The network alignment problem

Aligning protein-protein interaction (PPI) networks is very important to discover the functionally conserved sub-structures between different species. In recent years, the global PPI network alignment problem has been extensively studied aiming at finding the one-to-one alignment with the maximum matching score. However, finding large conserved components remains challenging due to its NP-hardness

18p vitzuyu2711 29-09-2021 13 1   Download

Network query problem aligns a small query network with an arbitrarily large target network. The complexity of this problem grows exponentially with the number of nodes in the query network if confidence in the optimality of result is desired. Scaling this problem to large query and target networks remains to be a challenge.

17p vikentucky2711 24-11-2020 10 1   Download

The alignment of protein-protein interaction networks was recently formulated as an integer quadratic programming problem, along with a linearization that can be solved by integer linear programming software tools.

14p vikentucky2711 24-11-2020 14 1   Download

In this paper, we present a novel global protein-protein interaction network alignment algorithm, which is enhanced with an extended large neighborhood search heuristics. Evaluated on benchmark datasets of yeast, fly, human and worm, the proposed algorithm outperforms state-of-the-art algorithms. Furthermore, the complexity of ours is polynomial, thus being scalable to large biological networks in practice.

11p tamynhan4 06-09-2020 13 3   Download

Several spectrally based pattern recognition problems appear in many areas e.g., image segmentation in computer vision, alignment of protein-protein interaction networks in bio-informatics, recognizing hard instances for combinatorial optimization problems such as the travelling salesman problem.

17p vinguyentuongdanh 19-12-2018 33 5   Download

Inspired by the incremental TER alignment, we re-designed the Indirect HMM (IHMM) alignment, which is one of the best hypothesis alignment methods for conventional MT system combination, in an incremental manner. One crucial problem of incremental alignment is to align a hypothesis to a confusion network (CN).

9p hongphan_1 14-04-2013 50 4   Download