A principled approach to programming with nested types in Haskell

Initial algebra semantics is one of the cornerstones of the theory of modern functional programming languages. For each inductive data type, it provides a Church encoding for that type, a build combinator which constructs data of that type, a fold combinator which encapsulates structured recursion over data of that type, and a fold/build rule which optimises modular programs by eliminating from them data constructed using the buildcombinator, and immediately consumed using the foldcombinator, for that type. It has long been thought that initial algebra semantics is not expressive enough to provide a similar foundation for programming with nested types in Haskell. Specifically, the standard folds derived from initial algebra semantics have been considered too weak to capture commonly occurring patterns of recursion over data of nested types in Haskell, and no build combinators or fold/build rules have until now been defined for nested types. This paper shows that standard folds are, in fact, sufficiently expressive for programming with nested types in Haskell. It also defines buildcombinators and fold/build fusion rules for nested types. It thus shows how initial algebra semantics provides a principled, expressive, and elegant foundation for programming with nested types in Haskell.     

Characterisation of flucloxacillin and 5-hydroxymethyl flucloxacillin haptenated HSA in vitro and in vivo

Flucloxacillin is a synthetic penicillin used in the treatment of Staphylococcal infections. Adverse reactions to the drug are believed to arise through covalent modification of proteins, with tissue damage occurring secondary to an immune reaction. Serum proteins have been shown by adduct-specific antibodies to be modified by flucloxacillin, but the nature and sites of modification have not been characterised. Here, in vitro studies on HSA have shown by MS that the modification of protein lysine residues occurs in a dose-, time- and site-dependent manner. Affinity, cation exchange and reversed phase chromatography prior to MS revealed in vivo modification of HSA with flucloxacillin in tolerant patients, with up to nine modified lysine residues being detected in each patient, and with modification of Lys190 and Lys212 being detected in 8/8 patients. It was also revealed for the first time that plasma proteins could be modified with the 5-hydroxymethyl metabolite of flucloxacillin, and that essentially the same Lys residues were targeted by both the parent drug and its metabolite. This study provides a detailed characterisation of sites of chemical modification of an endogenous target and reveals candidate peptides for T-cell and antibody assays of flucloxacillin hypersensitivity.     

Partitioning large networks without breaking communities

The identification of cohesive communities is a key process in social network analysis. However, the algorithms that are effective for finding communities do not scale well to very large problems, as their time complexity is worse than linear in the number of edges in the graph. This is an important issue for those interested in applying social network analysis techniques to very large networks, such as networks of mobile phone subscribers. In this respect, the contributions of this paper are twofold. First, we demonstrate these scaling issues using a prominent community-finding algorithm as a case study. Then, we show that a two-stage process, whereby the network is first decomposed into manageable subnetworks using a multilevel graph partitioning procedure, is effective in finding communities in networks with more than 10⁶ nodes.     

Efficient monitoring of parametric context-free patterns

Recent developments in runtime verification and monitoring show that parametric regular and temporal logic specifications can be efficiently monitored against large programs. However, these logics reduce to ordinary finite automata, limiting their expressivity. For example, neither can specify structured properties that refer to the call stack of the program. While context-free grammars (CFGs) are expressive and well-understood, existing techniques for monitoring CFGs generate large runtime overhead in real-life applications. This paper demonstrates that monitoring parametric CFGs is practical (with overhead on the order of 12% or lower in most cases). We present a monitor synthesis algorithm for CFGs based on an LR(1) parsing algorithm, modified to account for good prefix matching. In addition, a logic-independent mechanism is introduced to support matching against the suffixes of execution traces.     

FeynRules - Feynman rules made easy

In this paper we present FeynRules, a new Mathematica package that facilitates the implementation of new particle physics models. After the user implements the basic model information (e.g., particle content, parameters and Lagrangian), FeynRules derives the Feynman rules and stores them in a generic form suitable for translation to any Feynman diagram calculation program. The model can then be translated to the format specific to a particular Feynman diagram calculator via FeynRules translation interfaces. Such interfaces have been written for CalcHEP/CompHEP, FeynArts/FormCalc, MadGraph/MadEvent and Sherpa, making it possible to write a new model once and have it work in all of these programs. In this paper, we describe how to implement a new model, generate the Feynman rules, use a generic translation interface, and write a new translation interface. We also discuss the details of the FeynRules code.

Program summary

Program title: FeynRulesCatalogue identifier: AEDI_v1_0Program summary URL::http://cpc.cs.qub.ac.uk/summaries/AEDI_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 15 980No. of bytes in distributed program, including test data, etc.: 137 383Distribution format: tar.gzProgramming language: MathematicaComputer: Platforms on which Mathematica is availableOperating system: Operating systems on which Mathematica is availableClassification: 11.1, 11.2, 11.6Nature of problem: Automatic derivation of Feynman rules from a Lagrangian. Implementation of new models into Monte Carlo event generators and FeynArts.Solution method: FeynRules works in two steps:

1. derivation of the Feynman rules directly form the Lagrangian using canonical commutation relations among fields and creation operators.

2. implementation of the new physics model into FeynArts as well as various Monte Carlo programs via interfaces.

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Commitments and interaction norms in organisations

In an organisational setting such as an online marketplace, an entity called the ‘organisation’ or ‘institution’ defines interaction protocols, monitors agent interaction, and intervenes to enforce the interaction protocols. The organisation might be a software system that thus regulates the marketplace, for example. In this article we abstract over application-specific protocols and consider commitment lifecycles as generic interaction protocols. We model interaction protocols by explicitly-represented norms, such that we can operationalise the enforcement of protocols by means of norm enforcement, and we can analyse the protocols by a logical analysis of the norms. We adopt insights and methods from commitment-based approaches to agent interaction as well as from norm-based approaches to agent behaviour governance. First, we show how to use explicitly-represented norms to model commitment dynamics (lifecycles). Second, we introduce an operational semantics to operationalise norm enforcement. Third, we show how to logically analyse interaction protocols by means of commitment dynamics and norm enforcement. The model, semantics, and analysis are illustrated by a running example from a vehicle insurance domain.     

A new representation and associated algorithms for generalized planning

Constructing plans that can handle multiple problem instances is a longstanding open problem in AI. We present a framework for generalized planning that captures the notion of algorithm-like plans and unifies various approaches developed for addressing this problem. Using this framework, and building on the TVLA system for static analysis of programs, we develop a novel approach for computing generalizations of classical plans by identifying sequences of actions that will make measurable progress when placed in a loop. In a wide class of problems that we characterize formally in the paper, these methods allow us to find generalized plans with loops for solving problem instances of unbounded sizes and also to determine the correctness and applicability of the computed generalized plans. We demonstrate the scope and scalability of the proposed approach on a wide range of planning problems.