Monoidal computer III: A coalgebraic view of computability and complexity

Monoidal computer is a categorical model of intensional computation, where many different programs correspond to the same input-output behavior. The upshot of yet another model of computation is that a categorical formalism should provide a much needed high level language for theory of computation, flexible enough to allow abstracting away the low level implementation details when they are irrelevant, or taking them into account when they are genuinely needed. A salient feature of the approach through monoidal categories is the formal graphical language of string diagrams, which supports visual reasoning about programs and computations. In the present paper, we provide a coalgebraic characterization of monoidal computer. It turns out that the availability of interpreters and specializers, that make a monoidal category into a monoidal computer, is equivalent with the existence of a *universal state space*, that carries a weakly final state machine for any pair of input and output types. Being able to program state machines in monoidal computers allows us to represent Turing machines, to capture their execution, count their steps, as well as, e.g., the memory cells that they use. The coalgebraic view of monoidal computer thus provides a convenient diagrammatic language for studying computability and complexity.Comment: 34 pages, 24 figures; in this version: added the Appendi

Operations for Learning with Graphical Models

This paper is a multidisciplinary review of empirical, statistical learning from a graphical model perspective. Well-known examples of graphical models include Bayesian networks, directed graphs representing a Markov chain, and undirected networks representing a Markov field. These graphical models are extended to model data analysis and empirical learning using the notation of plates. Graphical operations for simplifying and manipulating a problem are provided including decomposition, differentiation, and the manipulation of probability models from the exponential family. Two standard algorithm schemas for learning are reviewed in a graphical framework: Gibbs sampling and the expectation maximization algorithm. Using these operations and schemas, some popular algorithms can be synthesized from their graphical specification. This includes versions of linear regression, techniques for feed-forward networks, and learning Gaussian and discrete Bayesian networks from data. The paper concludes by sketching some implications for data analysis and summarizing how some popular algorithms fall within the framework presented. The main original contributions here are the decomposition techniques and the demonstration that graphical models provide a framework for understanding and developing complex learning algorithms.Comment: See http://www.jair.org/ for any accompanying file

The computer-aided design of nano-scaled digital circuits

The use of CMOS-based transistors to implement digital logic is the prevalent means of modern computation. It is, however, not the only means. Advances in nano-science and engineering demonstrate that nano-scale integrated circuits are in fact a viable technology for computation. The dominant means for information propagation in these devices is quantum tunneling - a phenomenon that is not wholly compatible with current design techniques. This paper is an explanation of one process used to both design and simulate digital logic circuits utilizing the topology of the hypercube. The aim of the paper is to demonstrate the ease of designing and implementing a streamlined design environment and to demonstrate the utility that such an environment affords the designer. The hypercube topology is used as the dominant example for constructing 3D circuits. In this topology, each device is required to operate as a doubly gated switch and computation is performed utilizing a concept similar to pass-gate technology. The paper details the software required to generate the logic circuit and the means of simulation. Each device of the structure is modeled using a non-linear state-space representation. The paper concludes with two examples of implementable technologies: single-electron transistors (wrap-gate structures with quantum dots), and endohederal fullerenes acting as gate switches

An overview of existing modeling tools making use of model checking in the analysis of biochemical networks

Model checking is a well-established technique for automaticallyverifying complex systems. Recently, model checkers have appearedin computer tools for the analysis of biochemical (and generegulatory) networks. We survey several such tools to assess thepotential of model checking in computational biology. Next, our overviewfocuses on direct applications of existing model checkers, as well ason algorithms for biochemical network analysis influenced by modelchecking, such as those using binary decision diagrams or Booleansatisfiability solvers. We conclude with advantages and drawbacks ofmodel checking for the analysis of biochemical networks

On Formal Methods for Large-Scale Product Configuration

<p>In product development companies mass customization is widely used to achieve better customer satisfaction while keeping costs down. To efficiently implement mass customization, product platforms are often used. A product platform allows building a wide range of products from a set of predefined components. The process of matching these components to customers' needs is called product configuration. Not all components can be combined with each other due to restrictions of various kinds, for example, geometrical, marketing and legal reasons. Product design engineers develop configuration constraints to describe such restrictions. The number of constraints and the complexity of the relations between them are immense for complex product like a vehicle. Thus, it is both error-prone and time consuming to analyze, author and verify the constraints manually. Software tools based on formal methods can help engineers to avoid making errors when working with configuration constraints, thus design a correct product faster.</p> <p>This thesis introduces a number of formal methods to help engineers maintain, verify and analyze product configuration constraints. These methods provide automatic verification of constraints and computational support for analyzing and refactoring constraints. The methods also allow verifying the correctness of one specific type of constraints, item usage rules, for sets of mutually-exclusive required items, and automatic verification of equivalence of different formulations of the constraints. The thesis also introduces three methods for efficient enumeration of valid partial configurations, with benchmarking of the methods on an industrial dataset.</p> <p>Handling large-scale industrial product configuration problems demands high efficiency from the software methods. This thesis investigates a number of search-based and knowledge-compilation-based methods for working with large product configuration instances, including Boolean satisfiability solvers, binary decision diagrams and decomposable negation normal form. This thesis also proposes a novel method based on supervisory control theory for efficient reasoning about product configuration data. The methods were implemented in a tool, to investigate the applicability of the methods for handling large product configuration problems. It was found that search-based Boolean satisfiability solvers with incremental capabilities are well suited for industrial configuration problems.</p> <p>The methods proposed in this thesis exhibit good performance on practical configuration problems, and have a potential to be implemented in industry to support product design engineers in creating and maintaining configuration constraints, and speed up the development of product platforms and new products.</p