Efficient and Stable Unsupervised Feature Selection Based on Novel Structured Graph and Data Discrepancy Learning.

Unsupervised feature selection is an important tool in data mining, machine learning, and pattern recognition. Although data labels are often missing, the number of data classes can be known and exploited in many scenarios. Therefore, a structured graph, whose number of connected components is identical to the number of data classes, has been proposed and is frequently applied in unsupervised feature selection. However, methods based on the structured graph learning face two problems. First, their structured graphs are not always guaranteed to maintain the same number of connected components as the data classes with existing optimization algorithms. Second, they usually lack strategies for choosing moderate hyperparameters. To solve these problems, an efficient and stable unsupervised feature selection method based on a novel structured graph and data discrepancy learning (ESUFS) is proposed. Specifically, the novel structured graph, consisting of a pairwise data similarity matrix and an indicator matrix, can be efficiently learned by solving a discrete optimization problem. Data discrepancy learning focuses on features that maximize the difference among data and helps in selecting discriminative features. Extensive experiments conducted on various datasets show that ESUFS outperforms state-of-the-art methods not only in accuracy (ACC) but also in stability and speed.

HBcompare: Classifying Ligand Binding Preferences with Hydrogen Bond Topology.

This paper presents HBcompare, a method that classifies protein structures according to ligand binding preference categories by analyzing hydrogen bond topology. HBcompare excludes other characteristics of protein structure so that, in the event of accurate classification, it can implicate the involvement of hydrogen bonds in selective binding. This approach contrasts from methods that represent many aspects of protein structure because holistic representations cannot associate classification with just one characteristic. To our knowledge, HBcompare is the first technique with this capability. On five datasets of proteins that catalyze similar reactions with different preferred ligands, HBcompare correctly categorized proteins with similar ligand binding preferences 89.5% of the time. Using only hydrogen bond topology, classification accuracy with HBcompare surpassed standard structure-based comparison algorithms that use atomic coordinates. As a tool for implicating the role of hydrogen bonds in protein function categories, HBcompare represents a first step towards the automatic explanation of biochemical mechanisms.

Tensor-Based Multi-Modality Feature Selection and Regression for Alzheimer's Disease Diagnosis.

The assessment of Alzheimer's Disease (AD) and Mild Cognitive Impairment (MCI) associated with brain changes remains a challenging task. Recent studies have demonstrated that combination of multi-modality imaging techniques can better reflect pathological characteristics and contribute to more accurate diagnosis of AD and MCI. In this paper, we propose a novel tensor-based multi-modality feature selection and regression method for diagnosis and biomarker identification of AD and MCI from normal controls. Specifically, we leverage the tensor structure to exploit high-level correlation information inherent in the multi-modality data, and investigate tensor-level sparsity in the multilinear regression model. We present the practical advantages of our method for the analysis of ADNI data using three imaging modalities (VBM-MRI, FDG-PET and AV45-PET) with clinical parameters of disease severity and cognitive scores. The experimental results demonstrate the superior performance of our proposed method against the state-of-the-art for the disease diagnosis and the identification of disease-specific regions and modality-related differences. The code for this work is publicly available at https://github.com/junfish/BIOS22.

DeepVASP-E: A Flexible Analysis of Electrostatic Isopotentials for Finding and Explaining Mechanisms that Control Binding Specificity.

Amino acids that play a role in binding specificity can be identified with many methods, but few techniques identify the biochemical mechanisms by which they act. To address a part of this problem, we present DeepVASP-E, an algorithm that can suggest electrostatic mechanisms that influence specificity. DeepVASP-E uses convolutional neural networks to classify an electrostatic representation of ligand binding sites into specificity categories. It also uses class activation mapping to identify regions of electrostatic potential that are salient for classification. We hypothesize that electrostatic regions that are salient for classification are also likely to play a biochemical role in achieving specificity. Our findings, on two families of proteins with electrostatic influences on specificity, suggest that large salient regions can identify amino acids that have an electrostatic role in binding, and that DeepVASP-E is an effective classifier of ligand binding sites.

Color Image and Multispectral Image Denoising Using Block Diagonal Representation.

Filtering images of more than one channel are challenging in terms of both efficiency and effectiveness. By grouping similar patches to utilize the self-similarity and sparse linear approximation of natural images, recent nonlocal and transform-domain methods have been widely used in color and multispectral image (MSI) denoising. Many related methods focus on the modeling of group level correlation to enhance sparsity, which often resorts to a recursive strategy with a large number of similar patches. The importance of the patch level representation is understated. In this paper, we mainly investigate the influence and potential of representation at patch level by considering a general formulation with a block diagonal matrix. We further show that by training a proper global patch basis, along with a local principal component analysis transform in the grouping dimension, a simple transform-threshold-inverse method could produce very competitive results. Fast implementation is also developed to reduce the computational complexity. The extensive experiments on both the simulated and real datasets demonstrate its robustness, effectiveness, and efficiency.

A New 4-D Nonlocal Transform-Domain Filter for 3-D Magnetic Resonance Images Denoising.

The simultaneous removal of noise and preservation of the integrity of 3-D magnetic resonance (MR) images is a difficult and important task. In this paper, we consider characterizing MR images with 3-D operators, and present a novel 4-D transform-domain method termed 'modified nonlocal tensor-SVD (MNL-tSVD)' for MR image denoising. The proposed method is based on the grouping, hard-thresholding and aggregation paradigms, and can be viewed as a generalized nonlocal extension of tensor-SVD (t-SVD). By keeping MR images in its natural three-dimensional form, and collaboratively filtering similar patches, MNL-tSVD utilizes both the self-similarity property and 3-D structure of MR images to preserve more actual details and minimize the introduction of new artifacts. We show the adaptability of MNL-tSVD by incorporating it into a two-stage denoising strategy with a few adjustments. In addition, analysis of the relationship between MNL-tSVD and current the state-of-the-art 4-D transforms is given. Experimental comparisons over simulated and real brain data sets at different Rician noise levels show that MNL-tSVD can produce competitive performance compared with related approaches.