To ensure the safety of railroad operations, it is important to monitor and forecast track geometry irregularities. A higher safety requires forecasting with higher spatiotemporal frequencies, which in turn requires capturing spatial correlations. Additionally, track geometry irregularities are influenced by multiple exogenous factors. In this study, a method is proposed to forecast one type of track geometry irregularity, vertical alignment, by incorporating spatial and exogenous factor calculations. The proposed method embeds exogenous factors and captures spatiotemporal correlations using a convolutional long short-term memory. The proposed method is also experimentally compared with other methods in terms of the forecasting performance. Additionally, an ablation study on exogenous factors is conducted to examine their individual contributions to the forecasting performance. The results reveal that spatial calculations and maintenance record data improve the forecasting of vertical alignment.

Let $V_* : \mathbb{R}^d \to \mathbb{R}$ be some (possibly non-convex) potential function, and consider the probability measure $\pi \propto e^{-V_*}$. When $\pi$ exhibits multiple modes, it is known that sampling techniques based on Wasserstein gradient flows of the Kullback-Leibler (KL) divergence (e.g. Langevin Monte Carlo) suffer poorly in the rate of convergence, where the dynamics are unable to easily traverse between modes. In stark contrast, the work of Lu et al. (2019; 2022) has shown that the gradient flow of the KL with respect to the Fisher-Rao (FR) geometry exhibits a convergence rate to $\pi$ is that \textit{independent} of the potential function. In this short note, we complement these existing results in the literature by providing an explicit expansion of $\text{KL}(\rho_t^{\text{FR}}\|\pi)$ in terms of $e^{-t}$, where $(\rho_t^{\text{FR}})_{t\geq 0}$ is the FR gradient flow of the KL divergence. In turn, we are able to provide a clean asymptotic convergence rate, where the burn-in time is guaranteed to be finite. Our proof is based on observing a similarity between FR gradient flows and simulated annealing with linear scaling, and facts about cumulant generating functions. We conclude with simple synthetic experiments that demonstrate our theoretical findings are indeed tight. Based on our numerics, we conjecture that the asymptotic rates of convergence for Wasserstein-Fisher-Rao gradient flows are possibly related to this expansion in some cases.

We present a method to approximate Gaussian process regression models for large datasets by considering only a subset of the data. Our approach is novel in that the size of the subset is selected on the fly during exact inference with little computational overhead. From an empirical observation that the log-marginal likelihood often exhibits a linear trend once a sufficient subset of a dataset has been observed, we conclude that many large datasets contain redundant information that only slightly affects the posterior. Based on this, we provide probabilistic bounds on the full model evidence that can identify such subsets. Remarkably, these bounds are largely composed of terms that appear in intermediate steps of the standard Cholesky decomposition, allowing us to modify the algorithm to adaptively stop the decomposition once enough data have been observed.

We address the issue of detecting changes of models that lie behind a data stream. The model refers to an integer-valued structural information such as the number of free parameters in a parametric model. Specifically we are concerned with the problem of how we can detect signs of model changes earlier than they are actualized. To this end, we employ {\em continuous model selection} on the basis of the notion of {\em descriptive dimensionality}~(Ddim). It is a real-valued model dimensionality, which is designed for quantifying the model dimensionality in the model transition period. Continuous model selection is to determine the real-valued model dimensionality in terms of Ddim from a given data. We propose a novel methodology for detecting signs of model changes by tracking the rise-up of Ddim in a data stream. We apply this methodology to detecting signs of changes of the number of clusters in a Gaussian mixture model and those of the order in an auto regression model. With synthetic and real data sets, we empirically demonstrate its effectiveness by showing that it is able to visualize well how rapidly model dimensionality moves in the transition period and to raise early warning signals of model changes earlier than they are detected with existing methods.

We study the statistical properties of learning to defer (L2D) to multiple experts. In particular, we address the open problems of deriving a consistent surrogate loss, confidence calibration, and principled ensembling of experts. Firstly, we derive two consistent surrogates -- one based on a softmax parameterization, the other on a one-vs-all (OvA) parameterization -- that are analogous to the single expert losses proposed by Mozannar and Sontag (2020) and Verma and Nalisnick (2022), respectively. We then study the frameworks' ability to estimate P( m_j = y | x ), the probability that the jth expert will correctly predict the label for x. Theory shows the softmax-based loss causes mis-calibration to propagate between the estimates while the OvA-based loss does not (though in practice, we find there are trade offs). Lastly, we propose a conformal inference technique that chooses a subset of experts to query when the system defers. We perform empirical validation on tasks for galaxy, skin lesion, and hate speech classification.

Inferring causal structures from experimentation is a central task in many domains. For example, in biology, recent advances allow us to obtain single-cell expression data under multiple interventions such as drugs or gene knockouts. However, the targets of the interventions are often uncertain or unknown and the number of observations limited. As a result, standard causal discovery methods can no longer be reliably used. To fill this gap, we propose a Bayesian framework (BaCaDI) for discovering and reasoning about the causal structure that underlies data generated under various unknown experimental or interventional conditions. BaCaDI is fully differentiable, which allows us to infer the complex joint posterior over the intervention targets and the causal structure via efficient gradient-based variational inference. In experiments on synthetic causal discovery tasks and simulated gene-expression data, BaCaDI outperforms related methods in identifying causal structures and intervention targets.

This paper compares the performance of various data processing methods in terms of predictive performance for structured data. This paper also seeks to identify and recommend preprocessing methodologies for tree-based binary classification models, with a focus on eXtreme Gradient Boosting (XGBoost) models. Three data sets of various structures, interactions, and complexity were constructed, which were supplemented by a real-world data set from the Lending Club. We compare several methods for feature selection, categorical handling, and null imputation. Performance is assessed using relative comparisons among the chosen methodologies, including model prediction variability. This paper is presented by the three groups of preprocessing methodologies, with each section consisting of generalized observations. Each observation is accompanied by a recommendation of one or more preferred methodologies. Among feature selection methods, permutation-based feature importance, regularization, and XGBoost's feature importance by weight are not recommended. The correlation coefficient reduction also shows inferior performance. Instead, XGBoost importance by gain shows the most consistency and highest caliber of performance. Categorical featuring encoding methods show greater discrimination in performance among data set structures. While there was no universal "best" method, frequency encoding showed the greatest performance for the most complex data sets (Lending Club), but had the poorest performance for all synthetic (i.e., simpler) data sets. Finally, missing indicator imputation dominated in terms of performance among imputation methods, whereas tree imputation showed extremely poor and highly variable model performance.

Learning causal relationships from empirical observations is a central task in scientific research. A common method is to employ structural causal models that postulate noisy functional relations among a set of interacting variables. To ensure unique identifiability of causal directions, researchers consider restricted subclasses of structural causal models. Post-nonlinear (PNL) causal models constitute one of the most flexible options for such restricted subclasses, containing in particular the popular additive noise models as a further subclass. However, learning PNL models is not well studied beyond the bivariate case. The existing methods learn non-linear functional relations by minimizing residual dependencies and subsequently test independence from residuals to determine causal orientations. However, these methods can be prone to overfitting and, thus, difficult to tune appropriately in practice. As an alternative, we propose a new approach for PNL causal discovery that uses rank-based methods to estimate the functional parameters. This new approach exploits natural invariances of PNL models and disentangles the estimation of the non-linear functions from the independence tests used to find causal orientations. We prove consistency of our method and validate our results in numerical experiments.

Artificial intelligence (AI) systems utilizing deep neural networks (DNNs) and machine learning (ML) algorithms are widely used for solving important problems in bioinformatics, biomedical informatics, and precision medicine. However, complex DNNs or ML models, which are often perceived as opaque and black-box, can make it difficult to understand the reasoning behind their decisions. This lack of transparency can be a challenge for both end-users and decision-makers, as well as AI developers. Additionally, in sensitive areas like healthcare, explainability and accountability are not only desirable but also legally required for AI systems that can have a significant impact on human lives. Fairness is another growing concern, as algorithmic decisions should not show bias or discrimination towards certain groups or individuals based on sensitive attributes. Explainable artificial intelligence (XAI) aims to overcome the opaqueness of black-box models and provide transparency in how AI systems make decisions. Interpretable ML models can explain how they make predictions and the factors that influence their outcomes. However, most state-of-the-art interpretable ML methods are domain-agnostic and evolved from fields like computer vision, automated reasoning, or statistics, making direct application to bioinformatics problems challenging without customization and domain-specific adaptation. In this paper, we discuss the importance of explainability in the context of bioinformatics, provide an overview of model-specific and model-agnostic interpretable ML methods and tools, and outline their potential caveats and drawbacks. Besides, we discuss how to customize existing interpretable ML methods for bioinformatics problems. Nevertheless, we demonstrate how XAI methods can improve transparency through case studies in bioimaging, cancer genomics, and text mining.

In sponsored search advertising (SSA), keywords serve as the basic unit of business model, linking three stakeholders: consumers, advertisers and search engines. This paper presents an overarching framework for keyword decisions that highlights the touchpoints in search advertising management, including four levels of keyword decisions, i.e., domain-specific keyword pool generation, keyword targeting, keyword assignment and grouping, and keyword adjustment. Using this framework, we review the state-of-the-art research literature on keyword decisions with respect to techniques, input features and evaluation metrics. Finally, we discuss evolving issues and identify potential gaps that exist in the literature and outline novel research perspectives for future exploration.