Related papers: Analog computation with transcriptional networks

Data mining and data classification over biomedical data are two of the most important research fields in computer science. Among the great diversity of techniques that can be used for this purpose, Artifical Neural Networks (ANNs) is one…

Transcription factor proteins bind specific DNA sequences to control the expression of genes. They contain DNA binding domains which belong to several super-families, each with a specific mechanism of DNA binding. The total number of…

Operations typically used in machine learning al-gorithms (e.g. adds and soft max) can be implemented bycompact analog circuits. Analog Application-Specific Integrated Circuit (ASIC) designs that implement these algorithms using techniques…

We take a fresh look at analogue-digital systems focussing on their physical behaviour. We model a general analogue-digital system as a physical process controlled by an algorithm by viewing the physical process as physical oracle to the…

Cells integrate signals and make decisions about their future state in short amounts of time. A lot of theoretical effort has gone into asking how to best design gene regulatory circuits that fulfill a given function, yet little is known…

Living cells must control the reading out or "expression" of information encoded in their genomes, and this regulation often is mediated by transcription factors--proteins that bind to DNA and either enhance or repress the expression of…

Biological processes, including cell differentiation, organism development, and disease progression, can be interpreted as attractors (fixed points or limit cycles) of an underlying networked dynamical system. In this paper, we study the…

This paper considers the problem of decentralized analysis and control synthesis to verify and ensure properties like stability and dissipativity of a large-scale networked system comprised of linear subsystems interconnected in an…

Transformationally invariant processors constructed by transformed input vectors or operators have been suggested and applied to many applications. In this study, transformationally identical processing based on combining results of all…

Analog electrical networks have long been investigated as energy-efficient computing platforms for machine learning, leveraging analog physics during inference. More recently, resistor networks have sparked particular interest due to their…

We define all-to-all encode, a collective communication operation serving as a primitive in decentralized computation and storage systems. Consider a scenario where every processor initially has a data packet and requires a linear…

Logic Programming languages and combinational circuit synthesis tools share a common "combinatorial search over logic formulae" background. This paper attempts to reconnect the two fields with a fresh look at Prolog encodings for the…

To survive environmental conditions, cells transcribe their response activities into encoded mRNA sequences in order to produce certain amounts of protein concentrations. The external conditions are mapped into the cell through the…

Computer networks are hard to manage. Given a set of high-level requirements (e.g., reachability, security), operators have to manually figure out the individual configuration of potentially hundreds of devices running complex distributed…

Organisms are equipped with regulatory systems that display a variety of dynamical behaviours ranging from simple stable steady states, to switching and multistability, to oscillations. Earlier work has shown that oscillations in protein…

With the increasing amount of experimental data on gene expression and regulation, there is a growing need for quantitative models to describe the data and relate them to the different contexts. The thermodynamic models reviewed in the…

For cellular biochemical reaction systems where the numbers of molecules is small, significant noise is associated with chemical reaction events. This molecular noise can give rise to behavior that is very different from the predictions of…

This paper investigates the application of the transformer architecture in protein folding, as exemplified by DeepMind's AlphaFold project, and its implications for the understanding of so-called large language models. The prevailing…

Living organisms must respond to environmental changes. Generally, accurate and rapid responses are provided by simple, unidirectional networks that connect inputs with outputs. Besides accuracy and speed, biological responses should also…

The engineered control of cellular function through the design of synthetic genetic networks is becoming plausible. Here we show how a naturally occurring network can be used as a parts list for artificial network design, and how model…