Related papers: Experimental Biological Protocols with Formal Sema…
Automation is becoming ubiquitous in all laboratory activities, leading towards precisely defined and codified laboratory protocols. However, the integration between laboratory protocols and mathematical models is still lacking. Models…
Self-driving laboratories have begun to replace human experimenters in performing single experimental skills or predetermined experimental protocols. However, as the pace of idea iteration in scientific research has been intensified by…
Recent development in Artificial Intelligence (AI) models has propelled their application in scientific discovery, but the validation and exploration of these discoveries require subsequent empirical experimentation. The concept of…
Stochasticity is a key characteristic of intracellular processes such as gene regulation and chemical signalling. Therefore, characterising stochastic effects in biochemical systems is essential to understand the complex dynamics of living…
Probabilistic inference provides a language for describing how organisms may learn from and adapt to their environment. The computations needed to implement probabilistic inference often require specific representations, akin to having the…
We define a class of probabilistic models in terms of an operator algebra of stochastic processes, and a representation for this class in terms of stochastic parameterized grammars. A syntactic specification of a grammar is mapped to…
Stochastic processes offer a flexible mathematical formalism to model and reason about systems. Most analysis tools, however, start from the premises that models are fully specified, so that any parameters controlling the system's dynamics…
Biological systems typically involve large numbers of components with complex, highly parallel interactions and intrinsic stochasticity. To model this complexity, numerous programming languages based on process calculi have been developed,…
Automating science laboratories enables faster, safer, more accurate, and more reproducible execution of protocols, accelerating the discovery and testing of new materials, drugs, and more. However, setting up and running autonomous labs…
Formal semantics provides rigorous, mathematically precise definitions of programming languages, with which we can argue about program behaviour and program equivalence by formal means; in particular, we can describe and verify our…
The ability to automatically generate accurate protocols for scientific experiments would represent a major step towards the automation of science. Large Language Models (LLMs) have impressive capabilities on a wide range of tasks, such as…
Stochastic simulation can make the molecular processes of cellular control more vivid than the traditional differential-equation approach by generating typical system histories instead of just statistical measures such as the mean and…
Context: The Evidence-Based Software Engineering (EBSE) paradigm and the planning phase of a systematic literature review. Objective: A protocol to do a systematic literature review with detailed information about the processes suggested by…
Declarative modeling uses symbolic expressions to represent models. With such expressions one can formalize high-level mathematical computations on models that would be difficult or impossible to perform directly on a lower-level simulation…
Modern experimental platforms such as particle accelerators, fusion devices, telescopes, and industrial process control systems expose tens to hundreds of thousands of control and diagnostic channels accumulated over decades of evolution.…
We begin by reviewing a technique to approximate the dynamics of stochastic programs --written in a stochastic process algebra-- by a hybrid system, suitable to capture a mixed discrete/continuous evolution. In a nutshell, the discrete…
Surgical procedures are often not "standardised" (i.e., defined in a unique and unambiguous way), but rather exist as implicit knowledge in the minds of the surgeon and the surgical team. This reliance extends to pre-surgery planning and…
This paper introduces a simple formalism for dealing with deterministic, non- deterministic and stochastic cellular automata in an unified and composable manner. This formalism allows for local probabilistic correlations, a feature which is…
Synchronous languages rely on formal methods to ease the development of applications in an efficient and reusable way. Formal methods have been advocated as a means of increasing the reliability of systems, especially those which are safety…
We present a method for logical specification of the behavior of a system based on the specification of its components and for representing and specifying the effect of a class of communication "signaling pathways" among them. Variations in…