Learn More
In this article we present Supervised Semantic Indexing which defines a class of nonlinear (quadratic) models that are discriminatively trained to directly map from the word content in a query-document or document-document pair to a ranking score. Like Latent Semantic Indexing (LSI), our models take account of correlations between words (synonymy,(More)
Human immunodeficiency virus-1 (HIV-1) in acquired immune deficiency syndrome (AIDS) relies on human host cell proteins in virtually every aspect of its life cycle. Knowledge of the set of interacting human and viral proteins would greatly contribute to our understanding of the mechanisms of infection and subsequently to the design of new therapeutic(More)
Several years after sequencing the human genome and the mouse genome, much remains to be discovered about the functions of most human and mouse genes. Computational prediction of gene function promises to help focus limited experimental resources on the most likely hypotheses. Several algorithms using diverse genomic data have been applied to this task in(More)
MOTIVATION Protein complexes integrate multiple gene products to coordinate many biological functions. Given a graph representing pairwise protein interaction data one can search for subgraphs representing protein complexes. Previous methods for performing such search relied on the assumption that complexes form a clique in that graph. While this assumption(More)
We present a class of nonlinear (polynomial) models that are discriminatively trained to directly map from the word content in a query-document or documentdocument pair to a ranking score. Dealing with polynomial models on word features is computationally challenging. We propose a low-rank (but diagonal preserving) representation of our polynomial models to(More)
Latent semantic analysis (LSA), as one of the most popular unsupervised dimension reduction tools, has a wide range of applications in text mining and information retrieval. The key idea of LSA is to learn a projection matrix that maps the high dimensional vector space representations of documents to a lower dimensional latent space, i.e. so called latent(More)
One of the most important, but often ignored, parts of any clustering and classification algorithm is the computation of the similarity matrix. This is especially important when integrating high throughput biological data sources because of the high noise rates and the many missing values. In this paper we present a new method to compute such similarities(More)
High-throughput methods can directly detect the set of interacting proteins in model species but the results are often incomplete and exhibit high false positive and false negative rates. A number of researchers have recently presented methods for integrating direct and indirect data for predicting interactions. These methods utilize a common classifier for(More)
MOTIVATION Protein-protein interactions (PPIs) are critical for virtually every biological function. Recently, researchers suggested to use supervised learning for the task of classifying pairs of proteins as interacting or not. However, its performance is largely restricted by the availability of truly interacting proteins (labeled). Meanwhile, there(More)
In this paper, we explore supervised classification methods for video shot segmentation. We transform the temporal segmentation problem into a multi-class categorization issue. This approach provides a uniform framework for using different kinds of features extracted from the video and for detecting various types of shot boundaries. The approach utilizes(More)