Data-Driven Discovery of Mathematical and Physical Relations in Oncology Data Using Human-Understandable Machine Learning

For decades, researchers have used the concepts of rate of change and differential equations to model and forecast neoplastic processes. This expressive mathematical apparatus brought significant insights in oncology by describing the unregulated proliferation and host interactions of cancer cells,...

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Autores principales:	Daria Kurz, Carlos Salort Sánchez, Cristian Axenie
Formato:	article
Lenguaje:	EN
Publicado:	Frontiers Media S.A. 2021
Materias:	mathematical oncology machine learning mechanistic modeling data-driven predictions clinical data decision support system Electronic computers. Computer science QA75.5-76.95
Acceso en línea:	https://doaj.org/article/13337dfb05c64cd5a2f04d18df15cae3
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spelling	oai:doaj.org-article:13337dfb05c64cd5a2f04d18df15cae32021-11-30T22:53:47ZData-Driven Discovery of Mathematical and Physical Relations in Oncology Data Using Human-Understandable Machine Learning2624-821210.3389/frai.2021.713690https://doaj.org/article/13337dfb05c64cd5a2f04d18df15cae32021-11-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/frai.2021.713690/fullhttps://doaj.org/toc/2624-8212For decades, researchers have used the concepts of rate of change and differential equations to model and forecast neoplastic processes. This expressive mathematical apparatus brought significant insights in oncology by describing the unregulated proliferation and host interactions of cancer cells, as well as their response to treatments. Now, these theories have been given a new life and found new applications. With the advent of routine cancer genome sequencing and the resulting abundance of data, oncology now builds an “arsenal” of new modeling and analysis tools. Models describing the governing physical laws of tumor–host–drug interactions can be now challenged with biological data to make predictions about cancer progression. Our study joins the efforts of the mathematical and computational oncology community by introducing a novel machine learning system for data-driven discovery of mathematical and physical relations in oncology. The system utilizes computational mechanisms such as competition, cooperation, and adaptation in neural networks to simultaneously learn the statistics and the governing relations between multiple clinical data covariates. Targeting an easy adoption in clinical oncology, the solutions of our system reveal human-understandable properties and features hidden in the data. As our experiments demonstrate, our system can describe nonlinear conservation laws in cancer kinetics and growth curves, symmetries in tumor’s phenotypic staging transitions, the preoperative spatial tumor distribution, and up to the nonlinear intracellular and extracellular pharmacokinetics of neoadjuvant therapies. The primary goal of our work is to enhance or improve the mechanistic understanding of cancer dynamics by exploiting heterogeneous clinical data. We demonstrate through multiple instantiations that our system is extracting an accurate human-understandable representation of the underlying dynamics of physical interactions central to typical oncology problems. Our results and evaluation demonstrate that, using simple—yet powerful—computational mechanisms, such a machine learning system can support clinical decision-making. To this end, our system is a representative tool of the field of mathematical and computational oncology and offers a bridge between the data, the modeler, the data scientist, and the practicing clinician.Daria KurzCarlos Salort SánchezCristian AxenieFrontiers Media S.A.articlemathematical oncologymachine learningmechanistic modelingdata-driven predictionsclinical datadecision support systemElectronic computers. Computer scienceQA75.5-76.95ENFrontiers in Artificial Intelligence, Vol 4 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	mathematical oncology machine learning mechanistic modeling data-driven predictions clinical data decision support system Electronic computers. Computer science QA75.5-76.95
spellingShingle	mathematical oncology machine learning mechanistic modeling data-driven predictions clinical data decision support system Electronic computers. Computer science QA75.5-76.95 Daria Kurz Carlos Salort Sánchez Cristian Axenie Data-Driven Discovery of Mathematical and Physical Relations in Oncology Data Using Human-Understandable Machine Learning
description	For decades, researchers have used the concepts of rate of change and differential equations to model and forecast neoplastic processes. This expressive mathematical apparatus brought significant insights in oncology by describing the unregulated proliferation and host interactions of cancer cells, as well as their response to treatments. Now, these theories have been given a new life and found new applications. With the advent of routine cancer genome sequencing and the resulting abundance of data, oncology now builds an “arsenal” of new modeling and analysis tools. Models describing the governing physical laws of tumor–host–drug interactions can be now challenged with biological data to make predictions about cancer progression. Our study joins the efforts of the mathematical and computational oncology community by introducing a novel machine learning system for data-driven discovery of mathematical and physical relations in oncology. The system utilizes computational mechanisms such as competition, cooperation, and adaptation in neural networks to simultaneously learn the statistics and the governing relations between multiple clinical data covariates. Targeting an easy adoption in clinical oncology, the solutions of our system reveal human-understandable properties and features hidden in the data. As our experiments demonstrate, our system can describe nonlinear conservation laws in cancer kinetics and growth curves, symmetries in tumor’s phenotypic staging transitions, the preoperative spatial tumor distribution, and up to the nonlinear intracellular and extracellular pharmacokinetics of neoadjuvant therapies. The primary goal of our work is to enhance or improve the mechanistic understanding of cancer dynamics by exploiting heterogeneous clinical data. We demonstrate through multiple instantiations that our system is extracting an accurate human-understandable representation of the underlying dynamics of physical interactions central to typical oncology problems. Our results and evaluation demonstrate that, using simple—yet powerful—computational mechanisms, such a machine learning system can support clinical decision-making. To this end, our system is a representative tool of the field of mathematical and computational oncology and offers a bridge between the data, the modeler, the data scientist, and the practicing clinician.
format	article
author	Daria Kurz Carlos Salort Sánchez Cristian Axenie
author_facet	Daria Kurz Carlos Salort Sánchez Cristian Axenie
author_sort	Daria Kurz
title	Data-Driven Discovery of Mathematical and Physical Relations in Oncology Data Using Human-Understandable Machine Learning
title_short	Data-Driven Discovery of Mathematical and Physical Relations in Oncology Data Using Human-Understandable Machine Learning
title_full	Data-Driven Discovery of Mathematical and Physical Relations in Oncology Data Using Human-Understandable Machine Learning
title_fullStr	Data-Driven Discovery of Mathematical and Physical Relations in Oncology Data Using Human-Understandable Machine Learning
title_full_unstemmed	Data-Driven Discovery of Mathematical and Physical Relations in Oncology Data Using Human-Understandable Machine Learning
title_sort	data-driven discovery of mathematical and physical relations in oncology data using human-understandable machine learning
publisher	Frontiers Media S.A.
publishDate	2021
url	https://doaj.org/article/13337dfb05c64cd5a2f04d18df15cae3
work_keys_str_mv	AT dariakurz datadrivendiscoveryofmathematicalandphysicalrelationsinoncologydatausinghumanunderstandablemachinelearning AT carlossalortsanchez datadrivendiscoveryofmathematicalandphysicalrelationsinoncologydatausinghumanunderstandablemachinelearning AT cristianaxenie datadrivendiscoveryofmathematicalandphysicalrelationsinoncologydatausinghumanunderstandablemachinelearning
_version_	1718406186608361472

Data-Driven Discovery of Mathematical and Physical Relations in Oncology Data Using Human-Understandable Machine Learning

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