We predict disease-genes relations on the human interactome network using a methodology that jointly learns functional and connectivity patterns surrounding proteins. Contrary to other data structures, the interactome is characterised by high incompleteness and absence of explicit negative knowledge, which makes predictive tasks particularly challenging. To exploit at best latent information in the network, we propose an extended version of random walks, named Random Watcher-Walker (RW2), which is shown to perform better than other state-of-the-art algorithms. We also show that the performance of RW2 and other compared state-of-the-art algorithms is extremely sensitive to the interactome used, and to the adopted disease categorisations, since this influences the ability to capture regularities in presence of sparsity and incompleteness.
A Feature-Learning based method for the disease-gene prediction problem / Madeddu, Lorenzo; Stilo, Giovanni; Velardi, Paola. - In: INTERNATIONAL JOURNAL OF DATA MINING AND BIOINFORMATICS. - ISSN 1748-5673. - 24:1(2020). [10.1504/IJDMB.2020.10031422]
A Feature-Learning based method for the disease-gene prediction problem
Lorenzo Madeddu
;Giovanni Stilo;Paola Velardi
2020
Abstract
We predict disease-genes relations on the human interactome network using a methodology that jointly learns functional and connectivity patterns surrounding proteins. Contrary to other data structures, the interactome is characterised by high incompleteness and absence of explicit negative knowledge, which makes predictive tasks particularly challenging. To exploit at best latent information in the network, we propose an extended version of random walks, named Random Watcher-Walker (RW2), which is shown to perform better than other state-of-the-art algorithms. We also show that the performance of RW2 and other compared state-of-the-art algorithms is extremely sensitive to the interactome used, and to the adopted disease categorisations, since this influences the ability to capture regularities in presence of sparsity and incompleteness.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.