Search

Feature selection has devoted a consistently great amount of effort to dimension reduction for various machine learning tasks. Existing feature selection models focus on selecting the most discriminative features for learning targets. However, this strategy is weak in handling two kinds of features, that is, the irrelevant and redundant ones, which are collectively referred to as noisy features. These features may hamper the construction of optimal low-dimensional subspaces and compromise the learning performance of downstream tasks. In this study, we propose a novel multi-label feature selection approach by embedding label correlations (dubbed ELC) to address these issues. Particularly, we extract label correlations for reliable label space structures and employ them to steer feature selection. In this way, label and feature spaces can be expected to be consistent and noisy features can be effectively eliminated. An extensive experimental evaluation on public benchmarks validated the superiority of ELC. [ABSTRACT FROM AUTHOR]

Selecting functional genes is essential for analyzing microarray data. Among many available feature (gene) selection approaches, the ones on the basis of the large margin nearest neighbor receive more attention due to their low computational costs and high accuracies in analyzing the high-dimensional data. Yet, there still exist some problems that hamper the existing approaches in sifting real target genes, including selecting erroneous nearest neighbors, high sensitivity to irrelevant genes, and inappropriate evaluation criteria. Previous pioneer works have partly addressed some of the problems, but none of them are capable of solving these problems simultaneously. In this paper, we propose a new local-nearest-neighbors-based feature weighting approach to alleviate the above problems. The proposed approach is based on the trick of locally minimizing the within-class distances and maximizing the between-class distances with the $k$ nearest neighbors rule. We further define a feature weight vector, and construct it by minimizing the cost function with a regularization term. The proposed approach can be applied naturally to the multi-class problems and does not require extra modification. Experimental results on the UCI and the open microarray data sets validate the effectiveness and efficiency of the new approach. [ABSTRACT FROM AUTHOR]

The semantic information of documents needs to be represented because it is the basis for many applications, such as document summarization, web search, and text analysis. Although many studies have explored this problem by enriching document vectors with the relatedness of the words involved, the performance remains far from satisfactory because the physical boundaries of documents hinder the evaluation of the relatedness between words. To address this problem, we propose an effective approach to further infer the implicit relatedness between words via their common related words. To avoid overestimation of the implicit relatedness, we restrict the inference in terms of the marginal probabilities of the words based on the law of total probability. The proposed method measures the relatedness between words, which is confirmed theoretically and experimentally. Thorough evaluation on real datasets illustrates that significant improvement on document clustering has been achieved with the proposed method compared with state-of-the-art methods. [ABSTRACT FROM AUTHOR]

Feature selection is crucial, particularly for processing high-dimensional data. Existing selection methods generally compute a discriminant value for a feature with respect to class variable to indicate its classification ability. However, a scalar value can hardly reveal the multifaceted classification abilities of a feature for different subproblems of a complicated multiclass problem. In view of this, we propose to select features based on discrimination structure complementarity. To this end, the classification abilities of a feature for different subproblems are evaluated individually. Consequently, a discrimination structure vector can be obtained to indicate if the feature is discriminative respectively for different subproblems. Based on discrimination structure, indispensable and dispensable features (ID-features for short) are defined. In selection process, the ID-features, which are complementary in discrimination structure to the selected ones, are selected. The proposed method tries to equally treat all subproblems and hence can avoid falling into the pitfall that the discriminative features for difficult subproblems are prone to be covered by the features for easy ones in multi-class classification. Two algorithms are developed and compared with several feature selection methods using some open data sets. Experimental results demonstrate the effectiveness of the proposed method. [ABSTRACT FROM AUTHOR]

Feature selection is important and necessary especially for processing large scale data. Existing feature selection methods generally compute a discriminant value with respect to class variable for a feature to indicate its classification ability. Such a scalar value can hardly reveal the multi-faceted classification abilities of a feature for the different subproblems in a classification task. In this paper, an effective way is proposed for feature selection based on measurement of ability to classify subproblems and discrimination structure complementarity of features. The classification abilities of a feature for different subproblems are calculated respectively. Hence for the feature, a discrimination structure vector representing its classification abilities for all subproblems can be obtained. In feature selection, the features, which can individually classify as many subproblems as possible, are firstly evaluated and selected. Subsequently, their complementary features are selectively chosen, which can complementarily classify the subproblems that the selected features cannot classify. Two algorithms are designed for progressively selecting features, by firstly eliminating irrelevant features and then abandoning redundant features based on discrimination structure complementarity. The proposed algorithms are compared with some related methods for feature selection on some open gene expression datasets and UCI datasets. Experimental results demonstrate the effectiveness of the proposed method. [ABSTRACT FROM AUTHOR]

Many powerful computational methods based on graph neural networks (GNNs) have been proposed to predict drug-protein interactions (DPIs). It can effectively reduce laboratory workload and the cost of drug discovery and drug repurposing. However, many clinical functions of drugs and proteins are unknown due to their unobserved indications. Therefore, it is difficult to establish a reliable drug-protein heterogeneous network that can describe the relationships between drugs and proteins based on the available information. To solve this problem, we propose a DPI prediction method that can self-adaptively adjust the topological structure of the heterogeneous networks, and name it SATS. SATS establishes a representation learning module based on graph attention network to carry out the drug-protein heterogeneous network. It can self-adaptively learn the relationships among the nodes based on their attributes and adjust the topological structure of the network according to the training loss of the model. Finally, SATS predicts the interaction propensity between drugs and proteins based on their embeddings. The experimental results show that SATS can effectively improve the topological structure of the network. The performance of SATS outperforms several state-of-the-art DPI prediction methods under various evaluation metrics. These prove that SATS is useful to deal with incomplete data and unreliable networks. The case studies on the top section of the prediction results further demonstrate that SATS is powerful for discovering novel DPIs.

Detecting associations between an input gene set and annotated gene sets (e.g., pathways) is an important problem in modern molecular biology. In this paper, we propose two algorithms, termed NetPEA and NetPEA', for conducting network-based pathway enrichment analysis. Our algorithms consider not only shared genes but also gene-gene interactions. Both algorithms utilize a protein-protein interaction network and a random walk with a restart procedure to identify hidden relationships between an input gene set and pathways, but both use different randomization strategies to evaluate statistical significance and as a result emphasize different pathway properties. Compared to an over representation-based method, our algorithms can identify more statistically significant pathways. Compared to an existing network-based algorithm, EnrichNet, our algorithms have a higher sensitivity in revealing the true causal pathways while at the same time achieving a higher specificity. A literature review of selected results indicates that some of the novel pathways reported by our algorithms are biologically relevant and important. While the evaluations are performed only with KEGG pathways, we believe the algorithms can be valuable for general functional discovery from high-throughput experiments.

Background: The Receiver Operator Characteristic (ROC) curve is well-known in evaluating classification performance in biomedical field. Owing to its superiority in dealing with imbalanced and cost-sensitive data, the ROC curve has been exploited as a popular metric to evaluate and find out disease-related genes (features). The existing ROC-based feature selection approaches are simple and effective in evaluating individual features. However, these approaches may fail to find real target feature subset due to their lack of effective means to reduce the redundancy between features, which is essential in machine learning., Results: In this paper, we propose to assess feature complementarity by a trick of measuring the distances between the misclassified instances and their nearest misses on the dimensions of pairwise features. If a misclassified instance and its nearest miss on one feature dimension are far apart on another feature dimension, the two features are regarded as complementary to each other. Subsequently, we propose a novel filter feature selection approach on the basis of the ROC analysis. The new approach employs an efficient heuristic search strategy to select optimal features with highest complementarities. The experimental results on a broad range of microarray data sets validate that the classifiers built on the feature subset selected by our approach can get the minimal balanced error rate with a small amount of significant features., Conclusions: Compared with other ROC-based feature selection approaches, our new approach can select fewer features and effectively improve the classification performance.