Applicability of semi-supervised learning assumptions for gene ontology terms prediction

Gene Ontology (GO) is one of the most important resources in bioinformatics, aiming to provide a unified framework for the biological annotation of genes and proteins across all species. Predicting GO terms is an essential task for bioinformatics, but the number of available labelled proteins is in several cases insufficient for training reliable machine learning classifiers. Semi-supervised learning methods arise as a powerful solution that explodes the information contained in unlabelled data in order to improve the estimations of traditional supervised approaches. However, semi-supervised learning methods have to make strong assumptions about the nature of the training data and thus, the performance of the predictor is highly dependent on these assumptions. This paper presents an analysis of the applicability of semi-supervised learning assumptions over the specific task of GO terms prediction, focused on providing judgment elements that allow choosing the most suitable tools for specific GO terms. The results show that semi-supervised approaches significantly outperform the traditional supervised methods and that the highest performances are reached when applying the cluster assumption. Besides, it is experimentally demonstrated that cluster and manifold assumptions are complimentary to each other and an analysis of which GO terms can be more prone to be correctly predicted with each assumption, is provided.Postprint (published version

A novel two stage scheme utilizing the test set for model selection in text classification

Text classification is a natural application domain for semi-supervised learning, as labeling documents is expensive, but on the other hand usually an abundance of unlabeled documents is available. We describe a novel simple two stage scheme based on dagging which allows for utilizing the test set in model selection. The dagging ensemble can also be used by itself instead of the original classifier. We evaluate the performance of a meta classifier choosing between various base learners and their respective dagging ensembles. The selection process seems to perform robustly especially for small percentages of available labels for training

A novel spectral-spatial co-training algorithm for the transductive classification of hyperspectral imagery data

The automatic classification of hyperspectral data is made complex by several factors, such as the high cost of true sample labeling coupled with the high number of spectral bands, as well as the spatial correlation of the spectral signature. In this paper, a transductive collective classifier is proposed for dealing with all these factors in hyperspectral image classification. The transductive inference paradigm allows us to reduce the inference error for the given set of unlabeled data, as sparsely labeled pixels are learned by accounting for both labeled and unlabeled information. The collective inference paradigm allows us to manage the spatial correlation between spectral responses of neighboring pixels, as interacting pixels are labeled simultaneously. In particular, the innovative contribution of this study includes: (1) the design of an application-specific co-training schema to use both spectral information and spatial information, iteratively extracted at the object (set of pixels) level via collective inference; (2) the formulation of a spatial-aware example selection schema that accounts for the spatial correlation of predicted labels to augment training sets during iterative learning and (3) the investigation of a diversity class criterion that allows us to speed-up co-training classification. Experimental results validate the accuracy and efficiency of the proposed spectral-spatial, collective, co-training strategy