Kernel methods in genomics and computational biology

Support vector machines and kernel methods are increasingly popular in genomics and computational biology, due to their good performance in real-world applications and strong modularity that makes them suitable to a wide range of problems, from the classification of tumors to the automatic annotation of proteins. Their ability to work in high dimension, to process non-vectorial data, and the natural framework they provide to integrate heterogeneous data are particularly relevant to various problems arising in computational biology. In this chapter we survey some of the most prominent applications published so far, highlighting the particular developments in kernel methods triggered by problems in biology, and mention a few promising research directions likely to expand in the future

Exact and efficient top-K inference for multi-target prediction by querying separable linear relational models

Many complex multi-target prediction problems that concern large target spaces are characterised by a need for efficient prediction strategies that avoid the computation of predictions for all targets explicitly. Examples of such problems emerge in several subfields of machine learning, such as collaborative filtering, multi-label classification, dyadic prediction and biological network inference. In this article we analyse efficient and exact algorithms for computing the top-$K$ predictions in the above problem settings, using a general class of models that we refer to as separable linear relational models. We show how to use those inference algorithms, which are modifications of well-known information retrieval methods, in a variety of machine learning settings. Furthermore, we study the possibility of scoring items incompletely, while still retaining an exact top-K retrieval. Experimental results in several application domains reveal that the so-called threshold algorithm is very scalable, performing often many orders of magnitude more efficiently than the naive approach

Attentive monitoring of multiple video streams driven by a Bayesian foraging strategy

In this paper we shall consider the problem of deploying attention to subsets of the video streams for collating the most relevant data and information of interest related to a given task. We formalize this monitoring problem as a foraging problem. We propose a probabilistic framework to model observer's attentive behavior as the behavior of a forager. The forager, moment to moment, focuses its attention on the most informative stream/camera, detects interesting objects or activities, or switches to a more profitable stream. The approach proposed here is suitable to be exploited for multi-stream video summarization. Meanwhile, it can serve as a preliminary step for more sophisticated video surveillance, e.g. activity and behavior analysis. Experimental results achieved on the UCR Videoweb Activities Dataset, a publicly available dataset, are presented to illustrate the utility of the proposed technique.Comment: Accepted to IEEE Transactions on Image Processin