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

Structural Change and Technology. A Long View

change, technology

Identifying e-Commerce in Enterprises by means of Text Mining and Classification Algorithms

Monitoring specific features of the enterprises, for example, the adoption of e-commerce, is an important and basic task for several economic activities. This type of information is usually obtained by means of surveys, which are costly due to the amount of personnel involved in the task. An automatic detection of this information would allow consistent savings. This can actually be performed by relying on computer engineering, since in general this information is publicly available on-line through the corporate websites. This work describes how to convert the detection of e-commerce into a supervised classification problem, where each record is obtained from the automatic analysis of one corporate website, and the class is the presence or the absence of e-commerce facilities. The automatic generation of similar data records requires the use of several Text Mining phases; in particular we compare six strategies based on the selection of best words and best n-grams. After this, we classify the obtained dataset by means of four classification algorithms: Support Vector Machines; Random Forest; Statistical and Logical Analysis of Data; Logistic Classifier. This turns out to be a difficult case of classification problem. However, after a careful design and set-up of the whole procedure, the results on a practical case of Italian enterprises are encouraging

The potential of text mining in data integration and network biology for plant research : a case study on Arabidopsis

Despite the availability of various data repositories for plant research, a wealth of information currently remains hidden within the biomolecular literature. Text mining provides the necessary means to retrieve these data through automated processing of texts. However, only recently has advanced text mining methodology been implemented with sufficient computational power to process texts at a large scale. In this study, we assess the potential of large-scale text mining for plant biology research in general and for network biology in particular using a state-of-the-art text mining system applied to all PubMed abstracts and PubMed Central full texts. We present extensive evaluation of the textual data for Arabidopsis thaliana, assessing the overall accuracy of this new resource for usage in plant network analyses. Furthermore, we combine text mining information with both protein-protein and regulatory interactions from experimental databases. Clusters of tightly connected genes are delineated from the resulting network, illustrating how such an integrative approach is essential to grasp the current knowledge available for Arabidopsis and to uncover gene information through guilt by association. All large-scale data sets, as well as the manually curated textual data, are made publicly available, hereby stimulating the application of text mining data in future plant biology studies