Guppy: Process-Oriented Programming on Embedded Devices

Guppy is a new and experimental process-oriented programming language, taking much inspiration (and some code-base) from the existing occam-pi language. This paper reports on a variety of aspects related to this, specifically language, compiler and run-time system development, enabling Guppy programs to run on desktop and embedded systems. A native code-generation approach is taken, using C as the intermediate language, and with stack-space requirements determined at compile-time

To boldly go:an occam-π mission to engineer emergence

Future systems will be too complex to design and implement explicitly. Instead, we will have to learn to engineer complex behaviours indirectly: through the discovery and application of local rules of behaviour, applied to simple process components, from which desired behaviours predictably emerge through dynamic interactions between massive numbers of instances. This paper describes a process-oriented architecture for fine-grained concurrent systems that enables experiments with such indirect engineering. Examples are presented showing the differing complex behaviours that can arise from minor (non-linear) adjustments to low-level parameters, the difficulties in suppressing the emergence of unwanted (bad) behaviour, the unexpected relationships between apparently unrelated physical phenomena (shown up by their separate emergence from the same primordial process swamp) and the ability to explore and engineer completely new physics (such as force fields) by their emergence from low-level process interactions whose mechanisms can only be imagined, but not built, at the current time

Enabling high confidence detections of gravitational-wave bursts

With the advanced LIGO and Virgo detectors taking observations the detection of gravitational waves is expected within the next few years. Extracting astrophysical information from gravitational wave detections is a well-posed problem and thoroughly studied when detailed models for the waveforms are available. However, one motivation for the field of gravitational wave astronomy is the potential for new discoveries. Recognizing and characterizing unanticipated signals requires data analysis techniques which do not depend on theoretical predictions for the gravitational waveform. Past searches for short-duration un-modeled gravitational wave signals have been hampered by transient noise artifacts, or "glitches," in the detectors. In some cases, even high signal-to-noise simulated astrophysical signals have proven difficult to distinguish from glitches, so that essentially any plausible signal could be detected with at most 2-3 $\sigma$ level confidence. We have put forth the BayesWave algorithm to differentiate between generic gravitational wave transients and glitches, and to provide robust waveform reconstruction and characterization of the astrophysical signals. Here we study BayesWave's capabilities for rejecting glitches while assigning high confidence to detection candidates through analytic approximations to the Bayesian evidence. Analytic results are tested with numerical experiments by adding simulated gravitational wave transient signals to LIGO data collected between 2009 and 2010 and found to be in good agreement.Comment: 15 pages, 6 figures, submitted to PR

Life of occam-Pi

This paper considers some questions prompted by a brief review of the history of computing. Why is programming so hard? Why is concurrency considered an “advanced” subject? What’s the matter with Objects? Where did all the Maths go? In searching for answers, the paper looks at some concerns over fundamental ideas within object orientation (as represented by modern programming languages), before focussing on the concurrency model of communicating processes and its particular expression in the occam family of languages. In that focus, it looks at the history of occam, its underlying philosophy (Ockham’s Razor), its semantic foundation on Hoare’s CSP, its principles of process oriented design and its development over almost three decades into occam-? (which blends in the concurrency dynamics of Milner’s ?-calculus). Also presented will be an urgent need for rationalisation – occam-? is an experiment that has demonstrated significant results, but now needs time to be spent on careful review and implementing the conclusions of that review. Finally, the future is considered. In particular, is there a future

An occam Style Communications System for UNIX Networks

This document describes the design of a communications system which provides occam style communications primitives under a Unix environment, using TCP/IP protocols, and any number of other protocols deemed suitable as underlying transport layers. The system will integrate with a low overhead scheduler/kernel without incurring significant costs to the execution of processes within the run time environment. A survey of relevant occam and occam3 features and related research is followed by a look at the Unix and TCP/IP facilities which determine our working constraints, and a description of the T9000 transputer's Virtual Channel Processor, which was instrumental in our formulation. Drawing from the information presented here, a design for the communications system is subsequently proposed. Finally, a preliminary investigation of methods for lightweight access control to shared resources in an environment which does not provide support for critical sections, semaphores, or busy waiting, is made. This is presented with relevance to mutual exclusion problems which arise within the proposed design. Future directions for the evolution of this project are discussed in conclusion

Communicating Mobile Processes

This paper presents a new model for mobile processes in occam-pi. A process, embedded anywhere in a dynamically evolving network, may suspend itself mid-execution, be safely disconnected from its local environment, moved (by communication along a channel), reconnected to a new environment and reactivated. Upon reactivation, the process resumes execution from the same state (i.e. data values and code positions) it held when it suspended. Its view of its environment is unchanged, since that is abstracted by its synchronisation (e.g. channels and barriers) interface and that remains constant. The environment behind that interface will (usually) be completely different. The mobile process itself may contain any number of levels of dynamic sub-network. This model is simpler and, in some ways, more powerful than our earlier proposal, which required a process to terminate before it could be moved. Its formal semantics and implementation, however, throw up extra challenges. We present details and performance of an initial implementation

Calculus from the past: multiple delay systems arising in cancer cell modelling

Non-local calculus is often overlooked in the mathematics curriculum. In this paper we present an interesting new class of non-local problems that arise from modelling the growth and division of cells, especially cancer cells, as they progress through the cell cycle. The cellular biomass is assumed to be unstructured in size or position, and its evolution governed by a time-dependent system of ordinary differential equations with multiple time delays. The system is linear and taken to be autonomous. As a result, it is possible to reduce its solution to that of a nonlinear matrix eigenvalue problem. This method is illustrated by considering case studies, including the model of the cell cycle developed in Simms K, Bean N, & Koeber A. [10]. The paper concludes by explaining how asymptotic expressions for the distribution of cells across the compartments can be determined and used to assess the impact of different chemotherapeutic agents

Population of human ventricular cell models calibrated with in vivo measurements unravels ionic mechanisms of cardiac alternans

Cardiac alternansis an important risk factor in cardiac physiology, and is related to the initiation of many pathophysiological conditions. However, the mechanisms underlying the generation of alternans remain unclear. In this study, we used a population of computational human ventricle models based onthe O’Hara model [1] to explore the effect of 11 key factors experimentally reported to be related to alternans. In vivo experimental datasets coming from patients undergoing cardiac surgery were used in the calibration of our in silico population of models. The calibrated models in the population were divided into two groups (Normal and Alternans) depending on alternans occurrence. Our results showed that there were significant differences in the following 5 ionic currents between the two groups: fast sodium current, sodium calcium exchanger current, sodium potassium pump current, sarcoplasmic reticulum (SR) calcium release flux and SR calcium reuptake flux. Further analysis indicated that fast sodium current and SR calcium uptake were the two most significant currents that contributed to voltage and calcium alternans generation, respectively

A Spectral Algorithm with Additive Clustering for the Recovery of Overlapping Communities in Networks

This paper presents a novel spectral algorithm with additive clustering designed to identify overlapping communities in networks. The algorithm is based on geometric properties of the spectrum of the expected adjacency matrix in a random graph model that we call stochastic blockmodel with overlap (SBMO). An adaptive version of the algorithm, that does not require the knowledge of the number of hidden communities, is proved to be consistent under the SBMO when the degrees in the graph are (slightly more than) logarithmic. The algorithm is shown to perform well on simulated data and on real-world graphs with known overlapping communities.Comment: Journal of Theoretical Computer Science (TCS), Elsevier, A Para\^itr