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

Utjecaj NaCl na fermentaciju zrelih zelenih rajčica cv. Ailsa Braig u rasolu

The effect of osmotic strength on gene expression and activity of the major enzymes of fermentative metabolism of mature green tomato fruit (Solanum lycopersicum cv. Ailsa Craig) has been studied by exposing fruit to brine containing 0 (water), 5 and 10 % NaCl. The fruits were surface sterilized prior to treatment to prevent the growth of microbes naturally present on the skin of the fruit. Changes in fruit expression of fermentation genes and the activity of the respective enzymes as well as physicochemical quality characteristics (soluble solid content, titratable acidity, pH and firmness) were studied in both fruit and brine for 0.5, 1, 1.5, 2, 3, 7 and 14 days. Discrepancies in responses that resulted from the different salt concentrations were obtained at molecular and quality levels. The complex kinetics of solutes between the fruit and the surrounding solution due to osmotic potential has led to different responses of the tissue to fermentation. Tomato fruit showed cracking soon after storage in water; water-stored fruit had higher titratable acidity, lower soluble solid content, and higher induction of anaerobic metabolism as indicated by the expression or the activity of the fermentation enzymes compared to fruit stored in brine with 5 or 10 % NaCl. No cracking was observed in fruit stored in 5 (isotonic) or 10 % NaCl (hypertonic) brine, though in the latter, signs of dehydration were observed. The presence of salt in brine reduced the intensity of fermentative metabolism as indicated by the lower gene expression and enzyme activity. However, fruit stored in brine with 5 % NaCl survived longer than with 0 or 10 % NaCl. The presence of 5 % NaCl in brine caused mild changes of both the fermentative metabolism and the physicochemical characteristics and prevented fruit deterioration during storage.U radu je ispitan utjecaj osmoze na ekspresiju gena i aktivnost glavnih enzima koji sudjeluju u fermentaciji zrelih zelenih rajčica (Solanum lycopersicum cv. Ailsa Craig), i to uranjanjem plodova u vodu i rasol što sadržava 5 ili 10 % NaCl. Površina je plodova prije obrade sterilizirana da bi se spriječio rast mikroorganizama na pokožici ploda. Analizirani su plodovi rajčice i rasol tijekom 0,5; 1; 1,5; 2; 3; 7 i 14 dana skladištenja, te ispitani ovi parametri: promjena ekspresije gena i aktivnost enzima koji sudjeluju u fermentaciji, te fizikalno-kemijska svojstva plodova (udio topljivih tvari, titracijska kiselost, pH-vrijednost i čvrstoća). Utvrđene su razlike u dobivenim rezultatima, i to na molekularnoj razini te u kakvoći plodova. Zaključeno je da utjecaj fermentacije na tkivo ploda rajčice ovisi o složenoj kinetici prelaska otopljenih tvari iz plodova u otopinu zbog razlike osmotskih tlakova. Skladištenje u vodi uzrokovalo je pucanje plodova koji su imali veću titracijsku kiselost i manji udio topljivih tvari. Ekspresija gena i aktivnost enzima pokazali su da je došlo do povećanja anaerobnog metabolizma u tim plodovima, u usporedbi s onima skladištenim u rasolu. Skladištenje plodova u izotoničnoj otopini (5 % soli) nije uzrokovalo njihovo pucanje, a u hipertoničnoj (10 % soli) otopini nije došlo do pucanja već do dehidracije plodova. Dodatkom soli smanjen je intenzitet fermentacije, što je dovelo do manje ekspresije gena i aktivnosti enzima. Trajnost plodova skladištenih u izotoničnoj otopini bila je veća od onih skladištenih u vodi ili hipertoničnoj otopini. Manja koncentracija soli u otopini nije bitno utjecala na metabolizam fermentacije te kakvoću plodova, a spriječila je njihovo propadanje tijekom skladištenja