Related papers: Automated generation of bacterial resource allocat…

Reverse-phase protein array (RPPA) analysis is a powerful, relatively new platform that allows for high-throughput, quantitative analysis of protein networks. One of the challenges that currently limit the potential of this technology is…

This paper introduces ROmodel, an open source Python package extending the modeling capabilities of the algebraic modeling language Pyomo to robust optimization problems. ROmodel helps practitioners transition from deterministic to robust…

Surveys are an important research tool, providing unique measurements on subjective experiences such as sentiment and opinions that cannot be measured by other means. However, because survey data is collected from a self-selected group of…

Biological systems possess negative entropy. In them, one form of order produces another, more organized form of order. We propose a formal scheme to calculate robustness of an entire biological system by quantifying the negative entropy…

Reinforcement learning with verifiable rewards (RLVR) has become a central paradigm for improving reasoning and code generation in large language models, and GRPO-style training is widely adopted for its simplicity and effectiveness.…

We propose a new model to assess the mastery level of a given skill efficiently. The model, called Bayesian Adaptive Mastery Assessment (BAMA), uses information on the accuracy and the response time of the answers given and infers the…

RPA (Robotic Process Automation) helps automate repetitive tasks performed by users, often across different software solutions. Regardless of the RPA tool chosen, the key problem in automation is analyzing the steps of these tasks. This is…

Planning of biorefinery operations is complicated by the stochastic nature of physical and chemical characteristics of biomass feedstock, such as, moisture level and carbohydrate content. Biomass characteristics affect the performance of…

Bat Algorithm (BA) is a nature-inspired metaheuristic search algorithm designed to efficiently explore complex problem spaces and find near-optimal solutions. The algorithm is inspired by the echolocation behavior of bats, which acts as a…

This paper describes and illustrates the functionality of the baker R package. The package estimates a suite of nested partially-latent class models (NPLCM) for multivariate binary responses that are observed under a case-control design.…

Bacterial growth environment strongly influences the efficacy of antibiotic treatment, with slow growth often being associated with decreased susceptibility. Yet in many cases the connection between antibiotic susceptibility and pathogen…

RESPACK is a first-principles calculation software for evaluating the interaction parameters of materials and is able to calculate maximally localized Wannier functions, response functions based on the random phase approximation and related…

The solution space of genome-scale models of cellular metabolism provides a map between physically viable flux configurations and cellular metabolic phenotypes described, at the most basic level, by the corresponding growth rates. By…

Bacterial colonies can form a wide variety of shapes and structures based on ambient and internal conditions. To help understand the mechanisms that determine the structure of and the diversity within these colonies, various numerical…

Particle accelerators play a pivotal role in advancing scientific research, yet optimizing beamline configurations to maximize particle transmission remains a labor-intensive task requiring expert intervention. In this work, we introduce…

Analyzing and effectively communicating the efficacy and toxicity of treatment is the basis of risk benefit analysis (RBA). More efficient and objective tools are needed. We apply Chauhan Weighted Trajectory Analysis (CWTA) to perform RBA…

RNA-seq has become a de facto standard for measuring gene expression. Traditionally, RNA-seq experiments are mathematically averaged -- they sequence the mRNA of individuals from different treatment groups, hoping to correlate phenotype…

Various rod-shaped bacteria such as the canonical gram negative Escherichia coli or the well-studied gram positive Bacillus subtilis divide symmetrically after they approximately double their volume. Their size at division is not constant,…

Stochastic partition models divide a multi-dimensional space into a number of rectangular regions, such that the data within each region exhibit certain types of homogeneity. Due to the nature of their partition strategy, existing partition…

Cell-free protein synthesis (CFPS) systems are an attractive to complement the usual cell-based synthesis of proteins, especially for screening approaches. The literature describes a wide variety of CFPS systems, but their performance is…