Nonparametric Feature Extraction from Dendrograms

We propose feature extraction from dendrograms in a nonparametric way. The Minimax distance measures correspond to building a dendrogram with single linkage criterion, with defining specific forms of a level function and a distance function over that. Therefore, we extend this method to arbitrary dendrograms. We develop a generalized framework wherein different distance measures can be inferred from different types of dendrograms, level functions and distance functions. Via an appropriate embedding, we compute a vector-based representation of the inferred distances, in order to enable many numerical machine learning algorithms to employ such distances. Then, to address the model selection problem, we study the aggregation of different dendrogram-based distances respectively in solution space and in representation space in the spirit of deep representations. In the first approach, for example for the clustering problem, we build a graph with positive and negative edge weights according to the consistency of the clustering labels of different objects among different solutions, in the context of ensemble methods. Then, we use an efficient variant of correlation clustering to produce the final clusters. In the second approach, we investigate the sequential combination of different distances and features sequentially in the spirit of multi-layered architectures to obtain the final features. Finally, we demonstrate the effectiveness of our approach via several numerical studies

A study of hierarchical and flat classification of proteins

Automatic classification of proteins using machine learning is an important problem that has received significant attention in the literature. One feature of this problem is that expert-defined hierarchies of protein classes exist and can potentially be exploited to improve classification performance. In this article we investigate empirically whether this is the case for two such hierarchies. We compare multi-class classification techniques that exploit the information in those class hierarchies and those that do not, using logistic regression, decision trees, bagged decision trees, and support vector machines as the underlying base learners. In particular, we compare hierarchical and flat variants of ensembles of nested dichotomies. The latter have been shown to deliver strong classification performance in multi-class settings. We present experimental results for synthetic, fold recognition, enzyme classification, and remote homology detection data. Our results show that exploiting the class hierarchy improves performance on the synthetic data, but not in the case of the protein classification problems. Based on this we recommend that strong flat multi-class methods be used as a baseline to establish the benefit of exploiting class hierarchies in this area

Dynamic Metric Learning from Pairwise Comparisons

Recent work in distance metric learning has focused on learning transformations of data that best align with specified pairwise similarity and dissimilarity constraints, often supplied by a human observer. The learned transformations lead to improved retrieval, classification, and clustering algorithms due to the better adapted distance or similarity measures. Here, we address the problem of learning these transformations when the underlying constraint generation process is nonstationary. This nonstationarity can be due to changes in either the ground-truth clustering used to generate constraints or changes in the feature subspaces in which the class structure is apparent. We propose Online Convex Ensemble StrongLy Adaptive Dynamic Learning (OCELAD), a general adaptive, online approach for learning and tracking optimal metrics as they change over time that is highly robust to a variety of nonstationary behaviors in the changing metric. We apply the OCELAD framework to an ensemble of online learners. Specifically, we create a retro-initialized composite objective mirror descent (COMID) ensemble (RICE) consisting of a set of parallel COMID learners with different learning rates, demonstrate RICE-OCELAD on both real and synthetic data sets and show significant performance improvements relative to previously proposed batch and online distance metric learning algorithms.Comment: to appear Allerton 2016. arXiv admin note: substantial text overlap with arXiv:1603.0367