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Efficient sampling in biomolecular simulations is critical for accurately capturing the complex dynamical behaviors of biological systems. Adaptive sampling techniques aim to improve efficiency by focusing computational resources on the…

Biomolecules · Quantitative Biology 2024-10-22 Hassan Nadeem , Diwakar Shukla

Cancer and healthy cells have distinct distributions of molecular properties and thus respond differently to drugs. Cancer drugs ideally kill cancer cells while limiting harm to healthy cells. However, the inherent variance among cells in…

Other Quantitative Biology · Quantitative Biology 2013-08-07 Patrick N. Lawlor , Tomer Kalisky , Stephen Quake , Robert Rosner , Marsha Rich Rosner , Konrad P. Kording

Personalized cancer treatment is revolutionizing oncology by leveraging precision medicine and advanced computational techniques to tailor therapies to individual patients. Despite its transformative potential, challenges such as limited…

Machine Learning · Computer Science 2025-01-15 Sepinoud Azimi , Louise Spekking , Kateřina Staňková

Optimal design of a Phase I cancer trial can be formulated as a stochastic optimization problem. By making use of recent advances in approximate dynamic programming to tackle the problem, we develop an approximation of the Bayesian optimal…

Methodology · Statistics 2010-12-01 Jay Bartroff , Tze Leung Lai

Predictive modeling of the evolutionary dynamics of cancer is a challenge issue in computational cancer biology. In this paper, we propose a general mathematical model framework for the evolutionary dynamics of cancer with plasticity and…

Cell Behavior · Quantitative Biology 2020-01-10 Jinzhi Lei

We study a stochastic phase-field model for tumor growth dynamics coupling a stochastic Cahn-Hilliard equation for the tumor phase parameter with a stochastic reaction-diffusion equation governing the nutrient proportion. We prove strong…

Analysis of PDEs · Mathematics 2021-01-19 Carlo Orrieri , Elisabetta Rocca , Luca Scarpa

Precision medicine aims to tailor therapeutic decisions to individual patient characteristics. This objective is commonly formalized through dynamic treatment regimes, which use statistical and machine learning methods to derive sequential…

Machine Learning · Statistics 2026-03-23 Sophia Yazzourh , Erica E. M. Moodie

Traditionally, the major objective in phase I trials is to identify a working-dose for subsequent studies, whereas the major endpoint in phase II and III trials is treatment efficacy. The dose sought is typically referred to as the maximum…

Methodology · Statistics 2016-08-14 Mourad Tighiouart , André Rogatko

An optimal control problem for a model of tumor growth is studied. In a given subdomain, it is required to minimize the density of tumor cells, while the drug concentration in tissue is limited by given minimal and maximal values. Based on…

Optimization and Control · Mathematics 2024-07-12 Andrey Kovtanyuk , Christina Kuttler , Kristina Koshel , Alexander Chebotarev

Dynamic treatment regimes (DTRs) are used in medicine to tailor sequential treatment decisions to patients by considering patient heterogeneity. Common methods for learning optimal DTRs, however, have shortcomings: they are typically based…

Machine Learning · Statistics 2023-06-21 Theresa Blümlein , Joel Persson , Stefan Feuerriegel

To achieve the goal of providing the best possible care to each patient, physicians need to customize treatments for patients with the same diagnosis, especially when treating diseases that can progress further and require additional…

Methodology · Statistics 2022-10-25 Xiao Li , Brent R Logan , S M Ferdous Hossain , Erica E M Moodie

The aim is to create a method for accurately estimating the duration of post-cancer treatment, particularly focused on chemotherapy, to optimize patient care and recovery. This initiative seeks to improve the effectiveness of cancer…

Computers and Society · Computer Science 2025-04-24 Joyee Chakraborty , Mazahrul Islam Tohin , Danbir Rashid , Tanjil Ahmed Tanmoy , Md. Jehadul Islam Mony

The sequential treatment decisions made by physicians to treat chronic diseases are formalized in the statistical literature as dynamic treatment regimes. To date, methods for dynamic treatment regimes have been developed under the…

Methodology · Statistics 2022-02-22 Janie Coulombe , Erica E. M. Moodie , Susan M. Shortreed , Christel Renoux

Currently, most of the basic mechanisms governing tumor-immune system interactions, in combination with modulations of tumor-associated vasculature, are far from being completely understood. Here, we propose a mathematical model of…

Tissues and Organs · Quantitative Biology 2015-10-07 H. Hatzikirou , J. C. L. Alfonso , S. Muhle , C. Stern , S. Weiss , M. Meyer-Hermann

Cell heterogeneity plays an important role in patient responses to drug treatments. In many cancers, it is associated with poor treatment outcomes. Many modern drug combination therapies aim to exploit cell heterogeneity, but determining…

Quantitative Methods · Quantitative Biology 2025-02-18 Simon F. Martina-Perez , Samuel W. S. Johnson , Rebecca M. Crossley , Jennifer C. Kasemeier , Paul M. Kulesa , Ruth E. Baker

Adoptive Cell Transfer therapy of cancer is currently in full development and mathematical modeling is playing a critical role in this area. We study a stochastic model developed by Baar et al. in 2015 for modeling immunotherapy against…

Populations and Evolution · Quantitative Biology 2020-03-09 Modibo Diabate , Loren Coquille , Adeline Samson

A dynamic treatment regime is a sequence of treatment decision rules tailored to an individual's evolving status over time. In precision medicine, much focus has been placed on finding an optimal dynamic treatment regime which, if followed…

Other Statistics · Statistics 2025-10-13 Chunyu Wang , Brian DM Tom

Differential evolution is one of the most prestigious population-based stochastic optimization algorithm for black-box problems. The performance of a differential evolution algorithm depends highly on its mutation and crossover strategy and…

Neural and Evolutionary Computing · Computer Science 2021-02-09 Jianyong Sun , Xin Liu , Thomas Bäck , Zongben Xu

Adaptive machines have the potential to assist or interfere with human behavior in a range of contexts, from cognitive decision-making to physical device assistance. Therefore it is critical to understand how machine learning algorithms can…

Artificial Intelligence · Computer Science 2023-05-03 Benjamin J. Chasnov , Lillian J. Ratliff , Samuel A. Burden

Randomized experiments have been the gold standard for assessing the effectiveness of a treatment or policy. The classical complete randomization approach assigns treatments based on a prespecified probability and may lead to inefficient…

Methodology · Statistics 2023-10-26 Waverly Wei , Xinwei Ma , Jingshen Wang