News

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!

FONDA x Workflows Community Initiative


Since FONDA’s research is focussed on the area of Data Analysis Workflows, we are interested in working with researchers from the community. Therefore, we are especially grateful to spotlight our ongoing collaboration with the Workflows Community Initiative. The Workflows Community Initiative (WCI) is a community-centered effort for gathering and promoting long-standing and recent community-focused efforts. Learn More about WCI here.