Session Types in Abelian Logic

There was a PhD student who says "I found a pair of wooden shoes. I put a coin in the left and a key in the right. Next morning, I found those objects in the opposite shoes." We do not claim existence of such shoes, but propose a similar programming abstraction in the context of typed lambda calculi. The result, which we call the Amida calculus, extends Abramsky's linear lambda calculus LF and characterizes Abelian logic.Comment: In Proceedings PLACES 2013, arXiv:1312.221

On polymorphic sessions and functions: a tale of two (fully abstract) encodings

This work exploits the logical foundation of session types to determine what kind of type discipline for the Λ-calculus can exactly capture, and is captured by, Λ-calculus behaviours. Leveraging the proof theoretic content of the soundness and completeness of sequent calculus and natural deduction presentations of linear logic, we develop the first mutually inverse and fully abstract processes-as-functions and functions-as-processes encodings between a polymorphic session π-calculus and a linear formulation of System F. We are then able to derive results of the session calculus from the theory of the Λ-calculus: (1) we obtain a characterisation of inductive and coinductive session types via their algebraic representations in System F; and (2) we extend our results to account for value and process passing, entailing strong normalisation

On polymorphic sessions and functions: A tale of two (fully abstract) encodings

This work exploits the logical foundation of session types to determine what kind of type discipline for the -calculus can exactly capture, and is captured by, -calculus behaviours. Leveraging the proof theoretic content of the soundness and completeness of sequent calculus and natural deduction presentations of linear logic, we develop the first mutually inverse and fully abstract processes-as-functions and functions-as-processes encodings between a polymorphic session -calculus and a linear formulation of System F. We are then able to derive results of the session calculus from the theory of the -calculus: (1) we obtain a characterisation of inductive and coinductive session types via their algebraic representations in System F; and (2) we extend our results to account for value and process passing, entailing strong normalisation

Association of 5' estrogen receptor alpha gene polymorphisms with bone mineral density, vertebral bone area and fracture risk

This study investigates the influence of genetic variation of the estrogen receptor alpha (ESR1) gene locus on several bone parameters in 2042 individuals of The Rotterdam Study, a prospective population-based cohort study of elderly subjects. We analysed three polymorphic sites in the 5' region of the ESR1 gene; a (TA)(n)-repeat in the promoter region, and molecular haplotypes of the PvuII and XbaI RFLPs in intron 1, and inferred long-range haplotypes (LRH) thereof. We observed only three of the possible four PvuII-XbaI haplotypes in our population. A comparison with other Caucasian populations showed similar haplotype frequencies, while in Asian and African populations these were different. Linkage disequilibrium (LD) analysis between the PvuII-XbaI haplotype and the (TA)(n) repeat showed strong LD between the two sites. Reconstruction of long range haplotypes over the entire 5' region, revealed six frequent LRH. In men, we did not observe an association between the ESR1 polymorphisms studied

EpiToolKit—a web server for computational immunomics

Predicting the T-cell-mediated immune response is an important task in vaccine design and thus one of the key problems in computational immunomics. Various methods have been developed during the last decade and are available online. We present EpiToolKit, a web server that has been specifically designed to offer a problem-solving environment for computational immunomics. EpiToolKit offers a variety of different prediction methods for major histocompatibility complex class I and II ligands as well as minor histocompatibility antigens. These predictions are embedded in a user-friendly interface allowing refining, editing and constraining the searches conveniently. We illustrate the value of the approach with a set of novel tumor-associated peptides. EpiToolKit is available online at www.epitoolkit.org

Polymonad programming in Haskell

Polymonads were recently introduced by Hicks et al. as a unified approach to programming with different notions of monads. Their work was mainly focussed on foundational aspects of the approach. In this article, we show how to incorporate the notion of polymonads into Haskell, which is the first time this has been done in a full-scale language. In particular, we show how polymonads can be represented in Haskell, give a justification of the representation through proofs in Agda, and provide a plugin for the Glasgow Haskell Compiler (GHC) that enables their use in practice. Finally, we demonstrate the utility of our system by means of examples concerned with session types and the parameterized effect monad. This work provides a common representation of a number of existing approaches to generalized monads in Haskell

A logical foundation for session-based concurrent computation

Linear logic has long been heralded for its potential of providing a logical basis for concurrency. While over the years many research attempts were made in this regard, a Curry-Howard correspondence between linear logic and concurrent computation was only found recently, bridging the proof theory of linear logic and session-typed process calculus. Building upon this work, we have developed a theory of intuitionistic linear logic as a logical foundation for session-based concurrent computation, exploring several concurrency related phenomena such as value-dependent session types and polymorphic sessions within our logical framework in an arguably clean and elegant way, establishing with relative ease strong typing guarantees due to the logical basis, which ensure the fundamental properties of type preservation and global progress, entailing the absence of deadlocks in communication. We develop a general purpose concurrent programming language based on the logical interpretation, combining functional programming with a concurrent, session-based process layer through the form of a contextual monad, preserving our strong typing guarantees of type preservation and deadlock-freedom in the presence of general recursion and higher-order process communication. We introduce a notion of linear logical relations for session typed concurrent processes, developing an arguably uniform technique for reasoning about sophisticated properties of session-based concurrent computation such as termination or equivalence based on our logical approach, further supporting our goal of establishing intuitionistic linear logic as a logical foundation for sessionbased concurrency