Guoqiang Han

Incremental Semi-Supervised Clustering Ensemble for High Dimensional Data Clustering

Traditional cluster ensemble approaches have three limitations: (

SC³: Triple Spectral Clustering-Based Consensus Clustering Framework for Class Discovery from Cancer Gene Expression Profiles

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Hybrid Adaptive Classifier Ensemble

) They do not make use of prior knowledge of the datasets given by experts. (

Hybrid Fuzzy Cluster Ensemble Framework for Tumor Clustering from Biomolecular Data

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Semi-supervised ensemble classification in subspaces

) Most of the conventional cluster ensemble methods cannot obtain satisfactory results when handling high dimensional data. (

Adaptive Noise Immune Cluster Ensemble Using Affinity Propagation

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Adaptive fuzzy consensus clustering framework for clustering analysis of cancer data

) All the ensemble members are considered, even the ones without positive contributions. In order to address the limitations of conventional cluster ensemble approaches, we first propose an incremental semi-supervised clustering ensemble framework (ISSCE) which makes use of the advantage of the random subspace technique, the constraint propagation approach, the proposed incremental ensemble member selection process, and the normalized cut algorithm to perform high dimensional data clustering. The random subspace technique is effective for handling high dimensional data, while the constraint propagation approach is useful for incorporating prior knowledge. The incremental ensemble member selection process is newly designed to judiciously remove redundant ensemble members based on a newly proposed local cost function and a global cost function, and the normalized cut algorithm is adopted to serve as the consensus function for providing more stable, robust, and accurate results. Then, a measure is proposed to quantify the similarity between two sets of attributes, and is used for computing the local cost function in ISSCE. Next, we analyze the time complexity of ISSCE theoretically. Finally, a set of nonparametric tests are adopted to compare multiple semi-supervised clustering ensemble approaches over different datasets. The experiments on 18 real-world datasets, which include six UCI datasets and 12 cancer gene expression profiles, confirm that ISSCE works well on datasets with very high dimensionality, and outperforms the state-of-the-art semi-supervised clustering ensemble approaches.

Hybrid clustering solution selection strategy

In order to perform successful diagnosis and treatment of cancer, discovering, and classifying cancer types correctly is essential. One of the challenging properties of class discovery from cancer data sets is that cancer gene expression profiles not only include a large number of genes, but also contains a lot of noisy genes. In order to reduce the effect of noisy genes in cancer gene expression profiles, we propose two new consensus clustering frameworks, named as triple spectral clustering-based consensus clustering (SC^{3}) and double spectral clustering-based consensus clustering (SC^{2}Ncut) in this paper, for cancer discovery from gene expression profiles. SC^{3} integrates the spectral clustering (SC) algorithm multiple times into the ensemble framework to process gene expression profiles. Specifically, spectral clustering is applied to perform clustering on the gene dimension and the cancer sample dimension, and also used as the consensus function to partition the consensus matrix constructed from multiple clustering solutions. Compared with SC^{3}, SC^{2}Ncut adopts the normalized cut algorithm, instead of spectral clustering, as the consensus function. Experiments on both synthetic data sets and real cancer gene expression profiles illustrate that the proposed approaches not only achieve good performance on gene expression profiles, but also outperforms most of the existing approaches in the process of class discovery from these profiles.

From cluster ensemble to structure ensemble

Traditional random subspace-based classifier ensemble approaches (RSCE) have several limitations, such as viewing the same importance for the base classifiers trained in different subspaces, not considering how to find the optimal random subspace set. In this paper, we design a general hybrid adaptive ensemble learning framework (HAEL), and apply it to address the limitations of RSCE. As compared with RSCE, HAEL consists of two adaptive processes, i.e., base classifier competition and classifier ensemble interaction, so as to adjust the weights of the base classifiers in each ensemble and to explore the optimal random subspace set simultaneously. The experiments on the real-world datasets from the KEEL dataset repository for the classification task and the cancer gene expression profiles show that: 1) HAEL works well on both the real-world KEEL datasets and the cancer gene expression profiles and 2) it outperforms most of the state-of-the-art classifier ensemble approaches on 28 out of 36 KEEL datasets and 6 out of 6 cancer datasets.

Probabilistic cluster structure ensemble

Cancer class discovery using biomolecular data is one of the most important tasks for cancer diagnosis and treatment. Tumor clustering from gene expression data provides a new way to perform cancer class discovery. Most of the existing research works adopt single-clustering algorithms to perform tumor clustering is from biomolecular data that lack robustness, stability, and accuracy. To further improve the performance of tumor clustering from biomolecular data, we introduce the fuzzy theory into the cluster ensemble framework for tumor clustering from biomolecular data, and propose four kinds of hybrid fuzzy cluster ensemble frameworks (HFCEF), named as HFCEF-I, HFCEF-II, HFCEF-III, and HFCEF-IV, respectively, to identify samples that belong to different types of cancers. The difference between HFCEF-I and HFCEF-II is that they adopt different ensemble generator approaches to generate a set of fuzzy matrices in the ensemble. Specifically, HFCEF-I applies the affinity propagation algorithm (AP) to perform clustering on the sample dimension and generates a set of fuzzy matrices in the ensemble based on the fuzzy membership function and base samples selected by AP. HFCEF-II adopts AP to perform clustering on the attribute dimension, generates a set of subspaces, and obtains a set of fuzzy matrices in the ensemble by performing fuzzy c-means on subspaces. Compared with HFCEF-I and HFCEF-II, HFCEF-III and HFCEF-IV consider the characteristics of HFCEF-I and HFCEF-II. HFCEF-III combines HFCEF-I and HFCEF-II in a serial way, while HFCEF-IV integrates HFCEF-I and HFCEF-II in a concurrent way. HFCEFs adopt suitable consensus functions, such as the fuzzy c-means algorithm or the normalized cut algorithm (Ncut), to summarize generated fuzzy matrices, and obtain the final results. The experiments on real data sets from UCI machine learning repository and cancer gene expression profiles illustrate that 1) the proposed hybrid fuzzy cluster ensemble frameworks work well on real data sets, especially biomolecular data, and 2) the proposed approaches are able to provide more robust, stable, and accurate results when compared with the state-of-the-art single clustering algorithms and traditional cluster ensemble approaches.