An ML-based Approach to better Characterize Lung Diseases

Machine Learning at work.

An ML-based approach to better characterize lung diseases

THURSDAY, APRIL 27, 2023

Posted by Babak Behsaz, Software Engineer, and Andrew Carroll, Product Lead, Genomics

The combination of the environment an individual experiences and their genetic predispositions determines the majority of their risk for various diseases. Large national efforts, such as the UK Biobank, have created large, public resources to better understand the links between environment, genetics, and disease. This has the potential to help individuals better understand how to stay healthy, clinicians to treat illnesses, and scientists to develop new medicines.

One challenge in this process is how we make sense of the vast amount of clinical measurements — the UK Biobank has many petabytes of imaging, metabolic tests, and medical records spanning 500,000 individuals. To best use this data, we need to be able to represent the information present as succinct, informative labels about meaningful diseases and traits, a process called phenotyping. That is where we can use the ability of ML models to pick up on subtle intricate patterns in large amounts of data.

We’ve previously demonstrated the ability to use ML models to quickly phenotype at scale for retinal diseases. Nonetheless, these models were trained using labels from clinician judgment, and access to clinical-grade labels is a limiting factor due to the time and expense needed to create them.

In “Inference of chronic obstructive pulmonary disease with deep learning on raw spirograms identifies new genetic loci and improves risk models”, published in Nature Genetics, we’re excited to highlight a method for training accurate ML models for genetic discovery of diseases, even when using noisy and unreliable labels. We demonstrate the ability to train ML models that can phenotype directly from raw clinical measurement and unreliable medical record information. This reduced reliance on medical domain experts for labeling greatly expands the range of applications for our technique to a panoply of diseases and has the potential to improve their prevention, diagnosis, and treatment. We showcase this method with ML models that can better characterize lung function and chronic obstructive pulmonary disease (COPD). Additionally, we show the usefulness of these models by demonstrating a better ability to identify genetic variants associated with COPD, improved understanding of the biology behind the disease, and successful prediction of outcomes associated with COPD.

ML for deeper understanding of exhalation

For this demonstration, we focused on COPD, the third leading cause of worldwide death in 2019, in which airway inflammation and impeded airflow can progressively reduce lung function. Lung function for COPD and other diseases is measured by recording an individual’s exhalation volume over time (the record is called a spirogram; see an example below). Although there are guidelines (called GOLD) for determining COPD status from exhalation, these use only a few, specific data points in the curve and apply fixed thresholds to those values. Much of the rich data from these spirograms is discarded in this analysis of lung function.

We reasoned that ML models trained to classify spirograms would be able to use the rich data present more completely and result in more accurate and comprehensive measures of lung function and disease, similar to what we have seen in other classification tasks like mammography or histology. We trained ML models to predict whether an individual has COPD using the full spirograms as inputs.    .... '