Anthony J. Bonner

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An extension of predicate logic, called Transaction Logic, is proposed, which accounts in a clean and declarative fashion for the phenomenon of state changes in logic programs and databases. Transaction Logic has a natural model theory and a sound and complete proof theory, but unlike many other logics, it allows users to program transactions. The semantics(More)
Object-oriented databases have been introduced primarily to ease the development of database applications. However, the difficulties encountered when, for instance, trying to restructure data or integrate databases demonstrate that the models being used still lack flexibility. We claim that the natural way to overcome these shortcomings is to introduce a(More)
This paper presents an overview of Transaction Logic|a new formalism recently introduced in 11, 12] and designed to deal with the phenomenon of state changes in logic programming, databases, and AI. Transaction Logic has a natural model theory and a sound and complete proof theory. Unlike many other logics, however, it is suitable for programming procedures(More)
‘Transaction Datalog (abbreviated TV) is a concurrent programming language that provides process modeling, database access, and advanced transactions. This paper illustrates the use of TV for specifying and simulating workflows, with examples based on the needs of a highthroughpnt genome laboratory. In addition to traditional database support, these needs(More)
Seed germination is a complex trait of key ecological and agronomic significance. Few genetic factors regulating germination have been identified, and the means by which their concerted action controls this developmental process remains largely unknown. Using publicly available gene expression data from Arabidopsis thaliana, we generated a(More)
We present an extension of Horn-clause logic which can hypothetically add and delete tuples from a database. Such logics have been discussed in the literature, but their complexities and expressibilities have remained an open question. This paper examines two such logics in the function-free, predicate case. It is shown, in particular, that augmenting(More)
We propose an extension of classical predicate calculus, called Transaction Logic, which provides a logical foundation for the phenomenon of state changes in logic programs and databases. Transaction Logic comes with a natural model theory and a sound and complete proof theory. The proof theory not only veriies programs, but also executes them, which makes(More)
Deep learning has been successfully applied to perform non-linear embedding. In this paper, we present supervised embedding techniques that use a deep network to collapse classes. The network is pre-trained using a stack of RBMs, and finetuned using approaches that try to collapse classes. The finetuning is inspired by ideas from NCA, but it uses a Student(More)
Intuitionistic logic programming is an extension of Horn-clause logic programming in which implications may appear “embedded” on the right-hand side of a rule. Thus, rules of the form A(x) ← [B(x) ← C(x)] are allowed. These rules are called embedded implications. In this paper, we develop a language in which negationas-failure is combined with embedded(More)