L1pred: A Sequence-Based Prediction Tool for Catalytic Residues in Enzymes with the L1-logreg Classifier

To understand enzyme functions, identifying the catalytic residues is a usual first step. Moreover, knowledge about catalytic residues is also useful for protein engineering and drug-design. However, to experimentally identify catalytic residues remains challenging for reasons of time and cost. Therefore, computational methods have been explored to predict catalytic residues. Here, we developed a new algorithm, L1pred, for catalytic residue prediction, by using the L1-logreg classifier to integrate eight sequence-based scoring functions. We tested L1pred and compared it against several existing sequence-based methods on carefully designed datasets Data604 and Data63. With ten-fold cross-validation, L1pred showed the area under precision-recall curve (AUPR) and the area under ROC curve (AUC) of 0.2198 and 0.9494 on the training dataset, Data604, respectively. In addition, on the independent test dataset, Data63, it showed the AUPR and AUC values of 0.2636 and 0.9375, respectively. Compared with other sequence-based methods, L1pred showed the best performance on both datasets. We also analyzed the importance of each attribute in the algorithm, and found that all the scores contributed more or less equally to the L1pred performance

Distance Metric Learning with Eigenvalue Optimization

Copyright © 2012 Yiming Ying and Peng Li.The main theme of this paper is to develop a novel eigenvalue optimization framework for learning a Mahalanobis metric. Within this context, we introduce a novel metric learning approach called DML-eig which is shown to be equivalent to a well-known eigenvalue optimization problem called minimizing the maximal eigenvalue of a symmetric matrix (Overton, 1988; Lewis and Overton, 1996). Moreover, we formulate LMNN (Weinberger et al., 2005), one of the state-of-the-art metric learning methods, as a similar eigenvalue optimization problem. This novel framework not only provides new insights into metric learning but also opens new avenues to the design of efficient metric learning algorithms. Indeed, first-order algorithms are developed for DML-eig and LMNN which only need the computation of the largest eigenvector of a matrix per iteration. Their convergence characteristics are rigorously established. Various experiments on benchmark data sets show the competitive performance of our new approaches. In addition, we report an encouraging result on a difficult and challenging face verification data set called Labeled Faces in the Wild (LFW)

A Survey on Metric Learning for Feature Vectors and Structured Data

The need for appropriate ways to measure the distance or similarity between data is ubiquitous in machine learning, pattern recognition and data mining, but handcrafting such good metrics for specific problems is generally difficult. This has led to the emergence of metric learning, which aims at automatically learning a metric from data and has attracted a lot of interest in machine learning and related fields for the past ten years. This survey paper proposes a systematic review of the metric learning literature, highlighting the pros and cons of each approach. We pay particular attention to Mahalanobis distance metric learning, a well-studied and successful framework, but additionally present a wide range of methods that have recently emerged as powerful alternatives, including nonlinear metric learning, similarity learning and local metric learning. Recent trends and extensions, such as semi-supervised metric learning, metric learning for histogram data and the derivation of generalization guarantees, are also covered. Finally, this survey addresses metric learning for structured data, in particular edit distance learning, and attempts to give an overview of the remaining challenges in metric learning for the years to come.Comment: Technical report, 59 pages. Changes in v2: fixed typos and improved presentation. Changes in v3: fixed typos. Changes in v4: fixed typos and new method