Cell type deconvolution of methylated cell-free DNA at the resolution of individual reads

Cell-free DNA (cfDNA) are DNA fragments originating from dying cells that enter the plasma. Uncontrolled cell death, for example caused by cancer, induces an elevated concentration of cfDNA. As a result, determining the cell type origins of cfDNA can provide information about an individual's health. This research looks into how to increase the...

A multi-omic approach to discovering methylation-based markers of colon cancer in cfDNA

In recent years the advent of multi-omic techniques have shown great promise in the field of oncology. In light of these advancements, this thesis focuses on the use of multiple data types to find methylation markers around transcription start site regions for colorectal cancer in the cell-free DNA (cfDNA) domain. It combines several methods of...

Assessing the Capability of Multimodal Variational Auto-Encoders in Combining Information From Biological Layers in Cancer Cells

Personalized treatment methods for a complex disease such as cancer benefit from using multiple data modalities from a patient's cancer cells. Multiple modalities allow for analysis of dependencies between complex biological processes and downstream tasks, such as drug response and/or expected survival rate. To this end, it is important to gain...

Benchmarking the hyper-parameter sensitivity of VAE models for cancer treatment

Cancer has been known as a deadly and complex disease to tackle. By applying machine learning algorithms we hope to improve personalized treatment for cancer patients. These machine learning algorithms are trying to learn a (latent) representation of the input. The problem is that this representation is hard to interpret and to observe the...

Benchmarking VAE latent features in downstream tasks for cancer related predictions

Using RNA sequence data for predicting patient properties is fairly common by now. In this paper, Variational Auto-Encoders (VAEs) are used to assist in this process. VAEs are a type of neural network seeking to encode data into a smaller dimension called latent space. These latent features are then used to do downstream task analysis such as...

Finding disentangled representations using VAE

This study presents a comparison of different VariationalAutoencoder(VAE) models to see which VAE models arebetter at finding disentangled representations. Specificallytheir ability to encode biological processes into distinct la-tent dimensions. The biological processes that will be lookedat are the cell cycle and differentiation state. The...

The Effect of Different Initialization Methods on VAEs for Modeling Cancer using RNA Genome Expressions

Variational Auto-Encoders are a class of machine learning models that have been used in varying context, such as cancer research. Earlier research has shown that initialization plays a crucial part in training these models, since it can increase performance. Therefore, this paper studies the effect initialization methods on VAEs. This research...

Comparison of Linguistic Language Classification based on Origin and Data Driven Language Classification using the IPA and Clustering

Language similarity is very useful for enrichment data in both Natural Lanuguage Processing (NLP) and Automatic Speech Recognition (ASR). A clustering algorithm could provide an efficient means to define language similarity in a data-driven way. This research investigates the relation between linguistic classification by origin and data driven...

It sounds like Greek to me: Performance of phonetic representations for language identification

This paper compares the performance of two phonetic notations, IPA and ASJPcode, with the alphabetical notation for word-level language identification. Two machine learning models, a Multilayer Percerptron and a Logistic Regression model, are used to classify words using each of the three notations. With both models the IPA notation outperforms...

Detecting Rhyming Words

Rhyming words are one of the most important features in poems. They add rhythm to a poem, and poets use this literary device to portray emotion and meaning to their readers. Thus, detecting rhyming words will aid in adding emotions and enhancing readability when generating poems. Previous studies have been done on the topic of poem generation....

Extracting location context from transcripts: a comparison of ELMo and TF-IDF

Using transcripts of the TV-series FRIENDS, this paper explores the problem of predicting the location in which a sentence was said. The research focuses on using feature extraction on the sentences, and training a logistic regression model on those features. Specifically looking at the differences in performance between using ELMo and TF-IDF...

Using Skip-Gram Model to Predict from which Show a Given Line is

Text classification has a wide range of usage such as extracting the sentiment out of a product review, analyzing the topic of a document and spam detection. In this research, the text classification task is to predict from which TV-show a given line is. The skip-gram model, originally used to train the Word2Vec sentence embeddings [Mikolov et...

Gender bias in word embeddings of different languages

Word embeddings are useful for various applications, such as sentiment classification (Tang et al., 2014), word translation (Xing, Wang, Liu, & Lin, 2015) and résumé parsing (Nasser, Sreejith, & Irshad, 2018). Previous research has determined that word embeddings contain gender bias, which can be problematic in certain applications such...