Flexible sampling of discrete data correlations without the marginal distributions

Learning the joint dependence of discrete variables is a fundamental problem in machine learning, with many applications including prediction, clustering and dimensionality reduction. More recently, the framework of copula modeling has gained popularity due to its modular parametrization of joint distributions. Among other properties, copulas provide a recipe for combining flexible models for univariate marginal distributions with parametric families suitable for potentially high dimensional dependence structures. More radically, the extended rank likelihood approach of Hoff (2007) bypasses learning marginal models completely when such information is ancillary to the learning task at hand as in, e.g., standard dimensionality reduction problems or copula parameter estimation. The main idea is to represent data by their observable rank statistics, ignoring any other information from the marginals. Inference is typically done in a Bayesian framework with Gaussian copulas, and it is complicated by the fact this implies sampling within a space where the number of constraints increases quadratically with the number of data points. The result is slow mixing when using off-the-shelf Gibbs sampling. We present an efficient algorithm based on recent advances on constrained Hamiltonian Markov chain Monte Carlo that is simple to implement and does not require paying for a quadratic cost in sample size.Comment: An overhauled version of the experimental section moved to the main paper. Old experimental section moved to supplementary materia

Enforcing efficient equilibria in network design games via subsidies

The efficient design of networks has been an important engineering task that involves challenging combinatorial optimization problems. Typically, a network designer has to select among several alternatives which links to establish so that the resulting network satisfies a given set of connectivity requirements and the cost of establishing the network links is as low as possible. The Minimum Spanning Tree problem, which is well-understood, is a nice example. In this paper, we consider the natural scenario in which the connectivity requirements are posed by selfish users who have agreed to share the cost of the network to be established according to a well-defined rule. The design proposed by the network designer should now be consistent not only with the connectivity requirements but also with the selfishness of the users. Essentially, the users are players in a so-called network design game and the network designer has to propose a design that is an equilibrium for this game. As it is usually the case when selfishness comes into play, such equilibria may be suboptimal. In this paper, we consider the following question: can the network designer enforce particular designs as equilibria or guarantee that efficient designs are consistent with users' selfishness by appropriately subsidizing some of the network links? In an attempt to understand this question, we formulate corresponding optimization problems and present positive and negative results.Comment: 30 pages, 7 figure

Euro-Mediterranean Supply Chain Developments and Trends in Trade Structures, in the Fresh Fruit and Vegetable Sector

Supply chains for fresh fruit and vegetables, are going through considerable re-shaping phase worldwide. This study analyses the trends which impose those changes and focuses mainly at the wholesale and export trading of the Euro-Mediterranean supply chain (namely, on how fruit and vegetable producer, wholesale and export firms react to the market forces that direct them). Producer organizations and wholesale firms one the one hand of The Netherlands, Germany and other EU member countries, and of Non- EU Member Mediterranean countries, on the other hand, are the subject of this study. Two graphical representation of the Dutch and the German supply chains respectively are presented here as the main instrument to demonstrate the dynamics of the sectors structure, by describing the position, function size and development for the main chain partner in each of the aforementioned markets. The Euro-Med dimension of the fruit and vegetable supply chain, is analyzed by attempting an impact assessment and an estimation of the potential development of further supply chain integration or collaboration between firms in EU member countries and Mediterranean partner countries. The existing policy framework (the CMO for the fruit and vegetable sector of the CAP), is also taken into consideration as it particularly affects the relationships developed between producer organizations and wholesale firms and retail chains.Euro-Med Free Trade analysis, Supply chain restructure, supply chain efficiency, fresh fruit and vegetables trade, vertical coordination, Industrial Organization, International Relations/Trade,

Diversity and biosynthetic potential of culturable microbes associated with toxic marine animals

Tetrodotoxin (TTX) is a neurotoxin that has been reported from taxonomically diverse organisms across 14 different phyla. The biogenic origin of tetrodotoxin is still disputed, however, TTX biosynthesis by host-associated bacteria has been reported. An investigation into the culturable microbial populations from the TTX-associated blue-ringed octopus Hapalochlaena sp. and sea slug Pleurobranchaea maculata revealed a surprisingly high microbial diversity. Although TTX was not detected among the cultured isolates, PCR screening identifiedsome natural product biosynthesis genes putatively involved in its assembly. This study is the first to report on the microbial diversity of culturable communities from H. maculosa and P. maculata and common natural product biosynthesis genes from their microbiota. We also reassess the production of TTX reported from three bacterial strains isolated from the TTX-containing gastropod Nassarius semiplicatus

On the Configuration LP for Maximum Budgeted Allocation

We study the Maximum Budgeted Allocation problem, i.e., the problem of selling a set of $m$ indivisible goods to $n$ players, each with a separate budget, such that we maximize the collected revenue. Since the natural assignment LP is known to have an integrality gap of $\frac{3}{4}$, which matches the best known approximation algorithms, our main focus is to improve our understanding of the stronger configuration LP relaxation. In this direction, we prove that the integrality gap of the configuration LP is strictly better than $\frac{3}{4}$, and provide corresponding polynomial time roundings, in the following restrictions of the problem: (i) the Restricted Budgeted Allocation problem, in which all the players have the same budget and every item has the same value for any player it can be sold to, and (ii) the graph MBA problem, in which an item can be assigned to at most 2 players. Finally, we improve the best known upper bound on the integrality gap for the general case from $\frac{5}{6}$ to $2\sqrt{2}-2\approx 0.828$ and also prove hardness of approximation results for both cases.Comment: 29 pages, 4 figures. To appear in the 17th Conference on Integer Programming and Combinatorial Optimization (IPCO), 201

Job demands, job resources, safety behaviours, and burnout in air traffic management

A research report submitted to the Faculty of Humanities, University of the Witwatersrand, Johannesburg, in partial fulfilment of the requirements for the degree of Master of Arts (Organisational Psychology), 2017The aim of the present study was to utilise a mixed methods design as a means of investigating the relation between job demands, job resources, safety, and burnout in Air Traffic Management (ATM) technicians. It was also of interest to determine participants’ perspectives on the job demands and resources that may be present in their occupational environment, their participation in safety behaviours, and their perceptions regarding their work and safety performance. Non-probability, convenience sampling was employed to acquire the participants of the present research study. Participants included 33 ATM technicians (50.77% response rate) who took part in the quantitative component of the research study and 14 ATM who took part in the interview process. Participants’ ages ranged from 27 to 55 years (M = 38.91; SD = 8.76) and 90.1% were male (n = 30). Jackson and Rothmann’s (2005) original Job Demands-Resources Scale was used for the assessment of the job demands and resources sixteen items were also added to the original JDRS scale. Sixteen items were added to incorporate the possible job resources and demands experienced by ATM technicians, which were separated into the following sub-scales: shifts, weather conditions, travel, and equipment. Schaufeli, Leiter, Maslach, and Jackson’s (1996) Maslach Burnout Inventory-General Survey (MBIGS) was used to assess ATM technicians’ burnout. Safety behaviours were assessed through the integration of items found within two safety behaviour scales developed by Neal and Griffin (2006) and Hofmann and Morgeson (1999). A semi-structured interview process consisting of open-ended questions was used to discuss the following issues: job tasks, job demands, job resources, burnout, job safety, work-family spillover, and job performance. The findings depicted a weak, positive correlation between the perception of job demands and the experience of burnout (r = .376, p < .05) and a weak, negative correlation between the perception of job resources and the experience of burnout (r = -.383, p < .05). Job resources significantly predicted the experience of burnout (β = -.494, p = .002), as did job demands (β = .489, p = .003). A moderate, positive correlation between the perception of job resources and safety behaviours was obtained (r = .514, p < .01). The participants’ perceptions of job resources explained 26.5% of the variance in safety behaviours, (R2= .265, F(1, 31) = 11.16, p < 0.05. ATM technicians took part in the following safety behaviours: they consistently communicated with both management and air traffic controllers as a way of knowing exactly what the problem is before they went to a site, they took part in training programs as a means of keeping up to date with the latest technological knowledge, attended safety meetings, always communicated with management on how to increase safety, and made sure that a first aid kit was always available. ATM technician’s safety and performance appeared to be heavily influenced by their own personal understanding of the occupation’s risks, the weather conditions that take place on each specific site, the safety equipment that is worn, the knowledge of the possible repercussions that may arise from making any mistakes, and their own individual mood or disposition.XL201

A simple approach to ranking differentially expressed gene expression time courses through Gaussian process regression.

BACKGROUND: The analysis of gene expression from time series underpins many biological studies. Two basic forms of analysis recur for data of this type: removing inactive (quiet) genes from the study and determining which genes are differentially expressed. Often these analysis stages are applied disregarding the fact that the data is drawn from a time series. In this paper we propose a simple model for accounting for the underlying temporal nature of the data based on a Gaussian process. RESULTS: We review Gaussian process (GP) regression for estimating the continuous trajectories underlying in gene expression time-series. We present a simple approach which can be used to filter quiet genes, or for the case of time series in the form of expression ratios, quantify differential expression. We assess via ROC curves the rankings produced by our regression framework and compare them to a recently proposed hierarchical Bayesian model for the analysis of gene expression time-series (BATS). We compare on both simulated and experimental data showing that the proposed approach considerably outperforms the current state of the art. CONCLUSIONS: Gaussian processes offer an attractive trade-off between efficiency and usability for the analysis of microarray time series. The Gaussian process framework offers a natural way of handling biological replicates and missing values and provides confidence intervals along the estimated curves of gene expression. Therefore, we believe Gaussian processes should be a standard tool in the analysis of gene expression time series