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Generative Models and Feature Extraction on Patient Images and Structure Data in Radiation Therapy
KTH, School of Engineering Sciences (SCI), Mathematics (Dept.), Mathematical Statistics.
2018 (English)Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesisAlternative title
Generativamodeller för patientbilder inom strålterapi (Swedish)
Abstract [en]

This Master thesis focuses on generative models for medical patient data for radiation therapy. The objective with the project is to implement and investigate the characteristics of a Variational Autoencoder applied to this diverse and versatile data. The questions this thesis aims to answer are: (i) whether the VAE can capture salient features of medical image data, and (ii) if these features can be used to compare similarity between patients. Furthermore, (iii) if the VAE network can successfully reconstruct its input and lastly (iv) if the VAE can generate artificial data having a reasonable anatomical appearance. The experiments carried out conveyed that the VAE is a promising method for feature extraction, since it appeared to ascertain similarity between patient images. Moreover, the reconstruction of training inputs demonstrated that the method is capable of identifying and preserving anatomical details. Regarding the generative abilities, the artificial samples generally conveyed fairly realistic anatomical structures. Future work could be to investigate the VAEs ability to generalize, with respect to both the amount of data and probabilistic considerations as well as probabilistic assumptions.

Abstract [sv]

Fokuset i denna masteruppsats är generativa modeller för patientdata från strålningsbehandling. Syftet med projektet är att implementera och undersöka egenskaperna som en “Variational Autoencoder” (VAE) har på denna typ av mångsidiga och varierade data. Frågorna som ska besvaras är: (i) kan en VAE fånga särdrag hos medicinsk bild-data, och (ii) kan dessa särdrag användas för att jämföra likhet mellan patienter. Därutöver, (iii) kan VAE-nätverket återskapa sin indata väl och slutligen (iv) kan en VAE skapa artificiell data med ett rimligt anatomiskt utseende. De experiment som utfördes pekade på att en VAE kan vara en lovande metod för att extrahera framtydande drag hos patienter, eftersom metoden verkade utröna likheter mellan olika patienters bilder. Dessutom påvisade återskapningen av träningsdata att metoden är kapabel att identifiera och bevara anatomiska detaljer. Vidare uppvisade generellt den artificiellt genererade datan, en realistisk anatomisk struktur. Framtida arbete kan bestå i att undersöka hur väl en VAE kan generalisera, med avseende på både mängd data som krävs och sannolikhetsteorietiska avgränsningar och antaganden.

Place, publisher, year, edition, pages
2018.
Series
TRITA-SCI-GRU ; 2018:231
Keywords [en]
Variational Autoencoder, Feature extraction, Deep learning on medical images, Computed tomography, Radiation therapy
National Category
Probability Theory and Statistics
Identifiers
URN: urn:nbn:se:kth:diva-229407OAI: oai:DiVA.org:kth-229407DiVA, id: diva2:1215620
External cooperation
RaySearch Laboratories
Subject / course
Mathematical Statistics
Educational program
Master of Science - Applied and Computational Mathematics
Supervisors
Examiners
Available from: 2018-06-08 Created: 2018-06-08 Last updated: 2018-06-08Bibliographically approved

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CiteExportLink to record
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