Related papers: A Tractable Logic for Molecular Biology
In this paper, we study an extension of the stable model semantics for disjunctive logic programs where each true atom in a model is associated with an algebraic expression (in terms of rule labels) that represents its justifications. As in…
The development of logic has largely been through the 'deductive' paradigm: conclusions are inferred from established premisses. However, the use of logic in the context of both human and machine reasoning is typically through the dual…
Proteins are essential macromolecules defined by their amino acid sequences, which determine their three-dimensional structures and, consequently, their functions in all living organisms. Therefore, generative protein modeling necessitates…
The protein folding problem has attracted an increasing attention from physicists. The problem has a flavor of statistical mechanics, but possesses the most common feature of most biological problems -- the profound effects of evolution. I…
Communicating transactions is a form of distributed, non-isolated transactions which provides a simple construct for building concurrent systems. In this paper we develop a logical framework to express properties of the observable behaviour…
Formal logic has often been seen as uniquely placed to analyze mathematical argumentation. While formal logic is certainly necessary for a complete understanding of mathematical practice, it is not sufficient. Important aspects of…
We explore a fuzzy modal logic that can formalise probabilistic reasoning about actions and knowledge. In particular, we deal with contexts involving statements about events expressed via modal formulas, e.g., "after doing $a$, the…
We describe here a simple application of rational trees to the implementation of an interpreter for a procedural language written in a logic programming language. This is possible in languages designed to support rational trees (such as…
Biological organisms are composed of numerous interconnected biochemical processes. Diseases occur when normal functionality of these processes is disrupted. Thus, understanding these biochemical processes and their interrelationships is a…
Many semantical aspects of programming languages, such as their operational semantics and their type assignment calculi, are specified by describing appropriate proof systems. Recent research has identified two proof-theoretic features that…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
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…
This papers develops a logical language for representing probabilistic causal laws. Our interest in such a language is twofold. First, it can be motivated as a fundamental study of the representation of causal knowledge. Causality has an…
Compositional Explanations is a method for identifying logical formulas of concepts that approximate the neurons' behavior. However, these explanations are linked to the small spectrum of neuron activations (i.e., the highest ones) used to…
Non-normal modal logics, interpreted on neighbourhood models which generalise the usual relational semantics, have found application in several areas, such as epistemic, deontic, and coalitional reasoning. We present here preliminary…
Characteristic formulae give a complete logical description of the behaviour of processes modulo some chosen notion of behavioural semantics. They allow one to reduce equivalence or preorder checking to model checking, and are exactly the…
Classical higher-order logic, when utilized as a meta-logic in which various other (classical and non-classical) logics can be shallowly embedded, is well suited for realising a universal logic reasoning approach. Universal logic reasoning…
The paper introduces a new modular action language, ALM, and illustrates the methodology of its use. It is based on the approach of Gelfond and Lifschitz (1993; 1998) in which a high-level action language is used as a front end for a logic…
Nonmonotonic logics are usually characterized by the presence of some notion of 'conditional' that fails monotonicity. Research on nonmonotonic logics is therefore largely concerned with the defeasibility of argument forms and the…
Rational word languages can be defined by several equivalent means: finite state automata, rational expressions, finite congruences, or monadic second-order (MSO) logic. The robust subclass of aperiodic languages is defined by: counter-free…