Design for a Darwinian Brain: Part 1. Philosophy and Neuroscience

Physical symbol systems are needed for open-ended cognition. A good way to understand physical symbol systems is by comparison of thought to chemistry. Both have systematicity, productivity and compositionality. The state of the art in cognitive architectures for open-ended cognition is critically assessed. I conclude that a cognitive architecture that evolves symbol structures in the brain is a promising candidate to explain open-ended cognition. Part 2 of the paper presents such a cognitive architecture.Comment: Darwinian Neurodynamics. Submitted as a two part paper to Living Machines 2013 Natural History Museum, Londo

Automated Mapping of UML Activity Diagrams to Formal Specifications for Supporting Containment Checking

Business analysts and domain experts are often sketching the behaviors of a software system using high-level models that are technology- and platform-independent. The developers will refine and enrich these high-level models with technical details. As a consequence, the refined models can deviate from the original models over time, especially when the two kinds of models evolve independently. In this context, we focus on behavior models; that is, we aim to ensure that the refined, low-level behavior models conform to the corresponding high-level behavior models. Based on existing formal verification techniques, we propose containment checking as a means to assess whether the system's behaviors described by the low-level models satisfy what has been specified in the high-level counterparts. One of the major obstacles is how to lessen the burden of creating formal specifications of the behavior models as well as consistency constraints, which is a tedious and error-prone task when done manually. Our approach presented in this paper aims at alleviating the aforementioned challenges by considering the behavior models as verification inputs and devising automated mappings of behavior models onto formal properties and descriptions that can be directly used by model checkers. We discuss various challenges in our approach and show the applicability of our approach in illustrative scenarios.Comment: In Proceedings FESCA 2014, arXiv:1404.043

Empirical Potential Function for Simplified Protein Models: Combining Contact and Local Sequence-Structure Descriptors

An effective potential function is critical for protein structure prediction and folding simulation. Simplified protein models such as those requiring only $C_\alpha$ or backbone atoms are attractive because they enable efficient search of the conformational space. We show residue specific reduced discrete state models can represent the backbone conformations of proteins with small RMSD values. However, no potential functions exist that are designed for such simplified protein models. In this study, we develop optimal potential functions by combining contact interaction descriptors and local sequence-structure descriptors. The form of the potential function is a weighted linear sum of all descriptors, and the optimal weight coefficients are obtained through optimization using both native and decoy structures. The performance of the potential function in test of discriminating native protein structures from decoys is evaluated using several benchmark decoy sets. Our potential function requiring only backbone atoms or $C_\alpha$ atoms have comparable or better performance than several residue-based potential functions that require additional coordinates of side chain centers or coordinates of all side chain atoms. By reducing the residue alphabets down to size 5 for local structure-sequence relationship, the performance of the potential function can be further improved. Our results also suggest that local sequence-structure correlation may play important role in reducing the entropic cost of protein folding.Comment: 20 pages, 5 figures, 4 tables. In press, Protein

A short survey of discourse representation models

With the advancement of technology and the wide adoption of ontologies as knowledge representation formats, in the last decade, a handful of models were proposed for the externalization of the rhetoric and argumentation captured within scientific publications. Conceptually, most of these models share a similar representation form of the scientific publication, i.e. as a series of interconnected elementary knowledge items. The main differences are given by the terminology used, the types of rhetorical and/or argumentation relations connecting the knowledge items and the foundational theories supporting these relations. This paper analyzes the state of the art and provides a concise comparative overview of the five most prominent discourse representation models, with the goal of sketching an unified model for discourse representation

Array languages and the N-body problem

This paper is a description of the contributions to the SICSA multicore challenge on many body planetary simulation made by a compiler group at the University of Glasgow. Our group is part of the Computer Vision and Graphics research group and we have for some years been developing array compilers because we think these are a good tool both for expressing graphics algorithms and for exploiting the parallelism that computer vision applications require. We shall describe experiments using two languages on two different platforms and we shall compare the performance of these with reference C implementations running on the same platforms. Finally we shall draw conclusions both about the viability of the array language approach as compared to other approaches used in the challenge and also about the strengths and weaknesses of the two, very different, processor architectures we used

Understanding Hidden Memories of Recurrent Neural Networks

Recurrent neural networks (RNNs) have been successfully applied to various natural language processing (NLP) tasks and achieved better results than conventional methods. However, the lack of understanding of the mechanisms behind their effectiveness limits further improvements on their architectures. In this paper, we present a visual analytics method for understanding and comparing RNN models for NLP tasks. We propose a technique to explain the function of individual hidden state units based on their expected response to input texts. We then co-cluster hidden state units and words based on the expected response and visualize co-clustering results as memory chips and word clouds to provide more structured knowledge on RNNs' hidden states. We also propose a glyph-based sequence visualization based on aggregate information to analyze the behavior of an RNN's hidden state at the sentence-level. The usability and effectiveness of our method are demonstrated through case studies and reviews from domain experts.Comment: Published at IEEE Conference on Visual Analytics Science and Technology (IEEE VAST 2017