Alignment Pattern Analysis

This repository provides the code for the ICLR 2026 paper Only Brains Align with Brains: Cross-Region Alignment Patterns Expose Limits of Normative Models.

Preliminaries

Setup a virtual environment and install the python package provided by this repository.

We provide a definition file for a singularity container that can be built using the following command:

singularity build --fakeroot singularity/container.sif singularity/container.def

Download the BOLDMoments dataset from https://github.com/blahner/BOLDMomentsDataset to the datasets directory. Specifically, use the download script for versionB/fsLR32k. Also download the stimuli as detailed at this repository.

Reproducing alignment pattern analysis

We provide precomputed results from running the benchmarking pipeline. Alignment pattern analysis can be performed based on these results by executing

./run_aggregate_results.sh

Run figure shell scripts (run_figure_{x}.sh) to recreate the paper figures.

Evaluating models

Use the multitasking.benchmark script to evaluate a single model:

python -m multitasking.benchmark --config configs/benchmark.yaml

The tasks/ directory provides example setups for running the evaluation for multiple models or subjects in parallel on a slurm cluster.

# Run all models
python tasks/benchmark/launch.py --output-path path/to/output

# Run leave-one-out inter-subject comparison for all subjects
python tasks/benchmark_inter_subject_consistency/launch.py --output-path path/to/output

# Run pairwise inter-subject comparison for all subjects
python tasks/benchmark_inter_subject_consistency/launch.py --pairwise --output-path path/to/output

Citation

@inproceedings{
  title={Only Brains Align with Brains: Cross-Region Alignment Patterns Expose Limits of Normative Models},
  author={H{\"o}fling, Larissa and Tangemann, Matthias and Piefke, Lotta and Keller, Susanne and Bethge, Matthias and Franke, Katrin},
  booktitle={ICLR},
  year={2026},
  url={https://openreview.net/forum?id=cMGJcHHI7d}
}

This repository includes the code for the Opt-CWM model from Stojanov et al. (2025). Please cite all models and datasets used in your work.