Generative Flow Networks (GFlowNets), a class of generative models have recently emerged as a suitable framework for generating diverse and high-quality molecular structures by learning from unnormalized reward distributions. Previous works in this direction often restrict exploration by using predefined molecular fragments as building blocks, limiting the chemical space that can be accessed. In this work, we introduce Atomic GFlowNets (A-GFNs), a foundational generative model leveraging individual atoms as building blocks to explore drug-like chemical space more comprehensively. We propose an unsupervised pre-training approach using offline drug-like molecule datasets, which conditions A-GFNs on inexpensive yet informative molecular descriptors such as drug-likeliness, topological polar surface area, and synthetic accessibility scores. These properties serve as proxy rewards, guiding A-GFNs towards regions of chemical space that exhibit desirable pharmacological properties. We further our method by implementing a goal-conditioned fine-tuning process, which adapts A-GFNs to optimize for specific target properties. In this work, we pretrain A-GFN on the ZINC15 offline dataset and employ robust evaluation metrics to show the effectiveness of our approach when compared to other relevant baseline methods in drug design.

Abstract-- We present closed-form expressions for marginalizing and conditioning Gaussians onto linear manifolds, and demonstrate how to apply these expressions to smooth nonlinear manifolds through linearization. Although marginalization and conditioning onto axis-aligned manifolds are well-established procedures, doing so onto non-axis-aligned manifolds is not as well understood. We demonstrate the utility of our expressions through three applications: 1) approximation of the projected normal distribution, where the quality of our linearized approximation increases as problem nonlinearity decreases; 2) covariance extraction in Koopman SLAM, where our covariances are shown to be consistent on a real-world dataset; and 3) covariance extraction in constrained GTSAM, where our covariances are shown to be consistent in simulation. Figure 1: Marginalizing and conditioning Gaussians onto manifolds defined by linear constraints using Table II. Gaussians have rank-2 covariances, lying on the constraint plane.

The interplay between stochastic processes and optimal control has been extensively explored in the literature. With the recent surge in the use of diffusion models, stochastic processes have increasingly been applied to sample generation. This paper builds on the log transform, known as the Cole-Hopf transform in Brownian motion contexts, and extends it within a more abstract framework that includes a linear operator. Within this framework, we found that the well-known relationship between the Cole-Hopf transform and optimal transport is a particular instance where the linear operator acts as the infinitesimal generator of a stochastic process. We also introduce a novel scenario where the linear operator is the adjoint of the generator, linking to Bayesian inference under specific initial and terminal conditions. Leveraging this theoretical foundation, we develop a new algorithm, named the HJ-sampler, for Bayesian inference for the inverse problem of a stochastic differential equation with given terminal observations. The HJ-sampler involves two stages: (1) solving the viscous Hamilton-Jacobi partial differential equations, and (2) sampling from the associated stochastic optimal control problem. Our proposed algorithm naturally allows for flexibility in selecting the numerical solver for viscous HJ PDEs. We introduce two variants of the solver: the Riccati-HJ-sampler, based on the Riccati method, and the SGM-HJ-sampler, which utilizes diffusion models. We demonstrate the effectiveness and flexibility of the proposed methods by applying them to solve Bayesian inverse problems involving various stochastic processes and prior distributions, including applications that address model misspecifications and quantifying model uncertainty.

The Schrödinger bridge problem seeks a process, the Schrödinger bridge, with prescribed initial and terminal distributions, such that the distribution of the Schrödinger bridge minimizes the Kullback-Leibler (KL) divergence to the distribution of a reference process. Schrödinger bridges play a central role in measure transport theory (Marzouk et al., 2016). Notably, it is known that the initial-terminal distribution of a Schrödinger bridge provides a solution to a corresponding entropic optimal transport problem (Peyré & Cuturi, 2020). Schrödinger bridges thus provide an effective framework for finding an alignment between samples from two target distributions. Furthermore, diffusion-based generative models (Ho et al., 2020; Song et al., 2021) can be interpreted as solving trivial instances of the Schrödinger bridge problem (Peluchetti, 2023). Consequently, Schrödinger bridges offer a more general approach to contemporary generative applications. We consider the setting where samples are readily available from both target distributions, and where the reference process is a diffusion process solution to a stochastic differential equation (SDE).

Learning uncertain dynamics models using Gaussian process~(GP) regression has been demonstrated to enable high-performance and safety-aware control strategies for challenging real-world applications. Yet, for computational tractability, most approaches for Gaussian process-based model predictive control (GP-MPC) are based on approximations of the reachable set that are either overly conservative or impede the controller's safety guarantees. To address these challenges, we propose a robust GP-MPC formulation that guarantees constraint satisfaction with high probability. For its tractable implementation, we propose a sampling-based GP-MPC approach that iteratively generates consistent dynamics samples from the GP within a sequential quadratic programming framework. We highlight the improved reachable set approximation compared to existing methods, as well as real-time feasible computation times, using two numerical examples.

Nonreciprocal thermal emitters that break Kirchhoff's law of thermal radiation promise exciting applications for thermal and energy applications. The design of the bandwidth and angular range of the nonreciprocal effect, which directly affects the performance of nonreciprocal emitters, typically relies on physical intuition. In this study, we present a general numerical approach to maximize the nonreciprocal effect. We choose doped magneto-optic materials and magnetic Weyl semimetal materials as model materials and focus on pattern-free multilayer structures. The optimization randomly starts from a less effective structure and incrementally improves the broadband nonreciprocity through the combination of Bayesian optimization and reparameterization. Optimization results show that the proposed approach can discover structures that can achieve broadband nonreciprocal emission at wavelengths from 5 to 40 micrometers using only a fewer layers, significantly outperforming current state-of-the-art designs based on intuition in terms of both performance and simplicity.

As humans can explore and understand the world through the sense of touch, tactile sensing is also an important aspect of robotic perception. In unstructured environments, robots can encounter both known and novel objects, this calls for a method to address both known and novel objects. In this study, we combine a particle filter (PF) and Gaussian process implicit surface (GPIS) in a unified Bayesian framework. The framework can differentiate between known and novel objects, perform object recognition, estimate pose for known objects, and reconstruct shapes for unknown objects, in an active learning fashion. By grounding the selection of the GPIS prior with the maximum-likelihood-estimation (MLE) shape from the PF, the knowledge about known objects' shapes can be transferred to learn novel shapes. An exploration procedure with global shape estimation is proposed to guide active data acquisition and conclude the exploration when sufficient information is obtained. The performance of the proposed Bayesian framework is evaluated through simulations on known and novel objects, initialized with random poses. The results show that the proposed exploration procedure, utilizing global shape estimation, achieves faster exploration than a local exploration procedure based on rapidly explore random tree (RRT). Overall, our results indicate that the proposed framework is effective and efficient in object recognition, pose estimation and shape reconstruction. Moreover, we show that a learned shape can be included as a new prior and used effectively for future object recognition and pose estimation.

Organisms have to keep track of the information in the environment that is relevant for adaptive behaviour. Transmitting information in an economical and efficient way becomes crucial for limited-resourced agents living in high-dimensional environments. The efficient coding hypothesis claims that organisms seek to maximize the information about the sensory input in an efficient manner. Under Bayesian inference, this means that the role of the brain is to efficiently allocate resources in order to make predictions about the hidden states that cause sensory data. However, neither of those frameworks accounts for how that information is exploited downstream, leaving aside the action-oriented role of the perceptual system. Rate-distortion theory, which defines optimal lossy compression under constraints, has gained attention as a formal framework to explore goal-oriented efficient coding. In this work, we explore action-centric representations in the context of rate-distortion theory. We also provide a mathematical definition of abstractions and we argue that, as a summary of the relevant details, they can be used to fix the content of action-centric representations. We model action-centric representations using VAEs and we find that such representations i) are efficient lossy compressions of the data; ii) capture the task-dependent invariances necessary to achieve successful behaviour; and iii) are not in service of reconstructing the data. Thus, we conclude that full reconstruction of the data is rarely needed to achieve optimal behaviour, consistent with a teleological approach to perception.

We present the SynSUM benchmark, a synthetic dataset linking unstructured clinical notes to structured background variables. The dataset consists of 10,000 artificial patient records containing tabular variables (like symptoms, diagnoses and underlying conditions) and related notes describing the fictional patient encounter in the domain of respiratory diseases. The tabular portion of the data is generated through a Bayesian network, where both the causal structure between the variables and the conditional probabilities are proposed by an expert based on domain knowledge. We then prompt a large language model (GPT-4o) to generate a clinical note related to this patient encounter, describing the patient symptoms and additional context. The SynSUM dataset is primarily designed to facilitate research on clinical information extraction in the presence of tabular background variables, which can be linked through domain knowledge to concepts of interest to be extracted from the text - the symptoms, in the case of SynSUM. Secondary uses include research on the automation of clinical reasoning over both tabular data and text, causal effect estimation in the presence of tabular and/or textual confounders, and multi-modal synthetic data generation. The dataset can be downloaded from https://github.com/prabaey/SynSUM.

We consider the generative problem of sampling from an unknown distribution for which only a sufficiently large number of training samples are available. In this paper, we build on previous work combining Schrödinger bridges and Langevin dynamics. A key bottleneck of this approach is the exponential dependence of the required training samples on the dimension, d, of the ambient state space. We propose a localization strategy which exploits conditional independence of conditional expectation values. Localization thus replaces a single high-dimensional Schrödinger bridge problem by d low-dimensional Schrödinger bridge problems over the available training samples. As for the original approach, the localized sampler is stable and geometric ergodic. The sampler also naturally extends to conditional sampling and to Bayesian inference. We demonstrate the performance of our proposed scheme through experiments on a Gaussian problem with increasing dimensions and on a stochastic subgrid-scale parametrization conditional sampling problem. Keywords: generative modeling, Langevin dynamics, Schrödinger bridges, conditional independence, localization, Bayesian inference, conditional sampling, multi-scale closure AMS: 60H10,62F15,62F30,65C05,65C40 1. Introduction In this paper, we consider the problem of sampling from an unknown probability measure ν(dx) on R