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Two major extinction events in the evolutionary history of turtles: one caused by a meteorite, the other by hominins
(2022)bioRxivWe live in a time of highly accelerated extinction, which has the potential to mirror past mass extinction events. However, the rarity of these events and the restructuring of diversity that they cause complicate direct comparisons between the current extinction crisis and earlier mass extinctions. Among animals, turtles (Testudinata) are one of few groups which both have a sufficient fossil record and a sufficiently stable ecological ...Working Paper -
A Comprehensive Stochastic Programming Model for Transfer Synchronization in Transit Networks
(2024)arXivWe investigate the stochastic transfer synchronization problem, which seeks to synchronize the timetables of different routes in a transit network to reduce transfer waiting times, delay times, and unnecessary in-vehicle times. We present a sophisticated two-stage stochastic mixed-integer programming model that takes into account variability in passenger walking times between bus stops, bus running times, dwell times, and demand uncertainty. ...Working Paper -
Success Factors and Measures for Scaling Patient-Facing Digital Health Technologies from Leaders Insights
(2025)Research SquareBackground Europe’s healthcare systems face a triple burden: the rise of non-communicable diseases (NCDs), an aging population, and a shortage of healthcare professionals. NCDs, the leading causes of death, disproportionately affect older adults, placing significant pressure on healthcare services. By 2050, nearly 30% of Europe’s population will be aged 65 or older, up from 20% in 2023. These challenges demand urgent solutions to sustain ...Working Paper -
Dynamics and plasticity of stem cells in the regenerating human colonic epithelium
(2023)bioRxivThe human intestinal epithelium is a tissue with rapid turnover. Its complex regenerative process and differentiation trajectories have been challenging to study due to its inaccessibility and lack of temporal sampling. To this end, we developed a workflow to culture adult stem cell-derived human intestinal organoids from single cells to maturation. Extensive characterization of our model system indicated a transient regenerative response, ...Working Paper -
The G1/S transition in mammalian stem cells in vivo is autonomously regulated by cell size
(2024)bioRxivCell growth and division must be coordinated to maintain a stable cell size, but how this coordination is implemented in multicellular tissues remains unclear. In unicellular eukaryotes, autonomous cell size control mechanisms couple cell growth and division with little extracellular input. However, in multicellular tissues we do not know if autonomous cell size control mechanisms operate the same way or whether cell growth and cell cycle ...Working Paper -
Mechanochemical bistability of intestinal organoids enables robust morphogenesis
(2024)arXivHow pattern and form are generated in a reproducible manner during embryogenesis remains poorly understood. Intestinal organoid morphogenesis involves a number of mechanochemical regulators, including cell-type specific cytoskeletal forces and osmotically-driven lumen volume changes. However, whether and how these forces are coordinated in time and space via feedbacks to ensure robust morphogenesis remains unclear. Here, we propose a ...Working Paper -
Workshop on the Review and Future of State Space Stock Assessment Models in ICES (WKRFSAM)
(2020)ICES Scientific ReportsReport -
Socratic Reasoning Improves Positive Text Rewriting
(2024)arXivReframing a negative into a positive thought is at the crux of several cognitive approaches to mental health and psychotherapy that could be made more accessible by large language model-based solutions. Such reframing is typically non-trivial and requires multiple rationalization steps to uncover the underlying issue of a negative thought and transform it to be more positive. However, this rationalization process is currently neglected ...Working Paper -
How to Weight Multitask Finetuning? Fast Previews via Bayesian Model-Merging
(2024)arXivWhen finetuning multiple tasks altogether, it is important to carefully weigh them to get a good performance, but searching for good weights can be difficult and costly. Here, we propose to aid the search with fast previews to quickly get a rough idea of different reweighting options. We use model merging to create previews by simply reusing and averaging parameters of models trained on each task separately (no retraining required). To ...Working Paper -
Variational Low-Rank Adaptation Using IVON
(2024)arXivWe show that variational learning can significantly improve the accuracy and calibration of Low-Rank Adaptation (LoRA) without a substantial increase in the cost. We replace AdamW by the Improved Variational Online Newton (IVON) algorithm to finetune large language models. For Llama-2 with 7 billion parameters, IVON improves the accuracy over AdamW by 2.8% and expected calibration error by 4.6%. The accuracy is also better than the other ...Working Paper