相关论文: Attenuation Regulation as a Term Rewriting System
DNA methylation is usually treated as an epigenetic memory mark: transcriptional history is written into regulatory DNA and later stabilizes a chosen cell identity. This picture explains persistence, but it makes memory passive. Here we…
Reconstruction of gene regulatory networks is the process of identifying gene dependency from gene expression profile through some computation techniques. In our human body, though all cells pose similar genetic material but the activation…
Regular expressions are pervasive in modern systems. Many real-world regular expressions are inefficient, sometimes to the extent that they are vulnerable to complexity-based attacks, and while much research has focused on detecting…
A theory is developed which uses "networks" (directed acyclic graphs with some extra structure) as a formalism for expressions in multilinear algebra. It is shown that this formalism is valid for arbitrary PROPs (short for 'PROducts and…
The primary aim of automated performance improvement is to reduce the running time of programs while maintaining (or improving on) functionality. In this paper, Genetic Programming is used to find performance improvements in regular…
Binarization of gene expression data is a \textbf{critical prerequisite} for the synthesis of Boolean gene regulatory network (GRN) models from omics datasets. Because Boolean networks encode gene activity as binary variables, the accuracy…
Formulating an effective constraint model of a parameterised problem class is crucial to the efficiency with which instances of the class can subsequently be solved. It is difficult to know beforehand which of a set of candidate models will…
We propose a methodology for the identification of transcription factors involved in the deregulation of genes in tumoral cells. This strategy is based on the inference of a reference gene regulatory network that connects transcription…
We study an alternative model of infinitary term rewriting. Instead of a metric on terms, a partial order on partial terms is employed to formalise convergence of reductions. We consider both a weak and a strong notion of convergence and…
A deep generative model such as a GAN learns to model a rich set of semantic and physical rules about the target distribution, but up to now, it has been obscure how such rules are encoded in the network, or how a rule could be changed. In…
DNA amplification is the process of replication of a specified DNA sequence \emph{in vitro} through time-dependent manipulation of its external environment. A theoretical framework for determination of the optimal dynamic operating…
The advent of new experimental genomic technologies and the massive increase of DNA sequence information is helping researchers better understand how our genes work. Recently, experiments on mRNA abundance (gene expression) have revealed…
There are many evaluation strategies for term rewrite systems, but automatically proving termination or analyzing complexity is usually easiest for innermost rewriting. Several syntactic criteria exist when innermost termination implies…
A method based on Bayesian neural networks and genetic algorithm is proposed to control the fermentation process. The relationship between input and output variables is modelled using Bayesian neural network that is trained using hybrid…
Inference of gene regulatory networks has been an active area of research for around 20 years, leading to the development of sophisticated inference algorithms based on a variety of assumptions and approaches. With the always increasing…
While a mature body of work supports the study of rewriting systems, abstract tools for Probabilistic Rewriting are still limited. In this paper we study the question of uniqueness of the result (unique limit distribution), and develop a…
We propose a generic termination proof method for rewriting under strategies, based on an explicit induction on the termination property. Rewriting trees on ground terms are modeled by proof trees, generated by alternatively applying…
In this paper we examine a number of term rewriting system for integer number representations, building further upon the datatype defining systems described in [2]. In particular, we look at automated methods for proving confluence and…
Recently, microRNAs (miRNAs) have emerged as central posttranscriptional regulators of gene expression. miRNAs regulate many key biological processes, including cell growth, death, development and differentiation. This discovery is…
Various control schemes rely on a solution of a convex optimization problem involving a particular robust quadratic constraint, which can be reformulated as a linear matrix inequality using the well-known $\mathcal{S}$-lemma. However, the…