Learning Graphical Models
A Guide to Bayesian Optimization in Bioprocess Engineering
Siska, Maximilian, Pajak, Emma, Rosenthal, Katrin, Chanona, Antonio del Rio, von Lieres, Eric, Helleckes, Laura Marie
Bayesian optimization has become widely popular across various experimental sciences due to its favorable attributes: it can handle noisy data, perform well with relatively small datasets, and provide adaptive suggestions for sequential experimentation. While still in its infancy, Bayesian optimization has recently gained traction in bioprocess engineering. However, experimentation with biological systems is highly complex and the resulting experimental uncertainty requires specific extensions to classical Bayesian optimization. Moreover, current literature often targets readers with a strong statistical background, limiting its accessibility for practitioners. In light of these developments, this review has two aims: first, to provide an intuitive and practical introduction to Bayesian optimization; and second, to outline promising application areas and open algorithmic challenges, thereby highlighting opportunities for future research in machine learning.
BKP: An R Package for Beta Kernel Process Modeling
Zhao, Jiangyan, Qing, Kunhai, Xu, Jin
We present BKP, a user-friendly and extensible R package that implements the Beta Kernel Process (BKP) -- a fully nonparametric and computationally efficient framework for modeling spatially varying binomial probabilities. The BKP model combines localized kernel-weighted likelihoods with conjugate beta priors, resulting in closed-form posterior inference without requiring latent variable augmentation or intensive MCMC sampling. The package supports binary and aggregated binomial responses, allows flexible choices of kernel functions and prior specification, and provides loss-based kernel hyperparameter tuning procedures. In addition, BKP extends naturally to the Dirichlet Kernel Process (DKP) for modeling spatially varying multinomial or compositional data. To our knowledge, this is the first publicly available R package for implementing BKP-based methods. We illustrate the use of BKP through several synthetic and real-world datasets, highlighting its interpretability, accuracy, and scalability. The package aims to facilitate practical application and future methodological development of kernel-based beta modeling in statistics and machine learning.
Non-Stationary Restless Multi-Armed Bandits with Provable Guarantee
Hung, Yu-Heng, Hsieh, Ping-Chun, Wang, Kai
Online restless multi-armed bandits (RMABs) typically assume that each arm follows a stationary Markov Decision Process (MDP) with fixed state transitions and rewards. However, in real-world applications like healthcare and recommendation systems, these assumptions often break due to non-stationary dynamics, posing significant challenges for traditional RMAB algorithms. In this work, we specifically consider $N$-armd RMAB with non-stationary transition constrained by bounded variation budgets $B$. Our proposed \rmab\; algorithm integrates sliding window reinforcement learning (RL) with an upper confidence bound (UCB) mechanism to simultaneously learn transition dynamics and their variations. We further establish that \rmab\; achieves $\widetilde{\mathcal{O}}(N^2 B^{\frac{1}{4}} T^{\frac{3}{4}})$ regret bound by leveraging a relaxed definition of regret, providing a foundational theoretical framework for non-stationary RMAB problems for the first time.
Deep Learning in Classical and Quantum Physics
Heightman, Timothy, Płodzień, Marcin
Scientific progress is tightly coupled to the emergence of new research tools. Today, machine learning (ML)-especially deep learning (DL)-has become a transformative instrument for quantum science and technology. Owing to the intrinsic complexity of quantum systems, DL enables efficient exploration of large parameter spaces, extraction of patterns from experimental data, and data-driven guidance for research directions. These capabilities already support tasks such as refining quantum control protocols and accelerating the discovery of materials with targeted quantum properties, making ML/DL literacy an essential skill for the next generation of quantum scientists. At the same time, DL's power brings risks: models can overfit noisy data, obscure causal structure, and yield results with limited physical interpretability. Recognizing these limitations and deploying mitigation strategies is crucial for scientific rigor. These lecture notes provide a comprehensive, graduate-level introduction to DL for quantum applications, combining conceptual exposition with hands-on examples. Organized as a progressive sequence, they aim to equip readers to decide when and how to apply DL effectively, to understand its practical constraints, and to adapt AI methods responsibly to problems across quantum physics, chemistry, and engineering.
Nonlocal Monte Carlo via Reinforcement Learning
Dobrynin, Dmitrii, Mohseni, Masoud, Strachan, John Paul
Optimizing or sampling complex cost functions of combinatorial optimization problems is a longstanding challenge across disciplines and applications. When employing family of conventional algorithms based on Markov Chain Monte Carlo (MCMC) such as simulated annealing or parallel tempering, one assumes homogeneous (equilibrium) temperature profiles across input. This instance independent approach was shown to be ineffective for the hardest benchmarks near a computational phase transition when the so-called overlap-gap-property holds. In these regimes conventional MCMC struggles to unfreeze rigid variables, escape suboptimal basins of attraction, and sample high-quality and diverse solutions. In order to mitigate these challenges, Nonequilibrium Nonlocal Monte Carlo (NMC) algorithms were proposed that leverage inhomogeneous temperature profiles thereby accelerating exploration of the configuration space without compromising its exploitation. Here, we employ deep reinforcement learning (RL) to train the nonlocal transition policies of NMC which were previously designed phenomenologically. We demonstrate that the resulting solver can be trained solely by observing energy changes of the configuration space exploration as RL rewards and the local minimum energy landscape geometry as RL states. We further show that the trained policies improve upon the standard MCMC-based and nonlocal simulated annealing on hard uniform random and scale-free random 4-SAT benchmarks in terms of residual energy, time-to-solution, and diversity of solutions metrics.