Łukasiewicz-Moisil Many-Valued Logic Algebra of Highly-Complex Systems

A novel approach to self-organizing, highly-complex systems (HCS), such as living organisms and artificial intelligent systems (AIs), is presented which is relevant to Cognition, Medical Bioinformatics and Computational Neuroscience. Quantum Automata (QAs) were defined in our previous work as generalized, probabilistic automata with quantum state spaces (Baianu, 1971). Their next-state functions operate through transitions between quantum states defined by the quantum equations of motion in the Schroedinger representation, with both initial and boundary conditions in space-time. Such quantum automata operate with a quantum logic, or Q-logic, significantly different from either Boolean or Łukasiewicz many-valued logic. A new theorem is proposed which states that the category of quantum automata and automata--homomorphisms has both limits and colimits. Therefore, both categories of quantum automata and classical automata (sequential machines) are bicomplete. A second new theorem establishes that the standard automata category is a subcategory of the quantum automata category. The quantum automata category has a faithful representation in the category of Generalized (M,R)--Systems which are open, dynamic biosystem networks with defined biological relations that represent physiological functions of primordial organisms, single cells and higher organisms

Efficient minimization of multipole electrostatic potentials in torsion space

The development of models of macromolecular electrostatics capable of delivering improved fidelity to quantum mechanical calculations is an active field of research in computational chemistry. Most molecular force field development takes place in the context of models with full Cartesian coordinate degrees of freedom. Nevertheless, a number of macromolecular modeling programs use a reduced set of conformational variables limited to rotatable bonds. Efficient algorithms for minimizing the energies of macromolecular systems with torsional degrees of freedom have been developed with the assumption that all atom-atom interaction potentials are isotropic. We describe novel modifications to address the anisotropy of higher order multipole terms while retaining the efficiency of these approaches. In addition, we present a treatment for obtaining derivatives of atom-centered tensors with respect to torsional degrees of freedom. We apply these results to enable minimization of the Amoeba multipole electrostatics potential in a system with torsional degrees of freedom, and validate the correctness of the gradients by comparison to finite difference approximations. In the interest of enabling a complete model of electrostatics with implicit treatment of solvent-mediated effects, we also derive expressions for the derivative of solvent accessible surface area with respect to torsional degrees of freedom

Probabilistic Graphical Model Representation in Phylogenetics

Recent years have seen a rapid expansion of the model space explored in statistical phylogenetics, emphasizing the need for new approaches to statistical model representation and software development. Clear communication and representation of the chosen model is crucial for: (1) reproducibility of an analysis, (2) model development and (3) software design. Moreover, a unified, clear and understandable framework for model representation lowers the barrier for beginners and non-specialists to grasp complex phylogenetic models, including their assumptions and parameter/variable dependencies. Graphical modeling is a unifying framework that has gained in popularity in the statistical literature in recent years. The core idea is to break complex models into conditionally independent distributions. The strength lies in the comprehensibility, flexibility, and adaptability of this formalism, and the large body of computational work based on it. Graphical models are well-suited to teach statistical models, to facilitate communication among phylogeneticists and in the development of generic software for simulation and statistical inference. Here, we provide an introduction to graphical models for phylogeneticists and extend the standard graphical model representation to the realm of phylogenetics. We introduce a new graphical model component, tree plates, to capture the changing structure of the subgraph corresponding to a phylogenetic tree. We describe a range of phylogenetic models using the graphical model framework and introduce modules to simplify the representation of standard components in large and complex models. Phylogenetic model graphs can be readily used in simulation, maximum likelihood inference, and Bayesian inference using, for example, Metropolis-Hastings or Gibbs sampling of the posterior distribution

An "All Hands" Call to the Social Science Community: Establishing a Community Framework for Complexity Modeling Using Agent Based Models and Cyberinfrastructure

To date, many communities of practice (COP) in the social sciences have been struggling with how to deal with rapidly growing bodies of information. Many CoPs across broad disciplines have turned to community frameworks for complexity modeling (CFCMs) but this strategy has been slow to be discussed let alone adopted by the social sciences communities of practice (SS-CoPs). In this paper we urge the SS-CoPs that it is timely to develop and establish a CBCF for the social sciences for two major reasons: the rapid acquisition of data and the emergence of critical cybertools which can facilitate agent-based, spatially-explicit models. The goal of this paper is not to prescribe how a CFCM might be set up but to suggest of what components it might consist and what its advantages would be. Agent based models serve the establishment of a CFCM because they allow robust and diverse inputs and are amenable to output-driven modifications. In other words, as phenomena are resolved by a SS-CoP it is possible to adjust and refine ABMs (and their predictive ability) as a recursive and collective process. Existing and emerging cybertools such as computer networks, digital data collections and advances in programming languages mean the SS-CoP must now carefully consider committing the human organization to enabling a cyberinfrastructure tool. The combination of technologies with human interfaces can allow scenarios to be incorporated through 'if' 'then' rules and provide a powerful basis for addressing the dynamics of coupled and complex social ecological systems (cSESs). The need for social scientists to be more engaged participants in the growing challenges of characterizing chaotic, self-organizing social systems and predicting emergent patterns makes the application of ABMs timely. The enabling of a SS-CoP CFCM human-cyberinfrastructure represents an unprecedented opportunity to synthesize, compare and evaluate diverse sociological phenomena as a cohesive and recursive community-driven process.Community-Based Complex Models, Mathematics, Social Sciences

GRASS: Generative Recursive Autoencoders for Shape Structures

We introduce a novel neural network architecture for encoding and synthesis of 3D shapes, particularly their structures. Our key insight is that 3D shapes are effectively characterized by their hierarchical organization of parts, which reflects fundamental intra-shape relationships such as adjacency and symmetry. We develop a recursive neural net (RvNN) based autoencoder to map a flat, unlabeled, arbitrary part layout to a compact code. The code effectively captures hierarchical structures of man-made 3D objects of varying structural complexities despite being fixed-dimensional: an associated decoder maps a code back to a full hierarchy. The learned bidirectional mapping is further tuned using an adversarial setup to yield a generative model of plausible structures, from which novel structures can be sampled. Finally, our structure synthesis framework is augmented by a second trained module that produces fine-grained part geometry, conditioned on global and local structural context, leading to a full generative pipeline for 3D shapes. We demonstrate that without supervision, our network learns meaningful structural hierarchies adhering to perceptual grouping principles, produces compact codes which enable applications such as shape classification and partial matching, and supports shape synthesis and interpolation with significant variations in topology and geometry.Comment: Corresponding author: Kai Xu ([email protected]