Mechanistic, multicellular, agent-based models are commonly used to investigate tissue, organ, and organism-scale biology at single-cell resolution. The Cellular-Potts Model (CPM) is a powerful and popular framework for developing and interrogating these models. CPMs become computationally expensive at large space- and time- scales making application and investigation of developed models difficult. Surrogate models may allow for the accelerated evaluation of CPMs of complex biological systems. However, the stochastic nature of these models means each set of parameters may give rise to different model configurations, complicating surrogate model development. In this work, we leverage denoising diffusion probabilistic models to train a generative AI surrogate of a CPM used to investigate in vitro vasculogenesis. We describe the use of an image classifier to learn the characteristics that define unique areas of a 2-dimensional parameter space. We then apply this classifier to aid in surrogate model selection and verification. Our CPM model surrogate generates model configurations 20,000 timesteps ahead of a reference configuration and demonstrates approximately a 22x reduction in computational time as compared to native code execution. Our work represents a step towards the implementation of DDPMs to develop digital twins of stochastic biological systems.
Despite the growing interest in Explainable Artificial Intelligence (XAI), explainability is rarely considered during hyperparameter tuning or neural architecture optimization, where the focus remains primarily on minimizing predictive loss. In this work, we introduce the novel concept of XAI consistency, defined as the agreement among different feature attribution methods, and propose new metrics to quantify it. For the first time, we integrate XAI consistency directly into the hyperparameter tuning objective, creating a multi-objective optimization framework that balances predictive performance with explanation robustness. Implemented within the Sequential Parameter Optimization Toolbox (SPOT), our approach uses both weighted aggregation and desirability-based strategies to guide model selection. Through our proposed framework and supporting tools, we explore the impact of incorporating XAI consistency into the optimization process. This enables us to characterize distinct regions in the architecture configuration space: one region with poor performance and comparatively low interpretability, another with strong predictive performance but weak interpretability due to low \gls{xai} consistency, and a trade-off region that balances both objectives by offering high interpretability alongside competitive performance. Beyond introducing this novel approach, our research provides a foundation for future investigations into whether models from the trade-off zone-balancing performance loss and XAI consistency-exhibit greater robustness by avoiding overfitting to training performance, thereby leading to more reliable predictions on out-of-distribution data.
As machine learning (ML) models are increasingly deployed in high-stakes domains, trustworthy uncertainty quantification (UQ) is critical for ensuring the safety and reliability of these models. Traditional UQ methods rely on specifying a true generative model and are not robust to misspecification. On the other hand, conformal inference allows for arbitrary ML models but does not consider model selection, which leads to large interval sizes. We tackle these drawbacks by proposing a UQ method based on the predictability, computability, and stability (PCS) framework for veridical data science proposed by Yu and Kumbier. Specifically, PCS-UQ addresses model selection by using a prediction check to screen out unsuitable models. PCS-UQ then fits these screened algorithms across multiple bootstraps to assess inter-sample variability and algorithmic instability, enabling more reliable uncertainty estimates. Further, we propose a novel calibration scheme that improves local adaptivity of our prediction sets. Experiments across $17$ regression and $6$ classification datasets show that PCS-UQ achieves the desired coverage and reduces width over conformal approaches by $\approx 20\%$. Further, our local analysis shows PCS-UQ often achieves target coverage across subgroups while conformal methods fail to do so. For large deep-learning models, we propose computationally efficient approximation schemes that avoid the expensive multiple bootstrap trainings of PCS-UQ. Across three computer vision benchmarks, PCS-UQ reduces prediction set size over conformal methods by $20\%$. Theoretically, we show a modified PCS-UQ algorithm is a form of split conformal inference and achieves the desired coverage with exchangeable data.
Agricultural monitoring is critical for ensuring food security, maintaining sustainable farming practices, informing policies on mitigating food shortage, and managing greenhouse gas emissions. Traditional process-based physical models are often designed and implemented for specific situations, and their parameters could also be highly uncertain. In contrast, data-driven models often use black-box structures and does not explicitly model the inter-dependence between different ecological variables. As a result, they require extensive training data and lack generalizability to different tasks with data distribution shifts and inconsistent observed variables. To address the need for more universal models, we propose a knowledge-guided encoder-decoder model, which can predict key crop variables by leveraging knowledge of underlying processes from multiple physical models. The proposed method also integrates a language model to process complex and inconsistent inputs and also utilizes it to implement a model selection mechanism for selectively combining the knowledge from different physical models. Our evaluations on predicting carbon and nitrogen fluxes for multiple sites demonstrate the effectiveness and robustness of the proposed model under various scenarios.
Systematic reviews are comprehensive literature reviews that address highly focused research questions and represent the highest form of evidence in medicine. A critical step in this process is the development of complex Boolean queries to retrieve relevant literature. Given the difficulty of manually constructing these queries, recent efforts have explored Large Language Models (LLMs) to assist in their formulation. One of the first studies,Wang et al., investigated ChatGPT for this task, followed by Staudinger et al., which evaluated multiple LLMs in a reproducibility study. However, the latter overlooked several key aspects of the original work, including (i) validation of generated queries, (ii) output formatting constraints, and (iii) selection of examples for chain-of-thought (Guided) prompting. As a result, its findings diverged significantly from the original study. In this work, we systematically reproduce both studies while addressing these overlooked factors. Our results show that query effectiveness varies significantly across models and prompt designs, with guided query formulation benefiting from well-chosen seed studies. Overall, prompt design and model selection are key drivers of successful query formulation. Our findings provide a clearer understanding of LLMs' potential in Boolean query generation and highlight the importance of model- and prompt-specific optimisations. The complex nature of systematic reviews adds to challenges in both developing and reproducing methods but also highlights the importance of reproducibility studies in this domain.
Large language models (LLMs) often generate fluent but factually incorrect outputs, known as hallucinations, which undermine their reliability in real-world applications. While uncertainty estimation has emerged as a promising strategy for detecting such errors, current metrics offer limited interpretability and lack clarity about the types of uncertainty they capture. In this paper, we present a systematic framework for decomposing LLM uncertainty into four distinct sources, inspired by previous research. We develop a source-specific estimation pipeline to quantify these uncertainty types and evaluate how existing metrics relate to each source across tasks and models. Our results show that metrics, task, and model exhibit systematic variation in uncertainty characteristic. Building on this, we propose a method for task specific metric/model selection guided by the alignment or divergence between their uncertainty characteristics and that of a given task. Our experiments across datasets and models demonstrate that our uncertainty-aware selection strategy consistently outperforms baseline strategies, helping us select appropriate models or uncertainty metrics, and contributing to more reliable and efficient deployment in uncertainty estimation.
In this paper, we investigate the data-driven identification of asymmetric interaction kernels in the Motsch-Tadmor model based on observed trajectory data. The model under consideration is governed by a class of semilinear evolution equations, where the interaction kernel defines a normalized, state-dependent Laplacian operator that governs collective dynamics. To address the resulting nonlinear inverse problem, we propose a variational framework that reformulates kernel identification using the implicit form of the governing equations, reducing it to a subspace identification problem. We establish an identifiability result that characterizes conditions under which the interaction kernel can be uniquely recovered up to scale. To solve the inverse problem robustly, we develop a sparse Bayesian learning algorithm that incorporates informative priors for regularization, quantifies uncertainty, and enables principled model selection. Extensive numerical experiments on representative interacting particle systems demonstrate the accuracy, robustness, and interpretability of the proposed framework across a range of noise levels and data regimes.
Medical disease prediction, particularly through imaging, remains a challenging task due to the complexity and variability of medical data, including noise, ambiguity, and differing image quality. Recent deep learning models, including Knowledge Distillation (KD) methods, have shown promising results in brain tumor image identification but still face limitations in handling uncertainty and generalizing across diverse medical conditions. Traditional KD methods often rely on a context-unaware temperature parameter to soften teacher model predictions, which does not adapt effectively to varying uncertainty levels present in medical images. To address this issue, we propose a novel framework that integrates Ant Colony Optimization (ACO) for optimal teacher-student model selection and a novel context-aware predictor approach for temperature scaling. The proposed context-aware framework adjusts the temperature based on factors such as image quality, disease complexity, and teacher model confidence, allowing for more robust knowledge transfer. Additionally, ACO efficiently selects the most appropriate teacher-student model pair from a set of pre-trained models, outperforming current optimization methods by exploring a broader solution space and better handling complex, non-linear relationships within the data. The proposed framework is evaluated using three publicly available benchmark datasets, each corresponding to a distinct medical imaging task. The results demonstrate that the proposed framework significantly outperforms current state-of-the-art methods, achieving top accuracy rates: 98.01% on the MRI brain tumor (Kaggle) dataset, 92.81% on the Figshare MRI dataset, and 96.20% on the GastroNet dataset. This enhanced performance is further evidenced by the improved results, surpassing existing benchmarks of 97.24% (Kaggle), 91.43% (Figshare), and 95.00% (GastroNet).
Imori and Ing (2025) proposed the importance-weighted orthogonal greedy algorithm (IWOGA) for model selection in high-dimensional misspecified regression models under covariate shift. To determine the number of IWOGA iterations, they introduced the high-dimensional importance-weighted information criterion (HDIWIC). They argued that the combined use of IWOGA and HDIWIC, IWOGA + HDIWIC, achieves an optimal trade-off between variance and squared bias, leading to optimal convergence rates in terms of conditional mean squared prediction error. In this article, we provide a theoretical justification for this claim by establishing the optimality of IWOGA + HDIWIC under a set of reasonable assumptions.
This work presents an open-source unified benchmarking and evaluation framework for text-to-image generation models, with a particular focus on the impact of metadata augmented prompts. Leveraging the DeepFashion-MultiModal dataset, we assess generated outputs through a comprehensive set of quantitative metrics, including Weighted Score, CLIP (Contrastive Language Image Pre-training)-based similarity, LPIPS (Learned Perceptual Image Patch Similarity), FID (Frechet Inception Distance), and retrieval-based measures, as well as qualitative analysis. Our results demonstrate that structured metadata enrichments greatly enhance visual realism, semantic fidelity, and model robustness across diverse text-to-image architectures. While not a traditional recommender system, our framework enables task-specific recommendations for model selection and prompt design based on evaluation metrics.
The application of large language models (LLMs) to healthcare information extraction has emerged as a promising approach. This study evaluates the classification performance of five open-source LLMs: GEMMA-3-27B-IT, LLAMA3-70B, LLAMA4-109B, DEEPSEEK-R1-DISTILL-LLAMA-70B, and DEEPSEEK-V3-0324-UD-Q2_K_XL, across six healthcare-related classification tasks involving both social media data (breast cancer, changes in medication regimen, adverse pregnancy outcomes, potential COVID-19 cases) and clinical data (stigma labeling, medication change discussion). We report precision, recall, and F1 scores with 95% confidence intervals for all model-task combinations. Our findings reveal significant performance variability between LLMs, with DeepSeekV3 emerging as the strongest overall performer, achieving the highest F1 scores in four tasks. Notably, models generally performed better on social media tasks compared to clinical data tasks, suggesting potential domain-specific challenges. GEMMA-3-27B-IT demonstrated exceptionally high recall despite its smaller parameter count, while LLAMA4-109B showed surprisingly underwhelming performance compared to its predecessor LLAMA3-70B, indicating that larger parameter counts do not guarantee improved classification results. We observed distinct precision-recall trade-offs across models, with some favoring sensitivity over specificity and vice versa. These findings highlight the importance of task-specific model selection for healthcare applications, considering the particular data domain and precision-recall requirements rather than model size alone. As healthcare increasingly integrates AI-driven text classification tools, this comprehensive benchmarking provides valuable guidance for model selection and implementation while underscoring the need for continued evaluation and domain adaptation of LLMs in healthcare contexts.
The use of language models for automatically evaluating long-form text (LLM-as-a-judge) is becoming increasingly common, yet most LLM judges are optimized exclusively for English, with strategies for enhancing their multilingual evaluation capabilities remaining largely unexplored in the current literature. This has created a disparity in the quality of automatic evaluation methods for non-English languages, ultimately hindering the development of models with better multilingual capabilities. To bridge this gap, we introduce M-Prometheus, a suite of open-weight LLM judges ranging from 3B to 14B parameters that can provide both direct assessment and pairwise comparison feedback on multilingual outputs. M-Prometheus models outperform state-of-the-art open LLM judges on multilingual reward benchmarks spanning more than 20 languages, as well as on literary machine translation (MT) evaluation covering 4 language pairs. Furthermore, M-Prometheus models can be leveraged at decoding time to significantly improve generated outputs across all 3 tested languages, showcasing their utility for the development of better multilingual models. Lastly, through extensive ablations, we identify the key factors for obtaining an effective multilingual judge, including backbone model selection and training on natively multilingual feedback data instead of translated data. We release our models, training dataset, and code.
This lecture note is intended to prepare early-year master's and PhD students in data science or a related discipline with foundational ideas in machine learning. It starts with basic ideas in modern machine learning with classification as a main target task. These basic ideas include loss formulation, backpropagation, stochastic gradient descent, generalization, model selection as well as fundamental blocks of artificial neural networks. Based on these basic ideas, the lecture note explores in depth the probablistic approach to unsupervised learning, covering directed latent variable models, product of experts, generative adversarial networks and autoregressive models. Finally, the note ends by covering a diverse set of further topics, such as reinforcement learning, ensemble methods and meta-learning. After reading this lecture note, a student should be ready to embark on studying and researching more advanced topics in machine learning and more broadly artificial intelligence.
Comparing mathematical models offers a means to evaluate competing scientific theories. However, exact methods of model calibration are not applicable to many probabilistic models which simulate high-dimensional spatio-temporal data. Approximate Bayesian Computation is a widely-used method for parameter inference and model selection in such scenarios, and it may be combined with Topological Data Analysis to study models which simulate data with fine spatial structure. We develop a flexible pipeline for parameter inference and model selection in spatio-temporal models. Our pipeline identifies topological summary statistics which quantify spatio-temporal data and uses them to approximate parameter and model posterior distributions. We validate our pipeline on models of tumour-induced angiogenesis, inferring four parameters in three established models and identifying the correct model in synthetic test-cases.
In this paper, we conduct a simulation study to evaluate conventional meta-regression approaches (study-level random, fixed, and mixed effects) against seven methodology specifications new to meta-regressions that control joint heterogeneity in location and time (including a new one that we introduce). We systematically vary heterogeneity levels to assess statistical power, estimator bias and model robustness for each methodology specification. This assessment focuses on three aspects: performance under joint heterogeneity in location and time, the effectiveness of our proposed settings incorporating location fixed effects and study-level fixed effects with a time trend, as well as guidelines for model selection. The results show that jointly modeling heterogeneity when heterogeneity is in both dimensions improves performance compared to modeling only one type of heterogeneity.
Computer-generated holography (CGH) enables applications in holographic augmented reality (AR), 3D displays, systems neuroscience, and optical trapping. The fundamental challenge in CGH is solving the inverse problem of phase retrieval from intensity measurements. Physics-inspired neural networks (PINNs), especially Gerchberg-Saxton-based PINNs (GS-PINNs), have advanced phase retrieval capabilities. However, their performance strongly depends on forward models (FMs) and their hyperparameters (FMHs), limiting generalization, complicating benchmarking, and hindering hardware optimization. We present a systematic sensitivity analysis framework based on Saltelli's extension of Sobol's method to quantify FMH impacts on GS-PINN performance. Our analysis demonstrates that SLM pixel-resolution is the primary factor affecting neural network sensitivity, followed by pixel-pitch, propagation distance, and wavelength. Free space propagation forward models demonstrate superior neural network performance compared to Fourier holography, providing enhanced parameterization and generalization. We introduce a composite evaluation metric combining performance consistency, generalization capability, and hyperparameter perturbation resilience, establishing a unified benchmarking standard across CGH configurations. Our research connects physics-inspired deep learning theory with practical CGH implementations through concrete guidelines for forward model selection, neural network architecture, and performance evaluation. Our contributions advance the development of robust, interpretable, and generalizable neural networks for diverse holographic applications, supporting evidence-based decisions in CGH research and implementation.
Traditional Chinese Medicine (TCM) represents a rich repository of ancient medical knowledge that continues to play an important role in modern healthcare. Due to the complexity and breadth of the TCM literature, the integration of AI technologies is critical for its modernization and broader accessibility. However, this integration poses considerable challenges, including the interpretation of obscure classical Chinese texts and the modeling of intricate semantic relationships among TCM concepts. In this paper, we develop OpenTCM, an LLM-based system that combines a domain-specific TCM knowledge graph and Graph-based Retrieval-Augmented Generation (GraphRAG). First, we extract more than 3.73 million classical Chinese characters from 68 gynecological books in the Chinese Medical Classics Database, with the help of TCM and gynecology experts. Second, we construct a comprehensive multi-relational knowledge graph comprising more than 48,000 entities and 152,000 interrelationships, using customized prompts and Chinese-oriented LLMs such as DeepSeek and Kimi to ensure high-fidelity semantic understanding. Last, we integrate OpenTCM with this knowledge graph, enabling high-fidelity ingredient knowledge retrieval and diagnostic question-answering without model fine-tuning. Experimental evaluations demonstrate that our prompt design and model selection significantly improve knowledge graph quality, achieving a precision of 98. 55% and an F1 score of 99. 55%. In addition, OpenTCM achieves mean expert scores of 4.5 in ingredient information retrieval and 3.8 in diagnostic question-answering tasks, outperforming state-of-the-art solutions in real-world TCM use cases.
This paper presents a novel theoretical framework for reducing the computational complexity of multi-model adaptive control/estimation systems through systematic transformation to controllable canonical form. While traditional multi-model approaches face exponential growth in computational demands with increasing system dimension, we introduce a parameter-tying theorem that enables significant dimension reduction through careful analysis of system characteristics in canonical form. The approach leverages monotonicity properties and coordinated parameter relationships to establish minimal sets of identification models while preserving system stability and performance. We develop rigorous criteria for verifying plant inclusion within the convex hull of identification models and derive weight transformation relationships that maintain system properties across coordinate transformations. The effectiveness of the framework is demonstrated through application to coupled lateral-roll vehicle dynamics, where the dimension reduction enables real-time implementation while maintaining estimation accuracy. The results show that the proposed transformation approach can achieve comparable performance to conventional methods while requiring substantially fewer identification models, enabling practical deployment in high-dimensional systems.
Gaussian process (GP) models have been used in a wide range of battery applications, in which different kernels were manually selected with considerable expertise. However, to capture complex relationships in the ever-growing amount of real-world data, selecting a suitable kernel for the GP model in battery applications is increasingly challenging. In this work, we first review existing GP kernels used in battery applications and then extend an automatic kernel search method with a new base kernel and model selection criteria. The GP models with composite kernels outperform the baseline kernel in two numerical examples of battery applications, i.e., battery capacity estimation and residual load prediction. Particularly, the results indicate that the Bayesian Information Criterion may be the best model selection criterion as it achieves a good trade-off between kernel performance and computational complexity. This work should, therefore, be of value to practitioners wishing to automate their kernel search process in battery applications.
Model averaging (MA) and ensembling play a crucial role in statistical and machine learning practice. When multiple candidate models are considered, MA techniques can be used to weight and combine them, often resulting in improved predictive accuracy and better estimation stability compared to model selection (MS) methods. In this paper, we address two challenges in combining least squares estimators from both theoretical and practical perspectives. We first establish several oracle inequalities for least squares MA via minimizing a Mallows' $C_p$ criterion under an arbitrary candidate model set. Compared to existing studies, these oracle inequalities yield faster excess risk and directly imply the asymptotic optimality of the resulting MA estimators under milder conditions. Moreover, we consider candidate model construction and investigate the problem of optimal all-subset combination for least squares estimators, which is an important yet rarely discussed topic in the existing literature. We show that there exists a fundamental limit to achieving the optimal all-subset MA risk. To attain this limit, we propose a novel Mallows-type MA procedure based on a dimension-adaptive $C_p$ criterion. The implicit ensembling effects of several MS procedures are also revealed and discussed. We conduct several numerical experiments to support our theoretical findings and demonstrate the effectiveness of the proposed Mallows-type MA estimator.