Related papers: Maximum Cliques in Protein Structure Comparison
Subgraph matching is a basic operation widely used in many applications. However, due to its NP-hardness and the explosive growth of graph data, it is challenging to compute subgraph matching, especially in large graphs. In this paper, we…
We consider the problem of identifying a maximum clique in a given graph. We have proposed a mathematical model for this problem. The model resembles the matrix decomposition of the adjacency matrix of a given graph. The objective function…
The maximum clique problem is a well known NP-Hard problem with applications in data mining, network analysis, informatics, and many other areas. Although there exist several algorithms with acceptable runtimes for certain classes of…
Markov Networks are widely used through out computer vision and machine learning. An important subclass are the Associative Markov Networks which are used in a wide variety of applications. For these networks a good approximate minimum cost…
Approximate Nearest Neighbor Search with arbitrary filtering predicates (AFANNS) is essential for modern data applications, yet existing methods often incur substantial storage and computational costs. In this work, we introduce the Maximal…
A method to search for local structural similarities in proteins at atomic resolution is presented. It is demonstrated that a huge amount of structural data can be handled within a reasonable CPU time by using a conventional relational…
We present an alternate formulation of the partial assignment problem as matching random clique complexes, that are higher-order analogues of random graphs, designed to provide a set of invariants that better detect higher-order structure.…
Finding maximum cliques in large networks is a challenging combinatorial problem with many real-world applications. We present a fast algorithm to achieve the exact solution for the maximum clique problem in large sparse networks based on…
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…
Aligning multiple protein structures can yield valuable information about structural similarities among related proteins, as well as provide insight into evolutionary relationships between proteins in a family. We have developed an…
This report presents the implementation of a protein sequence comparison algorithm specifically designed for speeding up time consuming part on parallel hardware such as SSE instructions, multicore architectures or graphic boards. Three…
Fast, efficient and reliable algorithms for pairwise alignment of protein structures are in ever increasing demand for analyzing the rapidly growing data of protein structures. CLePAPS is a tool developed for this purpose. It distinguishes…
Mining cohesive subgraphs in attributed graphs is an essential problem in the domain of graph data analysis. The integration of fairness considerations significantly fuels interest in models and algorithms for mining fairness-aware cohesive…
We introduce an algorithm for the alignment of protein- coding sequences accounting for frameshifts. The main specificity of this algorithm as compared to previously published protein-coding sequence alignment methods is the introduction of…
The maximum clique problem, a well-known graph-based combinatorial optimization problem, has been addressed through various algorithmic approaches, though systematic analyses of the problem instances remain sparse. This study employs the…
Summary: Most cellular tasks are performed not by individual proteins, but by groups of functionally associated proteins, often referred to as modules. In a protein assocation network modules appear as groups of densely interconnected…
An algorithm is developed for finding a close to optimal junction tree of a given graph G. The algorithm has a worst case complexity O(c^k n^a) where a and c are constants, n is the number of vertices, and k is the size of the largest…
Proteins are the basic building blocks of life. They usually perform functions by folding to a particular structure. Understanding the folding process could help the researchers to understand the functions of proteins and could also help to…
Finding a maximum clique in a given graph is one of the fundamental NP-hard problems. We compare two multi-core thread-parallel adaptations of a state-of-the-art branch and bound algorithm for the maximum clique problem, and provide a novel…
Mining groups of genes that consistently co-express is an important problem in biomedical research, where it is critical for applications such as drug-repositioning and designing new disease treatments. Recently, Cooley et al. modeled this…