This paper proposes a unified approach to learning in environments in which patterns can be represented in variable-dimension domains, which nicely includes the case in which there are missing features. The proposal is based on the representation of the environment by pointwise constraints that are shown to model naturally pattern relationships that come out in problems of information retrieval, computer vision, and related fields. The given interpretation of learning leads to capturing the truly different aspects of similarity coming from the content at different dimensions and the pattern links. It turns out that functions that process real-valued features and functions that operate on symbolic entities are learned within a unified framework of regularization that can also be expressed using the kernel machines mathematical and algorithmic apparatus. Interestingly, in the extreme cases in which only the content or only the links are available, our theory returns classic kernel machines or graph regularization, respectively. We show experimental results that provide clear evidence of the remarkable improvements that are obtained when both types of similarities are exploited on artificial and real-world benchmarks.

BACKGROUND: Protein-protein interactions can be seen as a hierarchical process occurring at three related levels: proteins bind by means of specific domains, which in turn form interfaces through patches of residues. Detailed knowledge about which domains and residues are involved in a given interaction has extensive applications to biology, including better understanding of the binding process and more efficient drug/enzyme design. Alas, most current interaction prediction methods do not identify which parts of a protein actually instantiate an interaction. Furthermore, they also fail to leverage the hierarchical nature of the problem, ignoring otherwise useful information available at the lower levels; when they do, they do not generate predictions that are guaranteed to be consistent between levels. RESULTS: Inspired by earlier ideas of Yip et al. (BMC Bioinformatics 10:241, 2009), in the present paper we view the problem as a multi-level learning task, with one task per level (proteins, domains and residues), and propose a machine learning method that collectively infers the binding state of all object pairs. Our method is based on Semantic Based Regularization (SBR), a flexible and theoretically sound machine learning framework that uses First Order Logic constraints to tie the learning tasks together. We introduce a set of biologically motivated rules that enforce consistent predictions between the hierarchy levels. CONCLUSIONS: We study the empirical performance of our method using a standard validation procedure, and compare its performance against the only other existing multi-level prediction technique. We present results showing that our method substantially outperforms the competitor in several experimental settings, indicating that exploiting the hierarchical nature of the problem can lead to better predictions. In addition, our method is also guaranteed to produce interactions that are consistent with respect to the protein-domain-residue hierarchy.

Semantic Based Regularization (SBR) is a framework for injecting prior knowledge expressed as FOL clauses into a semi-supervised learning problem. The prior knowledge is converted into a set of continuous constraints, which are enforced during training. SBR employs the prior knowledge only at training time, hoping that the learning process is able to encode the knowledge via the training data into its parameters. This paper defines a collective classification approach employing the prior knowledge at test time, naturally reusing most of the mathematical apparatus developed for standard SBR. The experimental results show that the presented method outperforms state-of-the-art classification methods on multiple text categorization tasks.

Classical foundations of Statistical Learning Theory rely on the assumption that the input patterns are independently and identically distributed. However, in many applications, the inputs, represented as feature vectors, are also embedded into a network of pair wise relations. Transductive approaches like graph regularization rely on the network topology without considering the feature vectors. Semi-supervised approaches like Manifold Regularization learn a function taking the feature vectors as input, while being smooth over the network connections. In this latter case, the connectivity information is processed at training time, but is still neglected during generalization, as the final classification decision takes only the feature vector representations as input. This paper presents and evaluates a model merging the advantages of graph regularization and kernel machines for transductive classification problems.