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.

Predicting diseases solely from patient-side information, such as demographics and self-reported symptoms, has attracted significant research attention due to its potential to enhance patient awareness, facilitate early healthcare engagement, and improve healthcare system efficiency. However, existing approaches encounter critical challenges, including imbalanced disease distributions and a lack of interpretability, resulting in biased or unreliable predictions. To address these issues, we propose the Knowledge graph-enhanced, Prototype-aware, and Interpretable (KPI) framework. KPI systematically integrates structured and trusted medical knowledge into a unified disease knowledge graph, constructs clinically meaningful disease prototypes, and employs contrastive learning to enhance predictive accuracy, which is particularly important for long-tailed diseases. Additionally, KPI utilizes large language models (LLMs) to generate patient-specific, medically relevant explanations, thereby improving interpretability and reliability. Extensive experiments on real-world datasets demonstrate that KPI outperforms state-of-the-art methods in predictive accuracy and provides clinically valid explanations that closely align with patient narratives, highlighting its practical value for patient-centered healthcare delivery.

Electronic health records (EHRs) are designed to synthesize diverse data types, including unstructured clinical notes, structured lab tests, and time-series visit data. Physicians draw on these multimodal and temporal sources of EHR data to form a comprehensive view of a patient's health, which is crucial for informed therapeutic decision-making. Yet, most predictive models fail to fully capture the interactions, redundancies, and temporal patterns across multiple data modalities, often focusing on a single data type or overlooking these complexities. In this paper, we present CURENet, a multimodal model (Combining Unified Representations for Efficient chronic disease prediction) that integrates unstructured clinical notes, lab tests, and patients' time-series data by utilizing large language models (LLMs) for clinical text processing and textual lab tests, as well as transformer encoders for longitudinal sequential visits. CURENet has been capable of capturing the intricate interaction between different forms of clinical data and creating a more reliable predictive model for chronic illnesses. We evaluated CURENet using the public MIMIC-III and private FEMH datasets, where it achieved over 94\% accuracy in predicting the top 10 chronic conditions in a multi-label framework. Our findings highlight the potential of multimodal EHR integration to enhance clinical decision-making and improve patient outcomes.

Effective disease prediction in modern healthcare demands the twin goals of high accuracy and transparent, clinically meaningful explanations. Existing machine learning and large language model (LLM) based approaches often struggle to balance these goals. Many models yield accurate but unclear statistical outputs, while others generate fluent but statistically unsupported narratives, often undermining both the validity of the explanation and the predictive accuracy itself. This shortcoming comes from a shallow interaction with the data, preventing the development of a deep, detailed understanding similar to a human expert's. We argue that high accuracy and high-quality explanations are not separate objectives but are mutually reinforcing outcomes of a model that develops a deep, direct understanding of the data. To achieve this, we propose the Reflective Cognitive Architecture (RCA), a novel framework that coordinates multiple LLMs to learn from direct experience. RCA features an iterative rule refinement mechanism that improves its logic from prediction errors and a distribution-aware rules check mechanism that bases its reasoning in the dataset's global statistics. By using predictive accuracy as a signal to drive deeper comprehension, RCA builds a strong internal model of the data. We evaluated RCA on one private and two public datasets against 22 baselines. The results demonstrate that RCA not only achieves state-of-the-art accuracy and robustness with a relative improvement of up to 40\% over the baseline but, more importantly, leverages this deep understanding to excel in generating explanations that are clear, logical, evidence-based, and balanced, highlighting its potential for creating genuinely trustworthy clinical decision support systems. The code is available at \https://github.com/ssssszj/RCA.

Disease-symptom datasets are significant and in demand for medical research, disease diagnosis, clinical decision-making, and AI-driven health management applications. These datasets help identify symptom patterns associated with specific diseases, thus improving diagnostic accuracy and enabling early detection. The dataset presented in this study systematically compiles disease-symptom relationships from various online sources, medical literature, and publicly available health databases. The data was gathered through analyzing peer-reviewed medical articles, clinical case studies, and disease-symptom association reports. Only the verified medical sources were included in the dataset, while those from non-peer-reviewed and anecdotal sources were excluded. The dataset is structured in a tabular format, where the first column represents diseases, and the remaining columns represent symptoms. Each symptom cell contains a binary value, indicating whether a symptom is associated with a disease. Thereby, this structured representation makes the dataset very useful for a wide range of applications, including machine learning-based disease prediction, clinical decision support systems, and epidemiological studies. Although there are some advancements in the field of disease-symptom datasets, there is a significant gap in structured datasets for the Bangla language. This dataset aims to bridge that gap by facilitating the development of multilingual medical informatics tools and improving disease prediction models for underrepresented linguistic communities. Further developments should include region-specific diseases and further fine-tuning of symptom associations for better diagnostic performance

Human activity recognition (HAR) has gained significant attention due to its applications in health monitoring, intelligent environments, and human-computer interaction Hussain, Khan, Khan, Bhatt, Farouk, Bhola, and Baik (2024); Mishra, Gupta, Gupta, and Dutta (2022). Traditional HAR approaches employed wearable inertial sensors, vision-based methods, and environmental sensors for HAR. However, each method has inherent limitations such as discomfort, privacy concerns, or complex deployment requirements Wang, Huang, Zhao, Zhu, Huang, and Wu (2024); Mishra and Gupta (2025). The human body engages with its environment in diverse ways, one of which is the interaction between the lungs and the external environment through the act of breathing via the nose. The breathing pattern encompasses plenty of useful information that can be processed to fetch different behaviours and health information Mongelli, Orani, Cambiaso, Vaccari, Paglialonga, Braido, and Catalano (2020); Zhang, Wang, and Li (2024). Moreover, the breathing patterns are influenced by metabolic and physiological factors, offering a non-invasive and unobtrusive means of HAR.

Multi-omics data offer unprecedented insights into complex biological systems, yet their high dimensionality, sparsity, and intricate interactions pose significant analytical challenges. Network-based approaches have advanced multi-omics research by effectively capturing biologically relevant relationships among molecular entities. While these methods are powerful for representing molecular interactions, there remains a need for tools specifically designed to effectively utilize these network representations across diverse downstream analyses. To fulfill this need, we introduce BioNeuralNet, a flexible and modular Python framework tailored for end-to-end network-based multi-omics data analysis. BioNeuralNet leverages Graph Neural Networks (GNNs) to learn biologically meaningful low-dimensional representations from multi-omics networks, converting these complex molecular networks into versatile embeddings. BioNeuralNet supports all major stages of multi-omics network analysis, including several network construction techniques, generation of low-dimensional representations, and a broad range of downstream analytical tasks. Its extensive utilities, including diverse GNN architectures, and compatibility with established Python packages (e.g., scikit-learn, PyTorch, NetworkX), enhance usability and facilitate quick adoption. BioNeuralNet is an open-source, user-friendly, and extensively documented framework designed to support flexible and reproducible multi-omics network analysis in precision medicine.

Chronic diseases are long-term, manageable, yet typically incurable conditions, highlighting the need for effective preventive strategies. Machine learning has been widely used to assess individual risk for chronic diseases. However, many models rely on medical test data (e.g. blood results, glucose levels), which limits their utility for proactive self-assessment. Additionally, to gain public trust, machine learning models should be explainable and transparent. Although some research on self-assessment machine learning models includes explainability, their explanations are not validated against established medical literature, reducing confidence in their reliability. To address these issues, we develop deep learning models that predict the risk of developing 13 chronic diseases using only personal and lifestyle factors, enabling accessible, self-directed preventive care. Importantly, we use SHAP-based explainability to identify the most influential model features and validate them against established medical literature. Our results show a strong alignment between the models' most influential features and established medical literature, reinforcing the models' trustworthiness. Critically, we find that this observation holds across 13 distinct diseases, indicating that this machine learning approach can be broadly trusted for chronic disease prediction. This work lays the foundation for developing trustworthy machine learning tools for self-directed preventive care. Future research can explore other approaches for models' trustworthiness and discuss how the models can be used ethically and responsibly.

The scarcity of high-quality multimodal biomedical data limits the ability to effectively fine-tune pretrained Large Language Models (LLMs) for specialized biomedical tasks. To address this challenge, we introduce MINT (Multimodal Integrated kNowledge Transfer), a framework that aligns unimodal large decoder models with domain-specific decision patterns from multimodal biomedical data through preference optimization. While MINT supports different optimization techniques, we primarily implement it with the Odds Ratio Preference Optimization (ORPO) framework as its backbone. This strategy enables the aligned LLMs to perform predictive tasks using text-only or image-only inputs while retaining knowledge learnt from multimodal data. MINT leverages an upstream multimodal machine learning (MML) model trained on high-quality multimodal data to transfer domain-specific insights to downstream text-only or image-only LLMs. We demonstrate its effectiveness through two key applications: (1) Rare genetic disease prediction from texts, where MINT uses a multimodal encoder model, trained on facial photos and clinical notes, to generate a preference dataset for aligning a lightweight Llama 3.2-3B-Instruct. Despite relying on text input only, the MINT-derived model outperforms models trained with SFT, RAG, or DPO, and even outperforms Llama 3.1-405B-Instruct. (2) Tissue type classification using cell nucleus images, where MINT uses a vision-language foundation model as the preference generator, containing knowledge learnt from both text and histopathological images to align downstream image-only models. The resulting MINT-derived model significantly improves the performance of Llama 3.2-Vision-11B-Instruct on tissue type classification. In summary, MINT provides an effective strategy to align unimodal LLMs with high-quality multimodal expertise through preference optimization.

Machine learning has been successfully used in critical domains, such as medicine. However, extracting meaningful insights from biomedical data is often constrained by the lack of their available disease labels. In this research, we demonstrate how machine learning can be leveraged to enhance explainability and uncover biologically meaningful associations, even when predictive improvements in disease modeling are limited. We train LightGBM models from scratch on our dataset (10K) to impute metabolomics features and apply them to the UK Biobank (UKBB) for downstream analysis. The imputed metabolomics features are then used in survival analysis to assess their impact on disease-related risk factors. As a result, our approach successfully identified biologically relevant connections that were not previously known to the predictive models. Additionally, we applied a genome-wide association study (GWAS) on key metabolomics features, revealing a link between vascular dementia and smoking. Although being a well-established epidemiological relationship, this link was not embedded in the model's training data, which validated the method's ability to extract meaningful signals. Furthermore, by integrating survival models as inputs in the 10K data, we uncovered associations between metabolic substances and obesity, demonstrating the ability to infer disease risk for future patients without requiring direct outcome labels. These findings highlight the potential of leveraging external bio-banks to extract valuable biomedical insights, even in data-limited scenarios. Our results demonstrate that machine learning models trained on smaller datasets can still be used to uncover real biological associations when carefully integrated with survival analysis and genetic studies.