PABformer: A Multi-Channel Transformer for Physical Activity Behavior Representation and Health Outcome Assessment Using UK Biobank Accelerometer Data

Physical activity (PA) is a critical, modifiable determinant of health. The relationship between PA behavior and health outcomes has been increasingly examined using objectively measured accelerometer data. Accelerometer{square}derived PA features have been consistently associated with a wide range of health outcomes and have shown potential in predictive modeling. However, traditional summary{square}statistic features are limited in their ability to capture the high{square}resolution and dynamic accelerometer data, and the predictive utility of accelerometer data across diverse health outcomes has not been comprehensively evaluated. Here, we present PABformer, a foundation model for accelerometer data pretrained on the UK Biobank to learn behavior{square}level representations of PA. PABformer employs a channel{square}separation strategy to disentangle heterogeneities inherent in accelerometer data and leverages a multi{square}channel Transformer encoder to extract channel{square}specific representations. We finetuned PABformer on benchmark tasks, including demographic attribute inference and Parkinsons disease classification, where it consistently outperformed baseline models across multiple evaluation metrics. Extending beyond benchmarks, we applied the pretrained model to 157 chronic diseases spanning seven organ systems, as well as all{square}cause mortality. PABformer outperformed traditional covariate{square}based models in 48% of prevalent diseases, 54% of incident diseases, and mortality, with particularly marked improvements in three prevalent and nine incident diseases. These findings establish PABformer as a generalizable and scalable foundation model for accelerometer data, enhancing the utility of accelerometer measurements for health outcome assessment and offering the potential to advance disease risk prediction and enable precision health applications.