The space of ultrametric phylogenetic trees

The reliability of a phylogenetic inference method from genomic sequence data is ensured by its statistical consistency. Bayesian inference methods produce a sample of phylogenetic trees from the posterior distribution given sequence data. Hence the question of statistical consistency of such methods is equivalent to the consistency of the summary of the sample. More generally, statistical consistency is ensured by the tree space used to analyse the sample. In this paper, we consider two standard parameterisations of phylogenetic time-trees used in evolutionary models: inter-coalescent interval lengths and absolute times of divergence events. For each of these parameterisations we introduce a natural metric space on ultrametric phylogenetic trees. We compare the introduced spaces with existing models of tree space and formulate several formal requirements that a metric space on phylogenetic trees must possess in order to be a satisfactory space for statistical analysis, and justify them. We show that only a few known constructions of the space of phylogenetic trees satisfy these requirements. However, our results suggest that these basic requirements are not enough to distinguish between the two metric spaces we introduce and that the choice between metric spaces requires additional properties to be considered. Particularly, that the summary tree minimising the square distance to the trees from the sample might be different for different parameterisations. This suggests that further fundamental insight is needed into the problem of statistical consistency of phylogenetic inference methods.Comment: Minor changes. This version has been published in JTB. 27 pages, 9 figure

Optical computing by injection-locked lasers

A programmable optical computer has remained an elusive concept. To construct a practical computing primitive equivalent to an electronic Boolean logic, one should find a nonlinear phenomenon that overcomes weaknesses present in many optical processing schemes. Ideally, the nonlinearity should provide a functionally complete set of logic operations, enable ultrafast all-optical programmability, and allow cascaded operations without a change in the operating wavelength or in the signal encoding format. Here we demonstrate a programmable logic gate using an injection-locked Vertical-Cavity Surface-Emitting Laser (VCSEL). The gate program is switched between the AND and the OR operations at the rate of 1 GHz with Bit Error Ratio (BER) of 10e-6 without changes in the wavelength or in the signal encoding format. The scheme is based on nonlinearity of normalization operations, which can be used to construct any continuous complex function or operation, Boolean or otherwise.Comment: 47 pages, 7 figures in total, 2 tables. Intended for submission to Nature Physics within the next two week

Indeterminateness and `The' Universe of Sets: Multiversism, Potentialism, and Pluralism

In this article, I survey some philosophical attitudes to talk concerning `the' universe of sets. I separate out four different strands of the debate, namely: (i) Universism, (ii) Multiversism, (iii) Potentialism, and (iv) Pluralism. I discuss standard arguments and counterarguments concerning the positions and some of the natural mathematical programmes that are suggested by the various views

Proof-theoretic Semantics for Intuitionistic Multiplicative Linear Logic

This work is the first exploration of proof-theoretic semantics for a substructural logic. It focuses on the base-extension semantics (B-eS) for intuitionistic multiplicative linear logic (IMLL). The starting point is a review of Sandqvist’s B-eS for intuitionistic propositional logic (IPL), for which we propose an alternative treatment of conjunction that takes the form of the generalized elimination rule for the connective. The resulting semantics is shown to be sound and complete. This motivates our main contribution, a B-eS for IMLL , in which the definitions of the logical constants all take the form of their elimination rule and for which soundness and completeness are established

Improving Performance of Iterative Methods by Lossy Checkponting

Iterative methods are commonly used approaches to solve large, sparse linear systems, which are fundamental operations for many modern scientific simulations. When the large-scale iterative methods are running with a large number of ranks in parallel, they have to checkpoint the dynamic variables periodically in case of unavoidable fail-stop errors, requiring fast I/O systems and large storage space. To this end, significantly reducing the checkpointing overhead is critical to improving the overall performance of iterative methods. Our contribution is fourfold. (1) We propose a novel lossy checkpointing scheme that can significantly improve the checkpointing performance of iterative methods by leveraging lossy compressors. (2) We formulate a lossy checkpointing performance model and derive theoretically an upper bound for the extra number of iterations caused by the distortion of data in lossy checkpoints, in order to guarantee the performance improvement under the lossy checkpointing scheme. (3) We analyze the impact of lossy checkpointing (i.e., extra number of iterations caused by lossy checkpointing files) for multiple types of iterative methods. (4)We evaluate the lossy checkpointing scheme with optimal checkpointing intervals on a high-performance computing environment with 2,048 cores, using a well-known scientific computation package PETSc and a state-of-the-art checkpoint/restart toolkit. Experiments show that our optimized lossy checkpointing scheme can significantly reduce the fault tolerance overhead for iterative methods by 23%~70% compared with traditional checkpointing and 20%~58% compared with lossless-compressed checkpointing, in the presence of system failures.Comment: 14 pages, 10 figures, HPDC'1

Equivariant Seiberg-Witten Floer Homology

This paper circulated previously in a draft version. Now, upon general request, it is about time to distribute the more detailed (and much longer) version. The main technical issues revolve around the fine structure of the compactification of the moduli spaces of flow lines and the obstruction bundle technique, with related gluing theorems, needed in the proof of the topological invariance of the equivariant version of the Floer homology.Comment: 162 pages, LaTex, 1 figure, diagrams (xypic