Evaluation of classification algorithms for smooth pursuit eye movements : Evaluating current algorithms for smooth pursuit detection on Tobii Eye Trackers

Eye tracking is a field that has been growing immensely over the last decade. Accompanying this growth is a need for simplified and automatic analysis of eye tracking data. A part of that analysis is eye movement classification, and while there are many adequate classification methods for fixations and saccades, the tools for smooth pursuit classification are still lacking. This thesis gives an overview of the field,and analyses five different methods for classifying smooth pursuits, fixations,and saccades. The analysis also explores evaluation methods that avoid the laborious way of manually tagging data to get a reference classification. Despite earlier reports of decent performance, the overall results for all the analysed algorithms is poor. In particular, the slowest pursuits are consistently misclassified. Most certainly, the inclusion of the slow pursuits have skewed the results, but even disregarding them doesn’t yield particularly impressive results. This begs the question of what concessions one has to make in terms of prerequisites on the data, or qualifiers for the resulting analysis, to achieve adequate performance,and given those, when would such a classification be preferred to something tailored to the problem at hand

Sensitive Detection of Cell-Free Tumour DNA Using Optimised Targeted Sequencing Can Predict Prognosis in Gastro-Oesophageal Cancer

In this longitudinal study, cell-free tumour DNA (a liquid biopsy) from plasma was explored as a prognostic biomarker for gastro-oesophageal cancer. Both tumour-informed and tumour-agnostic approaches for plasma variant filtering were evaluated in 47 participants. This was possible through sequencing of DNA from tissue biopsies from all participants and cell-free DNA from plasma sampled before and after surgery (n = 42), as well as DNA from white blood cells (n = 21) using a custom gene panel with and without unique molecular identifiers (UMIs). A subset of the plasma samples (n = 12) was also assayed with targeted droplet digital PCR (ddPCR). In 17/31 (55%) diagnostic plasma samples, tissue-verified cancer-associated variants could be detected by the gene panel. In the tumour-agnostic approach, 26 participants (59%) had cancer-associated variants, and UMIs were necessary to filter the true variants from the technical artefacts. Additionally, clonal haematopoietic variants could be excluded using the matched white blood cells or follow-up plasma samples. ddPCR detected its targets in 10/12 (83%) and provided an ultra-sensitive method for follow-up. Detectable cancer-associated variants in plasma correlated to a shorter overall survival and shorter time to progression, with a significant correlation for the tumour-informed approaches. In summary, liquid biopsy gene panel sequencing using a tumour-agnostic approach can be applied to all patients regardless of the presence of a tissue biopsy, although this requires UMIs and the exclusion of clonal haematopoietic variants. However, if sequencing data from tumour biopsies are available, a tumour-informed approach improves the value of cell-free tumour DNA as a negative prognostic biomarker in gastro-oesophageal cancer patients