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undergraduate thesis
Graf neuronske mreže za de novo sastavljanje genoma
Zagreb: University of Zagreb, Faculty of Electrical Engineering and Computing, 2023. urn:nbn:hr:168:586262
Kolić, Jan
University of Zagreb
Faculty of Electrical Engineering and Computing

Institutional repository: FER Repository

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Kolić, J. (2023). Graf neuronske mreže za de novo sastavljanje genoma (Undergraduate thesis). Zagreb: University of Zagreb, Faculty of Electrical Engineering and Computing. Retrieved from https://urn.nsk.hr/urn:nbn:hr:168:586262

Kolić, Jan. "Graf neuronske mreže za de novo sastavljanje genoma." Undergraduate thesis, University of Zagreb, Faculty of Electrical Engineering and Computing, 2023. https://urn.nsk.hr/urn:nbn:hr:168:586262

Kolić, Jan. "Graf neuronske mreže za de novo sastavljanje genoma." Undergraduate thesis, University of Zagreb, Faculty of Electrical Engineering and Computing, 2023. https://urn.nsk.hr/urn:nbn:hr:168:586262

Kolić, J. (2023). 'Graf neuronske mreže za de novo sastavljanje genoma', Undergraduate thesis, University of Zagreb, Faculty of Electrical Engineering and Computing, accessed 11 July 2024, https://urn.nsk.hr/urn:nbn:hr:168:586262

Kolić J. Graf neuronske mreže za de novo sastavljanje genoma [Undergraduate thesis]. Zagreb: University of Zagreb, Faculty of Electrical Engineering and Computing; 2023 [cited 2024 July 11] Available at: https://urn.nsk.hr/urn:nbn:hr:168:586262

J. Kolić, "Graf neuronske mreže za de novo sastavljanje genoma", Undergraduate thesis, University of Zagreb, Faculty of Electrical Engineering and Computing, Zagreb, 2023. Available at: https://urn.nsk.hr/urn:nbn:hr:168:586262

Metadata
TitleGraf neuronske mreže za de novo sastavljanje genoma
Title (english)Graph Neural Networks for De Novo Genome assembly
AuthorJan Kolić
MentorMile Šikić (mentor)
Committee memberMile Šikić (predsjednik povjerenstva)
Committee memberRafael Josip Penić (član povjerenstva)
Committee memberFilip Tomas (član povjerenstva)
GranterUniversity of Zagreb
Faculty of Electrical Engineering and Computing
Zagreb
Defense date and country2023-07-05, Croatia
Scientific / art field,
discipline and subdiscipline		TECHNICAL SCIENCES
Computing
Abstract
Proces automatske rekonstrukcije sekvence genoma iz manjih sekvenci (očitanja) još uvijek nije potpuno usavršen. Jedan od problema je pojednostavljivanje grafa sastavljanja (strukture dobivene iz očitanja) tako da se može pronaći put kroz graf koji bi predstavljao cijelu sekvencu. U ovom radu, koristimo različite arhitekture graf neuronskih mreža (GCN, GAT, GraphSAGE, GatedGCN) za predviđanje koji bridovi grafa su dijelovi optimalnog puta kroz graf. Pokazujemo da se efikasnost modela podiže uporabom svojstava bridova i prenošenjem poruka u oba smjera usmjerenih bridova grafa. Najbolji u smislu točnosti, postotka lažno negativnih rezultata te F1 mjere se pokazao GatedGCN model, dok je najmanji postotak lažno pozitivnih postignut s GraphSAGE modelom.
Abstract (english)
The process of automatically reconstructing the full genome sequence, using smaller sequences called reads, hasn't yet been perfected. One of the problems is simplifying the assembly graph (a structure generated using the reads) so that a path through it, which represents the full sequence, can be found. In this paper, we train different graph neural network models (GCN, GAT, GraphSAGE, GatedGCN) to predict which edges are part of the optimal path through the graph. We show that bidirectional message passing (on a directed assembly graph) and using edge features improve the efficiency of the models. The GatedGCN models proved to be the best in terms of accuracy, false negative rate and F1 measure, while the GraphSAGE models produced the lowest false positive rates.
Keywords
Keywords (english)
Languageenglish
URN:NBNurn:nbn:hr:168:586262
Study programmeTitle: Computing
Study programme type: university
Study level: undergraduate
Academic / professional title: sveučilišni/a prvostupnik/ prvostupnica (baccalaureus/baccalaurea) inženjer/inženjerka računarstva (sveučilišni/a prvostupnik/ prvostupnica (baccalaureus/baccalaurea) inženjer/inženjerka računarstva)
Type of resourceText
File originBorn digital
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Created on2023-10-11 09:20:28