Related papers: Using biochemical circuits to approximately comput…
We consider the general problem of describing the dynamics of subnetworks of larger biochemical reaction networks, e.g. protein interaction networks involving complex formation and dissociation reactions. We propose the use of model…
Many studies have been performed to characterize the dynamics and stability of the microbiome across a range of environmental contexts [Costello et al., 2012, Faust et al., 2015]. For example, it is often of interest to identify time…
Unexpected stimuli induce "error" or "surprise" signals in the brain. The theory of predictive coding promises to explain these observations in terms of Bayesian inference by suggesting that the cortex implements variational inference in a…
Phenotypic variability in a population of cells can work as the bet-hedging of the cells under an unpredictably changing environment, the typical example of which is the bacterial persistence. To understand the strategy to control such…
The bioinformatical methods to detect lateral gene transfer events are mainly based on functional coding DNA characteristics. In this paper, we propose the use of DNA traits not depending on protein coding requirements. We introduce several…
Stochastic switching circuits are relay circuits that consist of stochastic switches called pswitches. The study of stochastic switching circuits has widespread applications in many fields of computer science, neuroscience, and…
The present manuscript studies signal detection by likelihood ratio tests in a number of spiked random matrix models, including but not limited to Gaussian mixtures and spiked Wishart covariance matrices. We work directly with multi-spiked…
We consider the problem of sequential signal detection in a multichannel system where the number and location of signals is a priori unknown. We assume that the data in each channel are sequentially observed and follow a general non-i.i.d.…
Implementing Boolean functions with circuits consisting of logic gates is fundamental in digital computer design. However, the implemented circuit must be exactly equivalent, which hinders generative neural approaches on this task due to…
We consider a lognormal diffusion process having a multisigmoidal logistic mean, useful to model the evolution of a population which reaches the maximum level of the growth after many stages. Referring to the problem of statistical…
Stochastic modeling and simulation provide powerful predictive methods for the intrinsic understanding of fundamental mechanisms in complex biochemical networks. Typically, such mathematical models involve networks of coupled jump…
Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. Delineating recombination events is important in the study of molecular evolution, as inference of such events provides a clearer…
Living organisms process information without any central control unit and without any ruling clock. We have been studying a novel computational strategy that uses a geometrically arranged excitable field, i.e., "field computation." As an…
Persistent currents in annular geometries have played an important role in disclosing the quantum phase coherence of superconductors and mesoscopic electronic systems. Ultracold atomic gases in multiply connected traps also exhibit…
Due to significant manufacturing process variations, the performance of integrated circuits (ICs) has become increasingly uncertain. Such uncertainties must be carefully quantified with efficient stochastic circuit simulators. This paper…
With the development of high throughput sequencing technology, it becomes possible to directly analyze mutation distribution in a genome-wide fashion, dissociating mutation rate measurements from the traditional underlying assumptions.…
A common goal in modern biostatistics is to form a biomarker signature from high dimensional gene expression data that is predictive of some outcome of interest. After learning this biomarker signature, an important question to answer is…
Gene expression in response to stimuli is regulated by transcription factors (TFs) through feedback loop motifs, aimed at maintaining the desired TF concentration despite uncertainties and perturbations. In this work, we consider a…
Resistance to therapy remains a significant challenge in cancer treatment, often due to the presence of a stem-like cell population that drives tumor recurrence post-treatment. Moreover, many anticancer therapies induce plasticity,…
Biochemical reaction networks in living cells usually involve reversible covalent modification of signaling molecules, such as protein phosphorylation. Under conditions of small molecule numbers, as is frequently the case in living cells,…