SBI Workflow Overview

Simulation-Based Inference: A Practical Guide

We provide a practical guide for applying SBI methods, outlining a structured workflow with guidelines and diagnostic tools for every stage—from setting up simulators to validating results.

August 2025 · Michael Deistler*, Jan Boelts*, Peter Steinbach, Guy Moss, Thomas Moreau, Manuel Gloeckler, Pedro L. C. Rodrigues, Julia Linhart, Janne K. Lappalainen, Benjamin Kurt Miller, Pedro J. Gonçalves, Jan-Matthis Lueckmann, Cornelius Schröder, Jakob H. Macke

sbi reloaded: A toolkit for simulation-based inference workflows

We present sbi reloaded, a comprehensive update to the sbi Python package that provides researchers with state-of-the-art algorithms and tools for simulation-based inference workflows across scientific domains.

April 2025 · Jan Boelts*, Michael Deistler*, Manuel Gloeckler, Álvaro Tejero-Cantero, Jan-Matthis Lueckmann, Guy Moss, Peter Steinbach, Thomas Moreau, Fabio Muratore, Julia Linhart, Conor Durkan, Julius Vetter, Benjamin Kurt Miller, Maternus Herold, Abolfazl Ziaeemehr, Matthijs Pals, Theo Gruner, Sebastian Bischoff, Nastya Krouglova, Richard Gao, Janne K. Lappalainen, Bálint Mucsányi, Felix Pei, Auguste Schulz, Zinovia Stefanidi, Pedro Rodrigues, Cornelius Schröder, Faried Abu Zaid, Jonas Beck, Jaivardhan Kapoor, David S. Greenberg, Pedro J. Gonçalves, Jakob H. Macke

Dissecting origins of wiring specificity in dense cortical connectomes

We dissect the origins of wiring specificity in dense cortical connectomes, revealing how geometric and biological constraints shape synaptic connectivity patterns.

December 2024 · Philipp Harth, Daniel Udvary, Jan Boelts, Daniel Baum, Jakob H. Macke, Hans-Christian Hege, Marcel Oberlaender
Simulation-based inference for computational connectomics

Simulation-based inference for efficient identification of generative models in connectomics

We demonstrate how simulation-based inference can efficiently identify synaptic connectivity rules in dense cortical connectomes, enabling analysis of complex brain circuit organization.

August 2023 · Jan Boelts, Philipp Harth, Richard Gao, Daniel Udvary, Felipe Yanez, Daniel Baum, Hans-Christian Hege, Marcel Oberlaender, Jakob H. Macke
Mixed Neural Likelihood Estimation

Flexible and efficient simulation-based inference for models of decision-making

We propose a new method to perform simulation-based inference for mixed data e.g., with continuous and discrete data types, like they often occur in models of decision-making.

July 2022 · Jan Boelts, Jan-Matthis Lueckmann, Richard Gao, Jakob H. Macke

GATSBI: Generative Adversarial Training for Simulation-Based Inference

We introduce GATSBI, a method that combines generative adversarial networks with simulation-based inference to achieve better sample efficiency and accuracy in posterior estimation.

April 2022 · Poornima Ramesh, Jan-Matthis Lueckmann, Jan Boelts, Álvaro Tejero-Cantero, David S. Greenberg, Jakob H. Macke

Benchmarking Simulation-Based Inference

We present a benchmark suite for simulation-based inference, systematically evaluating different methods across tasks with varying dimensionality, simulation budgets, and amortization requirements.

April 2021 · Jan-Matthis Lueckmann, Jan Boelts, David S. Greenberg, Pedro J. Gonçalves, Jakob H. Macke

sbi: A toolkit for simulation-based inference

We introduce sbi, a Python package providing a unified interface for simulation-based inference methods, making these powerful techniques accessible to researchers across disciplines.

August 2020 · Álvaro Tejero-Cantero*, Jan Boelts*, Michael Deistler*, Jan-Matthis Lueckmann*, Conor Durkan*, Pedro J. Gonçalves, David S. Greenberg, Jakob H. Macke