DILiS - News and Outreach Activities

January 7, 2025: DILiS goes BLISS

Join the BLISS lecture series on Tuesday, January 7, 6:45 pm, to listen to a talk by Katharina Baum who is going to present the group's work on informed ML and uncertainty. If you can't make it this time: The talk will be recorded and provided as a Youtube video. Please find more information here.

November 28, 2024: Presentation of our work at BIFOLD lunch seminar

You are warmly invited to the next issue of the BIFOLD lunch seminar, taking place on Thursday, Nov 28, at TU Berlin (Marchéstr) from 12-1pm (see more info here). Katharina Baum will talk about the group's progress in informed machine learning, and especially highlighting the differences between physically informing ML and biologically informing ML. There will be food available!

September 30 - October 2, 2024: DILiS at GCB 2024

We are presenting two of our projects at this year's German Conference on Bioinformatics in Bielefeld. Pascal Iversen will discuss about his work with Judith Bernett, Consistent and Biologically Meaningful Evaluation of Cancer Drug Response Prediction Models with DrEval, on appropriate evaluation of drug response prediction in a cooperation with two labs from TUM, that of Markus List and Mathias Wilhelm during the poster session. Katharina Baum's will present a project on informing machine learning, How to successfully inform machine learning for predictions in biological systems with prior knowledge from ordinary differential equation-based simulations, which has been selected as one of the contributed talks and will take place on October 1, 11 am in the Modeling and Systems Biology session. Check out the corresponding preprint here.

September 6, 2024: PEPerMINT paper published at Bioinformatics

Check out the paper to our new method PEPerMINT for GNN-based peptide abundance imputation that is now published at Bioinformatics (ECCB 2024 issue). It also includes a benchmark with various datasets. Special kudos to the first authors Tobias Pietz who did this work during his Master's thesis at HPI with us, and Sukrit Gupta for their great work, and of course a big thanks to the other contributors, Chris and Bernhard from the DACS chair at HPI, and Hanno and Saima from the Steen lab from Boston! We will be presenting the project as a talk in Turku, Finland, at ECCB2024 later in September. You can find the publication here.

July 26, 2024: Successful defense of BA thesis

We congratulate Jan Ehlting to the successful last step to his Bachelor thesis in Computer Science with the title "Computergestützte Methodik zur Simulation und Untersuchung struktureller Veränderungen in Proteinnetzwerken". We are looking forward to using your developed code of PyProteoNet for our research. All the best, Jan, we enjoyed the time time you spent in our group!

July 22, 2024: PhD position in ML open in our lab

Pending funding allocation, we are hiring a full-time PhD student in the BMBF-funded project Act-i-ML for 3 years. See the official job ad on the FU website here [German only, sorry, but applications in English are welcome].

June 24, 2024: Research internship on multi-omics data analysis

We are offering a 7-week research internship in collaboration with the Winter lab at University of Bonn. Join us to explore the fascinating function of lysosomes, just drop us an email if you are interested!

May 31, 2024: Paper accepted at ECCB 2024

Celebrate with us the acceptance of our paper PEPerMINT: Peptide Abundance Imputation in Mass Spectrometry-based Proteomics using Graph Neural Networks by Tobias Pietz & Sukrit Gupta et al. at this year's ECCB 2024. Big congrats and thanks to all collaborators! See the preprint on bioarxiv here.

April 25, 2024: Girl's Day

We offered a workshop at the Girl's Day 2024: On April 25, we found out together with 12 girls when to better be careful with ChatGPT as it turns out lying, and we introduced how to use it for programming with Python. There, ChatGPT can be really helpful! Link to our project: Der Mensch im Computer - wie Alexa, ChatGPT + Co. die Welt verändern und warum sie manchmal schwindeln