Probabilistic circuits (PCs) have emerged as a powerful framework to compactly represent probability distributions for efficient and exact probabilistic inference. It has been shown that PCs with a general directed acyclic graph (DAG) structure can be understood as a mixture of exponentially (in its height) many components, each of which is a product distribution over univariate marginals. However, existing structure learning algorithms for PCs often generate tree-structured circuits or use tree-structured circuits as intermediate steps to compress them into DAG-structured circuits. This leads to the intriguing question of whether there exists an exponential gap between DAGs and trees for the PC structure. In this paper, we provide a negative answer to this conjecture by proving that, for $n$ variables, there exists a quasi-polynomial upper bound $n^{O(\log n)}$ on the size of an equivalent tree computing the same probability distribution. On the other hand, we also show that given a depth restriction on the tree, there is a super-polynomial separation between tree and DAG-structured PCs. Our work takes an important step towards understanding the expressive power of tree-structured PCs, and our techniques may be of independent interest in the study of structure learning algorithms for PCs.

Neural posterior estimation (NPE), a simulation-based computational approach for Bayesian inference, has shown great success in situations where posteriors are intractable or likelihood functions are treated as "black boxes." Existing NPE methods typically rely on normalizing flows, which transform a base distributions into a complex posterior by composing many simple, invertible transformations. But flow-based models, while state of the art for NPE, are known to suffer from several limitations, including training instability and sharp trade-offs between representational power and computational cost. In this work, we demonstrate the effectiveness of conditional diffusions as an alternative to normalizing flows for NPE. Conditional diffusions address many of the challenges faced by flow-based methods. Our results show that, across a highly varied suite of benchmarking problems for NPE architectures, diffusions offer improved stability, superior accuracy, and faster training times, even with simpler, shallower models. These gains persist across a variety of different encoder or "summary network" architectures, as well as in situations where no summary network is required.

In neuroscience, researchers typically conduct experiments under multiple conditions to acquire neural responses in the form of high-dimensional spike train datasets. Analysing high-dimensional spike data is a challenging statistical problem. To this end, Gaussian process factor analysis (GPFA), a popular class of latent variable models has been proposed. GPFA extracts smooth, low-dimensional latent trajectories underlying high-dimensional spike train datasets. However, such analyses are often done separately for each experimental condition, contrary to the nature of neural datasets, which contain recordings under multiple experimental conditions. Exploiting the parametric nature of these conditions, we propose a multi-condition GPFA model and inference procedure to learn the underlying latent structure in the corresponding datasets in sample-efficient manner. In particular, we propose a non-parametric Bayesian approach to learn a smooth tuning function over the experiment condition space. Our approach not only boosts model accuracy and is faster, but also improves model interpretability compared to approaches that separately fit models for each experimental condition.

However, a unique challenge in nuclear engineering is data scarcity because experimentation on nuclear systems is usually more expensive and time-consuming than most other disciplines. Large amounts of data may be available for certain parts such as pipes, pumps and turbines, etc., due to large network of sensors, but not for many others, such as critical heat flux in thermal-hydraulics experiments, advanced materials qualification data like molten salts and multi-principal element alloys, etc. Particularly concerning is the lack of data for advanced reactor design and safety analysis, raising challenges for utilizing ML in licensing analyses of advanced nuclear reactors. In these cases, we need to move beyond "throw more data and re-train" at the problem, which is the common solution in areas such as computer vision and natural language processing that have access to "big data". One potential way to address the data scarcity issue is data augmentation using deep generative learning. Deep generative learning is an unsupervised ML technique that aims at discovering and learning the regularities or patterns in existing data using deep generative models (DGMs), in order to generate new samples that plausibly could have been drawn from the real dataset. DGMs are typically neural networks (NNs) trained to learn or approximate the underlying distribution of the training data. This enables them to generate synthetic samples that closely match the distribution of the original training data. By employing DGMs for data augmentation, one can significantly expand the training dataset for ML models to achieve better performance in other tasks, such as data-driven predictive ML models. Data augmentation with DGMs is still a relatively new research area in nuclear engineering, but has been studied for a few years in computer vision and natural language processing for datasets involving images, audios, videos, spoken words, etc.

We consider the problem of developing interpretable and computationally efficient matrix decomposition methods for matrices whose entries have bounded support. Such matrices are found in large-scale DNA methylation studies and many other settings. Our approach decomposes the data matrix into a Tucker representation wherein the number of columns in the constituent factor matrices is not constrained. We derive a computationally efficient sampling algorithm to solve for the Tucker decomposition. We evaluate the performance of our method using three criteria: predictability, computability, and stability. Empirical results show that our method has similar performance as other state-of-the-art approaches in terms of held-out prediction and computational complexity, but has significantly better performance in terms of stability to changes in hyper-parameters. The improved stability results in higher confidence in the results in applications where the constituent factors are used to generate and test scientific hypotheses such as DNA methylation analysis of cancer samples.

Causal discovery in real-world systems, such as biological networks, is often complicated by feedback loops and incomplete data. Standard algorithms, which assume acyclic structures or fully observed data, struggle with these challenges. To address this gap, we propose MissNODAG, a differentiable framework for learning both the underlying cyclic causal graph and the missingness mechanism from partially observed data, including data missing not at random. Our framework integrates an additive noise model with an expectation-maximization procedure, alternating between imputing missing values and optimizing the observed data likelihood, to uncover both the cyclic structures and the missingness mechanism. We demonstrate the effectiveness of MissNODAG through synthetic experiments and an application to real-world gene perturbation data.

LLMs show remarkable emergent abilities, such as inferring concepts from presumably out-of-distribution prompts, known as in-context learning. Though this success is often attributed to the Transformer architecture, our systematic understanding is limited. In complex real-world data sets, even defining what is out-of-distribution is not obvious. To better understand the OOD behaviour of autoregressive LLMs, we focus on formal languages, which are defined by the intersection of rules. We define a new scenario of OOD compositional generalization, termed rule extrapolation. Rule extrapolation describes OOD scenarios, where the prompt violates at least one rule. We evaluate rule extrapolation in formal languages with varying complexity in linear and recurrent architectures, the Transformer, and state space models to understand the architectures' influence on rule extrapolation. We also lay the first stones of a normative theory of rule extrapolation, inspired by the Solomonoff prior in algorithmic information theory.

Many Bayesian statistical inference problems come down to computing a maximum a-posteriori (MAP) assignment of latent variables. Yet, standard methods for estimating the MAP assignment do not have a finite time guarantee that the algorithm has converged to a fixed point. Previous research has found that MAP inference can be represented in dual form as a linear programming problem with a non-polynomial number of constraints. A Lagrangian relaxation of the dual yields a statistical inference algorithm as a linear programming problem. However, the decision as to which constraints to remove in the relaxation is often heuristic. We present a method for maximum a-posteriori inference in general Bayesian factor models that sequentially adds constraints to the fully relaxed dual problem using Benders' decomposition. Our method enables the incorporation of expressive integer and logical constraints in clustering problems such as must-link, cannot-link, and a minimum number of whole samples allocated to each cluster. Using this approach, we derive MAP estimation algorithms for the Bayesian Gaussian mixture model and latent Dirichlet allocation. Empirical results show that our method produces a higher optimal posterior value compared to Gibbs sampling and variational Bayes methods for standard data sets and provides certificate of convergence.

Proteins adopt multiple structural conformations to perform their diverse biological functions, and understanding these conformations is crucial for advancing drug discovery. Traditional physics-based simulation methods often struggle with sampling equilibrium conformations and are computationally expensive. Recently, deep generative models have shown promise in generating protein conformations as a more efficient alternative. However, these methods predominantly rely on the diffusion process within a 3D geometric space, which typically centers around the vicinity of metastable states and is often inefficient in terms of runtime. In this paper, we introduce Structure Language Modeling (SLM) as a novel framework for efficient protein conformation generation. Specifically, the protein structures are first encoded into a compact latent space using a discrete variational auto-encoder, followed by conditional language modeling that effectively captures sequencespecific conformation distributions. This enables a more efficient and interpretable exploration of diverse ensemble modes compared to existing methods. Based on this general framework, we instantiate SLM with various popular LM architectures as well as proposing the ESMDiff, a novel BERT-like structure language model fine-tuned from ESM3 with masked diffusion. We verify our approach in various scenarios, including the equilibrium dynamics of BPTI, conformational change pairs, and intrinsically disordered proteins. SLM provides a highly efficient solution, offering a 20-100x speedup than existing methods in generating diverse conformations, shedding light on promising avenues for future research. Protein structure dynamics are fundamental to understanding the biological functions of proteins. The ability of proteins to adopt multiple conformations is crucial for their function in influencing interactions with other biomolecules and the environment. Traditional computational methods, such as molecular dynamics (MD) simulations, have long been used to explore these dynamics. However, these methods are computationally expensive and time-consuming.

Rough set theory is one of the most widely used and significant approaches for handling incomplete information. It divides the universe in the beginning and uses equivalency relations to produce blocks. Numerous generalized rough set models have been put out and investigated in an effort to increase flexibility and extend the range of possible uses. We introduce four new generalized rough set models that draw inspiration from "neighborhoods and primals" in order to make a contribution to this topic. By minimizing the uncertainty regions, these models are intended to assist decision makers in more effectively analyzing and evaluating the provided data. We verify this goal by demonstrating that the existing models outperform certain current method approaches in terms of improving the approximation operators (upper and lower) and accuracy measurements. We claim that the current models can preserve nearly all significant aspects associated with the rough set model. Preserving the monotonic property, which enables us to assess data uncertainty and boost confidence in outcomes, is one of the intriguing characterizations derived from the existing models. With the aid of specific instances, we also compare the areas of the current approach. Finally, we demonstrate that the new strategy we define for our everyday health-related problem yields more accurate findings.