CUSBoost: Cluster-based Under-sampling with Boosting for Imbalanced Classification

Class imbalance classification is a challenging research problem in data mining and machine learning, as most of the real-life datasets are often imbalanced in nature. Existing learning algorithms maximise the classification accuracy by correctly classifying the majority class, but misclassify the minority class. However, the minority class instances are representing the concept with greater interest than the majority class instances in real-life applications. Recently, several techniques based on sampling methods (under-sampling of the majority class and over-sampling the minority class), cost-sensitive learning methods, and ensemble learning have been used in the literature for classifying imbalanced datasets. In this paper, we introduce a new clustering-based under-sampling approach with boosting (AdaBoost) algorithm, called CUSBoost, for effective imbalanced classification. The proposed algorithm provides an alternative to RUSBoost (random under-sampling with AdaBoost) and SMOTEBoost (synthetic minority over-sampling with AdaBoost) algorithms. We evaluated the performance of CUSBoost algorithm with the state-of-the-art methods based on ensemble learning like AdaBoost, RUSBoost, SMOTEBoost on 13 imbalance binary and multi-class datasets with various imbalance ratios. The experimental results show that the CUSBoost is a promising and effective approach for dealing with highly imbalanced datasets.Comment: CSITSS-201

An evaluation of DNA-damage response and cell-cycle pathways for breast cancer classification

Accurate subtyping or classification of breast cancer is important for ensuring proper treatment of patients and also for understanding the molecular mechanisms driving this disease. While there have been several gene signatures proposed in the literature to classify breast tumours, these signatures show very low overlaps, different classification performance, and not much relevance to the underlying biology of these tumours. Here we evaluate DNA-damage response (DDR) and cell cycle pathways, which are critical pathways implicated in a considerable proportion of breast tumours, for their usefulness and ability in breast tumour subtyping. We think that subtyping breast tumours based on these two pathways could lead to vital insights into molecular mechanisms driving these tumours. Here, we performed a systematic evaluation of DDR and cell-cycle pathways for subtyping of breast tumours into the five known intrinsic subtypes. Homologous Recombination (HR) pathway showed the best performance in subtyping breast tumours, indicating that HR genes are strongly involved in all breast tumours. Comparisons of pathway based signatures and two standard gene signatures supported the use of known pathways for breast tumour subtyping. Further, the evaluation of these standard gene signatures showed that breast tumour subtyping, prognosis and survival estimation are all closely related. Finally, we constructed an all-inclusive super-signature by combining (union of) all genes and performing a stringent feature selection, and found it to be reasonably accurate and robust in classification as well as prognostic value. Adopting DDR and cell cycle pathways for breast tumour subtyping achieved robust and accurate breast tumour subtyping, and constructing a super-signature which contains feature selected mix of genes from these molecular pathways as well as clinical aspects is valuable in clinical practice.Comment: 28 pages, 7 figures, 6 table

How to use the Kohonen algorithm to simultaneously analyse individuals in a survey

The Kohonen algorithm (SOM, Kohonen,1984, 1995) is a very powerful tool for data analysis. It was originally designed to model organized connections between some biological neural networks. It was also immediately considered as a very good algorithm to realize vectorial quantization, and at the same time pertinent classification, with nice properties for visualization. If the individuals are described by quantitative variables (ratios, frequencies, measurements, amounts, etc.), the straightforward application of the original algorithm leads to build code vectors and to associate to each of them the class of all the individuals which are more similar to this code-vector than to the others. But, in case of individuals described by categorical (qualitative) variables having a finite number of modalities (like in a survey), it is necessary to define a specific algorithm. In this paper, we present a new algorithm inspired by the SOM algorithm, which provides a simultaneous classification of the individuals and of their modalities.Comment: Special issue ESANN 0

Steps toward a classifier for the Virtual Observatory. I. Classifying the SDSS photometric archive

Modern photometric multiband digital surveys produce large amounts of data that, in order to be effectively exploited, need automatic tools capable to extract from photometric data an objective classification. We present here a new method for classifying objects in large multi-parametric photometric data bases, consisting of a combination of a clustering algorithm and a cluster agglomeration tool. The generalization capabilities and the potentialities of this approach are tested against the complexity of the Sloan Digital Sky Survey archive, for which an example of application is reported.Comment: To appear in the Proceedings of the "1st Workshop of Astronomy and Astrophysics for Students" - Naples, 19-20 April 200