Phylogenetic Stochastic Mapping without Matrix Exponentiation

Phylogenetic stochastic mapping is a method for reconstructing the history of trait changes on a phylogenetic tree relating species/organisms carrying the trait. State-of-the-art methods assume that the trait evolves according to a continuous-time Markov chain (CTMC) and work well for small state spaces. The computations slow down considerably for larger state spaces (e.g. space of codons), because current methodology relies on exponentiating CTMC infinitesimal rate matrices -- an operation whose computational complexity grows as the size of the CTMC state space cubed. In this work, we introduce a new approach, based on a CTMC technique called uniformization, that does not use matrix exponentiation for phylogenetic stochastic mapping. Our method is based on a new Markov chain Monte Carlo (MCMC) algorithm that targets the distribution of trait histories conditional on the trait data observed at the tips of the tree. The computational complexity of our MCMC method grows as the size of the CTMC state space squared. Moreover, in contrast to competing matrix exponentiation methods, if the rate matrix is sparse, we can leverage this sparsity and increase the computational efficiency of our algorithm further. Using simulated data, we illustrate advantages of our MCMC algorithm and investigate how large the state space needs to be for our method to outperform matrix exponentiation approaches. We show that even on the moderately large state space of codons our MCMC method can be significantly faster than currently used matrix exponentiation methods.Comment: 33 pages, including appendice

Fuzzy rule-based system applied to risk estimation of cardiovascular patients

Cardiovascular decision support is one area of increasing research interest. On-going collaborations between clinicians and computer scientists are looking at the application of knowledge discovery in databases to the area of patient diagnosis, based on clinical records. A fuzzy rule-based system for risk estimation of cardiovascular patients is proposed. It uses a group of fuzzy rules as a knowledge representation about data pertaining to cardiovascular patients. Several algorithms for the discovery of an easily readable and understandable group of fuzzy rules are formalized and analysed. The accuracy of risk estimation and the interpretability of fuzzy rules are discussed. Our study shows, in comparison to other algorithms used in knowledge discovery, that classifcation with a group of fuzzy rules is a useful technique for risk estimation of cardiovascular patients. © 2013 Old City Publishing, Inc

Improving Workplace Expertise to Meet Increasing Customer Requirements: The Impact of Training

This article focuses upon the training of engineers at a factory producing integrated circuits. Inadequate use of statistical process techniques by the engineers meant that the production process was not being optimised in the context of increasing customer requirements. A training needs analysis was undertaken and a training programme was developed, implemented and evaluated. The results of this programme are presented and conclusions drawn

Characteristic matrices for linear periodic delay differential equations

Szalai et al. (SIAM J. on Sci. Comp. 28(4), 2006) gave a general construction for characteristic matrices for systems of linear delay-differential equations with periodic coefficients. First, we show that matrices constructed in this way can have a discrete set of poles in the complex plane, which may possibly obstruct their use when determining the stability of the linear system. Then we modify and generalize the original construction such that the poles get pushed into a small neighborhood of the origin of the complex plane.Comment: 17 pages, 1 figur

Citizen Electronic Identities using TPM 2.0

Electronic Identification (eID) is becoming commonplace in several European countries. eID is typically used to authenticate to government e-services, but is also used for other services, such as public transit, e-banking, and physical security access control. Typical eID tokens take the form of physical smart cards, but successes in merging eID into phone operator SIM cards show that eID tokens integrated into a personal device can offer better usability compared to standalone tokens. At the same time, trusted hardware that enables secure storage and isolated processing of sensitive data have become commonplace both on PC platforms as well as mobile devices. Some time ago, the Trusted Computing Group (TCG) released the version 2.0 of the Trusted Platform Module (TPM) specification. We propose an eID architecture based on the new, rich authorization model introduced in the TCGs TPM 2.0. The goal of the design is to improve the overall security and usability compared to traditional smart card-based solutions. We also provide, to the best our knowledge, the first accessible description of the TPM 2.0 authorization model.Comment: This work is based on an earlier work: Citizen Electronic Identities using TPM 2.0, to appear in the Proceedings of the 4th international workshop on Trustworthy embedded devices, TrustED'14, November 3, 2014, Scottsdale, Arizona, USA, http://dx.doi.org/10.1145/2666141.266614

Generalized backward doubly stochastic differential equations and SPDEs with nonlinear Neumann boundary conditions

In this paper a new class of generalized backward doubly stochastic differential equations is investigated. This class involves an integral with respect to an adapted continuous increasing process. A probabilistic representation for viscosity solutions of semi-linear stochastic partial differential equations with a Neumann boundary condition is given.Comment: Published at http://dx.doi.org/10.3150/07-BEJ5092 in the Bernoulli (http://isi.cbs.nl/bernoulli/) by the International Statistical Institute/Bernoulli Society (http://isi.cbs.nl/BS/bshome.htm