Image Recognition for Atomic Force Microscopy

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dc.contributor Helsingin yliopisto, Matemaattis-luonnontieteellinen tiedekunta fi
dc.contributor University of Helsinki, Faculty of Science en
dc.contributor Helsingfors universitet, Matematisk-naturvetenskapliga fakulteten sv
dc.contributor.author Kurki, Lauri
dc.date.issued 2021
dc.identifier.uri URN:NBN:fi:hulib-202109233754
dc.identifier.uri http://hdl.handle.net/10138/334559
dc.description.abstract Atomic force microscopy (AFM) is a widely utilized characterization method capable of capturing atomic level detail in individual organic molecules. However, an AFM image contains relatively little information about the deeper atoms in a molecule and thus interpretation of AFM images of non-planar molecules offers significant challenges for human experts. An end-to-end solution starting from an AFM imaging system ending in an automated image interpreter would be a valuable asset for all research utilizing AFM. Machine learning has become a ubiquitous tool in all areas of science. Artificial neural networks (ANNs), a specific machine learning tool, have also arisen as a popular method many fields including medical imaging, self-driving cars and facial recognition systems. In recent years, progress towards interpreting AFM images from more complicated samples has been made utilizing ANNs. In this thesis, we aim to predict sample structures from AFM images by modeling the molecule as a graph and using a generative model to build the molecular structure atom-by-atom and bond-by-bond. The generative model uses two types of ANNs, a convolutional attention mechanism to process the AFM images and a graph neural network to process the generated molecule. The model is trained and tested using simulated AFM images. The results of the thesis show that the model has the capability to learn even slight details from complicated AFM images, especially when the model only adds a single atom to the molecule. However, there are challenges to overcome in the generative model for it to become a part of a fully capable end-to-end AFM process. en
dc.language.iso eng
dc.publisher Helsingin yliopisto fi
dc.publisher University of Helsinki en
dc.publisher Helsingfors universitet sv
dc.subject Atomic force microscopy
dc.subject machine learning
dc.subject deep learning
dc.subject convolutional neural networks
dc.title Image Recognition for Atomic Force Microscopy en
dc.title.alternative Kuvantunnistus atomivoimamikroskopiassa fi
dc.type.ontasot pro gradu -tutkielmat fi
dc.type.ontasot master's thesis en
dc.type.ontasot pro gradu-avhandlingar sv
dct.identifier.urn URN:NBN:fi:hulib-202109233754
dc.subject.specialization Laskennallinen materiaalifysiikka fi
dc.subject.specialization Computational Material Physics en
dc.subject.specialization Beräkningsmaterialfysik sv
dc.subject.degreeprogram Materiaalitutkimuksen maisteriohjelma fi
dc.subject.degreeprogram Master's Programme in Materials Research en
dc.subject.degreeprogram Magisterprogrammet i materialforskning sv

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