Tensor factorizations (TF) are powerful tools for the efficient representation and analysis of multidimensional data. However, classic TF methods based on maximum likelihood estimation underperform when applied to zero-inflated count data, such as single-cell RNA sequencing (scRNA-seq) data. Additionally, the stochasticity inherent in TFs results in factors that vary across repeated runs, making interpretation and reproducibility of the results challenging. In this paper, we introduce Zero Inflated Poisson Tensor Factorization (ZIPTF), a novel approach for the factorization of high-dimensional count data with excess zeros. To address the challenge of stochasticity, we introduce Consensus Zero Inflated Poisson Tensor Factorization (C-ZIPTF), which combines ZIPTF with a consensus-based meta-analysis. We evaluate our proposed ZIPTF and C-ZIPTF on synthetic zero-inflated count data and synthetic and real scRNA-seq data. ZIPTF consistently outperforms baseline matrix and tensor factorization methods in terms of reconstruction accuracy for zero-inflated data. When the probability of excess zeros is high, ZIPTF achieves up to $2.4\times$ better accuracy. Additionally, C-ZIPTF significantly improves the consistency and accuracy of the factorization. When tested on both synthetic and real scRNA-seq data, ZIPTF and C-ZIPTF consistently recover known and biologically meaningful gene expression programs.

Active Inference is a recent framework for modeling planning under uncertainty. Empirical and theoretical work have now begun to evaluate the strengths and weaknesses of this approach and how it might be improved. A recent extension - the sophisticated inference (SI) algorithm - improves performance on multi-step planning problems through recursive decision tree search. However, little work to date has been done to compare SI to other established planning algorithms. SI was also developed with a focus on inference as opposed to learning. The present paper has two aims. First, we compare performance of SI to Bayesian reinforcement learning (RL) schemes designed to solve similar problems. Second, we present an extension of SI - sophisticated learning (SL) - that more fully incorporates active learning during planning. SL maintains beliefs about how model parameters would change under the future observations expected under each policy. This allows a form of counterfactual retrospective inference in which the agent considers what could be learned from current or past observations given different future observations. To accomplish these aims, we make use of a novel, biologically inspired environment designed to highlight the problem structure for which SL offers a unique solution. Here, an agent must continually search for available (but changing) resources in the presence of competing affordances for information gain. Our simulations show that SL outperforms all other algorithms in this context - most notably, Bayes-adaptive RL and upper confidence bound algorithms, which aim to solve multi-step planning problems using similar principles (i.e., directed exploration and counterfactual reasoning). These results provide added support for the utility of Active Inference in solving this class of biologically-relevant problems and offer added tools for testing hypotheses about human cognition.

X-ray diffraction (XRD) is an essential technique to determine a material's crystal structure in high-throughput experimentation, and has recently been incorporated in artificially intelligent agents in autonomous scientific discovery processes. However, rapid, automated and reliable analysis method of XRD data matching the incoming data rate remains a major challenge. To address these issues, we present CrystalShift, an efficient algorithm for probabilistic XRD phase labeling that employs symmetry-constrained pseudo-refinement optimization, best-first tree search, and Bayesian model comparison to estimate probabilities for phase combinations without requiring phase space information or training. We demonstrate that CrystalShift provides robust probability estimates, outperforming existing methods on synthetic and experimental datasets, and can be readily integrated into high-throughput experimental workflows. In addition to efficient phase-mapping, CrystalShift offers quantitative insights into materials' structural parameters, which facilitate both expert evaluation and AI-based modeling of the phase space, ultimately accelerating materials identification and discovery.

Artificial intelligence (AI) is rapidly becoming one of the key technologies of this century. The majority of results in AI thus far have been achieved using deep neural networks trained with the error backpropagation learning algorithm. However, the ubiquitous adoption of this approach has highlighted some important limitations such as substantial computational cost, difficulty in quantifying uncertainty, lack of robustness, unreliability, and biological implausibility. It is possible that addressing these limitations may require schemes that are inspired and guided by neuroscience theories. One such theory, called predictive coding (PC), has shown promising performance in machine intelligence tasks, exhibiting exciting properties that make it potentially valuable for the machine learning community: PC can model information processing in different brain areas, can be used in cognitive control and robotics, and has a solid mathematical grounding in variational inference, offering a powerful inversion scheme for a specific class of continuous-state generative models. With the hope of foregrounding research in this direction, we survey the literature that has contributed to this perspective, highlighting the many ways that PC might play a role in the future of machine learning and computational intelligence at large.

A wide variety of NCM estimation methods have been proposed within the control community [1]. These methods Identifying the noise associated with a process, i.e., estimating can be classified into two categories: i) feedback free the Noise Covariance Matrix (NCM) is crucial for methods where the estimation is done by processing the state estimation and control of a dynamic system [1]. An entire data sequence offline and ii) feedback methods where incorrect NCM results in suboptimal gains (e.g., Kalman estimation is done online and. The feedback free methods are gain), significantly decreasing the quality of state estimation of two types: i) the correlation methods that are based on the and tracking. Hence, accurate NCM estimation has a wide analysis of the measurement error sequence, such as Indirect scope of applications that include robotics, signal processing, Correlation (ICM) [9], Input-Output Correlation (IOCM) fault detection, optimal controller design, system identification, [10], Weighted Correlation (WCM) [11], Measurement Average etc. However, most of the NCM estimation algorithms Correlation (MACM) [12], Direct Correlation (DCM) assume a white noise condition, which may not be true in [13] and Measurement Difference Correlation (MDCM) [14], practice. In many real-world applications the noise is colored and ii) the Maximum-Likelihood Methods (MLM) [15] that (e.g., there are temporal autocorrelations). This makes NCM maximises the likelihood function over the data.

Multidimensional scaling (MDS) is a widely used approach to representing high-dimensional, dependent data. MDS works by assigning each observation a location on a low-dimensional geometric manifold, with distance on the manifold representing similarity. We propose a Bayesian approach to multidimensional scaling when the low-dimensional manifold is hyperbolic. Using hyperbolic space facilitates representing tree-like structures common in many settings (e.g. text or genetic data with hierarchical structure). A Bayesian approach provides regularization that minimizes the impact of measurement error in the observed data and assesses uncertainty. We also propose a case-control likelihood approximation that allows for efficient sampling from the posterior distribution in larger data settings, reducing computational complexity from approximately $O(n^2)$ to $O(n)$. We evaluate the proposed method against state-of-the-art alternatives using simulations, canonical reference datasets, Indian village network data, and human gene expression data.

We propose OCDaf, a novel order-based method for learning causal graphs from observational data. We establish the identifiability of causal graphs within multivariate heteroscedastic noise models, a generalization of additive noise models that allow for non-constant noise variances. Drawing upon the structural similarities between these models and affine autoregressive normalizing flows, we introduce a continuous search algorithm to find causal structures. Our experiments demonstrate state-of-the-art performance across the Sachs and SynTReN benchmarks in Structural Hamming Distance (SHD) and Structural Intervention Distance (SID). Furthermore, we validate our identifiability theory across various parametric and nonparametric synthetic datasets and showcase superior performance compared to existing baselines.

This paper studies the performance of the spectral method in the estimation and uncertainty quantification of the unobserved preference scores of compared entities in a very general and more realistic setup in which the comparison graph consists of hyper-edges of possible heterogeneous sizes and the number of comparisons can be as low as one for a given hyper-edge. Such a setting is pervasive in real applications, circumventing the need to specify the graph randomness and the restrictive homogeneous sampling assumption imposed in the commonly-used Bradley-Terry-Luce (BTL) or Plackett-Luce (PL) models. Furthermore, in the scenarios when the BTL or PL models are appropriate, we unravel the relationship between the spectral estimator and the Maximum Likelihood Estimator (MLE). We discover that a two-step spectral method, where we apply the optimal weighting estimated from the equal weighting vanilla spectral method, can achieve the same asymptotic efficiency as the MLE. Given the asymptotic distributions of the estimated preference scores, we also introduce a comprehensive framework to carry out both one-sample and two-sample ranking inferences, applicable to both fixed and random graph settings. It is noteworthy that it is the first time effective two-sample rank testing methods are proposed. Finally, we substantiate our findings via comprehensive numerical simulations and subsequently apply our developed methodologies to perform statistical inferences on statistics journals and movie rankings.

Quantifying uncertainty about a policy's long-term performance is important to solve sequential decision-making tasks. We study the problem from a model-based Bayesian reinforcement learning perspective, where the goal is to learn the posterior distribution over value functions induced by parameter (epistemic) uncertainty of the Markov decision process. Previous work restricts the analysis to a few moments of the distribution over values or imposes a particular distribution shape, e.g., Gaussians. Inspired by distributional reinforcement learning, we introduce a Bellman operator whose fixed-point is the value distribution function. Based on our theory, we propose Epistemic Quantile-Regression (EQR), a model-based algorithm that learns a value distribution function that can be used for policy optimization. Evaluation across several continuous-control tasks shows performance benefits with respect to established model-based and model-free algorithms.

Semantic communications are expected to accomplish various semantic tasks with relatively less spectrum resource by exploiting the semantic feature of source data. To simultaneously serve both the data transmission and semantic tasks, joint data compression and semantic analysis has become pivotal issue in semantic communications. This paper proposes a deep separate source-channel coding (DSSCC) framework for the joint task and data oriented semantic communications (JTD-SC) and utilizes the variational autoencoder approach to solve the rate-distortion problem with semantic distortion. First, by analyzing the Bayesian model of the DSSCC framework, we derive a novel rate-distortion optimization problem via the Bayesian inference approach for general data distributions and semantic tasks. Next, for a typical application of joint image transmission and classification, we combine the variational autoencoder approach with a forward adaption scheme to effectively extract image features and adaptively learn the density information of the obtained features. Finally, an iterative training algorithm is proposed to tackle the overfitting issue of deep learning models. Simulation results reveal that the proposed scheme achieves better coding gain as well as data recovery and classification performance in most scenarios, compared to the classical compression schemes and the emerging deep joint source-channel schemes.