paper_figures.md

Figures from the paper

I. Aitsahalia et al., "Inferring cognitive strategies from groups of animals in natural environments," presented at the NeurIPS Workshop on Data on the Brain & Mind Findings, 2025.

Figure 2

The video alignment was done manually using the scripts in collab_env/tracking. Detailed instructions appear in tracking/README.md and an example notebook is available at tracking/full_pipeline.ipynb.

Figure 4

Requires running alignment/align.ipynb and alignment/reprojection.ipynb sequentially.

• Default parameters for camera alignment
• The following parameters for reprojection:
  • n_agents = 20
  • n_min_frames = 150

Figure 5

Instructions on running the boids simulation appear in sim/README.md.

Figure 6

Instructions for training and analyzing GNNs appear in gnn/GNNReadMe.md.

• For Figure 6(B) see ../figures/gnn/A-rollout.ipynb
• For Figure 6(C) see ../figures/gnn/B-attention_weights_food.ipynb

Figure 7

See ../figures/gnn/appendix-rollout_perturb.ipynb

Figure 8

See ../figures/gnn/Z-tracked-data.ipynb