Related papers: A Tractable Logic for Molecular Biology
Metabolism displays striking and robust regularities in the forms of modularity and hierarchy, whose composition may be compactly described. This renders metabolic architecture comprehensible as a system, and suggests the order in which…
Distributed representations (such as those based on embeddings) and discrete representations (such as those based on logic) have complementary strengths. We explore one possible approach to combining these two kinds of representations. We…
Justification logics are modal-like logics with the additional capability of recording the reason, or justification, for modalities in syntactic structures, called justification terms. Justification logics can be seen as explicit…
We axiomatize the molecular-biology reasoning style, show compliance of the standard reference: Ptashne, A Genetic Switch, and present proof-theory-induced technologies to help infer phenotypes and to predict life cycles from genotypes. The…
Networks of gene regulation govern morphogenesis, determine cell identity and regulate cell function. But we have little understanding, at the local level, of which logics are biologically preferred or even permitted. To solve this puzzle,…
To appear in Theory and Practice of Logic Programming (TPLP). Tabling is a commonly used technique in logic programming for avoiding cyclic behavior of logic programs and enabling more declarative program definitions. Furthermore, tabling…
We look at characterizing which formulas are expressible in rich decidable logics such as guarded fixpoint logic, unary negation fixpoint logic, and guarded negation fixpoint logic. We consider semantic characterizations of definability, as…
Recent research in molecular discovery has primarily been devoted to small, drug-like molecules, leaving many similarly important applications in material design without adequate technology. These applications often rely on more complex…
First-order logic is the basis for many knowledge representation formalisms and methods. Providing technological support for learning to write first-order formulas for natural language specifications requires methods to test formulas for…
We propose a novel logic, called Frame Logic (FL), that extends first-order logic (with recursive definitions) using a construct Sp(.) that captures the implicit supports of formulas -- the precise subset of the universe upon which their…
Standard epistemic logics introduce a modal operator K to represent knowledge, but in doing so they presuppose the logical apparatus they aim to explain. By contrast, this paper explores how logic may be derived from the structure of…
Tarski gave a general semantics for deductive reasoning: a formula a may be deduced from a set A of formulas iff a holds in all models in which each of the elements of A holds. A more liberal semantics has been considered: a formula a may…
In complex inferential tasks like question answering, machine learning models must confront two challenges: the need to implement a compositional reasoning process, and, in many applications, the need for this reasoning process to be…
The importance of transformations and normal forms in logic programming, and generally in computer science, is well documented. This paper investigates transformations and normal forms in the context of Defeasible Logic, a simple but…
Proteins are the common constituents of all living cells. They are molecular machines that interact with each other as well as with other cell products and carry out a dizzying array of functions with distinction. These interactions follow…
Our goal is to define an algebraic language for reasoning about non-deterministic computations. Towards this goal, we introduce an algebra of string-to-string transductions. Specifically, it is an algebra of partial functions on words over…
Circuit representations are becoming the lingua franca to express and reason about tractable generative and discriminative models. In this paper, we show how complex inference scenarios for these models that commonly arise in machine…
Logical formalisms provide a natural and concise means for specifying and reasoning about preferences. In this paper, we propose lexicographic logic, an extension of classical propositional logic that can express a variety of preferences,…
We bring forward a logical system of transition algebras that enhances many-sorted first-order logic using features from dynamic logics. The sentences we consider include compositions, unions, and transitive closures of transition…
A plausible definition of "reasoning" could be "algebraically manipulating previously acquired knowledge in order to answer a new question". This definition covers first-order logical inference or probabilistic inference. It also includes…