Machine-Learned Biomarker Discovery from Standard-of-Care Data
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Solution Overview
Problem
Existing biomarker discovery processes in oncology rely heavily on small clinical trials and require assays not typically collected as part of standard-of-care (SoC), making them underpowered and slow to adopt broadly.
Innovation Solution
A machine learning model is trained on both medical images and molecular analyte data from separate cohorts to predict molecular analyte activity in patients, enabling the imputation of missing biological measurements from SoC data, allowing for patient stratification and treatment recommendations.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If predictive biomarkers are discovered using small clinical trials with targeted assays, then measurement precision can be achieved, but the sample size is insufficient for robust discovery and the process is slow to adopt
Solution Approach 1:
The patent introduces machine learning models as an intermediary that bridges the gap between standard-of-care data and predictive biomarker discovery. The ML models process routine clinical data (imaging, lab results, demographics) to infer molecular analyte activity, enabling robust biomarker discovery without requiring specialized assays or large dedicated cohorts. This intermediary approach allows the system to extract meaningful biomarker signals from existing SoC data, resolving the contradiction between measurement precision and sample size requirements.
2Measurement precision
If new biomarkers are identified using assays not collected as part of standard-of-care, then measurement precision improves, but the process becomes complex and slow to obtain broad adoption
Solution Approach 1:
The patent leverages inexpensive, routinely collected standard-of-care data (medical images, lab results, demographics) as substitute proxies for complex molecular assays. Instead of implementing new specialized assays, the system uses readily available SoC data that can be processed by machine learning models to infer molecular analyte activity. This approach replaces complex, costly assays with simple, abundant data sources, dramatically reducing implementation complexity while maintaining biomarker detection precision.
3Measurement precision
If biological measurements not currently collected as part of SoC are used for biomarker discovery, then measurement precision improves, but the data is hard to ascertain robustly and slow to obtain broad adoption
Solution Approach 1:
The patent enables the system to serve itself by using machine learning models to extract molecular analyte activity information from existing standard-of-care data collections. Rather than requiring separate robust data collection infrastructure for biological measurements, the system processes routinely collected SoC data through ML algorithms that automatically infer molecular activity patterns. This self-service approach eliminates the need for additional robust data collection systems while maintaining measurement precision, as the ML models learn to extract meaningful signals from the inherent variability in SoC data.
Data Source
AI summary
The present disclosure relates generally to biomarker discovery and patient stratification, and more specifically to machine learning techniques for discovering relevant biomarkers using data collected as part of the standard-of-care (SoC), which can be used to identify a relevant patient population for a therapeutic with a known mechanism of action (MoA). An exemplary method for predicting activity of a molecular analyte of a patient comprises: training a first module of a machine learning model based on a plurality of medical images of a first cohort; training a second module of the machine learning model based on one or more molecular analyte data sets obtained from a second cohort; receiving a medical image from the patient; and predicting, using the trained first and second modules of the machine learning model, the activity of the molecular analyte from the medical image of the patient.


