PHAISTOS: A framework for Markov chain Monte Carlo simulation and inference of protein structure. - Wouter Boomsma; Jes Frellsen; Tim Harder; Sandro Bottaro; Kristoffer E. Johansson; Pengfei Tian; Kasper Stovgaard; Christian Andreetta; Simon Olsson; Jan B. Valentin; Lubomir D. Antonov; Anders S. Christensen; et al. (J. Comput. Chem., 2013)

Ecosystem Models Based on Artificial Intelligence. - Claes Strannegård; Niklas Engsner; Jesper Eisfeldt; John A. Endler; Amanda Hansson; Rasmus Lindgren; Petter Mostad; Simon Olsson; Irene Perini; Heather Reese; Fulya Taylan; Simon Ulfsbäcker; et al. (SAIS, 2022)

De Novo Drug Design Using Reinforcement Learning with Graph-Based Deep Generative Models. - Sara Romeo Atance; Juan Viguera Diez; Ola Engkvist; Simon Olsson; Rocío Mercado (J. Chem. Inf. Model., 2022)

Implicit Transfer Operator Learning: Multiple Time-Resolution Models for Molecular Dynamics. - Mathias Schreiner; Ole Winther; Simon Olsson (NeurIPS, 2023)

Exploring local effects of economic activities using agent-based ecosystem models. - Claes Strannegård; Niklas Engsner; Rasmus Lindgren; Simon Olsson; John A. Endler (CoRR, 2023)

Rescuing off-equilibrium simulation data through dynamic experimental data with dynAMMo. - Christopher Kolloff; Simon Olsson (Mach. Learn. Sci. Technol., 2023)

Efficient 3D Molecular Generation with Flow Matching and Scale Optimal Transport. - Ross Irwin; Alessandro Tibo; Jon Paul Janet; Simon Olsson (CoRR, 2024)

Generation of conformational ensembles of small molecules via surrogate model-assisted molecular dynamics. - Juan Viguera Diez; Sara Romeo Atance; Ola Engkvist; Simon Olsson (Mach. Learn. Sci. Technol., 2024)

SemlaFlow - Efficient 3D Molecular Generation with Latent Attention and Equivariant Flow Matching. - Ross Irwin; Alessandro Tibo; Jon Paul Janet; Simon Olsson (AISTATS, 2025)

Boltzmann priors for Implicit Transfer Operators. - Juan Viguera Diez; Mathias Jacob Schreiner; Ola Engkvist; Simon Olsson (ICLR, 2025)

Compositional Flows for 3D Molecule and Synthesis Pathway Co-design. - Tony Shen; Seonghwan Seo; Ross Irwin; Kieran Didi; Simon Olsson; Woo Youn Kim; Martin Ester (CoRR, 2025)

FLOWR: Flow Matching for Structure-Aware De Novo, Interaction- and Fragment-Based Ligand Generation. - Julian Cremer; Ross Irwin; Alessandro Tibo; Jon Paul Janet; Simon Olsson; Djork-Arné Clevert (CoRR, 2025)

Minimum-Excess-Work Guidance. - Christopher Kolloff; Tobias Höppe; Emmanouil Angelis; Mathias Jacob Schreiner; Stefan Bauer; Andrea Dittadi; Simon Olsson (CoRR, 2025)