Related papers: A Tractable Logic for Molecular Biology
We develop a classical propositional logic for reasoning about combinatory logic. We define its syntax, axiomatic system and semantics. The syntax and axiomatic system are presented based on classical propositional logic, with typed…
Protein structure prediction and folding are fundamental to understanding biology, with recent deep learning advances reshaping the field. Diffusion-based generative models have revolutionized protein design, enabling the creation of novel…
While modal extensions of decidable fragments of first-order logic are usually undecidable, their monodic counterparts, in which formulas in the scope of modal operators have at most one free variable, are typically decidable. This only…
Metabolic networks, formed by a series of metabolic pathways, are made of intracellular and extracellular reactions that determine the biochemical properties of a cell, and by a set of interactions that guide and regulate the activity of…
Equilibrium logic is an approach to nonmonotonic reasoning that extends the stable-model and answer-set semantics for logic programs. In particular, it includes the general case of nested logic programs, where arbitrary Boolean combinations…
A logic is defined that allows to express information about statistical probabilities and about degrees of belief in specific propositions. By interpreting the two types of probabilities in one common probability space, the semantics given…
The purpose of this paper is to give an easy to understand with step-by-step explanation to allow interested people to fully appreciate the power of natural deduction for first-order logic. Natural deduction as a proof system can be used to…
Fiore and Hur recently introduced a conservative extension of universal algebra and equational logic from first to second order. Second-order universal algebra and second-order equational logic respectively provide a model theory and a…
Temporal logics over finite traces have recently seen wide application in a number of areas, from business process modelling, monitoring, and mining to planning and decision making. However, real-life dynamic systems contain a degree of…
Justification theory is a unifying framework for semantics of non-monotonic logics. It is built on the notion of a justification, which intuitively is a graph that explains the truth value of certain facts in a structure. Knowledge…
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…
This paper makes a first step towards a logic of learning from experiments. For this, we investigate formal frameworks for modeling the interaction of causal and (qualitative) epistemic reasoning. Crucial for our approach is the idea that…
We describe an approach for compiling preferences into logic programs under the answer set semantics. An ordered logic program is an extended logic program in which rules are named by unique terms, and in which preferences among rules are…
We define a family of intuitionistic non-normal modal logics; they can bee seen as intuitionistic counterparts of classical ones. We first consider monomodal logics, which contain only one between Necessity and Possibility. We then consider…
Mathematical methods provide useful framework for the analysis and design of complex systems. In newer contexts such as biology, however, there is a need to both adapt existing methods as well as to develop new ones. Using a combination of…
We extend the simply-typed guarded $\lambda$-calculus with discrete probabilities and endow it with a program logic for reasoning about relational properties of guarded probabilistic computations. This provides a framework for programming…
Pearl observes that causal knowledge enables predicting the effects of interventions, such as actions, whereas descriptive knowledge only permits drawing conclusions from observation. This paper extends Pearl's approach to causality and…
The emergence of tools based on artificial intelligence has also led to the need of producing explanations which are understandable by a human being. In most approaches, the system is considered a black box, making it difficult to generate…
Over the past few decades, non-monotonic reasoning has developed to be one of the most important topics in computational logic and artificial intelligence. Different ways to introduce non-monotonic aspects to classical logic have been…
Game semantics aim at describing the interactive behaviour of proofs by interpreting formulas as games on which proofs induce strategies. In this article, we introduce a game semantics for a fragment of first order propositional logic. One…