ProDis-ContSHC: learning protein dissimilarity measures and hierarchical context coherently for protein-protein comparison in protein database retrieval

Large-Scale Multi-modal Distance Metric Learning with Application to Content-Based Information Retrieval and Image Classification

Metric learning algorithms aim to make the conceptually related data items closer and keep dissimilar ones at a distance. The most common approach for metric learning on the Mahalanobis method. Despite its success, this method is limited to find a linear projection and also suffer from scalability respecting both the dimensionality and the size of input data. To address these problems, this paper presents a new scalable metric learning algorithm for multi-modal data. Our method learns an optimal metric for any feature set of the multi-modal data in an online fashion. We also combine the learned metrics with a novel Passive/Aggressive (PA)-based algorithm which results in a higher convergence rate compared to the state-of-the-art methods. To address scalability with respect to dimensionality, Dual Random Projection (DRP) is adopted in this paper. The present method is evaluated on some challenging machine vision datasets for image classification and Content-Based Information Retrieval (CBIR) tasks. The experimental results confirm that the proposed method significantly surpasses other state-of-the-art metric learning methods in most of these datasets in terms of both accuracy and efficiency.

A Guaranteed Similarity Metric Learning Framework for Biological Sequence Comparison

Similarity of sequences is a key mathematical notion for Classification and Phylogenetic studies in Biology. The distance and similarity between two sequence are very important and widely studied. During the last decades, Similarity(distance) metric learning is one of the hottest topics of machine learning/data mining as well as their applications in the bioinformatics field. It is feasible to introduce machine learning technology to learn similarity metric from biological data. In this paper, we propose a novel framework of guaranteed similarity metric learning (GMSL) to perform alignment of biology sequences in any feature vector space. It introduces the (ϵ, γ, τ)-goodness similarity theory to Mahalanobis metric learning. As a theoretical guaranteed similarity metric learning approach, GMSL guarantees that the learned similarity function performs well in classification and clustering. Our experiments on the most used datasets demonstrate that our approach outperforms the state-of-the-art biological sequences alignment methods and other similarity metric learning algorithms in both accuracy and stability.

CMsearch: simultaneous exploration of protein sequence space and structure space improves not only protein homology detection but also protein structure prediction

MOTIVATION

Protein homology detection, a fundamental problem in computational biology, is an indispensable step toward predicting protein structures and understanding protein functions. Despite the advances in recent decades on sequence alignment, threading and alignment-free methods, protein homology detection remains a challenging open problem. Recently, network methods that try to find transitive paths in the protein structure space demonstrate the importance of incorporating network information of the structure space. Yet, current methods merge the sequence space and the structure space into a single space, and thus introduce inconsistency in combining different sources of information.

METHOD

We present a novel network-based protein homology detection method, CMsearch, based on cross-modal learning. Instead of exploring a single network built from the mixture of sequence and structure space information, CMsearch builds two separate networks to represent the sequence space and the structure space. It then learns sequence-structure correlation by simultaneously taking sequence information, structure information, sequence space information and structure space information into consideration.

RESULTS

We tested CMsearch on two challenging tasks, protein homology detection and protein structure prediction, by querying all 8332 PDB40 proteins. Our results demonstrate that CMsearch is insensitive to the similarity metrics used to define the sequence and the structure spaces. By using HMM-HMM alignment as the sequence similarity metric, CMsearch clearly outperforms state-of-the-art homology detection methods and the CASP-winning template-based protein structure prediction methods.

AVAILABILITY AND IMPLEMENTATION

Our program is freely available for download from http://sfb.kaust.edu.sa/Pages/Software.aspx

CONTACT

: xin.gao@kaust.edu.sa

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

LigandRFs: random forest ensemble to identify ligand-binding residues from sequence information alone

Background

Protein-ligand binding is important for some proteins to perform their functions. Protein-ligand binding sites are the residues of proteins that physically bind to ligands. Despite of the recent advances in computational prediction for protein-ligand binding sites, the state-of-the-art methods search for similar, known structures of the query and predict the binding sites based on the solved structures. However, such structural information is not commonly available.

Results

In this paper, we propose a sequence-based approach to identify protein-ligand binding residues. We propose a combination technique to reduce the effects of different sliding residue windows in the process of encoding input feature vectors. Moreover, due to the highly imbalanced samples between the ligand-binding sites and non ligand-binding sites, we construct several balanced data sets, for each of which a random forest (RF)-based classifier is trained. The ensemble of these RF classifiers forms a sequence-based protein-ligand binding site predictor.

Conclusions

Experimental results on CASP9 and CASP8 data sets demonstrate that our method compares favorably with the state-of-the-art protein-ligand binding site prediction methods.