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Protein-protein interactions play a key role in many biological systems. High-throughput methods can directly detect the set of interacting proteins in yeast, but the results are often incomplete and exhibit high false-positive and false-negative rates. Recently, many different research groups independently suggested using supervised learning methods to(More)
In this article we present Supervised Semantic Indexing (SSI) 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)
Although deep neural networks (DNNs) have achieved great success in many computer vision tasks, recent studies have shown they are vulnerable to adversarial examples. Such examples, typically generated by adding small but purposeful distortions, can frequently fool DNN models. Previous studies to defend against ad-versarial examples mostly focused on(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)
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)
In this paper, we propose an efficient embedding for modeling higher-order (n-gram) phrases that projects the n-grams to low-dimensional latent semantic space, where a classification function can be defined. We utilize a deep neural network to build a unified discriminative framework that allows for estimating the parameters of the latent space as well as(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 document-document 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(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)