Using Natural Language Processing with Deep Learning to Explore Clinical Notes

In recent years, the deep learning community and technology have grown substantially, both in terms of research and applications. However, some application areas have lagged behind. The medical domain is an example of a field with a lot of untapped potential, partly caused by complex issues related to privacy and ethics. Still, deep learning is a very powerful tool to utilize structured and unstructured data, and could help save lives. In this thesis, we use natural language processing to interpret clinical notes and predict the mortality rate of subjects. We explore if language models trained on a specific domain would become more performant, and we compared them to language models trained on an intermediate data set. We found that our language model trained on an intermediate data set that had some resemblance to our target data set performed slightly better than its counterpart language model. We found that text classifiers built on top of the language models were capable of correctly predicting if a subject would die or not. Furthermore, we extracted the free-text features from the text classifiers and combined them, using stacking, with heterogeneous data as an attempt to increase the efficacy of the classifiers and to explore the relative performance boost gained by including free-text features. We found a correlation between the quality of text classifiers that produced the text features and the stacking classifiers' performances. The classifier that was trained on a data set without text features performed the worst, and the classifier trained on a data set with the best text features performed the best. We also discuss the central concerns that come with applying deep learning in a medical domain with regards to privacy and ethics. It is our intention that this thesis serves as a contribution to the advancement of deep learning within the medical domain, and as a testament as to what can be achieved with today's technology.Masteroppgave i Programutvikling samarbeid med HVLPROG399MAMN-PRO

Politisamarbeid mellom Norge og Russland: En studie av bilateral regimeeffektivitet i et endret landskap

Master i samfunnsvitenskap - 202

Practical Implementation of a Graphics Turing Test

We present a practical implementation of a variation of the Turing Test for realistic computer graphics. The test determines whether virtual representations of objects appear as real as genuine objects. Two experiments were conducted wherein a real object and a similar virtual object is presented to test subjects under specific restrictions. A criterion for passing the test is presented based on the probability for the subjects to be unable to recognise a computer generated object as virtual. The experiments show that the specific setup can be used to determine the quality of virtual reality graphics. Based on the results from these experiments, future versions of the Graphics Turing Test could ease the restrictions currently necessary in order to test object telepresence under more general conditions. Furthermore, the test could be used to determine the minimum requirements to achieve object telepresence.</p

Mitigation of conductor line galloping by a direct cable-connection to non-conductive composite power pylons

Steel lattice towers with suspended insulator strings are typically used to carry high-voltage overhead transmission lines. The installation of non-conductive power pylons made of glass fibre reinforced plastics enables a direct cable-pylon connection, as the composite structure acts as an unibody insulator. At the same time, wind-induced vibrations, such as the severe cable vibration phenomenon galloping, will consequently be directly transferred to the slender composite mast structure, potentially leading to extensive damage. The aim of the study is therefore to investigate the galloping behaviour of iced conductor lines with regard to different cable support conditions. Furthermore, additional damping in the composite power pylon structure is assumed to mitigate conductor line galloping and therefore reduce the risk of phase flash-overs between adjacent conductor lines. A numerical galloping simulation is carried out in order to evaluate the effect of a rigid cable-pylon connection with enhanced damping properties on the cable vibration amplitudes. A pylon-cable system, consisting of 3×300 m spans, is investigated. It was found that the support conditions of the conductor lines have a significant influence on the galloping mode, the vibration amplitudes and the orientation of the characteristic galloping ellipse. The addition of damping to the pylon decreases the vibration amplitudes slightly and leads to a re-orientation of the galloping ellipse

Using a Graphics Turing Test to Evaluate the Effect of Frame Rate and Motion Blur on Telepresence of Animated Objects

A limited Graphics Turing Test is used to determine the frame rate that is required to achieve telepresence of an animated object. For low object velocities of 2.25 and 4.5 degrees of visual angle per second at 60 frames per second a rotating object with no added motion blur is able to pass the test. The results of the experiments confirm previous results in psychophysics and show that the Graphics Turing Test is a useful tool in computer graphics. Even with simulated motion blur, our Graphics Turing Test could not be passed with frame rates of 30 and 20 frames per second. Our results suggest that 60 frames per second (instead of 30 frames per second) should be considered the minimum frame rate to achieve object telepresence and that motion blur provides only limited benefits.</p

Elevated serum YKL-40, IL-6, CRP, CEA, and CA19-9 combined as a prognostic biomarker panel after resection of colorectal liver metastases

Background The inflammatory biomarkers, YKL-40 and interleukin-6 (IL-6), are elevated in patients with metastatic colorectal cancer. We examined their associations with relapse-free survival and overall survival in combination with serum C-reactive protein (CRP), carcinoembryonic antigen (CEA), and carbohydrate antigen 19–9 (CA19-9) in patients with colorectal liver metastases. Methods Altogether 441 consecutive patients undergoing liver resection at Helsinki University Hospital between 1998 and 2013 were included in the study. Pre- and postoperative YKL-40 and IL-6 were determined from serum samples with commercially available enzyme-linked immunosorbent assay (ELISA) kits, and CRP, CEA, and CA19-9 by routine methods. Associations between these biomarkers and relapse-free and overall survival were examined using Cox regression analysis. Results Patients with 2–5 elevated biomarkers were at an increased risk of relapse compared to those with 0–1 elevated biomarkers, preoperatively (HR 1.37, 95% CI 1.1–1.72) or postoperatively (HR 1.54, 95% CI 1.23–1.92). Patients with 2–5 elevated biomarkers were also at an increased risk of death compared to those with 0–1 elevated biomarkers, preoperatively (HR 1.76, 95% CI 1.39–2.24) or postoperatively (HR 1.83, 95% CI 1.44–2.33). Conclusion The results suggest that a protein panel of the inflammatory biomarkers YKL-40, IL-6, and CRP, and the cancer biomarkers CEA and CA19-9 might identify patients that benefit from more aggressive treatment and surveillance, although the additional value of IL-6 and CRP in this aspect is limited.Peer reviewe

Local Gamma Augmentation for Ischemic Stroke Lesion Segmentation on MRI

The identification and localisation of pathological tissues in medical images continues to command much attention among deep learning practitioners. When trained on abundant datasets, deep neural networks can match or exceed human performance. However, the scarcity of annotated data complicates the training of these models. Data augmentation techniques can compensate for a lack of training samples. However, many commonly used augmentation methods can fail to provide meaningful samples during model fitting. We present local gamma augmentation, a technique for introducing new instances of intensities in pathological tissues. We leverage local gamma augmentation to compensate for a bias in intensities corresponding to ischemic stroke lesions in human brain MRIs. On three datasets, we show how local gamma augmentation can improve the image-level sensitivity of a deep neural network tasked with ischemic lesion segmentation on magnetic resonance images.Comment: Camera-ready version for Northern Lights Deep Learning Conference 2024, 7 pages, 2 figure

In vitro micro-CT analyse av demineraliseringslesjoner på emaljeoverflaten

Målsetting: Målet med dette masterforsøket er å danne demineraliseringslesjoner som ligner på initialkaries ved hjelp av 4 ulike syreløsninger på emaljeoverflaten in vitro, og deretter sammenlikne bildene utfra de diagnostiske kriteriene, definert under, for å se hvilken som gir det beste resultatet. Metode: 40 tenner ble samlet inn fra UTK og TkNN, hvor deretter 12 tenner ble randomisert valgt ut til bruk i dette studiet. Hver krone ble spaltet fra roten og delt videre inn i 2, slik at vi fikk 24 kronebiter. De 24 kronebitene ble utsatt for 4 forskjellige syreløsninger og 2 forskjellige tidsparametere slik at vi fikk 8 grupper totalt. Coca-Cola® (The Coca-Cola Company, USA) (pH 2.4), syreløsning med pH 2.4 og pH 4.4 ble utsatt for syreløsningen i 96 timer og 144 timer. I gruppene hvor Total Etch® (Ivoclar Vivadent, Lichtenstein) 37 % forforsyre-gel med pH<1 ble brukt, var tidsintervallene 30 min og 6 timer. Kronebitene ble scannet før og etter de ble utsatt for syreløsningene med micro-CT (Skyscan 1272, Brukers, Kontich, Belgia). I DataViewer (Brukers, Kontich, Belgia) vises snittbildene av tannkronen i tre ulike plan (sagitalt, koronalt og transversalt). Resultat: I gruppen Coca-Cola® (The Coca-Cola Company, USA), med målt pH til 2.4, viste en liten demineralisiering. Gruppen syreløsning 1 (pH 2.4) viste en klar demineralisering med gjenværende emalje i overflaten. Gruppen syreløsning 2 (pH 4.4) ga ingen synlig demineraliseringslesjon. Total Etch® (Ivoclar Vivadent, Lichtenstein) 37% fosforsyre gel med en pH på <1.00, ga en svak demineraliseringslesjon. Konklusjon: I analysene av in vitro demineraliseringslesjonene fant vi ut at demineralisering med syreløsning 1 (pH 2.4) ga den tydeligste demineraliseringslesjonen (mest likt initialkaries). Videre forsøk kan benytte seg av denne løsningen, og de valgte tidsparametrene. Coca-Cola® med pH 2.4 og Total Etch® med pH<1.00 kan også brukes i dannelsen av in vitro demineraliseringslesjoner. Syreløsning 2 (pH 4.4.) ga minst tydelig demineralisering, så hvis denne skal benyttes bør tidsparametret økes. Det er behov for flere studier med økt antall kronebiter og statistiske analyser, for å få mer bekreftende resultater