392160 | Schönhuth / Pianesi | Summer 2025 | Tue 16-18 in V2-105/115 (S) and Thu 10-12 in V10-118 (Ü) |
The recent surge of Machine Learning (ML) has opened up various opportunities when analysing biological datasets. Graph Neural Networks (GNNs) are a fairly new deep learning model capable of handling biological data in the best way overall. The seminar will start with a few (around 4 or 5) introductory lectures on Graph Representation Learning basics and Graph Neural Networks. The earliest and most recent approaches will be discussed, together with their use cases and drawbacks. The initial set of lectures will be followed by two lectures in which it will be presented how to write technical reports and how to prepare a good presentation. Then seminar presentations will take place, and they will need to be presented in small groups of 1-2 students. The course will be seminar+tutorial style, thus students will: 1. present a chosen paper; 2. deliver a final report of around 10 pages; 3. weekly deliver a summary of the presentation that took place during that week (around 500 words long).
The course will is entirely held in English.
If there is any problem with accessing a paper, write an email to Luna Pianesi.
Please, see on Moodle
Authors | Title | Year | Source |
Gilmer et al. | Neural message passing for quantum chemistry | 2017 | https://arxiv.org/abs/1704.01212 |
Zitnik et al. | Modelling polypharmacy side effects with graph convolutional networks | 2018 | https://academic.oup.com/bioinformatics/article/34/13/i457/5045770 |
Date | Topic |
15.04.2025 | Prof. Schönhuth: Organization (slides), How to present, How to write reports |
22.04.2025 | Introduction (slides), Glossary (slides), How to write summaries |
29.04.2025 | Prof. Schönhuth: Lecture 1 |
06.05.2025 | Prof. Schönhuth: Lecture 2 |
13.05.2025 | Prof. Schönhuth: Lecture 3 |
20.05.2025 | Prof. Schönhuth: Lecture 4 |
27.05.2025 | Prof. Schönhuth: Lecture 5, and deadline for choosing paper |
03.06.2025 | Q&A if needed |
10.06.2025 | Q&A if needed |
17.06.2025 | Q&A if needed |
24.06.2025 | Block presentations: 4 people |
01.07.2025 | Block presentations: 4 people |
08.07.2025 | Block presentations: 4 people |
15.07.2025 | Block presentations: 4 people |
18.07.2025 | End of lectures |
26.08.2025 | Deadline for report and paper journal |
30.09.2025 | End of semester |