Algebraic shortcuts for leave-one-out cross-validation in supervised network inference

Supervised machine learning techniques have traditionally been very successful at reconstructing biological networks, such as protein-ligand interaction, protein-protein interaction and gene regulatory networks. Many supervised techniques for network prediction use linear models on a possibly nonlinear pairwise feature representation of edges. Recently, much emphasis has been placed on the correct evaluation of such supervised models. It is vital to distinguish between using a model to either predict new interactions in a given network or to predict interactions for a new vertex not present in the original network. This distinction matters because (i) the performance might dramatically differ between the prediction settings and (ii) tuning the model hyperparameters to obtain the best possible model depends on the setting of interest. Specific cross-validation schemes need to be used to assess the performance in such different prediction settings. In this work we discuss a state-of-the-art kernel-based network inference technique called two-step kernel ridge regression. We show that this regression model can be trained efficiently, with a time complexity scaling with the number of vertices rather than the number of edges. Furthermore, this framework leads to a series of cross-validation shortcuts that allow one to rapidly estimate the model performance for any relevant network prediction setting. This allows computational biologists to fully assess the capabilities of their models

Efficient Regularized Least-Squares Algorithms for Conditional Ranking on Relational Data

In domains like bioinformatics, information retrieval and social network analysis, one can find learning tasks where the goal consists of inferring a ranking of objects, conditioned on a particular target object. We present a general kernel framework for learning conditional rankings from various types of relational data, where rankings can be conditioned on unseen data objects. We propose efficient algorithms for conditional ranking by optimizing squared regression and ranking loss functions. We show theoretically, that learning with the ranking loss is likely to generalize better than with the regression loss. Further, we prove that symmetry or reciprocity properties of relations can be efficiently enforced in the learned models. Experiments on synthetic and real-world data illustrate that the proposed methods deliver state-of-the-art performance in terms of predictive power and computational efficiency. Moreover, we also show empirically that incorporating symmetry or reciprocity properties can improve the generalization performance

A kernel-based framework for learning graded relations from data

Driven by a large number of potential applications in areas like bioinformatics, information retrieval and social network analysis, the problem setting of inferring relations between pairs of data objects has recently been investigated quite intensively in the machine learning community. To this end, current approaches typically consider datasets containing crisp relations, so that standard classification methods can be adopted. However, relations between objects like similarities and preferences are often expressed in a graded manner in real-world applications. A general kernel-based framework for learning relations from data is introduced here. It extends existing approaches because both crisp and graded relations are considered, and it unifies existing approaches because different types of graded relations can be modeled, including symmetric and reciprocal relations. This framework establishes important links between recent developments in fuzzy set theory and machine learning. Its usefulness is demonstrated through various experiments on synthetic and real-world data.Comment: This work has been submitted to the IEEE for possible publication. Copyright may be transferred without notice, after which this version may no longer be accessibl

High-Level Concepts for Affective Understanding of Images

This paper aims to bridge the affective gap between image content and the emotional response of the viewer it elicits by using High-Level Concepts (HLCs). In contrast to previous work that relied solely on low-level features or used convolutional neural network (CNN) as a black-box, we use HLCs generated by pretrained CNNs in an explicit way to investigate the relations/associations between these HLCs and a (small) set of Ekman's emotional classes. As a proof-of-concept, we first propose a linear admixture model for modeling these relations, and the resulting computational framework allows us to determine the associations between each emotion class and certain HLCs (objects and places). This linear model is further extended to a nonlinear model using support vector regression (SVR) that aims to predict the viewer's emotional response using both low-level image features and HLCs extracted from images. These class-specific regressors are then assembled into a regressor ensemble that provide a flexible and effective predictor for predicting viewer's emotional responses from images. Experimental results have demonstrated that our results are comparable to existing methods, with a clear view of the association between HLCs and emotional classes that is ostensibly missing in most existing work