Related papers: Athena: Modular CAM/CAD Software for Synthetic Bio…
The application of Artificial Intelligence (AI) to synthetic biology will provide the foundation for the creation of a high throughput automated platform for genetic design, in which a learning machine is used to iteratively optimise the…
Mathematical models are increasingly used in both academia and the pharmaceutical industry to understand how phenotypes emerge from systems of molecular interactions. However, their current construction as monolithic sets of equations…
Epigenetic Tracking (ET) is an Artificial Embryology system which allows for the evolution and development of large complex structures built from artificial cells. In terms of the number of cells, the complexity of the bodies generated with…
NeuroAI is an emerging field at the intersection of neuroscience and artificial intelligence, where insights from brain function guide the design of intelligent systems. A central area within this field is synthetic biological intelligence…
In this paper, we explore relationships between two models of systems which are governed by only the local interactions of large collections of simple components: cellular automata (CA) and the abstract Tile Assembly Model (aTAM). While…
Dynamical systems are capable of performing computation in a reservoir computing paradigm. This paper presents a general representation of these systems as an artificial neural network (ANN). Initially, we implement the simplest dynamical…
Cellular automata are a class of computational models based on simple rules and algorithms that can simulate a wide range of complex phenomena. However, when using conventional computers, these 'simple' rules are only encapsulated at the…
Cellular research and development (R&D) is throttled by six structural processes that each consume months of manual engineering work per iteration: (i) synthesizing new features from standards or research papers into production code; (ii)…
With the advancement of synthetic biology, several new tools have been conceptualized over the years as alternative treatments for current medical procedures. Most of those applications are applied to various chronic diseases. This work…
We describe a hybrid agent-based model and simulation of urban morphogenesis. It consists of a cellular automata grid coupled to a dynamic network topology. The inherently heterogeneous properties of urban structure and function are taken…
The focus of this thesis is on the applications of nonlinear dynamical systems in bioengineering which are mainly used in large-scale and generally categorised into two groups: (1) dynamical systems from biology (2) dynamical systems for…
Many Embedded Systems are indeed Software Based Control Systems, that is control systems whose controller consists of control software running on a microcontroller device. This motivates investigation on Formal Model Based Design approaches…
Solving math word problems depends on how to articulate the problems, the lens through which models view human linguistic expressions. Real-world settings count on such a method even more due to the diverse practices of the same…
Scientific discovery can be modeled as a sequence of probabilistic decisions that map physical problems to numerical solutions. Recent agentic AI systems automate individual scientific tasks by orchestrating LLM-driven planners, solvers,…
Motivated by the need to emulate workload execution characteristics on high-performance and distributed heterogeneous resources, we introduce Synapse. Synapse is used as a proxy application (or "representative application") for real…
As computer scientists working in bioinformatics/computational biology, we often face the challenge of coming up with an algorithm to answer a biological question. This occurs in many areas, such as variant calling, alignment, and assembly.…
A central problem in systems biology is to identify parameter values such that a biological model satisfies some behavioral constraints (\eg, time series). In this paper we focus on parameter synthesis for hybrid (continuous/discrete)…
The automatic generation of computer programs is one of the main applications with practical relevance in the field of evolutionary computation. With program synthesis techniques not only software developers could be supported in their…
Computational models have emerged as powerful tools for multi-scale energy modeling research at the building and urban scale, supporting data-driven analysis across building and urban energy systems. However, these models require large…
Nearly all cell models explicitly or implicitly deal with the biophysical constraints that must be respected for life to persist. Despite this, there is almost no systematicity in how these constraints are implemented, and we lack a…