Informing agent-based models with spatial data using convolutional autoencoders.
MOTIVATION: Spatial computational models such as agent-based models (ABMs) offer powerful in silico tools to study tumor dynamics, yet imaging data are still rarely used to inform these models directly. RESULTS: We present an ABM optimization framework that leverages convolutional encoders to compare spatial patterns between experimental imaging data and ABM-generated outputs within a shared latent space. This quantitative comparison was used to estimate ABM parameters across three datasets, ranging from synthetic data to 3D tumoroid-T cell co-culture microscopy and histopathology images from The Cancer Genome Atlas skin cutaneous melanoma samples. Estimated parameters were evaluated using data-derived features and experimental knowledge, including experimental conditions and gene expressions. Simulations using optimized parameters reproduced key spatial features of the training images, such as tumor boundary complexity and tumor-tumor neighborhood structure. Together, these results demonstrate a flexible framework for ABM parameter optimization using spatial data across modalities, enabling systematic investigation of how spatial architecture influences tumor progression and immune interactions. AVAILABILITY AND IMPLEMENTATION: Source code is available at https://github.com/SysBioOncology/ AutoencoderABM under the GPL-3.0 license, with corresponding data sets at https://zenodo.org/records/19022344.