Related papers: Proofs of life: molecular-biology reasoning simula…

We propose a novel approach for the formal verification of biological systems based on the use of a modal linear logic. We show how such a logic can be used, with worlds as instants of time, as an unified framework to encode both biological…

We design a proof system for propositional classical logic that integrates two languages for Boolean functions: standard conjunction-disjunction-negation and binary decision trees. We give two reasons to do so. The first is…

Cells with the same genome can exist in different phenotypes. and can change between distinct phenotypes when subject to specific stimuli and microenvironments. Some examples include cell differentiation during development, reprogramming…

This series presents an approach to mathematical biology which makes precise the function of biological molecules. Because biological systems compute, the theory is a general purpose computer language. I build a language for efficiently…

Understanding how genotypes map onto phenotypes, fitness, and eventually organisms is arguably the next major missing piece in a fully predictive theory of evolution. We refer to this generally as the problem of the genotype-phenotype map.…

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…

Structural proof theory is praised for being a symbolic approach to reasoning and proofs, in which one can define schemas for reasoning steps and manipulate proofs as a mathematical structure. For this to be possible, proof systems must be…

We advocate here the use of computational logic for systems biology, as a \emph{unified and safe} framework well suited for both modeling the dynamic behaviour of biological systems, expressing properties of them, and verifying these…

Recent research has extended methods from the fields of thermodynamics and statistical mechanics into other disciplines. Most notably, one recent work creates a unified theoretical framework to understand evolutionary biology, machine…

Molecular phenotypes are important links between genomic information and organismic functions, fitness, and evolution. Complex phenotypes, which are also called quantitative traits, often depend on multiple genomic loci. Their evolution…

We introduce a logic for knowledge representation and reasoning on protein-protein interactions. Modulo a theory, formulas describe protein structures and dynamic changes. They can be composed in order to add or remove static and dynamic…

This paper develops an algorithmic-based approach for proving inductive properties of propositional sequent systems such as admissibility, invertibility, cut-elimination, and identity expansion. Although undecidable in general, these…

We study induction on the program structure as a proof method for bisimulation-based compiler correctness. We consider a first-order language with mutually recursive function definitions, system calls, and an environment semantics. The…

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…

While model checking has often been considered as a practical alternative to building formal proofs, we argue here that the theory of sequent calculus proofs can be used to provide an appealing foundation for model checking. Since the…

In this paper we will try to provide a formalization of some characteristics of the development of biological systems aiming at the highest level of adequacy: justificative adequacy, that is, not only what we observe (descriptive adequacy)…

In this study, we provide a relatively simple simulation framework for constructing artificial life (ALife) with both autonomous and evolutionary aspects by extending chemoton model. While the original chemoton incorporates metabolism,…

We present a framework to formally describe probabilistic system behavior and symbolically reason about it. In particular we aim at reasoning about possible failures and fault tolerance. We regard systems which are composed of different…

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…

Phenotypically structured equations arise in population biology to describe the interaction of species with their environment that brings the nutrients. This interaction usually leads to selection of the fittest individuals. Models used in…