Related papers: Constrained Allocation Flux Balance Analysis
The Bayesian approach to feature extraction, known as factor analysis (FA), has been widely studied in machine learning to obtain a latent representation of the data. An adequate selection of the probabilities and priors of these bayesian…
Cooperative coevolution (CC) has shown great potential in solving large scale optimization problems (LSOPs). However, traditional CC algorithms often waste part of computation resource (CR) as they equally allocate CR among all the…
One important problem in microbiome analysis is to identify the bacterial taxa that are associated with a response, where the microbiome data are summarized as the composition of the bacterial taxa at different taxonomic levels. This paper…
The expansion of biological species in natural environments is usually described as the combined effect of individual spatial dispersal and growth. In the case of aquatic ecosystems flow transport can also be extremely relevant as an extra,…
Protein synthesis is an important determinant of microbial growth and response that demands a high amount of metabolic and biosynthetic resources. Despite these costs, microbial species from different taxa and habitats massively synthesize…
Due to its implication in cancer treatment, the Warburg Effect has received extensive in silico investigation. Flux Balance Analysis (FBA), based on constrained optimization, was successfully applied in the Warburg Effect modelling. Yet,…
We consider the problem of inferring the probability distribution of flux configurations in metabolic network models from empirical flux data. For the simple case in which experimental averages are to be retrieved, data are described by a…
Flow and diffusion models achieve high-fidelity, high-resolution image synthesis, but often require many function evaluations (NFEs) at sampling time. Existing acceleration methods either require additional training through distillation or…
The function of biomolecules such as proteins depends on their ability to interconvert between a wide range of structures or "conformations." Researchers have endeavored for decades to develop computational methods to predict the…
Nutrient gradients and limitations play a pivotal role in the life of all microbes, both in their natural habitat as well as in artificial, microfluidic systems. Spatial concentration gradients of nutrients in densely packed cell…
Many organisms repartition their proteome in a circadian fashion in response to the daily nutrient changes in their environment. A striking example is provided by cyanobacteria, which perform photosynthesis during the day to fix carbon.…
Stochastic optimization finds a wide range of applications in operations research and management science. However, existing stochastic optimization techniques usually require the information of random samples (e.g., demands in the…
Identifying genetic interactions for a given microorganism such as yeast is difficult. Quantitative Fitness Analysis (QFA) is a high-throughput experimental and computational methodology for quantifying the fitness of microbial cultures.…
The target of inference in microbiome analyses is usually relative abundance (RA) because RA in a sample (e.g., stool) can be considered as an approximation of RA in an entire ecosystem (e.g., gut). However, inference on RA suffers from the…
The regulation of metabolic activity by tuning enzyme expression levels is crucial to sustain cellular growth in changing environments. Metabolic networks are often studied at steady state using constraint-based models and optimization…
Phylogenetic comparative methods explore the relationships between quantitative traits adjusting for shared evolutionary history. This adjustment often occurs through a Brownian diffusion process along the branches of the phylogeny that…
To leverage data and computation capabilities of mobile devices, machine learning algorithms are deployed at the network edge for training artificial intelligence (AI) models, resulting in the new paradigm of edge learning. In this paper,…
Motivation: Flux balance analysis, and its variants, are widely used methods for predicting steady-state reaction rates in biochemical reaction networks. The exploration of high dimensional networks with such methods is currently hampered…
Accurate quantification of intracellular metabolic fluxes is central to systems biology and biotechnology. Flux estimation relies on biochemical network models, with $^{13}$C metabolic flux analysis (MFA) being the state-of-the-art…
Metagenomics has revealed hundreds of bacterial species in almost all microbiota. In a few well-studied cases, bacterial communities have been observed to coordinate their metabolic fluxes. In principle, bacteria can divide tasks to reap…