Related papers: A Tractable Logic for Molecular Biology
In this paper we explore the boundary between biology and the study of formal systems (logic). In the end, we arrive at a summary formalism, a chapter in "boundary mathematics" where there are not only containers <> but also extainers ><,…
Biological information processing as implemented by regulatory and signaling networks in living cells requires sufficient specificity of molecular interaction to distinguish signals from one another, but much of regulation and signaling…
Computational analysis of time-course data with an underlying causal structure is needed in a variety of domains, including neural spike trains, stock price movements, and gene expression levels. However, it can be challenging to determine…
We introduce a new family of temporal logics designed to finely balance the trade-off between expressivity and complexity. Their key feature is the possibility of defining operators of a new kind that we call transformation operators. Some…
A major issue in biology is the understanding of the interactions between proteins. These interactions can be described by a network, where the proteins are modeled by nodes and the interactions by edges. The origin of these protein…
Proof search has been used to specify a wide range of computation systems. In order to build a framework for reasoning about such specifications, we make use of a sequent calculus involving induction and co-induction. These proof principles…
We present a way to apply quantum logic to the study of quantum programs. This is made possible by using an extension of the usual propositional language in order to make transformations performed on the system appear explicitly. This way,…
A logic programming paradigm which expresses solutions to problems as stable models has recently been promoted as a declarative approach to solving various combinatorial and search problems, including planning problems. In this paradigm,…
Molecular dynamics simulations of folding in an off-lattice protein model reveal a nucleation scenario, in which a few well-defined contacts are formed with high probability in the transition state ensemble of conformations. Their…
Modular logic programs provide a way of viewing logic programs as consisting of many independent, meaningful modules. This paper introduces first-order modular logic programs, which can capture the meaning of many answer set programs. We…
Logic is playing an increasingly important role in the engineering of real-time, hybrid, and cyber-physical systems, but mostly in the form of posterior verification and high-level analysis. The core methodology in the design of real-world…
An inductive logic can be formulated in which the elements are not propositions or probability distributions, but information systems. The logic is complete for information systems with binary hypotheses, i.e., it applies to all such…
In this work we propose a multi-valued extension of logic programs under the stable models semantics where each true atom in a model is associated with a set of justifications, in a similar spirit than a set of proof trees. The main…
We provide a denotational semantics for first-order logic that captures the two-level view of the computation process typical for constraint programming. At one level we have the usual program execution. At the other level an automatic…
Argumentation problems are concerned with determining the acceptability of a set of arguments from their relational structure. When the available information is uncertain, probabilistic argumentation frameworks provide modelling tools to…
It is here proposed an analysis of symbolic and sub-symbolic models for studying cognitive processes, centered on emergence and logical openness notions.The Theory of Logical Openness connects the Physics of system/environment relationships…
The induction of a signaling pathway is characterized by transient complex formation and mutual posttranslational modification of proteins. To faithfully capture this combinatorial process in a mathematical model is an important challenge…
Recently, symbolic structures were proposed as finite representations of potentially infinite first-order structures, where Linear Integer Arithmetic terms and formulas define the domain and interpretations of a structure. We generalize…
Ontologies formalise how the concepts from a given domain are interrelated. Despite their clear potential as a backbone for explainable AI, existing ontologies tend to be highly incomplete, which acts as a significant barrier to their more…
Model theoretic results such as Characterization and Definability give important information about different logics. It is well known that the proofs of those results for several modal logics have, somehow, the same 'taste'. A general proof…