====== Thesis Topics & Student Projects ======
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===== GENERATING GENOMES USING LANGUAGE MODELS=====
  * Genomes, the DNA of living organisms, follow a grammatical structure
  * The rules are implied by the laws of genetics
  * Idea: Structure DNA in terms of applicable words and sentences
  * Make language model pick up the grammar that underlies the resulting sentences
  * Application: Language models capture the structure of diseases and other (biomedically) relevant particularities of (human) genomes

===== GRAPH DATABASES / DRUG REACTION PREDICTION =====
  * We know functional relationships for many drugs and genes I Would like to predict new drugs and their behaviour
  * Use advanced machine learning for prediction
  * Exploit knowledge arranged in graph databases
  * Project involves implementation of advanced prediction techniques not yet exploited in clinical practice

===== GRAPH NEURAL NETWORKS / POLYPHAMARCY SIDE EFFECTS =====
  * Identify biological pathway of interest
  * Screen drugs relative to their effect on pathway
  * Implement graph neural networks to systematically exploit effects
  * Investigate pathways using Gaussian graphical model
  * Project involves analysis of multilevel, complex data hierarchies

===== INDEX STRUCTURES FOR PANGENOME GRAPHS =====
  * Pangenome graphs are modern, advanced data structures for storing (hundreds of) thousands of genomes in compressed form
  * Indexes enable us to navigate these graphs systematically 
  * Project involves algorithmically tricky techniques

===== PREDICTING ANTIMICROBIAL RESISTANCE USING TRANSFORMERS / CAPSULE NETWORKS =====
  * Idea: predict resistance behaviour of pathogenic strains
  * Use advance machine learning to predict this from genome (DNA) data
  * Project involves implementation of advanced machine learning techniques for novel, clinically relevant application scenarios
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Just come and talk to us on in our offices at U10 and we will work out an exciting project with you!