Related papers: Automated generation of bacterial resource allocat…
We describe the R package acebayes and demonstrate its use to find Bayesian optimal experimental designs. A decision-theoretic approach is adopted, with the optimal design maximising an expected utility. Finding Bayesian optimal designs for…
Physiological changes which result in changes in bacterial gene expression are often accompanied by changes in the growth rate for fast adapting enteric bacteria. Since the availability of RNA polymerase (RNAP) in cells is dependent on the…
We describe the development of a new toolkit for data analysis. The analysis package is based on Bayes' Theorem, and is realized with the use of Markov Chain Monte Carlo. This gives access to the full posterior probability distribution.…
Nested data structures arise when observations are grouped into distinct units, such as patients within hospitals or students within schools. Accounting for this hierarchical organization is essential for valid inference, as ignoring it can…
Optimal resource allocation is gaining a renewed interest due its relevance as a core problem in managing, over time, cloud and high-performance computing facilities. Semi-Bandit Feedback (SBF) is the reference method for efficiently…
Observational studies are often conducted to estimate causal effects of treatments or exposures on event-time outcomes. Since treatments are not randomized in observational studies, techniques from causal inference are required to adjust…
Self-monitoring of blood glucose (SMBG) and continuous glucose monitoring (CGM) are commonly used by type 1 diabetes (T1D) patients to measure glucose concentrations. The proposed adaptive basal-bolus algorithm (ABBA) supports inputs from…
Analytical join queries over unstructured data are increasingly prevalent in data analytics. Applying machine learning (ML) models to label every pair in the cross product of tables can achieve state-of-the-art accuracy, but the cost of…
Dormancy is an essential strategy for microorganisms to cope with environmental stress. However, global ecosystem models typically ignore microbial dormancy, resulting in major model uncertainties. To facilitate the consideration of…
To improve accuracy and speed of regressions and classifications, we present a data-based prediction method, Random Bits Regression (RBR). This method first generates a large number of random binary intermediate/derived features based on…
Bat algorithm (BA) is a recent optimization algorithm based on swarm intelligence and inspiration from the echolocation behavior of bats. One of the issues in the standard bat algorithm is the premature convergence that can occur due to the…
Protein distributions measured under a broad set of conditions in bacteria and yeast were shown to exhibit a common skewed shape, with variances depending quadratically on means. For bacteria these properties were reproduced by temporal…
Big data sets must be carefully partitioned into statistically similar data subsets that can be used as representative samples for big data analysis tasks. In this paper, we propose the random sample partition (RSP) data model to represent…
We present an approach for flux analysis in process algebra models of biological systems. We perceive flux as the flow of resources in stochastic simulations. We resort to an established correspondence between event structures, a broadly…
Production of chemicals from engineered organisms in a batch culture involves an inherent trade-off between productivity, yield, and titer. Existing strategies for strain design typically focus on designing mutations that achieve the…
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 cycle of scientific discovery is frequently bottlenecked by the slow, manual creation of software to support computational experiments\cite{hannay2009how}. To address this, we present Empirical Research Assistance (ERA), an AI system…
Task-based programming models are emerging as a promising alternative to make the most of multi-/many-core systems. These programming models rely on runtime systems, and their goal is to improve application performance by properly…
Erythropoiesis is a mechanism for the production of red blood cells by cellular differentiation. It is based on amplification steps due to an interplay between renewal and differentiation in the successive cell compartments from stem cells…
Two fundamental research tasks in science and engineering are forward predictions and data inversion. This article introduces a recent R package RobustCalibration for Bayesian data inversion and model calibration by experiments and field…