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In eukaryotes, protein ubiquitylation is an important type of post-translation modification, in which the ubiquitin conjugates to a substrate protein. To have a better insight of the mechanisms underlying ubiquitylation, a key step is to identify protein ubiquitylation sites. Many existing computational methods are based on feature engineering, which may lead to biased and incomplete features. Deep...
In functional genomics, small interfering RNA (siRNA) can be used to knockdown gene expression. Usually, a target gene has numerous potential siRNAs, but their efficiencies of gene silencing often varies. Thus, for a successful RNA interference (RNAi), selecting the most effective siRNA is a critical step. Despite various computational algorithms have been developed, the efficacy prediction accuracy...
Formal program verification is a powerful technique to ensure the correctness of programs. To perform this technique, one oftentimes needs to manually specify assertions, which is a time-consuming and error-prone task. Generating assertions automatically can significantly improve the usability of formal program verification. To decide where an assertion is needed heavily and which value range of the...
The curse of dimensionality in machine learning we are introducing in this paper is caused by increasing data, and the research focus of feature selection is described. The formalized definitions of redundancy and relevance of feature are presented. Based on entropy and mutual information of information theory, the issue of how to measure the relevance between features is discussed. The main contributions...
This letter focuses on solving the challenging problem of detecting natural image boundaries. A boundary usually refers to the border between two regions with different semantic meanings. Therefore, a measurement of dissimilarity between image regions plays a pivotal role in boundary detection of natural images. To improve the performance of boundary detection, a Learning-based Boundary Metric (LBM)...
In case of the unknown production quality information, the clustering method with process data is used to acquire the production status. Feature extraction is an important factor to ensure the accurate rate of clustering. As a common non-linear feature extraction method, kernel principal component analysis uses the variance as the information metric. Because the variance is not always effective in...
Due to the general lack of experimental data for biochemical pathway model identification, cell-level time series experimental design is particularly important in current systems biology research. This paper investigates the problem of experimental design for signal transduction pathway modeling, and in particular, focuses on methods for parametric feature selection. An important problem is the estimation...
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