netReg: network-regularized linear models for biological association studies. - Simon Dirmeier; Christiane Fuchs; Nikola S. Müller; Fabian J. Theis (Bioinform., 2018)

datastructures: An R package for organisation and storage of data. - Simon Dirmeier (J. Open Source Softw., 2018)

PyBDA: a command line tool for automated analysis of big biological data sets. - Simon Dirmeier; Mario Emmenlauer; Christoph Dehio; Niko Beerenwinkel (BMC Bioinform., 2019)

Host factor prioritization for pan-viral genetic perturbation screens using random intercept models and network propagation. - Simon Dirmeier; Christopher Dächert; Martijn van Hemert; Ali Tas; Natacha S. Ogando; Frank J. M. van Kuppeveld; Ralf Bartenschlager; Lars Kaderali; Marco Binder; Niko Beerenwinkel (PLoS Comput. Biol., 2020)

Simulation-based inference using surjective sequential neural likelihood estimation. - Simon Dirmeier; Carlo Albert; Fernando Pérez-Cruz (CoRR, 2023)

Uncertainty quantification and out-of-distribution detection using surjective normalizing flows. - Simon Dirmeier; Ye Hong; Yanan Xin 001; Fernando Pérez-Cruz (CoRR, 2023)

Diffusion models for probabilistic programming. - Simon Dirmeier; Fernando Pérez-Cruz (CoRR, 2023)

Revealing behavioral impact on mobility prediction networks through causal interventions. - Ye Hong; Yanan Xin 001; Simon Dirmeier; Fernando Pérez-Cruz; Martin Raubal (CoRR, 2023)

Synthetic location trajectory generation using categorical diffusion models. - Simon Dirmeier; Ye Hong; Fernando Pérez-Cruz (CoRR, 2024)

Simulation-based inference with the Python Package sbijax. - Simon Dirmeier; Simone Ulzega; Antonietta Mira; Carlo Albert (CoRR, 2024)

High Resolution Seismic Waveform Generation using Denoising Diffusion. - Andreas Bergmeister; Kadek Hendrawan Palgunadi; Andrea Bosisio; Laura Ermert; Maria Koroni; Nathanaël Perraudin; Simon Dirmeier; Men-Andrin Meier (CoRR, 2024)

Surjectors: surjection layers for density estimation with normalizing flows. - Simon Dirmeier (J. Open Source Softw., 2024)

Simulation-based Inference for High-dimensional Data using Surjective Sequential Neural Likelihood Estimation. - Simon Dirmeier; Carlo Albert; Fernando Pérez-Cruz (UAI, 2025)

Causal Posterior Estimation. - Simon Dirmeier; Antonietta Mira (CoRR, 2025)