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The evolution of antibiotic resistance among bacteria threatens our continued ability to treat infectious diseases. The need for sustainable strategies to cure bacterial infections has never been greater. So far, all attempts to restore…

Populations and Evolution · Quantitative Biology 2015-06-12 Christiane P. Goulart , Mentar Mahmudi , Kristina A. Crona , Stephen D. Jacobs , Marcelo Kallmann , Barry G. Hall , Devin C. Greene , Miriam Barlow

Antimicrobial resistance (AMR) poses a mounting global health crisis, requiring rapid and reliable prediction frameworks that capture its complex evolutionary dynamics. Traditional antimicrobial susceptibility testing (AST), while accurate,…

Populations and Evolution · Quantitative Biology 2025-11-18 Anshul Bagaria

Bacterial infections are responsible for high mortality worldwide. Antimicrobial resistance underlying the infection, and multifaceted patient's clinical status can hamper the correct choice of antibiotic treatment. Randomized clinical…

Machine Learning · Statistics 2022-07-18 Inyoung Jun , Simone Marini , Christina A. Boucher , J. Glenn Morris , Jiang Bian , Mattia Prosperi

Multiobjective stochastic programming is a field well located to tackle problems arising in emergencies, given that uncertainty and multiple objectives are usually present in such problems. A new concept of solution is proposed in this…

Optimization and Control · Mathematics 2021-02-08 Javier León , Justo Puerto , Begoña Vitoriano

This paper studies flexible multi-facility capacity expansion with risk aversion. In this setting, the decision maker can periodically expand the capacity of facilities given observations of uncertain demand. We model this situation as a…

Optimization and Control · Mathematics 2019-05-15 Sixiang Zhao , William B. Haskell , Michel-Alexandre Cardin

In a typical stochastic multi-armed bandit problem, the objective is often to maximize the expected sum of rewards over some time horizon $T$. While the choice of a strategy that accomplishes that is optimal with no additional information,…

Machine Learning · Computer Science 2023-11-01 Reda Alami , Mohammed Mahfoud , Mastane Achab

Antibiotic resistance presents a growing global health threat by diminishing the effectiveness of treatments and allowing once-manageable bacterial infections to persist. This study develops and analyzes an optimization-based mathematical…

Populations and Evolution · Quantitative Biology 2025-09-23 Uzzwal Kumar Mallick , Jobayer Ahmed , Khan Anik Islam , Pulak Kundu

In this paper, we consider a risk-averse decision problem for controlled-diffusion processes, with dynamic risk measures, in which there are two risk-averse decision makers (i.e., {\it leader} and {\it follower}) with different risk-averse…

Optimization and Control · Mathematics 2016-10-25 Getachew K. Befekadu , Eduardo L. Pasiliao

Understanding how antibiotics inhibit bacteria can help to reduce antibiotic use and hence avoid antimicrobial resistance - yet few theoretical models exist for bacterial growth inhibition by a clinically relevant antibiotic treatment…

Cell Behavior · Quantitative Biology 2017-12-06 Philip Greulich , Jakub Dolezal , Matthew Scott , Martin R. Evans , Rosalind J. Allen

Two approaches to time consistency of risk averse multistage stochastic problems were discussed in the recent literature. In one approach certain properties of the cor-responding risk measure are postulated which imply its decomposability.…

Optimization and Control · Mathematics 2018-06-06 Alexander Shapiro , Kerem Ugurlu

Antimicrobial resistance (AMR) is escalating and outpacing current antibiotic development. Thus, discovering antibiotics effective against emerging pathogens is becoming increasingly critical. However, existing approaches cannot rapidly…

Machine Learning · Computer Science 2025-07-11 Tianang Leng , Fangping Wan , Marcelo Der Torossian Torres , Cesar de la Fuente-Nunez

The rapid rise of antibiotic resistance is a serious threat to global public health. Without further incentives, pharmaceutical companies have little interest in developing antibiotics, since the success probability is low and development…

Populations and Evolution · Quantitative Biology 2022-06-22 Lucas Böttcher , Hans Gersbach

The translation of comparative genomics into clinical decision support tools often depends on the quality of sequence alignments. However, currently used methods of multiple sequence alignments suffer from significant biases and problems…

Genomics · Quantitative Biology 2023-11-30 Manal Helal , Vitali Sintchenko

Antimicrobial resistance is a threat to public health with millions of deaths linked to drug resistant infections every year. To mitigate resistance, common strategies that are used are combination therapies and therapy switching. However,…

Populations and Evolution · Quantitative Biology 2025-06-02 Juan Magalang , Javier Aguilar , Jose Perico Esguerra , Édgar Roldán , Daniel Sanchez-Taltavull

We use Markov risk measures to formulate a risk-averse version of the undiscounted total cost problem for a transient controlled Markov process. We derive risk-averse dynamic programming equations and we show that a randomized policy may be…

Optimization and Control · Mathematics 2014-03-25 Ozlem Cavus , Andrzej Ruszczynski

We consider a risk-averse stochastic capacity planning problem under uncertain demand in each period. Using a scenario tree representation of the uncertainty, we formulate a multistage stochastic integer program to adjust the capacity…

Optimization and Control · Mathematics 2024-11-05 Xian Yu , Siqian Shen

Contextual bandits with average-case statistical guarantees are inadequate in risk-averse situations because they might trade off degraded worst-case behaviour for better average performance. Designing a risk-averse contextual bandit is…

Machine Learning · Statistics 2023-07-11 Mónika Farsang , Paul Mineiro , Wangda Zhang

Purpose: Antimicrobial resistance is a major global health concern, affecting hospital admissions and treatment success. This study aims to introduce an experimental setup for monitoring bacterial activity over time using image-based…

Quantitative Methods · Quantitative Biology 2025-06-12 M. A. Gameiro , R. F. Pinto , N. V. Lopes

Trajectory optimization under uncertainty underpins a wide range of applications in robotics. However, existing methods are limited in terms of reasoning about sources of epistemic and aleatoric uncertainty, space and time correlations,…

Robotics · Computer Science 2023-09-28 Thomas Lew , Riccardo Bonalli , Marco Pavone

We develop a new classification framework based on the theory of coherent risk measures and systemic risk. The proposed approach is suitable for multi-class problems when the data is noisy, scarce (relative to the dimension of the problem),…

Machine Learning · Statistics 2026-05-29 Darinka Dentcheva , Xiangyu Tian