Related papers: Regulated Multiset Rewriting Systems
Neuromorphic control is receiving growing attention due to the multifaceted advantages it brings over more classical control approaches, including: sparse and on-demand sensing, information transmission, and actuation; energy-efficient…
We study the termination problem for probabilistic term rewrite systems. We prove that the interpretation method is sound and complete for a strengthening of positive almost sure termination, when abstract reduction systems and term rewrite…
Context: Refactoring is the art of modifying the design of a system without altering its behavior. The idea is to reorganize variables, classes and methods to facilitate their future adaptations and comprehension. As the concept of behavior…
Synthetic biology is a recent area of biological engineering, whose aim is to provide cells with novel functionalities. A number of important results regarding the development of control circuits in synthetic biology have been achieved…
Monotone systems constitute one of the most important classes of dynamical systems used in mathematical biology modeling. The objective of this paper is to extend the notion of monotonicity to systems with inputs and outputs, a necessary…
Can language models read biomedical texts and explain the biomedical mechanisms discussed? In this work we introduce a biomedical mechanism summarization task. Biomedical studies often investigate the mechanisms behind how one entity (e.g.,…
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…
Robotic systems are multi-dimensional entities, combining both hardware and software, that are heavily dependent on, and influenced by, interactions with the real world. They can be variously categorised as embedded, cyberphysical,…
Multisets are an intuitive extension of the traditional concept of sets that allow repetition of elements, with the number of times each element appears being understood as the respective multiplicity. Recent generalizations of multisets to…
We show that biological networks with serial regulation (each node regulated by at most one other node) are constrained to {\it direct functionality}, in which the sign of the effect of an environmental input on a target species depends…
We show in this paper how managed multi-context systems (mMCSs) can be turned into a reactive formalism suitable for continuous reasoning in dynamic environments. We extend mMCSs with (abstract) sensors and define the notion of a run of the…
Regulatory networks (RNs) are a well-accepted modelling formalism in computational systems biology. The control of RNs is currently receiving a lot of attention because it provides a computational basis for cell reprogramming -- an…
In this paper we present a formal framework for analysis and optimisation of the requirements specifications of systems developed to apply in several countries. As different countries typically have different regulations/laws as well as…
We recently presented the so-called allagmatic method, which includes a system metamodel providing a framework for describing, modelling, simulating, and interpreting complex systems. Its development and programming was guided by…
The multifarious internal workings of organisms are difficult to reconcile with a single feature defining a state of being alive. Indeed, definitions of life rely on emergent properties (growth, capacity to evolve, agency) only symptomatic…
Recent studies have shown that the majority of published computational models in systems biology and physiology are not repeatable or reproducible. There are a variety of reasons for this. One of the most likely reasons is that given how…
Regulatory functions are essential in both socioeconomic and biological systems, from corporate managers to regulatory genes. Regulatory functions come with substantial costs and benefits, and the balance of the two is often taken for…
Neural controllable text generation is an important area gaining attention due to its plethora of applications. Although there is a large body of prior work in controllable text generation, there is no unifying theme. In this work, we…
Counterfactuals are a concept inherited from the field of logic and in general attain to the existence of causal relations between sentences or events. In particular, this concept has been introduced also in the context of interpretability…
Gene Regulatory Networks are networks of interactions in biological organisms responsible for determining the production levels of proteins and peptides. Proteins are workers of a cell factory, and their production defines the goal of a…