# A Multi-target Bayesian Transformer Framework for Predicting Cardiovascular Disease Biomarkers during Pandemics

arXiv: https://arxiv.org/abs/2509.01794 · HTML: https://mlsanity.com/paper/2509.01794/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 11 of its 38 references that are in the map.
- First posted on arXiv 1 Sep 2025.

## Builds on (most cited first, 11 of 11)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Simple and Scalable Predictive Uncertainty Estimation using Deep Ensembles](https://mlsanity.com/paper/1612.01474/) (2016)
- [A Time Series is Worth 64 Words: Long-term Forecasting with Transformers](https://mlsanity.com/paper/2211.14730/) (2022)
- [BioBERT: a pre-trained biomedical language representation model for biomedical text mining](https://mlsanity.com/paper/1901.08746/) (2019)
- [iTransformer: Inverted Transformers Are Effective for Time Series Forecasting](https://mlsanity.com/paper/2310.06625/) (2023)
- [Simple and Principled Uncertainty Estimation with Deterministic Deep Learning via Distance Awareness](https://mlsanity.com/paper/2006.10108/) (2020)
- [BayesFormer: Transformer with Uncertainty Estimation](https://mlsanity.com/paper/2206.00826/) (2022)
- [Uncertainty Estimation of Transformers' Predictions via Topological Analysis of the Attention Matrices](https://mlsanity.com/paper/2308.11295/) (2023)
- [Bayesian Neural Networks with Domain Knowledge Priors](https://mlsanity.com/paper/2402.13410/) (2024)
- [Heart Disease Detection using Vision-Based Transformer Models from ECG Images](https://mlsanity.com/paper/2310.12630/) (2023)

## Abstract (arXiv)

The COVID-19 pandemic disrupted healthcare systems worldwide, disproportionately impacting individuals with chronic conditions such as cardiovascular disease (CVD). These disruptions -- through delayed care and behavioral changes, affected key CVD biomarkers, including LDL cholesterol (LDL-C), HbA1c, BMI, and systolic blood pressure (SysBP). Accurate modeling of these changes is crucial for predicting disease progression and guiding preventive care. However, prior work has not addressed multi-target prediction of CVD biomarker from Electronic Health Records (EHRs) using machine learning (ML), while jointly capturing biomarker interdependencies, temporal patterns, and predictive uncertainty. In this paper, we propose MBT-CB, a Multi-target Bayesian Transformer (MBT) with pre-trained BERT-based transformer framework to jointly predict LDL-C, HbA1c, BMI and SysBP CVD biomarkers from EHR data. The model leverages Bayesian Variational Inference to estimate uncertainties, embeddings to capture temporal relationships and a DeepMTR model to capture biomarker inter-relationships. We evaluate MBT-CT on retrospective EHR data from 3,390 CVD patient records (304 unique patients) in Central Massachusetts during the Covid-19 pandemic. MBT-CB outperformed a comprehensive set of baselines including other BERT-based ML models, achieving an MAE of 0.00887, RMSE of 0.0135 and MSE of 0.00027, while effectively capturing data and model uncertainty, patient biomarker inter-relationships, and temporal dynamics via its attention and embedding mechanisms. MBT-CB's superior performance highlights its potential to improve CVD biomarker prediction and support clinical decision-making during pandemics.