Prediction of protein-protein interactions using one-class classification methods and integrating diverse data

This research addresses the problem of prediction of protein-protein interactions (PPI) when integrating diverse kinds of biological information. This task has been commonly viewed as a binary classification problem (whether any two proteins do or do not interact) and several different machine learning techniques have been employed to solve this task. However the nature of the data creates two major problems which can affect results. These are firstly imbalanced class problems due to the number of positive examples (pairs of proteins which really interact) being much smaller than the number of negative ones. Secondly the selection of negative examples can be based on some unreliable assumptions which could introduce some bias in the classification results. Here we propose the use of one-class classification (OCC) methods to deal with the task of prediction of PPI. OCC methods utilise examples of just one class to generate a predictive model which consequently is independent of the kind of negative examples selected; additionally these approaches are known to cope with imbalanced class problems. We have designed and carried out a performance evaluation study of several OCC methods for this task, and have found that the Parzen density estimation approach outperforms the rest. We also undertook a comparative performance evaluation between the Parzen OCC method and several conventional learning techniques, considering different scenarios, for example varying the number of negative examples used for training purposes. We found that the Parzen OCC method in general performs competitively with traditional approaches and in many situations outperforms them. Finally we evaluated the ability of the Parzen OCC approach to predict new potential PPI targets, and validated these results by searching for biological evidence in the literature

A Comparative Review of Dimension Reduction Methods in Approximate Bayesian Computation

Approximate Bayesian computation (ABC) methods make use of comparisons between simulated and observed summary statistics to overcome the problem of computationally intractable likelihood functions. As the practical implementation of ABC requires computations based on vectors of summary statistics, rather than full data sets, a central question is how to derive low-dimensional summary statistics from the observed data with minimal loss of information. In this article we provide a comprehensive review and comparison of the performance of the principal methods of dimension reduction proposed in the ABC literature. The methods are split into three nonmutually exclusive classes consisting of best subset selection methods, projection techniques and regularization. In addition, we introduce two new methods of dimension reduction. The first is a best subset selection method based on Akaike and Bayesian information criteria, and the second uses ridge regression as a regularization procedure. We illustrate the performance of these dimension reduction techniques through the analysis of three challenging models and data sets.Comment: Published in at http://dx.doi.org/10.1214/12-STS406 the Statistical Science (http://www.imstat.org/sts/) by the Institute of Mathematical Statistics (http://www.imstat.org

Evaluating probabilistic forecasts with scoringRules

Probabilistic forecasts in the form of probability distributions over future events have become popular in several fields including meteorology, hydrology, economics, and demography. In typical applications, many alternative statistical models and data sources can be used to produce probabilistic forecasts. Hence, evaluating and selecting among competing methods is an important task. The scoringRules package for R provides functionality for comparative evaluation of probabilistic models based on proper scoring rules, covering a wide range of situations in applied work. This paper discusses implementation and usage details, presents case studies from meteorology and economics, and points to the relevant background literature

Consistent tests of conditional moment restrictions

We propose two classes of consistent tests in parametric econometric models defined through multiple conditional moment restrictions. The first type of tests relies on nonparametric estimation, while the second relies on a functional of a marked empirical process. For both tests, a simulation procedure for obtaining critical values is shown to be asymptotically valid. Finite sample performances of the tests are investigated by means of several Monte-Carlo experiments.Publicad

Technological change and industry competitiveness through the evolution of localised comparative advantages - The case of Italy

The influence of technological change on industry performances is nowadays being increasingly investigated under the broad category of "national systemic competitiveness". Moreover theoretical works have shown that the relationship between technology and economic performance not only takes different forms in different socio-economic contexts, but is also powerfully influenced by the way that innovation processes evolve over time along strongly localised patterns. The present study is focused on the evolution of trade competitiveness of the manufacturing sector in Italy over the past ten years and addresses to the role played by localised comparative advantages in shaping the model of national competitiveness. The data used in the analysis, drawn by the Enea Observatory on high tech industries, are based on trade statistics at the SITC five digit level and are spatially referenced to the Italy NUT3 regional partition. The effects of localised trade specialisation on manufacturing competitiveness are first assessed through spatial econometric tecniques. Spatial variation in the relationships found is further explored in order to give additional hints on the specific contribution of localised comparative advantages. According to major trends which have recently characterised manufacturing trade competitiveness in Italy, the analysis is expected to bring into evidence significant changes in the contribution of industrial localities to national competitiveness.