Identifying Spurious Interactions in the Protein-Protein Interaction Networks Using Local Similarity Preserving Embedding
| Autor: | De-Shuang Huang, Lin Zhu, Su-Ping Deng, Zhu-Hong You |
|---|---|
| Rok vydání: | 2017 |
| Předmět: |
0301 basic medicine
Saccharomyces cerevisiae Proteins Similarity (geometry) Computer science 0206 medical engineering 02 engineering and technology computer.software_genre Machine learning Protein protein interaction network 03 medical and health sciences Protein Interaction Mapping Genetics Computer Simulation Protein Interaction Maps Databases Protein Spurious relationship business.industry Applied Mathematics Rank (computer programming) Computational Biology Embedding algorithm ComputingMethodologies_PATTERNRECOGNITION 030104 developmental biology Benchmark (computing) Embedding Data mining Noise (video) Artificial intelligence business computer Algorithms 020602 bioinformatics Biotechnology |
| Zdroj: | IEEE/ACM Transactions on Computational Biology and Bioinformatics. 14:345-352 |
| ISSN: | 1545-5963 |
| Popis: | In recent years, a remarkable amount of protein-protein interaction (PPI) data are being available owing to the advance made in experimental high-throughput technologies. However, the experimentally detected PPI data usually contain a large amount of spurious links, which could contaminate the analysis of the biological significance of protein links and lead to incorrect biological discoveries, thereby posing new challenges to both computational and biological scientists. In this paper, we develop a new embedding algorithm called local similarity preserving embedding (LSPE) to rank the interaction possibility of protein links. By going beyond limitations of current geometric embedding methods for network denoising and emphasizing the local information of PPI networks, LSPE can avoid the unstableness of previous methods. We demonstrate experimental results on benchmark PPI networks and show that LSPE was the overall leader, outperforming the state-of-the-art methods in topological false links elimination problems. |
| Databáze: | OpenAIRE |
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