Feature selection techniques have become an apparent need in many bioinformatics applications. In addition to the large pool of techniques that have already been developed in the machine learning and data mining fields, specific applications in bioinformatics have led to a wealth of newly proposed techniques.

In this article, we make the interested reader aware of the possibilities of feature selection, providing a basic taxonomy of feature selection techniques, and discussing their use, variety and potential in a number of both common as well as upcoming bioinformatics applications.

Contact: yvan.saeys@psb.ugent.be

Supplementary information: http://bioinformatics.psb.ugent.be/supplementary_data/yvsae/fsreview

A review of feature selection techniques in bioinformatics

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评《Oxford Advanced Learner’s Dictionary of Current English》第五版

This chapter introduces the subject of statistical pattern recognition (SPR). It starts by considering how features are defined and emphasizes that the nearest neighbor algorithm achieves error rates comparable with those of an ideal Bayes’ classifier. The concepts of an optimal number of features, representativeness of the training data, and the need to avoid overfitting to the training data are stressed. The chapter shows that methods such as the support vector machine and artificial neural networks are subject to these same training limitations, although each has its advantages. For neural networks, the multilayer perceptron architecture and back-propagation algorithm are described. The chapter distinguishes between supervised and unsupervised learning, demonstrating the advantages of the latter and showing how methods such as clustering and principal components analysis fit into the SPR framework. The chapter also defines the receiver operating characteristic, which allows an optimum balance between false positives and false negatives to be achieved.

Statistical Pattern Recognition

Ensemble learning is an intensively studies technique in machine learning and pattern recognition. Recent work in computational biology has seen an increasing use of ensemble learning methods due to their unique advantages in dealing with small sample size, high-dimensionality, and complexity data structures. The aim of this article is two-fold. First, it is to provide a review of the most widely used ensemble learning methods and their application in various bioinformatics problems, including the main topics of gene expression, mass spectrometry-based proteomics, gene-gene interaction identification from genome-wide association studies, and prediction of regulatory elements from DNA and protein sequences. Second, we try to identify and summarize future trends of ensemble methods in bioinformatics. Promising directions such as ensemble of support vector machine, meta-ensemble, and ensemble based feature selection are discussed.

A Review of Ensemble Methods in Bioinformatics

Image segmentation is a critical and important step in (GEographic) Object-Based Image Analysis (GEOBIA or OBIA). The final feature extraction and classification in OBIA is highly dependent on the quality of image segmentation. Segmentation has been used in remote sensing image processing since the advent of the Landsat-1 satellite. However, after the launch of the high-resolution IKONOS satellite in 1999, the paradigm of image analysis moved from pixel-based to object-based. As a result, the purpose of segmentation has been changed from helping pixel labeling to object identification. Although several articles have reviewed segmentation algorithms, it is unclear if some segmentation algorithms are generally more suited for (GE)OBIA than others. This article has conducted an extensive state-of-the-art survey on OBIA techniques, discussed different segmentation techniques and their applicability to OBIA. Conceptual details of those techniques are explained along with the strengths and weaknesses. The available tools and software packages for segmentation are also summarized. The key challenge in image segmentation is to select optimal parameters and algorithms that can general image objects matching with the meaningful geographic objects. Recent research indicates an apparent movement towards the improvement of segmentation algorithms, aiming at more accurate, automated, and computationally efficient techniques.

Segmentation for Object-Based Image Analysis (OBIA): A review of algorithms and challenges from remote sensing perspective

The use of mass spectrometry as a proteomics tool is poised to revolutionize early disease diagnosis and biomarker identification. Unfortunately, before standard supervised classification algorithms can be employed, the "curse of dimensionality" needs to be solved. Due to the sheer amount of information contained within the mass spectra, most standard machine learning techniques cannot be directly applied. Instead, feature selection techniques are used to first reduce the dimensionality of the input space and thus enable the subsequent use of classification algorithms. This paper examines feature selection techniques for proteomic mass spectrometry. This study examines the performance of the nearest centroid classifier coupled with the following feature selection algorithms. Student-t test, Kolmogorov-Smirnov test, and the P-test are univariate statistics used for filter-based feature ranking. From the wrapper approaches we tested sequential forward selection and a modified version of sequential backward selection. Embedded approaches included shrunken nearest centroid and a novel version of boosting based feature selection we developed. In addition, we tested several dimensionality reduction approaches, namely principal component analysis and principal component analysis coupled with linear discriminant analysis. To fairly assess each algorithm, evaluation was done using stratified cross validation with an internal leave-one-out cross-validation loop for automated feature selection. Comprehensive experiments, conducted on five popular cancer data sets, revealed that the less advocated sequential forward selection and boosted feature selection algorithms produce the most consistent results across all data sets. In contrast, the state-of-the-art performance reported on isolated data sets for several of the studied algorithms, does not hold across all data sets. This study tested a number of popular feature selection methods using the nearest centroid classifier and found that several reportedly state-of-the-art algorithms in fact perform rather poorly when tested via stratified cross-validation. The revealed inconsistencies provide clear evidence that algorithm evaluation should be performed on several data sets using a consistent (i.e., non-randomized, stratified) cross-validation procedure in order for the conclusions to be statistically sound.

/pdf/feature-selection-and-nearest-centroid-classification-for-1r31gstjjb.pdf

Feature selection and nearest centroid classification for protein mass spectrometry

This paper presents a novel approach for creation of topographical function and object markers used within watershed segmentation. Typically, marker-driven watershed segmentation extracts seeds indicating the presence of objects or background at specific image locations. The marker locations are then set to be regional minima within the topological surface (typically, the gradient of the original input image), and the watershed algorithm is applied. In contrast, our approach uses two classifiers, one trained to produce markers, the other trained to produce object boundaries. As a result of using machine-learned pixel classification, the proposed algorithm is directly applicable to both single channel and multichannel image data. Additionally, rather than flooding the gradient image, we use the inverted probability map produced by the second aforementioned classifier as input to the watershed algorithm. Experimental results demonstrate the superior performance of the classification-driven watershed segmentation algorithm for the tasks of 1) image-based granulometry and 2) remote sensing

Classification-Driven Watershed Segmentation

Ore image segmentation by learning image and shape features

Admissible and consistent heuristic functions are usually preferred in single-agent heuristic search as they guarantee optimal solutions with complete search methods such as A* and IDA*. Larger problems, however, frequently make a complete search intractable due to space and/or time limitations. In particular, a path-planning agent in a real-time strategy game may need to take an action before its complete search has the time to finish. In such cases, incomplete search techniques (such as RTA*, SRTA*, RTDP, DTA*) can be used. Such algorithms conduct a limited ply lookahead and then evaluate the states envisioned using a heuristic function. The action selected on the basis of such evaluations can be suboptimal due to the incompleteness of search and inaccuracies in the heuristic. It is usually believed that deeper lookahead increases the chances of taking the optimal action. In this paper, we demonstrate that this is not necessarily the case, even when admissible and consistent heuristic functions are used.

/pdf/lookahead-pathologies-for-single-agent-search-3pclrp7ju9.pdf

Lookahead pathologies for single agent search

Automated image interpretation is an important task with numerous applications. Until recently, designing such systems required extensive subject matter and computer vision expertise resulting in poor cross-domain portability and expensive maintenance. Recently, a machine-learned system (ADORE) was successfully applied in an aerial image interpretation domain. Subsequently, it was re-trained for another man-made object recognition task. In this paper we propose and implement several extensions of ADORE addressing its primary limitations. These extensions enable the first successful application of this emerging AI technology to a natural image interpretation domain. The resulting system is shown to be robust with respect to noise in the training data, illumination, and camera angle variations as well as competitively adaptive with respect to novel images.

/pdf/machine-learning-for-adaptive-image-interpretation-4fg66bvuc7.pdf

Ilya Levner

Papers

Feature selection and nearest centroid classification for protein mass spectrometry

Classification-Driven Watershed Segmentation

Ore image segmentation by learning image and shape features

Lookahead pathologies for single agent search

Machine learning for adaptive image interpretation