Replicators in Fine-grained Environment: Adaptation and Polymorphism

Selection in a time-periodic environment is modeled via the two-player replicator dynamics. For sufficiently fast environmental changes, this is reduced to a multi-player replicator dynamics in a constant environment. The two-player terms correspond to the time-averaged payoffs, while the three and four-player terms arise from the adaptation of the morphs to their varying environment. Such multi-player (adaptive) terms can induce a stable polymorphism. The establishment of the polymorphism in partnership games [genetic selection] is accompanied by decreasing mean fitness of the population.Comment: 4 pages, 2 figure

Statistical Mechanics of Learning in the Presence of Outliers

Using methods of statistical mechanics, we analyse the effect of outliers on the supervised learning of a classification problem. The learning strategy aims at selecting informative examples and discarding outliers. We compare two algorithms which perform the selection either in a soft or a hard way. When the fraction of outliers grows large, the estimation errors undergo a first order phase transition.Comment: 24 pages, 7 figures (minor extensions added

Genome-wide DNA methylation meta-analysis in the brains of suicide completers

Suicide is the second leading cause of death globally among young people representing a significant global health burden. Although the molecular correlates of suicide remains poorly understood, it has been hypothesised that epigenomic processes may play a role. The objective of this study was to identify suicide-associated DNA methylation changes in the human brain by utilising previously published and unpublished methylomic datasets. We analysed prefrontal cortex (PFC, n = 211) and cerebellum (CER, n = 114) DNA methylation profiles from suicide completers and non-psychiatric, sudden-death controls, meta-analysing data from independent cohorts for each brain region separately. We report evidence for altered DNA methylation at several genetic loci in suicide cases compared to controls in both brain regions with suicide-associated differentially methylated positions enriched among functional pathways relevant to psychiatric phenotypes and suicidality, including nervous system development (PFC) and regulation of long-term synaptic depression (CER). In addition, we examined the functional consequences of variable DNA methylation within a PFC suicide-associated differentially methylated region (PSORS1C3 DMR) using a dual luciferase assay and examined expression of nearby genes. DNA methylation within this region was associated with decreased expression of firefly luciferase but was not associated with expression of nearby genes, PSORS1C3 and POU5F1. Our data suggest that suicide is associated with DNA methylation, offering novel insights into the molecular pathology associated with suicidality.This article is freely available via Open Access. Click on the Publisher URL to access it via the publisher's site.NA/Fondation Brain Canada (Fondation Neuro Canada) MR/K013807/1/MRC_/Medical Research Council/United Kingdom NIMH 1R21MH094771/U.S. Department of Health & Human Services | NIH | National Institute of Mental Health (NIMH) MR/K013807/1/Brain and Behavior Research Foundation (Brain & Behavior Research Foundation) MR/K013807/1/RCUK | MRC | Medical Research Foundation NA/Fonds de Recherche du Québec-Société et Culture (FRQSC) R21 MH094771/MH/NIMH NIH HHS/United Statespublished version, accepted version, submitted versio

Inducing Probabilistic Grammars by Bayesian Model Merging

We describe a framework for inducing probabilistic grammars from corpora of positive samples. First, samples are {\em incorporated} by adding ad-hoc rules to a working grammar; subsequently, elements of the model (such as states or nonterminals) are {\em merged} to achieve generalization and a more compact representation. The choice of what to merge and when to stop is governed by the Bayesian posterior probability of the grammar given the data, which formalizes a trade-off between a close fit to the data and a default preference for simpler models (`Occam's Razor'). The general scheme is illustrated using three types of probabilistic grammars: Hidden Markov models, class-based $n$-grams, and stochastic context-free grammars.Comment: To appear in Grammatical Inference and Applications, Second International Colloquium on Grammatical Inference; Springer Verlag, 1994. 13 page

Inferential models: A framework for prior-free posterior probabilistic inference

Posterior probabilistic statistical inference without priors is an important but so far elusive goal. Fisher's fiducial inference, Dempster-Shafer theory of belief functions, and Bayesian inference with default priors are attempts to achieve this goal but, to date, none has given a completely satisfactory picture. This paper presents a new framework for probabilistic inference, based on inferential models (IMs), which not only provides data-dependent probabilistic measures of uncertainty about the unknown parameter, but does so with an automatic long-run frequency calibration property. The key to this new approach is the identification of an unobservable auxiliary variable associated with observable data and unknown parameter, and the prediction of this auxiliary variable with a random set before conditioning on data. Here we present a three-step IM construction, and prove a frequency-calibration property of the IM's belief function under mild conditions. A corresponding optimality theory is developed, which helps to resolve the non-uniqueness issue. Several examples are presented to illustrate this new approach.Comment: 29 pages with 3 figures. Main text is the same as the published version. Appendix B is an addition, not in the published version, that contains some corrections and extensions of two of the main theorem

Data Mining and Machine Learning in Astronomy

We review the current state of data mining and machine learning in astronomy. 'Data Mining' can have a somewhat mixed connotation from the point of view of a researcher in this field. If used correctly, it can be a powerful approach, holding the potential to fully exploit the exponentially increasing amount of available data, promising great scientific advance. However, if misused, it can be little more than the black-box application of complex computing algorithms that may give little physical insight, and provide questionable results. Here, we give an overview of the entire data mining process, from data collection through to the interpretation of results. We cover common machine learning algorithms, such as artificial neural networks and support vector machines, applications from a broad range of astronomy, emphasizing those where data mining techniques directly resulted in improved science, and important current and future directions, including probability density functions, parallel algorithms, petascale computing, and the time domain. We conclude that, so long as one carefully selects an appropriate algorithm, and is guided by the astronomical problem at hand, data mining can be very much the powerful tool, and not the questionable black box.Comment: Published in IJMPD. 61 pages, uses ws-ijmpd.cls. Several extra figures, some minor additions to the tex

Long-term effects of gestational nicotine exposure and food-restriction on gene expression in the striatum of adolescent rats

Gestational exposure to environmental toxins such as nicotine may result in detectable gene expression changes in later life. To investigate the direct toxic effects of prenatal nicotine exposure on later brain development, we have used transcriptomic analysis of striatal samples to identify gene expression differences between adolescent Lister Hooded rats exposed to nicotine in utero and controls. Using an additional group of animals matched for the reduced food intake experienced in the nicotine group, we were also able to assess the impact of imposed food-restriction on gene expression profiles. We found little evidence for a role of gestational nicotine exposure on altered gene expression in the striatum of adolescent offspring at a significance level of p0.5|, although we cannot exclude the possibility of nicotine-induced changes in other brain regions, or at other time points. We did, however, find marked gene expression differences in response to imposed food-restriction. Food-restriction resulted in significant group differences for a number of immediate early genes (IEGs) including Fos, Fosb, Fosl2, Arc, Junb, Nr4a1 and Nr4a3. These genes are associated with stress response pathways and therefore may reflect long-term effects of nutritional deprivation on the development of the stress system

A Method of Hidden Markov Model Optimization for Use with Geophysical Data Sets

Abstract. Geophysics research has been faced with a growing need for automated techniques with which to process large quantities of data. A successful tool must meet a number of requirements: it should be consistent, require minimal parameter tuning, and produce scienti¯cally meaningful results in reasonable time. We introduce a hidden Markov model (HMM)-based method for analysis of geophysical data sets that attempts to address these issues. Our method improves on standard HMM methods and is based on the systematic analysis of structural local maxima of the HMM objective function. Preliminary results of the method as applied to geodetic and seismic records are presented.

Analysis of Fourier transform valuation formulas and applications

The aim of this article is to provide a systematic analysis of the conditions such that Fourier transform valuation formulas are valid in a general framework; i.e. when the option has an arbitrary payoff function and depends on the path of the asset price process. An interplay between the conditions on the payoff function and the process arises naturally. We also extend these results to the multi-dimensional case, and discuss the calculation of Greeks by Fourier transform methods. As an application, we price options on the minimum of two assets in L\'evy and stochastic volatility models.Comment: 26 pages, 3 figures, to appear in Appl. Math. Financ