Stable Feature Selection for Biomarker Discovery

Feature selection techniques have been used as the workhorse in biomarker discovery applications for a long time. Surprisingly, the stability of feature selection with respect to sampling variations has long been under-considered. It is only until recently that this issue has received more and more attention. In this article, we review existing stable feature selection methods for biomarker discovery using a generic hierarchal framework. We have two objectives: (1) providing an overview on this new yet fast growing topic for a convenient reference; (2) categorizing existing methods under an expandable framework for future research and development

Use of pre-transformation to cope with outlying values in important candidate genes

Outlying values in predictors often strongly affect the results of statistical analyses in high-dimensional settings. Although they frequently occur with most high-throughput techniques, the problem is often ignored in the literature. We suggest to use a very simple transformation, proposed before in a different context by Royston and Sauerbrei, as an intermediary step between array normalization and high-level statistical analysis. This straightforward univariate transformation identifies extreme values and reduces the influence of outlying values considerably in all further steps of statistical analysis without eliminating the incriminated observation or feature. The use of the transformation and its effects are demonstrated for diverse univariate and multivariate statistical analyses using nine publicly available microarray data sets

Identification of functionally related enzymes by learning-to-rank methods

Enzyme sequences and structures are routinely used in the biological sciences as queries to search for functionally related enzymes in online databases. To this end, one usually departs from some notion of similarity, comparing two enzymes by looking for correspondences in their sequences, structures or surfaces. For a given query, the search operation results in a ranking of the enzymes in the database, from very similar to dissimilar enzymes, while information about the biological function of annotated database enzymes is ignored. In this work we show that rankings of that kind can be substantially improved by applying kernel-based learning algorithms. This approach enables the detection of statistical dependencies between similarities of the active cleft and the biological function of annotated enzymes. This is in contrast to search-based approaches, which do not take annotated training data into account. Similarity measures based on the active cleft are known to outperform sequence-based or structure-based measures under certain conditions. We consider the Enzyme Commission (EC) classification hierarchy for obtaining annotated enzymes during the training phase. The results of a set of sizeable experiments indicate a consistent and significant improvement for a set of similarity measures that exploit information about small cavities in the surface of enzymes

Learning Deep Context-aware Features over Body and Latent Parts for Person Re-identification

Person Re-identification (ReID) is to identify the same person across different cameras. It is a challenging task due to the large variations in person pose, occlusion, background clutter, etc How to extract powerful features is a fundamental problem in ReID and is still an open problem today. In this paper, we design a Multi-Scale Context-Aware Network (MSCAN) to learn powerful features over full body and body parts, which can well capture the local context knowledge by stacking multi-scale convolutions in each layer. Moreover, instead of using predefined rigid parts, we propose to learn and localize deformable pedestrian parts using Spatial Transformer Networks (STN) with novel spatial constraints. The learned body parts can release some difficulties, eg pose variations and background clutters, in part-based representation. Finally, we integrate the representation learning processes of full body and body parts into a unified framework for person ReID through multi-class person identification tasks. Extensive evaluations on current challenging large-scale person ReID datasets, including the image-based Market1501, CUHK03 and sequence-based MARS datasets, show that the proposed method achieves the state-of-the-art results.Comment: Accepted by CVPR 201