Naslov
A step towards neural genome assembly

Autori
Vrček, Lovro ; Veličković, Petar ; Šikić, Mile

Vrsta, podvrsta i kategorija rada
Sažeci sa skupova, neobjavljeni rad, ostalo

Skup
NeurIPS 2020 Learning Meets Combinatorial Algorithms Workshop

Mjesto i datum
Online; konferencija, 06.12.2020. - 12.12.2020

Vrsta sudjelovanja
Poster

Vrsta recenzije
Međunarodna recenzija

Ključne riječi
Graph neural networks ; Genome assembly ; Neural execution

Sažetak
De novo genome assembly focuses on finding connections between a vast amount of short sequences in order to reconstruct the original genome. The central problem of genome assembly could be described as finding a Hamiltonian path through a large directed graph with a constraint that an unknown number of nodes and edges should be avoided. However, due to local structures in the graph and biological features, the problem can be reduced to graph simplification, which includes removal of redundant information. Motivated by recent advancements in graph representation learning and neural execution of algorithms, in this work we train the MPNN model with max-aggregator to execute several algorithms for graph simplification. We show that the algorithms were learned successfully and can be scaled to graphs of sizes up to 20 times larger than the ones used in training. We also test on graphs obtained from real-world genomic data--- that of a lambda phage and E. coli.

Izvorni jezik
Engleski

Znanstvena područja
Biologija, Računarstvo

POVEZANOST RADA