Finally, we present a Role-aware Multi-agent Reinforcement Learning approach that learns traffic policies conditioned on the dynamically roles. Extensive experiments across four public traffic scenarios show that RMTC outperforms existing traffic light control methods by significantly reducing emergency vehicle travel time, while effectively preserving traffic efficiency for regular vehicles.

Neurosymbolic (NeSy) predictors combine neural perception with symbolic reasoning to solve tasks like visual reasoning. However, standard NeSy predictors assume conditional independence between the symbols they extract, thus limiting their ability to model interactions and uncertainty -- often leading to overconfident predictions and poor out-of-distribution generalisation. To overcome the limitations of the independence assumption, we introduce neurosymbolic diffusion models (NESYDMS), a new class of NeSy predictors that use discrete diffusion to model dependencies between symbols.

Designing protein sequences of both high fitness and novelty is a challenging task in data-efficient protein engineering. Exploration beyond wild-type neighborhoods often leads to biologically implausible sequences or relies on surrogate models that lose fidelity in novel regions. Here, we propose PROSPERO, an active learning framework in which a frozen pre-trained generative model is guided by a surrogate updated from oracle feedback. By integrating fitness-relevant residue selection with biologically-constrained Sequential Monte Carlo sampling, our approach enables exploration beyond wild-type neighborhoods while preserving biological plausibility. We show that our framework remains effective even when the surrogate is misspecified. PROSPERO consistently outperforms or matches existing methods across diverse protein engineering tasks, retrieving sequences of both high fitness and novelty.

Recent advances in flow-based generative modelling have provided scalable methods for computing the Schr odinger Bridge (SB) between distributions, a dynamic form of entropy-regularised Optimal Transport (OT) for the quadratic cost. The successful Iterative Markovian Fitting (IMF) procedure solves the SB problem via sequential bridge-matching steps, presenting an elegant and practical approach with many favourable properties over the more traditional Iterative Proportional Fitting (IPF) procedure. Beyond the standard setting, optimal transport can be generalised to the multi-marginal case in which the objective is to minimise a cost defined over several marginal distributions. Of particular importance are costs defined over a tree structure, from which Wasserstein barycentres can be recovered as a special case. In this work, we extend the IMF procedure to solve for the tree-structured SB problem. Our resulting algorithm inherits the many advantages of IMF over IPF approaches in the tree-based setting. In the case of Wasserstein barycentres, our approach can be viewed as extending the widely used fixed-point approach to use flow-based entropic OT solvers, while requiring only simple bridge-matching steps at each iteration.

Causal discovery from observational data is a fundamental task in artificial intelligence, with far-reaching implications for decision-making, predictions, and interventions. Despite significant advances, existing methods can be broadly categorized as constraint-based or score-based approaches. Constraint-based methods offer rigorous causal discovery but are often hindered by small sample sizes, while score-based methods provide flexible optimization but typically forgo explicit conditional independence testing. This work explores a third avenue: developing differentiable d-separation scores, obtained through a percolation theory using soft logic. This enables the implementation of a new type of causal discovery method: gradient-based optimization of conditional independence constraints. Empirical evaluations demonstrate the robust performance of our approach in low-sample regimes, surpassing traditional constraint-based and score-based baselines on a real-world dataset.