A team of researchers at the University of Utah has developed a quantum mechanics-based artificial intelligence and machine learning method, which they say can improve the prediction of cancer outcomes and identify treatment targets using the comprehensive molecular background of individual patients. The approach, described in APL Quantum, addresses a major roadblock to leveraging conventional AI for predicting patient outcomes in clinical trials, namely the vast amounts of data needed to train large language models and to account for the complexity of disease drivers.
“It’s much more than just one gene—everything that’s happening in the cells of the patient matters,” said Orly Alter, PhD, associate professor of biomedical engineering at the University of Utah’s Scientific Computing & Imaging Institute. To take this into account, the team developed a method that is capable of analyzing multiple layers of molecular information simultaneously, including tumor DNA, blood DNA, and tumor RNA.
Clinical trials can enroll as few as 20 to 100 patients, while existing genomic datasets often contain data detailing millions to billions of molecular features. According to the researchers, many existing AI and machine-learning methods need more patient samples than genetic features to properly train the model. For instance, they pointed to a recent large language model of the 30,000-nucleotide genome of the COVID-19 virus, which needed 110 million samples. Extrapolating from this, the Utah team said that a complete modeling of the three billion nucleotides in the human genome would require 33 trillion patient samples.
To overcome this constraint, the investigators used a collection of algorithms known as multitensor comparative spectral decompositions, which Alter developed based on the quantum mechanical concepts of entanglement and superposition. The result, the team said, is analogous to a prism splitting light into its individual color components, providing data on multiple layers of a patient’s molecular makeup, including tumor and blood genomes and RNA transcriptomics, able to demonstrate linked patterns in cancer that can predict individual patient outcomes.
“The model rewrites a set of multiple omic profiles from one patient as a superposition of phenotypes, each represented by a set of multiple entangled patterns,” the researchers wrote. Importantly, data from one molecular profile can approximate an analysis from other profiles, which allows predictions to remain consistent among different types of biological data.
The researchers tested their model using an open-source dataset of the childhood cancer neuroblastoma. Their analysis found two previously unrecognized predictors of survival and treatment response, with each predictive element found in three separate, but interconnected data types: tumor genomes, blood genomes, and tumor transcriptomes. The study found that these predictors outperformed the currently used biomarker, the MYCN gene, for predicting treatment response and outcomes.
The new method builds on the substantial body of work by Alter and colleagues. Earlier research in this area had used related comparative spectral decomposition methods to analyze genomic and transcriptomic data in other tumor types, including glioblastoma.
The team will continue its work as it looks to develop an approach that can be used in the clinic. “That’s the ultimate precision medicine,” Alter said. “You have a single person. Can you take the data from just that one person and come up with a treatment for them? I think we can get there.”
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