The interaction of a protein with its environment can be understood and controlled via its 3D structure. Experimental methods for protein structure determination, such as X-ray crystallography or cryogenic electron microscopy, shed light on biological processes but introduce challenging inverse problems. Learning-based approaches have emerged as accurate and efficient methods to solve these inverse problems for 3D structure determination, but are specialized for a predefined type of measurement. Here, we introduce a versatile framework to turn raw biophysical measurements of varying types into 3D atomic models. Our method combines a physics-based forward model of the measurement process with a pretrained generative model providing a task-agnostic, data-driven prior. Our method outperforms posterior sampling baselines on both linear and non-linear inverse problems. In particular, it is the first diffusion-based method for refining atomic models from cryo-EM density maps.

Discovering causal relationships from observational data, particularly in the presence of latent variables, poses a challenging problem. While current local structure learning methods have proven effective and efficient when the focus lies solely on the local relationships of a target variable, they operate under the assumption of causal sufficiency. This assumption implies that all the common causes of the measured variables are observed, leaving no room for latent variables. Such a premise can be easily violated in various real-world applications, resulting in inaccurate structures that may adversely impact downstream tasks. In light of this, our paper delves into the primary investigation of locally identifying potential parents and children of a target from observational data that may include latent variables. Specifically, we harness the causal information from m-separation and V-structures to derive theoretical consistency results, effectively bridging the gap between global and local structure learning. Together with the newly developed stop rules, we present a principled method for determining whether a variable is a direct cause or effect of a target. Further, we theoretically demonstrate the correctness of our approach under the standard causal Markov and faithfulness conditions, with infinite samples. Experimental results on both synthetic and real-world data validate the effectiveness and efficiency of our approach.

The decisions of individuals and organizations are often suboptimal because normative decision strategies are too demanding in the real world. Recent work suggests that some errors can be prevented by leveraging artificial intelligence to discover and teach prescriptive decision strategies that take people's constraints into account. So far, this line of research has been limited to simplified decision problems. This article is the first to extend this approach to a real-world decision problem, namely project selection. We develop a computational method (MGPS) that automatically discovers project selection strategies that are optimized for real people and develop an intelligent tutor that teaches the discovered strategies. We evaluated MGPS on a computational benchmark and tested the intelligent tutor in a training experiment with two control conditions. MGPS outperformed a state-of-the-art method and was more computationally efficient. Moreover, the intelligent tutor significantly improved people's decision strategies. Our results indicate that our method can improve human decision-making in naturalistic settings similar to real-world project selection, a first step towards applying strategy discovery to the real world.

Recent advances in probabilistic deep learning enable efficient amortized Bayesian inference in settings where the likelihood function is only implicitly defined by a simulation program (simulation-based inference; SBI). But how faithful is such inference if the simulation represents reality somewhat inaccurately, that is, if the true system behavior at test time deviates from the one seen during training? We conceptualize the types of such model misspecification arising in SBI and systematically investigate how the performance of neural posterior approximators gradually deteriorates as a consequence, making inference results less and less trustworthy. To notify users about this problem, we propose a new misspecification measure that can be trained in an unsupervised fashion (i.e., without training data from the true distribution) and reliably detects model misspecification at test time. Our experiments clearly demonstrate the utility of our new measure both on toy examples with an analytical ground-truth and on representative scientific tasks in cell biology, cognitive decision making, disease outbreak dynamics, and computer vision. We show how the proposed misspecification test warns users about suspicious outputs, raises an alarm when predictions are not trustworthy, and guides model designers in their search for better simulators.

In recent years, solving optimization problems involving black-box simulators has become a point of focus for the machine learning community due to their ubiquity in science and engineering. The simulators describe a forward process $f_{\mathrm{sim}}: (\psi, x) \rightarrow y$ from simulation parameters $\psi$ and input data $x$ to observations $y$, and the goal of the optimization problem is to find parameters $\psi$ that minimize a desired loss function. Sophisticated optimization algorithms typically require gradient information regarding the forward process, $f_{\mathrm{sim}}$, with respect to the parameters $\psi$. However, obtaining gradients from black-box simulators can often be prohibitively expensive or, in some cases, impossible. Furthermore, in many applications, practitioners aim to solve a set of related problems. Thus, starting the optimization ``ab initio", i.e. from scratch, each time might be inefficient if the forward model is expensive to evaluate. To address those challenges, this paper introduces a novel method for solving classes of similar black-box optimization problems by learning an active learning policy that guides a differentiable surrogate's training and uses the surrogate's gradients to optimize the simulation parameters with gradient descent. After training the policy, downstream optimization of problems involving black-box simulators requires up to $\sim$90\% fewer expensive simulator calls compared to baselines such as local surrogate-based approaches, numerical optimization, and Bayesian methods.

Current approaches to model-based offline Reinforcement Learning (RL) often incorporate uncertainty-based reward penalization to address the distributional shift problem. While these approaches have achieved some success, we argue that this penalization introduces excessive conservatism, potentially resulting in suboptimal policies through underestimation. We identify as an important cause of over-penalization the lack of a reliable uncertainty estimator capable of propagating uncertainties in the Bellman operator. The common approach to calculating the penalty term relies on sampling-based uncertainty estimation, resulting in high variance. To address this challenge, we propose a novel method termed Moment Matching Offline Model-Based Policy Optimization (MOMBO). MOMBO learns a Q-function using moment matching, which allows us to deterministically propagate uncertainties through the Q-function. We evaluate MOMBO's performance across various environments and demonstrate empirically that MOMBO is a more stable and sample-efficient approach.

High-dimensional Bayesian optimization (BO) tasks such as molecular design often require > 10,000 function evaluations before obtaining meaningful results. While methods like sparse variational Gaussian processes (SVGPs) reduce computational requirements in these settings, the underlying approximations result in suboptimal data acquisitions that slow the progress of optimization. In this paper we modify SVGPs to better align with the goals of BO: targeting informed data acquisition rather than global posterior fidelity. Using the framework of utility-calibrated variational inference, we unify GP approximation and data acquisition into a joint optimization problem, thereby ensuring optimal decisions under a limited computational budget. Our approach can be used with any decision-theoretic acquisition function and is compatible with trust region methods like TuRBO. We derive efficient joint objectives for the expected improvement and knowledge gradient acquisition functions in both the standard and batch BO settings. Our approach outperforms standard SVGPs on high-dimensional benchmark tasks in control and molecular design.

The diffusion bridge is a type of diffusion process that conditions on hitting a specific state within a finite time period. It has broad applications in fields such as Bayesian inference, financial mathematics, control theory, and shape analysis. However, simulating the diffusion bridge for natural data can be challenging due to both the intractability of the drift term and continuous representations of the data. Although several methods are available to simulate finite-dimensional diffusion bridges, infinite-dimensional cases remain unresolved. In the paper, we present a solution to this problem by merging score-matching techniques with operator learning, enabling a direct approach to score-matching for the infinite-dimensional bridge. We construct the score to be discretization invariant, which is natural given the underlying spatially continuous process. We conduct a series of experiments, ranging from synthetic examples with closed-form solutions to the stochastic nonlinear evolution of real-world biological shape data, and our method demonstrates high efficacy, particularly due to its ability to adapt to any resolution without extra training.

Olfaction sensing in autonomous robotics faces challenges in dynamic operations, energy efficiency, and edge processing. It necessitates a machine learning algorithm capable of managing real-world odor interference, ensuring resource efficiency for mobile robotics, and accurately estimating gas features for critical tasks such as odor mapping, localization, and alarm generation. This paper introduces a hybrid approach that exploits neuromorphic computing in combination with probabilistic inference to address these demanding requirements. Our approach implements a combination of a convolutional spiking neural network for feature extraction and a Bayesian spiking neural network for odor detection and identification. The developed algorithm is rigorously tested on a dataset for sensor drift compensation for robustness evaluation. Additionally, for efficiency evaluation, we compare the energy consumption of our model with a non-spiking machine learning algorithm under identical dataset and operating conditions. Our approach demonstrates superior efficiency alongside comparable accuracy outcomes.

Reconstructing jets, which provide vital insights into the properties and histories of subatomic particles produced in high-energy collisions, is a main problem in data analyses in collider physics. This intricate task deals with estimating the latent structure of a jet (binary tree) and involves parameters such as particle energy, momentum, and types. While Bayesian methods offer a natural approach for handling uncertainty and leveraging prior knowledge, they face significant challenges due to the super-exponential growth of potential jet topologies as the number of observed particles increases. To address this, we introduce a Combinatorial Sequential Monte Carlo approach for inferring jet latent structures. As a second contribution, we leverage the resulting estimator to develop a variational inference algorithm for parameter learning. Building on this, we introduce a variational family using a pseudo-marginal framework for a fully Bayesian treatment of all variables, unifying the generative model with the inference process. We illustrate our method's effectiveness through experiments using data generated with a collider physics generative model, highlighting superior speed and accuracy across a range of tasks.