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 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

GraphFC: Customs Fraud Detection with Label Scarcity

Custom officials across the world encounter huge volumes of transactions. With increased connectivity and globalization, the customs transactions continue to grow every year. Associated with customs transactions is the customs fraud - the intentional manipulation of goods declarations to avoid the taxes and duties. With limited manpower, the custom offices can only undertake manual inspection of a limited number of declarations. This necessitates the need for automating the customs fraud detection by machine learning (ML) techniques. Due the limited manual inspection for labeling the new-incoming declarations, the ML approach should have robust performance subject to the scarcity of labeled data. However, current approaches for customs fraud detection are not well suited and designed for this real-world setting. In this work, we propose $\textbf{GraphFC}$ ($\textbf{Graph}$ neural networks for $\textbf{C}$ustoms $\textbf{F}$raud), a model-agnostic, domain-specific, semi-supervised graph neural network based customs fraud detection algorithm that has strong semi-supervised and inductive capabilities. With upto 252% relative increase in recall over the present state-of-the-art, extensive experimentation on real customs data from customs administrations of three different countries demonstrate that GraphFC consistently outperforms various baselines and the present state-of-art by a large margin

Transforming Graph Representations for Statistical Relational Learning

Relational data representations have become an increasingly important topic due to the recent proliferation of network datasets (e.g., social, biological, information networks) and a corresponding increase in the application of statistical relational learning (SRL) algorithms to these domains. In this article, we examine a range of representation issues for graph-based relational data. Since the choice of relational data representation for the nodes, links, and features can dramatically affect the capabilities of SRL algorithms, we survey approaches and opportunities for relational representation transformation designed to improve the performance of these algorithms. This leads us to introduce an intuitive taxonomy for data representation transformations in relational domains that incorporates link transformation and node transformation as symmetric representation tasks. In particular, the transformation tasks for both nodes and links include (i) predicting their existence, (ii) predicting their label or type, (iii) estimating their weight or importance, and (iv) systematically constructing their relevant features. We motivate our taxonomy through detailed examples and use it to survey and compare competing approaches for each of these tasks. We also discuss general conditions for transforming links, nodes, and features. Finally, we highlight challenges that remain to be addressed

A Very Brief Introduction to Machine Learning With Applications to Communication Systems

Given the unprecedented availability of data and computing resources, there is widespread renewed interest in applying data-driven machine learning methods to problems for which the development of conventional engineering solutions is challenged by modelling or algorithmic deficiencies. This tutorial-style paper starts by addressing the questions of why and when such techniques can be useful. It then provides a high-level introduction to the basics of supervised and unsupervised learning. For both supervised and unsupervised learning, exemplifying applications to communication networks are discussed by distinguishing tasks carried out at the edge and at the cloud segments of the network at different layers of the protocol stack