Metric learning pairwise kernel for graph inference

Much recent work in bioinformatics has focused on the inference of various types of biological networks, representing gene regulation, metabolic processes, protein-protein interactions, etc. A common setting involves inferring network edges in a supervised fashion from a set of high-confidence edges, possibly characterized by multiple, heterogeneous data sets (protein sequence, gene expression, etc.). Here, we distinguish between two modes of inference in this setting: direct inference based upon similarities between nodes joined by an edge, and indirect inference based upon similarities between one pair of nodes and another pair of nodes. We propose a supervised approach for the direct case by translating it into a distance metric learning problem. A relaxation of the resulting convex optimization problem leads to the support vector machine (SVM) algorithm with a particular kernel for pairs, which we call the metric learning pairwise kernel (MLPK). We demonstrate, using several real biological networks, that this direct approach often improves upon the state-of-the-art SVM for indirect inference with the tensor product pairwise kernel

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

Person re-identification via efficient inference in fully connected CRF

In this paper, we address the problem of person re-identification problem, i.e., retrieving instances from gallery which are generated by the same person as the given probe image. This is very challenging because the person's appearance usually undergoes significant variations due to changes in illumination, camera angle and view, background clutter, and occlusion over the camera network. In this paper, we assume that the matched gallery images should not only be similar to the probe, but also be similar to each other, under suitable metric. We express this assumption with a fully connected CRF model in which each node corresponds to a gallery and every pair of nodes are connected by an edge. A label variable is associated with each node to indicate whether the corresponding image is from target person. We define unary potential for each node using existing feature calculation and matching techniques, which reflect the similarity between probe and gallery image, and define pairwise potential for each edge in terms of a weighed combination of Gaussian kernels, which encode appearance similarity between pair of gallery images. The specific form of pairwise potential allows us to exploit an efficient inference algorithm to calculate the marginal distribution of each label variable for this dense connected CRF. We show the superiority of our method by applying it to public datasets and comparing with the state of the art.Comment: 7 pages, 4 figure

Extracting Biomolecular Interactions Using Semantic Parsing of Biomedical Text

We advance the state of the art in biomolecular interaction extraction with three contributions: (i) We show that deep, Abstract Meaning Representations (AMR) significantly improve the accuracy of a biomolecular interaction extraction system when compared to a baseline that relies solely on surface- and syntax-based features; (ii) In contrast with previous approaches that infer relations on a sentence-by-sentence basis, we expand our framework to enable consistent predictions over sets of sentences (documents); (iii) We further modify and expand a graph kernel learning framework to enable concurrent exploitation of automatically induced AMR (semantic) and dependency structure (syntactic) representations. Our experiments show that our approach yields interaction extraction systems that are more robust in environments where there is a significant mismatch between training and test conditions.Comment: Appearing in Proceedings of the Thirtieth AAAI Conference on Artificial Intelligence (AAAI-16