Related papers: Granular clustering of de novo protein models

As an important technology in artificial intelligence Granular Computing (GrC) has emerged as a new multi-disciplinary paradigm and received much attention in recent years. Information granules forming an abstract and efficient…

We derive an efficient method to perform clustering of nodes in Gaussian graphical models directly from sample data. Nodes are clustered based on the similarity of their network neighborhoods, with edge weights defined by partial…

Deep clustering as an important branch of unsupervised representation learning focuses on embedding semantically similar samples into the identical feature space. This core demand inspires the exploration of contrastive learning and…

Cluster analysis of biological samples using gene expression measurements is a common task which aids the discovery of heterogeneous biological sub-populations having distinct mRNA profiles. Several model-based clustering algorithms have…

We present a novel approach for finding and evaluating structural models of small metallic nanoparticles. Rather than fitting a single model with many degrees of freedom, the approach algorithmically builds libraries of nanoparticle…

Engineering new molecules with desirable functions and properties has the potential to extend our ability to engineer proteins beyond what nature has so far evolved. Advances in the so-called "de novo" design problem have recently been…

The most popular and universally predictive protein simulation models employ all-atom molecular dynamics (MD), but they come at extreme computational cost. The development of a universal, computationally efficient coarse-grained (CG) model…

This paper presents a new, parallel implementation of clustering and demonstrates its utility in greatly speeding up the process of identifying homologous proteins. Clustering is a technique to reduce the number of comparison needed to find…

Traditional clustering algorithms often focus on the most fine-grained information and achieve clustering by calculating the distance between each pair of data points or implementing other calculations based on points. This way is not…

Cluster analysis is one of the essential tasks in data mining and knowledge discovery. Each type of data poses unique challenges in achieving relatively efficient partitioning of the data into homogeneous groups. While the algorithms for…

We use a semisupervised learning algorithm based on a topological data analysis approach to assign functional categories to yeast proteins using similarity graphs. This new approach to analyzing biological networks yields results that are…

Genome wide comparisons between enteric bacteria yield large sets of conserved putative regulatory sites on a gene by gene basis that need to be clustered into regulons. Using the assumption that regulatory sites can be represented as…

Coarse-graining (CG) of molecular simulations simplifies the particle representation by grouping selected atoms into pseudo-beads and drastically accelerates simulation. However, such CG procedure induces information losses, which makes…

In this paper, a novel method to perform model-based clustering of time series is proposed. The procedure relies on two iterative steps: (i) K global forecasting models are fitted via pooling by considering the series pertaining to each…

Constrained clustering has gained significant attention in the field of machine learning as it can leverage prior information on a growing amount of only partially labeled data. Following recent advances in deep generative models, we…

Identifying one or more biologically-active/native decoys from millions of non-native decoys is one of the major challenges in computational structural biology. The extreme lack of balance in positive and negative samples (native and…

A model involving Gaussian processes (GPs) is introduced to simultaneously handle multi-task learning, clustering, and prediction for multiple functional data. This procedure acts as a model-based clustering method for functional data as…

Partially recorded data are frequently encountered in many applications and usually clustered by first removing incomplete cases or features with missing values, or by imputing missing values, followed by application of a clustering…

Training generative models like Generative Adversarial Network (GAN) is challenging for noisy data. A novel curriculum learning algorithm pertaining to clustering is proposed to address this issue in this paper. The curriculum construction…

Background: The development, optimization and validation of protein modeling methods require efficient tools for structural comparison. Frequently, a large number of models need to be compared with the target native structure. The main…