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These lecture notes are intended to cover some introductory topics in stochastic simulation for scientific computing courses offered by the IT department at Uppsala University, as taught by the author. Basic concepts in probability theory are provided in the Appendix A, which you may review before starting the upcoming sections or refer to as needed throughout the text.
Using the National Academies report, {\em Data Science for Undergraduates: Opportunities and Options}, we connect data science curricula to the more familiar pedagogy used by many mathematical scientists. We use their list of ``data acumen" components to ground a discussion, which hopes to connect data science curricula to the more familiar pedagogy used by many mathematical scientists.
This commentary proposes a framework for understanding the role of statistics in policy-making, regulation, and bureaucratic systems. I introduce the concept of "ex ante policy," describing statistical rules and procedures designed before data collection to govern future actions. Through examining examples, particularly clinical trials, I explore how ex ante policy serves as a calculus of bureaucracy, providing numerical foundations for governance through clear, transparent rules. The ex ante frame obviates heated debates about inferential interpretations of probability and statistical tests, p-values, and rituals. I conclude by calling for a deeper appreciation of statistics' bureaucratic function and suggesting new directions for research in policy-oriented statistical methodology.
Occupational data play a vital role in research, official statistics, and policymaking, yet their collection and accurate classification remain a challenge. This study investigates the effects of occupational question wording on data variability and the performance of automatic coding tools. We conducted and replicated a split-ballot survey experiment in Germany using two common occupational question formats: one focusing on "job title" (Berufsbezeichnung) and another on "berufliche Tätigkeit" (loosely translated as occupation or occupational task). Our analysis reveals that automatic coding tools, such as CASCOT and OccuCoDe, exhibit sensitivity to the form and origin of the data. Specifically, these tools were more efficient when coding responses to the job title question format than the occupational task format, suggesting a potential way to improve the respective questions for many German surveys. In a subsequent "detailed tasks and duties" question, providing a guiding example prompted respondents to give longer answers without broadening the range of unique words they used. These findings highlight the importance of harmonising survey questions and and ensuring that automatic coding tools are robust to differences in question wording. Further research is needed to optimise question design and coding tools for greater accuracy and applicability in occupational data collection.
Misclassified binary outcome or mediator variables can cause unpredictable bias in resulting parameter estimates. As more datasets that were not originally collected for research purposes are being used for studies in the social and health sciences, the need for methods that address data quality concerns is growing. In this paper, we describe two R packages, COMBO and COMMA, that implement bias-correction methods for misclassified binary outcome and mediator variables, respectively. These likelihood-based approaches do not require gold standard measures and allow for estimation of sensitivity and specificity rates for the misclassified variable(s). In addition, these R packages automatically apply crucial label switching corrections, allowing researchers to circumvent the inherent permutation invariance of the misclassification model likelihood. We demonstrate COMBO for single-outcome cases using a study of bar exam passage. We develop and evaluate a risk prediction model based on noisy indicators in a pretrial risk assessment study to demonstrate COMBO for multi-outcome cases. In addition, we use COMMA to evaluate the mediating effect of potentially misdiagnosed gestational hypertension on the maternal ethnicity-birthweight relationship.
Recent methods have been developed to map single-cell lineage statistics to population growth. Because population growth selects for exponentially rare phenotypes, these methods inherently depend on sampling large deviations from finite data, which introduces systematic errors. A comprehensive understanding of these errors in the context of finite data remains elusive. To address this gap, we study the error in growth rate estimates across different models. We show that under the usual bias-variance decomposition, the bias can be decomposed into a finite-time bias and nonlinear averaging bias. We demonstrate that finite-time bias, which dominates at short times, can be mitigated by fitting its monotonic behavior. In contrast, at longer times, nonlinear averaging bias becomes the predominant source of error, leading to a phase transition. This transition can be understood through the Random Energy Model, a mean-field model of disordered systems, where a few lineages dominate the estimator. Applying these methods to experimental data demonstrates that correcting for biases in lineage-based approaches yields consistent results for the long-term growth rate across multiple methods and enables the reverse-engineering of dynamic models. This new framework provides a quantitative understanding of growth rate estimators, clarifies the conditions under which they can be effectively applied to finite data, and introduces model-free approaches for studying the connections between physiology and cell growth.
Random fuzzy variables join the modeling of the impreciseness (due to their ``fuzzy part'') and randomness. Statistical samples of such objects are widely used, and their direct, numerically effective generation is therefore necessary. Usually, these samples consist of triangular or trapezoidal fuzzy numbers. In this paper, we describe theoretical results and simulation algorithms for another family of fuzzy numbers -- LR fuzzy numbers with interval-valued cores. Starting from a simulation perspective on the piecewise linear LR fuzzy numbers with the interval-valued cores, their limiting behavior is then considered. This leads us to the numerically efficient algorithm for simulating a sample consisting of such fuzzy values.
A finite-horizon variant of the quickest change detection problem is investigated, which is motivated by a change detection problem that arises in piecewise stationary bandits. The goal is to minimize the \emph{latency}, which is smallest threshold such that the probability that the detection delay exceeds the threshold is below a desired low level, while controlling the false alarm probability to a desired low level. When the pre- and post-change distributions are unknown, two tests are proposed as candidate solutions. These tests are shown to attain order optimality in terms of the horizon. Furthermore, the growth in their latencies with respect to the false alarm probability and late detection probability satisfies a property that is desirable in regret analysis for piecewise stationary bandits. Numerical results are provided to validate the theoretical performance results.
Recent work [ 14 ] has introduced a method for prior elicitation that utilizes records of expert decisions to infer a prior distribution. While this method provides a promising approach to eliciting expert uncertainty, it has only been demonstrated using tabular data, which may not entirely represent the information used by experts to make decisions. In this paper, we demonstrate how analysts can adopt a deep learning approach to utilize the method proposed in [14 ] with the actual information experts use. We provide an overview of deep learning models that can effectively model expert decision-making to elicit distributions that capture expert uncertainty and present an example examining the risk of colon cancer to show in detail how these models can be used.
This expository paper introduces a simplified approach to image-based quality inspection in manufacturing using OpenAI's CLIP (Contrastive Language-Image Pretraining) model adapted for few-shot learning. While CLIP has demonstrated impressive capabilities in general computer vision tasks, its direct application to manufacturing inspection presents challenges due to the domain gap between its training data and industrial applications. We evaluate CLIP's effectiveness through five case studies: metallic pan surface inspection, 3D printing extrusion profile analysis, stochastic textured surface evaluation, automotive assembly inspection, and microstructure image classification. Our results show that CLIP can achieve high classification accuracy with relatively small learning sets (50-100 examples per class) for single-component and texture-based applications. However, the performance degrades with complex multi-component scenes. We provide a practical implementation framework that enables quality engineers to quickly assess CLIP's suitability for their specific applications before pursuing more complex solutions. This work establishes CLIP-based few-shot learning as an effective baseline approach that balances implementation simplicity with robust performance, demonstrated in several manufacturing quality control applications.
The unseen-species problem assumes $n\geq1$ samples from a population of individuals belonging to different species, possibly infinite, and calls for estimating the number $K_{n,m}$ of hitherto unseen species that would be observed if $m\geq1$ new samples were collected from the same population. This is a long-standing problem in statistics, which has gained renewed relevance in biological and physical sciences, particularly in settings with large values of $n$ and $m$. In this paper, we adopt a Bayesian nonparametric approach to the unseen-species problem under the Pitman-Yor prior, and propose a novel methodology to derive large $m$ asymptotic credible intervals for $K_{n,m}$, for any $n\geq1$. By leveraging a Gaussian central limit theorem for the posterior distribution of $K_{n,m}$, our method improves upon competitors in two key aspects: firstly, it enables the full parameterization of the Pitman-Yor prior, including the Dirichlet prior; secondly, it avoids the need of Monte Carlo sampling, enhancing computational efficiency. We validate the proposed method on synthetic and real data, demonstrating that it improves the empirical performance of competitors by significantly narrowing the gap between asymptotic and exact credible intervals for any $m\geq1$.
Generation of realistic synthetic data has garnered considerable attention in recent years, particularly in the health research domain due to its utility in, for instance, sharing data while protecting patient privacy or determining optimal clinical trial design. While much work has been concentrated on synthetic image generation, generation of realistic and complex synthetic tabular data of the type most commonly encountered in classic epidemiological or clinical studies is still lacking, especially with regards to generating data for randomized controlled trials (RTCs). There is no consensus regarding the best way to generate synthetic tabular RCT data such that the underlying multivariate data distribution is preserved. Motivated by an RCT in the treatment of Human Immunodeficiency Virus, we empirically compared the ability of several strategies and two generation techniques (one machine learning, the other a more classical statistical method) to faithfully reproduce realistic data. Our results suggest that using a sequential generation approach with a R-vine copula model to generate baseline variables, followed by a simple random treatment allocation to mimic the RCT setting, and subsequent regression models for variables post-treatment allocation (such as the trial outcome) is the most effective way to generate synthetic tabular RCT data that capture important and realistic features of the real data.
The Unit Weibull distribution with parameters $α$ and $β$ is considered to study in the context of dual generalized order statistics. For the analysis purpose, Bayes estimators based on symmetric and asymmetric loss functions are obtained. The methods which are utilized for Bayesian estimation are approximation and simulation tools such as Lindley, Tierney-Kadane and Markov chain Monte Carlo methods. The authors have considered squared error loss function as symmetric and LINEX and general entropy loss function as asymmetric loss functions. After presenting the mathematical results, a simulation study is conducted to exhibit the performances of various derived estimators. As this study is considered for the dual generalized order statistics that is unification of models based distinct ordered random variable such as order statistics, record values, etc. This provides flexibility in our results and in continuation of this, the cotton production data of USA is analyzed for both submodels of ordered random variables: order statistics and record values.
This paper introduces Monotone Delta, an order-theoretic measure designed to enhance the reliability assessment of survey-based instruments in human-machine interactions. Traditional reliability measures, such as Cronbach's Alpha and McDonald's Omega, often yield misleading estimates due to their sensitivity to redundancy, multidimensional constructs, and assumptions of normality and uncorrelated errors. These limitations can compromise decision-making in human-centric evaluations, where survey instruments inform adaptive interfaces, cognitive workload assessments, and human-AI trust models. Monotone Delta addresses these issues by quantifying internal consistency through the minimization of ordinal contradictions and alignment with a unidimensional latent order using weighted tournaments. Unlike traditional approaches, it operates without parametric or model-based assumptions. We conducted theoretical analyses and experimental evaluations on four challenging scenarios: tau-equivalence, redundancy, multidimensionality, and non-normal distributions, and proved that Monotone Delta provides more stable reliability assessments compared to existing methods. The Monotone Delta is a valuable alternative for evaluating questionnaire-based assessments in psychology, human factors, healthcare, and interactive system design, enabling organizations to optimize survey instruments, reduce costly redundancies, and enhance confidence in human-system interactions.
This paper examines the foundational concept of random variables in probability theory and statistical inference, demonstrating that their mathematical definition requires no reference to randomization or hypothetical repeated sampling. We show how measure-theoretic probability provides a framework for modeling populations through distributions, leading to three key contributions. First, we establish that random variables, properly understood as measurable functions, can be fully characterized without appealing to infinite hypothetical samples. Second, we demonstrate how this perspective enables statistical inference through logical rather than probabilistic reasoning, extending the reductio ad absurdum argument from deductive to inductive inference. Third, we show how this framework naturally leads to information-based assessment of statistical procedures, replacing traditional inference metrics that emphasize bias and variance with information-based approaches that better describe the families of distributions used in parametric inference. This reformulation addresses long-standing debates in statistical inference while providing a more coherent theoretical foundation. Our approach offers an alternative to traditional frequentist inference that maintains mathematical rigor while avoiding the philosophical complications inherent in repeated sampling interpretations.
Modeling has become a widespread, useful tool in mathematics applied to diverse fields, from physics to economics to biomedicine. Practitioners of modeling may use algebraic or differential equations, to the elements of which they attribute an intuitive relationship with some relevant aspect of reality they wish to represent. More sophisticated expressions may include stochasticity, either as observation error or system noise. However, a clear, unambiguous mathematical definition of what a model is and of what is the relationship between the model and the real-life phenomena it purports to represent has so far not been formulated. The present work aims to fill this gap, motivating the definition of a mathematical model as an operator on a Hilbert space of random variables, identifying the experimental realization as the map between the theoretical space of model construction and the computational space of statistical model identification, and tracing the relationship of the geometry of the model manifold in the abstract setting with the corresponding geometry of the prediction surfaces in statistical estimation.
Dimensionality reduction is a fundamental technique in machine learning and data analysis, enabling efficient representation and visualization of high-dimensional data. This paper explores five key methods: Principal Component Analysis (PCA), Kernel PCA (KPCA), Sparse Kernel PCA, t-Distributed Stochastic Neighbor Embedding (t-SNE), and Uniform Manifold Approximation and Projection (UMAP). PCA provides a linear approach to capturing variance, whereas KPCA and Sparse KPCA extend this concept to non-linear structures using kernel functions. Meanwhile, t-SNE and UMAP focus on preserving local relationships, making them effective for data visualization. Each method is examined in terms of its mathematical formulation, computational complexity, strengths, and limitations. The trade-offs between global structure preservation, computational efficiency, and interpretability are discussed to guide practitioners in selecting the appropriate technique based on their application needs.
Longitudinal models with dynamics governed by differential equations may require numerical integration alongside parameter estimation. We have identified a situation where the numerical integration introduces error in such a way that it becomes a novel source of non-uniqueness in estimation. We obtain two very different sets of parameters, one of which is a good estimate of the true values and the other a very poor one. The two estimates have forward numerical projections statistically indistinguishable from each other because of numerical error. In such cases, the posterior distribution for parameters is bimodal, with a dominant mode closer to the true parameter value, and a second cluster around the errant value. We demonstrate that multi-modality exists both theoretically and empirically for an affine first order differential equation, that a simulation workflow can test for evidence of the issue more generally, and that Markov Chain Monte Carlo sampling with a suitable solution can avoid bimodality. The issue of multi-modal posteriors arising from numerical error has consequences for Bayesian inverse methods that rely on numerical integration more broadly.