Related papers: Constrained Allocation Flux Balance Analysis
Balancing influential covariates is crucial for valid treatment comparisons in clinical studies. While covariate-adaptive randomization is commonly used to achieve balance, its performance can be inadequate when the number of baseline…
This article is concerned with the mathematical analysis of a family of adaptive importance sampling algorithms applied to diffusion processes. These methods, referred to as Adaptive Biasing Potential methods, are designed to efficiently…
Recent studies have demonstrated that learned Bloom filters, which combine machine learning with the classical Bloom filter, can achieve superior memory efficiency. However, existing learned Bloom filters face two critical unresolved…
Microalgae are an important source of precursors (e.g. lipids) for a variety of biosynthetic processes (e.g. biofuel production). Their co-culturing with other organisms providing essential substrates for growth may reduce cost and provide…
Metabolic heterogeneity is widely recognised as the next challenge in our understanding of non-genetic variation. A growing body of evidence suggests that metabolic heterogeneity may result from the inherent stochasticity of intracellular…
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…
Discrete data such as counts of microbiome taxa resulting from next-generation sequencing are routinely encountered in bioinformatics. Taxa count data in microbiome studies are typically high-dimensional, over-dispersed, and can only reveal…
We propose the covariate-balanced-and-adjusted response-adaptive randomization (CBARA) procedure for adaptive design in clinical trials, which integrates the complementary strengths of covariate-adjusted response-adaptive randomization…
In order to grow in any given environment, bacteria need to collect information about the medium composition and implement suitable growth strategies by adjusting their regulatory and metabolic degrees of freedom. In the standard sense,…
The life of a cell is governed by highly dynamical microscopic processes. Two notable examples are the diffusion of membrane receptors and the kinetics of transcription factors governing the rates of gene expression. Different fluorescence…
Evolutionary algorithms have been frequently applied to constrained continuous optimisation problems. We carry out feature based comparisons of different types of evolutionary algorithms such as evolution strategies, differential evolution…
A hallmark of bacterial populations cultured in vitro is their homogeneity of growth, where the majority of cells display identical growth rate, cell size and content. Recent insights, however, have revealed that even cells growing in…
Ecological and evolutionary dynamics have been historically regarded as unfolding at broadly separated timescales. However, these two types of processes are nowadays well documented to much more tightly than traditionally assumed,…
Biomolecular machines consume free energy to break symmetry and make directed progress. Nonequilibrium ATP concentrations are the typical free energy source, with one cycle of a molecular machine consuming a certain number of ATP, providing…
A new implementation of an adiabatically-trained ensemble model is derived that shows significant improvements over classical methods. In particular, empirical results of this new algorithm show that it offers not just higher performance,…
We present the results of a numerical study, with 20 qubits, of the performance of the Quantum Adiabatic Algorithm on randomly generated instances of MAX 2-SAT with a unique assignment that maximizes the number of satisfied clauses. The…
A Bayesian feature allocation model (FAM) is presented for identifying cell subpopulations based on multiple samples of cell surface or intracellular marker expression level data obtained by cytometry by time of flight (CyTOF). Cell…
Part I of this work [2] developed the exact diffusion algorithm to remove the bias that is characteristic of distributed solutions for deterministic optimization problems. The algorithm was shown to be applicable to a larger set of…
Predicting protein properties, functions and localizations are important tasks in bioinformatics. Recent progress in machine learning offers an opportunities for improving existing methods. We developed a new approach called ProtBoost,…
Enzyme costs play a major role in the choice of metabolic routes, both in evolution and bioengineering. Given desired fluxes, necessary enzyme levels can be estimated based on known rate laws and on a principle of minimal enzyme cost. With…