Abstract Discrete stochastic processes are widespread across physics, chemistry, ecology, and beyond. In computational biology and epidemiology, however, most simulators still assume Markovian kinetics with memoryless dynamics, despite growing evidence for history-dependent effects in gene regulation, RNA transcription...
A. Pélissier, Miroslav Phan, N. Beerenwinkel et al.· Briefings in Bioinformatics· 0 citations
This work tests the reliability of perturbations and their alignment with shared perturbation responses, classifying each perturbation as specific, shared, or unreliable, and applies these quality labels to published benchmarks shows that model comparisons depend on perturbation quality.
Xi Wang, J. Kuipers, Florian Hugi et al.· bioRxiv· 0 citations
Two numerical approximations of population size distributions for multi-type branching processes on directed graphs on directed graphs with arbitrary initialization are introduced and provided computational building blocks for future likelihood-based inference in cancer evolution and other expanding populations.
Xiang-Ge Luo, J. Kuipers, N. Beerenwinkel· 0 citations
It is demonstrated that integrated multimodal tumor profiling can inform personalized maintenance treatment decisions and that chemotherapy reshapes tumor cell diversity.
Francis Jacob, R. Wegmann, Joanna Ficek-Pascual et al.· Nature Communications· 0 citations
HIVMedQA is developed, a clinician-curated benchmark of HIV-related open-ended medical question-answer pairs spanning basic knowledge, clinical reasoning, complex patient vignettes, and bias-modified scenarios that provides a structured benchmark for evaluating LLMs in HIV clinical decision support.
Gonzalo Cardenal-Antolin, J. Fellay, Bashkim Jaha et al.· Communications Medicine· 1 citation
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