Modeling sparse count data, which arise across numerous scientific fields, presents significant statistical challenges. This chapter addresses these challenges in the context of infectious disease prediction, with a focus on predicting outbreaks in geographic regions that have historically reported zero cases. To this end, we present the detailed computational framework and experimental application of the Poisson Hierarchical Indian Buffet Process (PHIBP), with demonstrated success in handling sparse count data in microbiome and ecological studies. The PHIBP's architecture, grounded in the concept of absolute abundance, systematically borrows statistical strength from related regions and circumvents the known sensitivities of relative-rate methods to zero counts. Through a series of experiments on infectious disease data, we show that this principled approach provides a robust foundation for generating coherent predictive distributions and for the effective use of comparative measures such as alpha and beta diversity. The chapter's emphasis on algorithmic implementation and experimental results confirms that this unified framework delivers both accurate outbreak predictions and meaningful epidemiological insights in data-sparse settings.

Feature and Interaction Importance (FII) methods are essential in supervised learning for assessing the relevance of input variables and their interactions in complex prediction models. In many domains, such as personalized medicine, local interpretations for individual predictions are often required, rather than global scores summarizing overall feature importance. Random Forests (RFs) are widely used in these settings, and existing interpretability methods typically exploit tree structures and split statistics to provide model-specific insights. However, theoretical understanding of local FII methods for RF remains limited, making it unclear how to interpret high importance scores for individual predictions. We propose a novel, local, model-specific FII method that identifies frequent co-occurrences of features along decision paths, combining global patterns with those observed on paths specific to a given test point. We prove that our method consistently recovers the true local signal features and their interactions under a Locally Spike Sparse (LSS) model and also identifies whether large or small feature values drive a prediction. We illustrate the usefulness of our method and theoretical results through simulation studies and a real-world data example.

This paper investigates bias in GLLM annotations by conceptually replicating manual annotations of Boukes (2024). Using various GLLMs (Llama3.1:8b, Llama3.3:70b, GPT4o, Qwen2.5:72b) in combination with five different prompts for five concepts (political content, interactivity, rationality, incivility, and ideology). We find GLLMs perform adequate in terms of F1 scores, but differ from manual annotations in terms of prevalence, yield substantively different downstream results, and display systematic bias in that they overlap more with each other than with manual annotations. Differences in F1 scores fail to account for the degree of bias.

In the intensive care unit, the underlying causes of critical illness vary substantially across diagnoses, yet prediction models accounting for diagnostic heterogeneity have not been systematically studied. To address the gap, we evaluate transfer learning approaches for diagnosis-specific mortality prediction and apply both GLM- and XGBoost-based models to the eICU Collaborative Research Database. Our results demonstrate that transfer learning consistently outperforms models trained only on diagnosis-specific data and those using a well-known ICU severity-of-illness score, i.e., APACHE IVa, alone, while also achieving better calibration than models trained on the pooled data. Our findings also suggest that the Youden cutoff is a more appropriate decision threshold than the conventional 0.5 for binary outcomes, and that transfer learning maintains consistently high predictive performance across various cutoff criteria.

Evaluating rare-event forecasts is challenging because standard metrics collapse as event prevalence declines. Measures such as F1-score, AUPRC, MCC, and accuracy induce degenerate thresholds -- converging to zero or one -- and their values become dominated by class imbalance rather than tail discrimination. We develop a family of rare-event-stable (RES) metrics whose optimal thresholds remain strictly interior as the event probability approaches zero, ensuring coherent decision rules under extreme rarity. Simulations spanning event probabilities from 0.01 down to one in a million show that RES metrics maintain stable thresholds, consistent model rankings, and near-complete prevalence invariance, whereas traditional metrics exhibit statistically significant threshold drift and structural collapse. A credit-default application confirms these results: RES metrics yield interpretable probability-of-default cutoffs (4-9%) and remain robust under subsampling, while classical metrics fail operationally. The RES framework provides a principled, prevalence-invariant basis for evaluating extreme-risk forecasts.

Deep learning models are prone to learning shortcut solutions to problems using spuriously correlated yet irrelevant features of their training data. In high-risk applications such as medical image analysis, this phenomenon may prevent models from using clinically meaningful features when making predictions, potentially leading to poor robustness and harm to patients. We demonstrate that different types of shortcuts (those that are diffuse and spread throughout the image, as well as those that are localized to specific areas) manifest distinctly across network layers and can, therefore, be more effectively targeted through mitigation strategies that target the intermediate layers. We propose a novel knowledge distillation framework that leverages a teacher network fine-tuned on a small subset of task-relevant data to mitigate shortcut learning in a student network trained on a large dataset corrupted with a bias feature. Through extensive experiments on CheXpert, ISIC 2017, and SimBA datasets using various architectures (ResNet-18, AlexNet, DenseNet-121, and 3D CNNs), we demonstrate consistent improvements over traditional Empirical Risk Minimization, augmentation-based bias-mitigation, and group-based bias-mitigation approaches. In many cases, we achieve comparable performance with a baseline model trained on bias-free data, even on out-of-distribution test data. Our results demonstrate the practical applicability of our approach to real-world medical imaging scenarios where bias annotations are limited and shortcut features are difficult to identify a priori.

Public health agencies face critical challenges in identifying high-risk neighborhoods for childhood lead exposure with limited resources for outreach and intervention programs. To address this, we develop a Priority Score integrating untested children proportions, elevated blood lead prevalence, and public health coverage patterns to support optimized resource allocation decisions across 136 neighborhoods in Chicago, New York City, and Washington, D.C. We leverage these allocation tasks, which require integrating multiple vulnerability indicators and interpreting empirical evidence, to evaluate whether large language models (LLMs) with agentic reasoning and deep research capabilities can effectively allocate public health resources when presented with structured allocation scenarios. LLMs were tasked with distributing 1,000 test kits within each city based on neighborhood vulnerability indicators. Results reveal significant limitations: LLMs frequently overlooked neighborhoods with highest lead prevalence and largest proportions of untested children, such as West Englewood in Chicago, while allocating disproportionate resources to lower-priority areas like Hunts Point in New York City. Overall accuracy averaged 0.46, reaching a maximum of 0.66 with ChatGPT 5 Deep Research. Despite their marketed deep research capabilities, LLMs struggled with fundamental limitations in information retrieval and evidence-based reasoning, frequently citing outdated data and allowing non-empirical narratives about neighborhood conditions to override quantitative vulnerability indicators.

Data-driven methods for electrocardiogram (ECG) interpretation are rapidly progressing. Large datasets have enabled advances in artificial intelligence (AI) based ECG analysis, yet limitations in annotation quality, size, and scope remain major challenges. Here we present CODE-II, a large-scale real-world dataset of 2,735,269 12-lead ECGs from 2,093,807 adult patients collected by the Telehealth Network of Minas Gerais (TNMG), Brazil. Each exam was annotated using standardized diagnostic criteria and reviewed by cardiologists. A defining feature of CODE-II is a set of 66 clinically meaningful diagnostic classes, developed with cardiologist input and routinely used in telehealth practice. We additionally provide an open available subset: CODE-II-open, a public subset of 15,000 patients, and the CODE-II-test, a non-overlapping set of 8,475 exams reviewed by multiple cardiologists for blinded evaluation. A neural network pre-trained on CODE-II achieved superior transfer performance on external benchmarks (PTB-XL and CPSC 2018) and outperformed alternatives trained on larger datasets.

For a dataset of label-count pairs, an anonymized histogram is the multiset of counts.