News

PI Lecture Series Part 4

Our fourth set of PI-Lectures will be Monday, February 17th starting at 15:00 in Humboldt-Universität zu Berlin’s main building, Unter den Linden 6. The following PIs will give talks about their ongoing research:

  • Anna-Lena Lamprecht – Workflomics
  • Florian Schintke – SIMD Vectorization of Positional Population Count
  • Dagmar Kainmueller – The Helmholtz Foundation Model Initiative

PI-Lecture Series Part 3

We had the third session of PI-Lectures on Monday, February 3rd. Tilmann Hickel presented on his work in computational materials science, “Workflows as an enabler for computational materials design”. This was followed by a tutorial on using the FONDA cluster by Vasilis Bountris, and the second part of Ulf Leser’s tutorial on workflow systems.

There will not be a lecture next week. We will meet again on February 17th at Unter den Linden 6 for our next set of talks.

PI-Lecture Series part 2

Our second set of PI-Lectures will be today at 15:00 at Einstein Center Digital Future. The following PIs will be presenting their research areas:

  • Patrick Hostert – Satellite Remote Sensing
  • Matthias Boehm – System Infrastructure for Data-centric ML Pipelines
  • Tillman Rabl – Carbon-efficient Data Systems
  • Odej Kao – LLMOps for Reliability and Availability of Massive AI Infrastructures

FONDA contributed the first non-Bioinformatics Workflow to nf-core

We have successfully ported and contributed our Rangeland workflow [1], [2] to the nf-core workflow repository. This milestone marks the release of the first non-bioinformatics workflow on nf-core, which now serves as a blueprint for workflows in remote sensing and other domains. Being a part of the nf-core community confirms that our workflow uses best practices and ensures accessibility to researchers worldwide.


The Rangeland workflow analyzes trends in grassland changes, providing valuable insights for environmental research.

This achievement was made possible by subproject B5: Felix Kummer, Katarzyna Ewa Lewińska, Fabian Lehmann, and David Frantz.

-Fabian Lehmann

FONDA Winter Retreat 2024

Members from both phases of FONDA met for our retreat in Kremmen from December 4th to 6th. Scientists from the first phase passed the torch to the incoming cohort with presentations of the work so far and lively scientific discussions about the future.

We also elected the following board members during the General Assembly:

  • Speaker – Prof. Ulf Leser
  • Deputy Speaker – Prof. Matthias Weidlich
  • Equality and Diversity Commissioner – Prof.  Anna-Lena Lamprecht
  • Prof. Odej Kao
  • Luisa Gerlach
  • Christopher Lazik

FONDA PhD student Mario Sänger successfully defends his PhD thesis on “Representation Learning for Biomedical Text Mining”

Mario Sänger, a member of the group “Human-computer interaction for Scientific Software”, successfully defended his PhD thesis on November 25, 2024. His work focuses on using representation learning to extract meaningful connections between biomedical entities, such as genes, diseases, proteins, and pharmaceuticals from a corpus of PubMed abstracts, as well as biomedical knowledge bases. In addition to demonstrating the feasibility of this corpus-wide approach, he also benchmarked and tested existing pre-trained language models (PLMs) for sentence-level relation prediction. His results show that additional context from biomedical knowledge databases does not enhance the most robust carefully tuned PLMs.

In FONDA, he collaborated with Prof. Dr. Thomas Kosch, exploring the use of ChatGPT as a tool to support users in designing and implementing scientific workflows.

Congratulations Mario, and all the best!

FONDA PHD student Sarah Kleest-Meißner successfully defends her PhD thesis on “Exploring the Complexity of Event Query Discovery”

Sarah Kleest-Meißner, research group “Logic in Computer Science” at HU Berlin’s computer science department, successfully defended her PhD thesis on September 10, 2024. She proposed an expressive, theoretical query model for sequence data based on subsequences and patterns with variables which captures the core of Complex Event Processing (CEP) languages. Based thereon, she presented an algorithm for solving the task of discovering a query that describes best a given finite set of finite sequences of events. The theoretical basis of her query model enabled a comprehensive analysis of the complexity of event query discovery, whereas a prototypical implementation and an experimental evaluation with synthetic and real-world datasets complemented the formal results.

Congratulations!

FONDA PHD student Masoud Jami successfully defends his PhD thesis on “Optimizing Checkpoint/Restart and Input/Output for Large Scale Applications”

Masoud Jami, né Gholami, of ZIB successfully defended his PhD thesis at the Institute of Computer Science, Humboldt-Universität zu Berlin on October 10, 2024. He enhanced C/R techniques by reducing overhead by more than 10% compared to state-of-the-art, and outperforms Reed-Solomon codes by combining XOR and partner checkpointing in terms of resiliency and computational overhead. His IOSIG plugin for GCC adds pragma annotations to specify I/O characteristics of certain streams, enabling injected code to choose optimal devices during runtime. His accurate I/O models of the Linux kernel that consider page caching behavior estimate I/O costs with over 80-90% accuracy.

Congratulations!