Related papers: A Tractable Logic for Molecular Biology
There is a growing need for abstractions in logic specification languages such as FO(.) and ASP. One technique to achieve these abstractions are templates (sometimes called macros). While the semantics of templates are virtually always…
How we choose to represent our data has a fundamental impact on our ability to subsequently extract information from them. Machine learning promises to automatically determine efficient representations from large unstructured datasets, such…
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…
Logics of limited belief aim at enabling computationally feasible reasoning in highly expressive representation languages. These languages are often dialects of first-order logic with a weaker form of logical entailment that keeps reasoning…
The formal construction of the second-order logic or predicate calculus essentially adds quantifiers to propositional logic. Why second-order logic cannot be reduced to that of the first order? How to demonstrate that certain predicates are…
Information processing and decision making is based upon logic operations, which in cellular networks has been well characterized at the level of transcription. In recent years however, both experimentalists and theorists have begun to…
We study two extensions of FO2[<], first-order logic interpreted in finite words, in which formulas are restricted to use only two variables. We adjoin to this language two-variable atomic formulas that say, "the letter $a$ appears between…
This paper presents matching logic, a first-order logic (FOL) variant for specifying and reasoning about structure by means of patterns and pattern matching. Its sentences, the patterns, are constructed using variables, symbols, connectives…
The 21st century is presenting humankind with unprecedented environmental and medical challenges. The ability to design novel proteins tailored for specific purposes could transform our ability to respond timely to these issues. Recent…
Semantics of logic programs has been given by proof theory, model theory and by fixpoint of the immediate-consequence operator. If clausal logic is a programming language, then it should also have a compositional semantics. Compositional…
We analyse so-called computable laws, i.e., laws that can be enforced by automatic procedures. These laws should be logically perfect and unambiguous, but sometimes they are not. We use a regulation on road transport to illustrate this…
We regard explanations as a blending of the input sample and the model's output and offer a few definitions that capture various desired properties of the function that generates these explanations. We study the links between these…
We introduce a new logic that combines Adjoint Logic with Graded Necessity Modalities. This results in a very expressive system capable of controlling when and how structural rules are used. We give a sequent calculus, natural deduction,…
Robotic cell injection is used for automatically delivering substances into a cell and is an integral component of drug development, genetic engineering and many other areas of cell biology. Traditionally, the correctness of functionality…
The molecular computing has been successfully employed to solve more and more complex computation problems. However, as an important complex problem, the model checking are still far from fully resolved under the circumstance of molecular…
Drug discovery aims to find novel compounds with specified chemical property profiles. In terms of generative modeling, the goal is to learn to sample molecules in the intersection of multiple property constraints. This task becomes…
The internal dynamics of strongly interacting systems and that of biomolecules such as proteins display several important analogies, despite the huge difference in their characteristic energy and length scales. For example, in all such…
Adjoint logic is a general approach to combining multiple logics with different structural properties, including linear, affine, strict, and (ordinary) intuitionistic logics, where each proposition has an intrinsic mode of truth. It has…
A logic program is an executable specification. For example, merge sort in pure Prolog is a logical formula, yet shows creditable performance on long linked lists. But such executable specifications are a compromise: the logic is distorted…
For any first order theory T we construct a Boolean valued model M, in which precisely the T--provable formulas hold, and in which every (Boolean valued) subset which is invariant under all automorphisms of M is definable by a first order…