Prediction of Drug Induced Gene Expression Perturbations through Drug Target and Protein-Protein Interaction Information

Background Transcriptomics provide insights into gene expression and with it the ability to analyze one of the fundamental processes of life - the translation from gene to protein. Single Cell RNA sequencing (scRNAseq) is a technology that measures transcriptomics on the single cell level. However, biological data is highly complex, variability and noisy, making it challenging to analyze and work with. The goal of the project is to evaluate if deep learning can infer gene expression profiles of specific conditions (exposures) by only receiving prior information about an exposure, such as a drug’s known gene targets as well as a general protein-protein interaction network. The aim is to evaluate the model based on its zero-shot performance (e.g. unseen drugs). ...

May 21, 2024

Transfer learning & Training of (Explainable) Deep Learning Model for Single Cell Transcriptomics

Background Transcriptomics provide insights into gene expression and with it the ability to analyse one of the fundamental processes of life - the translation from gene to protein. single Cell RNA sequencing (scRNAseq) is a technology that measures transcriptomics on the single cell level. However, biological data is highly complex, variability and noisy, making it challenging to analyse and wo. By building on pre-trained general scRNAseq deep learning model we want to fine-tune and train the model task specific. Examples of existing models are Geneformer https://www.nature.com/articles/s41586-023-06139-9 or scGPT https://www.nature.com/articles/s41592-024-02201-0. If the student decides that existing models are not suitable there is also the option to build/train from scratch. ...

May 21, 2024