Nonlinear Models of Neural and Genetic Network Dynamics:\ud \ud Natural Transformations of Łukasiewicz Logic LM-Algebras in a Łukasiewicz-Topos as Representations of Neural Network Development and Neoplastic Transformations \ud

A categorical and Łukasiewicz-Topos framework for Algebraic Logic models of nonlinear dynamics in complex functional systems such as Neural Networks, Cell Genome and Interactome Networks is introduced. Łukasiewicz Algebraic Logic models of both neural and genetic networks and signaling pathways in cells are formulated in terms of nonlinear dynamic systems with n-state components that allow for the generalization of previous logical models of both genetic activities and neural networks. An algebraic formulation of variable next-state/transfer functions is extended to a Łukasiewicz Topos with an N-valued Łukasiewicz Algebraic Logic subobject classifier description that represents non-random and nonlinear network activities as well as their transformations in developmental processes and carcinogenesis.\u

Neural Networks, Cell Genome and Interactome Nonlinear Dynamic Models

Operational logic and bioinformatics models of nonlinear dynamics in complex functional systems such as neural networks, genomes and cell interactomes are proposed. Łukasiewicz Algebraic Logic models of genetic networks and signaling pathways in cells are formulated in terms of nonlinear dynamic systems with n-state components that allow for the generalization of previous logical models of both genetic activities and neural networks. An algebraic formulation of variable 'next-state functions' is extended to a Łukasiewicz Topos with an n-valued Łukasiewicz Algebraic Logic subobject classifier description that represents non-random and nonlinear network activities as well as their transformations in developmental processes and carcinogenesis

Łukasiewicz-Topos Models of Neural Networks, Cell Genome and Interactome Nonlinear Dynamic Models

A categorical and Łukasiewicz-Topos framework for Algebraic Logic models of nonlinear dynamics in complex functional systems such as Neural Networks, Cell Genome and Interactome Networks is introduced. Łukasiewicz Algebraic Logic models of both neural and genetic networks and signaling pathways in cells are formulated in terms of nonlinear dynamic systems with n-state components that allow for the generalization of previous logical models of both genetic activities and neural networks. An algebraic formulation of variable 'next-state functions' is extended to a Łukasiewicz Topos with an n-valued Łukasiewicz Algebraic Logic subobject classifier description that represents non-random and nonlinear network activities as well as their transformations in developmental processes and carcinogenesis

"Not not bad" is not "bad": A distributional account of negation

With the increasing empirical success of distributional models of compositional semantics, it is timely to consider the types of textual logic that such models are capable of capturing. In this paper, we address shortcomings in the ability of current models to capture logical operations such as negation. As a solution we propose a tripartite formulation for a continuous vector space representation of semantics and subsequently use this representation to develop a formal compositional notion of negation within such models.Comment: 9 pages, to appear in Proceedings of the 2013 Workshop on Continuous Vector Space Models and their Compositionalit

A novel Boolean kernels family for categorical data

Kernel based classifiers, such as SVM, are considered state-of-the-art algorithms and are widely used on many classification tasks. However, this kind of methods are hardly interpretable and for this reason they are often considered as black-box models. In this paper, we propose a new family of Boolean kernels for categorical data where features correspond to propositional formulas applied to the input variables. The idea is to create human-readable features to ease the extraction of interpretation rules directly from the embedding space. Experiments on artificial and benchmark datasets show the effectiveness of the proposed family of kernels with respect to established ones, such as RBF, in terms of classification accuracy

Computational core and fixed-point organisation in Boolean networks

In this paper, we analyse large random Boolean networks in terms of a constraint satisfaction problem. We first develop an algorithmic scheme which allows to prune simple logical cascades and under-determined variables, returning thereby the computational core of the network. Second we apply the cavity method to analyse number and organisation of fixed points. We find in particular a phase transition between an easy and a complex regulatory phase, the latter one being characterised by the existence of an exponential number of macroscopically separated fixed-point clusters. The different techniques developed are reinterpreted as algorithms for the analysis of single Boolean networks, and they are applied to analysis and in silico experiments on the gene-regulatory networks of baker's yeast (saccaromices cerevisiae) and the segment-polarity genes of the fruit-fly drosophila melanogaster.Comment: 29 pages, 18 figures, version accepted for publication in JSTA

Probabilistic Inference Modulo Theories

We present SGDPLL(T), an algorithm that solves (among many other problems) probabilistic inference modulo theories, that is, inference problems over probabilistic models defined via a logic theory provided as a parameter (currently, propositional, equalities on discrete sorts, and inequalities, more specifically difference arithmetic, on bounded integers). While many solutions to probabilistic inference over logic representations have been proposed, SGDPLL(T) is simultaneously (1) lifted, (2) exact and (3) modulo theories, that is, parameterized by a background logic theory. This offers a foundation for extending it to rich logic languages such as data structures and relational data. By lifted, we mean algorithms with constant complexity in the domain size (the number of values that variables can take). We also detail a solver for summations with difference arithmetic and show experimental results from a scenario in which SGDPLL(T) is much faster than a state-of-the-art probabilistic solver.Comment: Submitted to StarAI-16 workshop as closely revised version of IJCAI-16 pape