Coarse-grained (CG) models play a crucial role in the study of protein structures, protein thermodynamic properties, and protein conformation dynamics. Due to the information loss in the coarse-graining process, backmapping from CG to all-atom configurations is essential in many protein design and drug discovery applications when detailed atomic representations are needed for in-depth studies. Despite recent progress in data-driven backmapping approaches, devising a backmapping method that can be universally applied across various CG models and proteins remains unresolved. In this work, we propose BackDiff, a new generative model designed to achieve generalization and reliability in the protein backmapping problem. BackDiff leverages the conditional score-based diffusion model with geometric representations. Since different CG models can contain different coarse-grained sites which include selected atoms (CG atoms) and simple CG auxiliary functions of atomistic coordinates (CG auxiliary variables), we design a self-supervised training framework to adapt to different CG atoms, and constrain the diffusion sampling paths with arbitrary CG auxiliary variables as conditions. Our method facilitates end-to-end training and allows efficient sampling across different proteins and diverse CG models without the need for retraining. Comprehensive experiments over multiple popular CG models demonstrate BackDiff's superior performance to existing state-of-the-art approaches, and generalization and flexibility that these approaches cannot achieve. A pretrained BackDiff model can offer a convenient yet reliable plug-and-play solution for protein researchers, enabling them to investigate further from their own CG models.

This study investigated the performance, explainability, and robustness of deployed artificial intelligence (AI) models in predicting mortality during the COVID-19 pandemic and beyond. The first study of its kind, we found that Bayesian Neural Networks (BNNs) and intelligent training techniques allowed our models to maintain performance amidst significant data shifts. Our results emphasize the importance of developing robust AI models capable of matching or surpassing clinician predictions, even under challenging conditions. Our exploration of model explainability revealed that stochastic models generate more diverse and personalized explanations thereby highlighting the need for AI models that provide detailed and individualized insights in real-world clinical settings. Furthermore, we underscored the importance of quantifying uncertainty in AI models which enables clinicians to make better-informed decisions based on reliable predictions. Our study advocates for prioritizing implementation science in AI research for healthcare and ensuring that AI solutions are practical, beneficial, and sustainable in real-world clinical environments. By addressing unique challenges and complexities in healthcare settings, researchers can develop AI models that effectively improve clinical practice and patient outcomes.

Jamming and intrusion detection are critical in 5G research, aiming to maintain reliability, prevent user experience degradation, and avoid infrastructure failure. This paper introduces an anonymous jamming detection model for 5G based on signal parameters from the protocol stacks. The system uses supervised and unsupervised learning for real-time, high-accuracy detection of jamming, including unknown types. Supervised models reach an AUC of 0.964 to 1, compared to LSTM models with an AUC of 0.923 to 1. However, the need for data annotation limits the supervised approach. To address this, an unsupervised auto-encoder-based anomaly detection is presented with an AUC of 0.987. The approach is resistant to adversarial training samples. For transparency and domain knowledge injection, a Bayesian network-based causation analysis is introduced.

Computing Continuum (CC) systems are challenged to ensure the intricate requirements of each computational tier. Given the system's scale, the Service Level Objectives (SLOs) which are expressed as these requirements, must be broken down into smaller parts that can be decentralized. We present our framework for collaborative edge intelligence enabling individual edge devices to (1) develop a causal understanding of how to enforce their SLOs, and (2) transfer knowledge to speed up the onboarding of heterogeneous devices. Through collaboration, they (3) increase the scope of SLO fulfillment. We implemented the framework and evaluated a use case in which a CC system is responsible for ensuring Quality of Service (QoS) and Quality of Experience (QoE) during video streaming. Our results showed that edge devices required only ten training rounds to ensure four SLOs; furthermore, the underlying causal structures were also rationally explainable. The addition of new types of devices can be done a posteriori, the framework allowed them to reuse existing models, even though the device type had been unknown. Finally, rebalancing the load within a device cluster allowed individual edge devices to recover their SLO compliance after a network failure from 22% to 89%.

Bayesian learning, a fundamental concept in statistical inference and decision-making, has gained significant traction across various fields due to its ability to integrate prior knowledge with new information. As a robust methodology, Bayesian learning has been widely acknowledged for its adaptability and precision in handling uncertainty and updating beliefs (Gelman et al., 1995). This manuscript expands upon the Bayesian learning framework (Baley and Veldkamp, 2023) through uniquely addressing the action and state-dependent signal variance in the agents' information set. At the core of this framework is the concept that the precision of the signal received by an agent is contingent upon both the agent's action and the actual state, for example, based on their congruence or tracking error (Daly, 2018; du Sart and van Vuuren, 2021; Orlik and Veldkamp, 2014; Rompotis, 2011; Stone et al., 2013; Yang and Huang, 2022).

Most scientific challenges can be framed into one of the following three levels of complexity of function approximation. Type 1: Approximate an unknown function given input/output data. Type 2: Consider a collection of variables and functions, some of which are unknown, indexed by the nodes and hyperedges of a hypergraph (a generalized graph where edges can connect more than two vertices). Given partial observations of the variables of the hypergraph (satisfying the functional dependencies imposed by its structure), approximate all the unobserved variables and unknown functions. Type 3: Expanding on Type 2, if the hypergraph structure itself is unknown, use partial observations of the variables of the hypergraph to discover its structure and approximate its unknown functions. While most Computational Science and Engineering and Scientific Machine Learning challenges can be framed as Type 1 and Type 2 problems, many scientific problems can only be categorized as Type 3. Despite their prevalence, these Type 3 challenges have been largely overlooked due to their inherent complexity. Although Gaussian Process (GP) methods are sometimes perceived as well-founded but old technology limited to Type 1 curve fitting, their scope has recently been expanded to Type 2 problems. In this paper, we introduce an interpretable GP framework for Type 3 problems, targeting the data-driven discovery and completion of computational hypergraphs. Our approach is based on a kernel generalization of Row Echelon Form reduction from linear systems to nonlinear ones and variance-based analysis. Here, variables are linked via GPs and those contributing to the highest data variance unveil the hypergraph's structure. We illustrate the scope and efficiency of the proposed approach with applications to (algebraic) equation discovery, network discovery (gene pathways, chemical, and mechanical) and raw data analysis.

A Bayesian approach to machine learning is attractive when we need to quantify uncertainty, deal with missing observations, when samples are scarce, or when the data is sparse. All of these commonly apply when analysing healthcare data. To address these analytical requirements, we propose a deep generative model for multinomial count data where both the weights and hidden units of the network are Dirichlet distributed. A Gibbs sampling procedure is formulated that takes advantage of a series of augmentation relations, analogous to the Zhou-Cong-Chen model. We apply the model on small handwritten digits, and a large experimental dataset of DNA mutations in cancer, and we show how the model is able to extract biologically meaningful meta-signatures in a fully data-driven way.

Nonparametric estimation of nonlocal interaction kernels is crucial in various applications involving interacting particle systems. The inference challenge, situated at the nexus of statistical learning and inverse problems, comes from the nonlocal dependency. A central question is whether the optimal minimax rate of convergence for this problem aligns with the rate of $M^{-\frac{2\beta}{2\beta+1}}$ in classical nonparametric regression, where $M$ is the sample size and $\beta$ represents the smoothness exponent of the radial kernel. Our study confirms this alignment for systems with a finite number of particles. We introduce a tamed least squares estimator (tLSE) that attains the optimal convergence rate for a broad class of exchangeable distributions. The tLSE bridges the smallest eigenvalue of random matrices and Sobolev embedding. This estimator relies on nonasymptotic estimates for the left tail probability of the smallest eigenvalue of the normal matrix. The lower minimax rate is derived using the Fano-Tsybakov hypothesis testing method. Our findings reveal that provided the inverse problem in the large sample limit satisfies a coercivity condition, the left tail probability does not alter the bias-variance tradeoff, and the optimal minimax rate remains intact. Our tLSE method offers a straightforward approach for establishing the optimal minimax rate for models with either local or nonlocal dependency.

Simulation-Based Inference (SBI) is a common name for an emerging family of approaches that infer the model parameters when the likelihood is intractable. Existing SBI methods either approximate the likelihood, such as Approximate Bayesian Computation (ABC), or directly model the posterior, such as Sequential Neural Posterior Estimation (SNPE). While ABC is efficient on low-dimensional problems, on higher-dimensional tasks, it is generally outperformed by SNPE which leverages function approximation. In this paper, we propose Pseudo-Likelihood Inference (PLI), a new method that brings neural approximation into ABC, making it competitive on challenging Bayesian system identification tasks. By utilizing integral probability metrics, we introduce a smooth likelihood kernel with an adaptive bandwidth that is updated based on information-theoretic trust regions. Thanks to this formulation, our method (i) allows for optimizing neural posteriors via gradient descent, (ii) does not rely on summary statistics, and (iii) enables multiple observations as input. In comparison to SNPE, it leads to improved performance when more data is available. The effectiveness of PLI is evaluated on four classical SBI benchmark tasks and on a highly dynamic physical system, showing particular advantages on stochastic simulations and multi-modal posterior landscapes.

Loss functions serve as the foundation of supervised learning and are often chosen prior to model development. To avoid potentially ad hoc choices of losses, statistical decision theory describes a desirable property for losses known as \emph{properness}, which asserts that Bayes' rule is optimal. Recent works have sought to \emph{learn losses} and models jointly. Existing methods do this by fitting an inverse canonical link function which monotonically maps $\mathbb{R}$ to $[0,1]$ to estimate probabilities for binary problems. In this paper, we extend monotonicity to maps between $\mathbb{R}^{C-1}$ and the projected probability simplex $\tilde{\Delta}^{C-1}$ by using monotonicity of gradients of convex functions. We present {\sc LegendreTron} as a novel and practical method that jointly learns \emph{proper canonical losses} and probabilities for multiclass problems. Tested on a benchmark of domains with up to 1,000 classes, our experimental results show that our method consistently outperforms the natural multiclass baseline under a $t$-test at 99% significance on all datasets with greater than 10 classes.