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The Drosha-DGCR8 complex initiates microRNA maturation by precise cleavage of the stem loops that are embedded in primary transcripts (pri-miRNAs). Here we propose a model for this process that is based upon evidence from both computational and biochemical analyses. A typical metazoan pri-miRNA consists of a stem of approximately 33 bp, with a terminal loop(More)
We consider the problem of learning a local metric to enhance the performance of nearest neighbor classification. Conventional metric learning methods attempt to separate data distributions in a purely discriminative manner; here we show how to take advantage of information from parametric generative models. We focus on the bias in the information-theoretic(More)
Genetic programming is distinguished from other evolutionary algorithms in that it uses tree representations of variable size instead of linear strings of fixed length. The flexible representation scheme is very important because it allows the underlying structure of the data to be discovered automatically. One primary difficulty, however, is that the(More)
Genetic algorithms have been used for neural networks in two main ways: to optimize the network architecture and to train the weights of a xed architecture. While most previous work focuses on only one of these two options, this paper investigates an alternative evolutionary approach called Breeder Genetic Programming (BGP) in which the architecture and the(More)
A genetic programming method is investigated for optimizing both the architecture and the connection weights of multilayer feedforward neural networks. The genotype of each n e t work is represented as a tree whose depth and width are dynamically adapted to the particular application by speciically deened genetic operators. The weights are trained by a(More)
Protein-protein interaction (PPI) extraction has been an important research topic in bio-text mining area, since the PPI information is critical for understanding biological processes. However, there are very few open systems available on the Web and most of the systems focus on keyword searching based on predefined PPIs. PIE (Protein Interaction(More)
In this paper we introduce PubMiner, an intelligent machine learning based text mining system for mining biological information from the literature. PubMiner employs natural language processing techniques and machine learning based data mining techniques for mining useful biological information such as protein-protein interaction from the massive(More)
Most document classification systems consider only the distribution of content words of the documents, ignoring the syntactic information underlying the documents though it is also an important factor. In this paper, we present an approach for classifying large scale unstructured documents by incorporating both the lexical and the syntactic information of(More)
In evolutionary continuous optimization by building and using probabilistic models, the multivariate Gaussian distribution and their variants or extensions such as the mixture of Gaussians have been used popularly. However, this Gaussian assumption is often violated in many real problems. In this paper, we propose a new continuous estimation of distribution(More)