Integrating Specialized Classifiers Based on Continuous Time Markov Chain

Specialized classifiers, namely those dedicated to a subset of classes, are often adopted in real-world recognition systems. However, integrating such classifiers is nontrivial. Existing methods, e.g. weighted average, usually implicitly assume that all constituents of an ensemble cover the same set of classes. Such methods can produce misleading predictions when used to combine specialized classifiers. This work explores a novel approach. Instead of combining predictions from individual classifiers directly, it first decomposes the predictions into sets of pairwise preferences, treating them as transition channels between classes, and thereon constructs a continuous-time Markov chain, and use the equilibrium distribution of this chain as the final prediction. This way allows us to form a coherent picture over all specialized predictions. On large public datasets, the proposed method obtains considerable improvement compared to mainstream ensemble methods, especially when the classifier coverage is highly unbalanced.Comment: Published at IJCAI-17, typo fixe

Multi-class protein fold classification using a new ensemble machine learning approach.

Protein structure classification represents an important process in understanding the associations between sequence and structure as well as possible functional and evolutionary relationships. Recent structural genomics initiatives and other high-throughput experiments have populated the biological databases at a rapid pace. The amount of structural data has made traditional methods such as manual inspection of the protein structure become impossible. Machine learning has been widely applied to bioinformatics and has gained a lot of success in this research area. This work proposes a novel ensemble machine learning method that improves the coverage of the classifiers under the multi-class imbalanced sample sets by integrating knowledge induced from different base classifiers, and we illustrate this idea in classifying multi-class SCOP protein fold data. We have compared our approach with PART and show that our method improves the sensitivity of the classifier in protein fold classification. Furthermore, we have extended this method to learning over multiple data types, preserving the independence of their corresponding data sources, and show that our new approach performs at least as well as the traditional technique over a single joined data source. These experimental results are encouraging, and can be applied to other bioinformatics problems similarly characterised by multi-class imbalanced data sets held in multiple data sources

Dissimilarity-based Ensembles for Multiple Instance Learning

In multiple instance learning, objects are sets (bags) of feature vectors (instances) rather than individual feature vectors. In this paper we address the problem of how these bags can best be represented. Two standard approaches are to use (dis)similarities between bags and prototype bags, or between bags and prototype instances. The first approach results in a relatively low-dimensional representation determined by the number of training bags, while the second approach results in a relatively high-dimensional representation, determined by the total number of instances in the training set. In this paper a third, intermediate approach is proposed, which links the two approaches and combines their strengths. Our classifier is inspired by a random subspace ensemble, and considers subspaces of the dissimilarity space, defined by subsets of instances, as prototypes. We provide guidelines for using such an ensemble, and show state-of-the-art performances on a range of multiple instance learning problems.Comment: Submitted to IEEE Transactions on Neural Networks and Learning Systems, Special Issue on Learning in Non-(geo)metric Space

Integrative machine learning approach for multi-class SCOP protein fold classification

Classification and prediction of protein structure has been a central research theme in structural bioinformatics. Due to the imbalanced distribution of proteins over multi SCOP classification, most discriminative machine learning suffers the well-known ‘False Positives ’ problem when learning over these types of problems. We have devised eKISS, an ensemble machine learning specifically designed to increase the coverage of positive examples when learning under multiclass imbalanced data sets. We have applied eKISS to classify 25 SCOP folds and show that our learning system improved over classical learning methods

Training of Convolutional Networks on Multiple Heterogeneous Datasets for Street Scene Semantic Segmentation

We propose a convolutional network with hierarchical classifiers for per-pixel semantic segmentation, which is able to be trained on multiple, heterogeneous datasets and exploit their semantic hierarchy. Our network is the first to be simultaneously trained on three different datasets from the intelligent vehicles domain, i.e. Cityscapes, GTSDB and Mapillary Vistas, and is able to handle different semantic level-of-detail, class imbalances, and different annotation types, i.e. dense per-pixel and sparse bounding-box labels. We assess our hierarchical approach, by comparing against flat, non-hierarchical classifiers and we show improvements in mean pixel accuracy of 13.0% for Cityscapes classes and 2.4% for Vistas classes and 32.3% for GTSDB classes. Our implementation achieves inference rates of 17 fps at a resolution of 520x706 for 108 classes running on a GPU.Comment: IEEE Intelligent Vehicles 201