Machine learning for biomedical applications and time-to-event data

Jagannath Ghosh Chair
Medivant Pharma, LLC
 
Sunday, Aug 3: 4:00 PM - 5:50 PM
4020 
Contributed Papers 
Music City Center 
Room: CC-103B 

Main Sponsor

Section on Statistical Learning and Data Science

Presentations

A Monotonic Single-Index Model Powered by Deep Neural Networks for Non-Gaussian Periodontal Data

Periodontal pocket depth is a widely used biomarker for diagnosing risk of periodontal disease. However, pocket depth typically exhibits skewness and heavy-tailedness, and its relationship with clinical risk factors is often nonlinear. Motivated by periodontal studies, this paper develops a robust single-index modal regression framework for analyzing skewed and heavy-tailed data. Our method has the following novel features: (1) a flexible two-piece scale Student-t error distribution that generalizes both normal and two-piece scale normal distributions; (2) a deep neural network with guaranteed monotonicity constraints to estimate the unknown single-index function; and (3) theoretical guarantees, including model identifiability and a universal approximation theorem. Our single-index model combines the flexibility of neural networks and the two-piece scale Student-t distribution, delivering robust mode-based estimation that is resistant to outliers, while retaining clinical interpretability through parametric index coefficients. We demonstrate the performance of our method through simulation studies and an application to periodontal disease data from the HealthPartners Institute of Minnesota. The proposed methodology is implemented in the R package DNNSIM. 

Keywords

deep neural network

single index model

skewness

heavy-tailed

modal regression 

Co-Author(s)

Shijie Wang, Gauss Lab
Ray Bai, University of South Carolina
Dipankar Bandyopadhyay, Virginia Commonwealth University

First Author

Qingyang Liu, University of Wisconsin - Madison

Presenting Author

Qingyang Liu, University of Wisconsin - Madison

A simulation study evaluating the predictive performance of Cox proportional hazards model and machine learning methods for time-to-event data

Many data-driven risk prediction models have been developed for analysing time-to-event data. However, choosing the most suitable model for accurate predictions in a specific medical application remains a challenge. Simulation enables effective comparison based on equal-sized datasets. This study provided a comprehensive evaluation of the survival prediction performance of random survival forests, eXtreme Gradient Boosting, deep neural networks (DeepSurv), and Cox proportional hazards (PH) model, using both simulated and real datasets. We assessed model performance using C-index and Integrated Brier Score. The evaluation was performed under varying sample sizes, censoring proportions, addition of noise variables, and in the presence of different types of model misspecification. All the models improved in predictive performance with larger sample sizes but declined with higher censoring and with increase in number of noise variables. Tree-based models demonstrated promising predictive performance compared to the Cox PH model and DeepSurv in the presence of misspecification and large number of noise variables. The Cox PH model performed well with larger sample sizes and fewer noise variables. It also performed well when the model was correctly specified or had only minor misspecification. 

Keywords

Simulation

Machine Learning

Survival analysis

Prediction modelling

Stroke 

Co-Author(s)

Jenny Häggström, Umeå University
Marie Eriksson, Umeå University

First Author

Josline Adhiambo Otieno, Umeå University

Presenting Author

Josline Adhiambo Otieno, Umeå University

Adaptive Neural-Fuzzy Rule Generation with Attention Mechanisms for Anthropometric Prediction

Accurate decision support in healthcare often requires effective handling of uncertainty inherent in clinical data. Traditional fuzzy systems rely on manually crafted rule bases, which can be inflexible and labor-intensive to design. In this work, we propose an adaptive rule generation framework that integrates neural networks with fuzzy logic to automatically derive fuzzy rules from numerical health indicators and demographic variables. Our method utilizes learnable fuzzy membership functions to transform raw data into fuzzy representations and employs an attention mechanism to dynamically assign weights to the generated rules. The overall architecture consists of a fuzzy encoding layer, an adaptive rule generation module, and a subsequent prediction layer, enabling end-to-end training for regression tasks such as the prediction of Body Mass Index (BMI), weight, and waist circumference. By eliminating the reliance on manually defined rules, the proposed framework enhances model flexibility and interpretability, paving the way for more robust and data-driven decision support systems in healthcare. 

Keywords

fuzzy system

healthcare prediction

attention mechanism 

Co-Author(s)

Honggang Wang, Yeshiva University
Hua Fang

First Author

Dengyi Liu, Yeshiva University

Presenting Author

Dengyi Liu, Yeshiva University

Machine Learning Prediction Models for Chronic Kidney Disease with Imbalanced Data.

Chronic kidney disease (CKD) is a disease characterized by the gradual decline of kidney function over time due to which kidneys slowly lose their ability to filter waste and excess fluid from the blood. This causes a buildup of toxin in the body leading to kidney failure (End-Stage Renal Disease, ESRD) and other serious health complications. The prevalence of CKD has become a major concerning public health issue globally and in the United States, with its prevalence steadily increasing over the years. Early detection of CKD is crucial for effective management and treatment so that the progression of ESRD can be prevented or delayed thus reducing the overly expensive treatment cost. In this paper, we explore the use of machine learning (ML) techniques to predict Chronic Kidney Disease (CKD) based on the South Carolina Behavioral Risk Factor Surveillance System (BRFSS) dataset. However, the dataset is imbalanced, with a much smaller number of CKD cases compared to healthy individuals. The study compares different ML algorithms and tackles the challenges of imbalanced data. 

Keywords

Machine Learning

Chronic kidney disease

imbalanced data

South Carolina

BRFSS 

First Author

Dilli Bhatta, University of South Carolina Upstate

Presenting Author

Dilli Bhatta, University of South Carolina Upstate

Machine Learning-Driven Mediation CNN (Med-CNN) Model for High-Dimensional Mediation Data

Complex biological features like the microbiome and gene expressions mediate disease progression by influencing immune and metabolic processes. Understanding these mediation roles is crucial for disease pathogenesis and treatment. However, high-dimensional mediation analysis is challenging due to structural dependencies, correlations, and hierarchical relationships, such as microbial taxonomies and gene pathways. The many mediators also complicate conventional approaches.
We propose Med-CNN, a Convolutional Neural Network (CNN)-based model that integrates biological networks to estimate mediation effects. Network-specific CNN outputs are condensed into an Integrative Mediation Metric (IMM) to capture key biological information while handling high-dimensional data and non-linear interactions. Our model accommodates complex structures and improves interpretability in mediation analysis.
Through simulations, Med-CNN showed lower mediation effect biases compared to conventional methods. In a real data application, it identified a mediation effect between ethnicity and vaginal pH levels, demonstrating its robustness in analyzing high-dimensional mediators. 

Keywords

High-dimensional

Mediation analysis

Microbiome

Deep learning 

Co-Author(s)

Jasper Zhongyuan Zhang, University of Toronto
Olli Saarela, University of Toronto
Divya Sharma, University of Toronto/University Health Network
Wei Xu, University of Toronto

First Author

Yao Li

Presenting Author

Jasper Zhongyuan Zhang, University of Toronto

Non-Crossing Deep Quantile Regression for Time-to-Event Analysis

Deep learning (DL) has garnered increasing attention in time-to-event prediction due to its ability to model complex nonlinear relationships while offering greater flexibility than traditional methods. In this work, we propose a non-crossing quantile regression framework that estimates multiple quantiles of event time simultaneously in right-censored survival data while ensuring valid quantile ordering. Unlike existing approaches that rely on multilayer perceptrons (MLPs), we leverage Kolmogorov-Arnold Networks (KAN) for efficient function approximation and Transformers for capturing intricate feature dependencies through self attention. To provide theoretical insights, we establish upper bounds on the prediction error of our quantile estimators. We evaluate our framework on both simulated and real-world datasets, benchmarking its performance against existing quantile-based and non-quantile-based methods. As shown in these experiments, our DL framework can achieve 30% to 50% error reduction in real data analysis compared with various baseline methods. 

Keywords

Deep Learning

Non-Crossing Quantile Regression

Time-to-Event Prediction

Transformer

KAN

Survival Analysis 

First Author

Shuai Huang

Presenting Author

Shuai Huang

Quantization Aware Training Enabled CNN for On-Device Sleep Disorder Detection

Quantization-Aware Training (QAT) was integrated into a 1D 6-layer convolutional neural network (CNN) using the Sleep-EDF Database Expanded to detect sleep disorders by classifying sleep stages. This approach enables efficient on-device execution with limited memory while preserving performance despite quantization. QAT CNN consistently demonstrates reliable performance across all sleep stages, with its 8-bit and 16-bit quantized versions achieving high specificity (99.7%–100%) and lower sensitivity across most stages, and peak sensitivity at Stage R (100%) with lower specificity. These findings highlight QAT CNN's suitability for edge devices, ensuring stage-specific reliability, ie., sensitivity for Stage R and specificity for other stages. In contrast, non-QAT CNN exhibits lower sensitivity and higher specificity (82.1%–99%) across all stages and inconsistent performance in its quantized forms: 8-bit CNN shows high sensitivity and low specificity at Stage 3/4 and the reverse at other stages, while 16-bit CNN shows similar inconsistencies at Stage 1, instead. Overall, this QAT-guided CNN provides consistent and dependable performance for deploying quantized models on-device. 

Keywords

Quantization Aware Training

CNN

on-device

Sleep-EDF Database Expanded

sleep disorder detection


QAT 

First Author

Anna Wang

Presenting Author

Anna Wang