Add auxiliary-task and annotator analyses for manuscript revision

paper/nature_neuroscience_revision/auxiliary_task_assessment/.gitignore

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+__pycache__/
+*.py[cod]
+.ipynb_checkpoints/
+*.pt
+*.pth
+*.ckpt
+*.npy
+*.npz
+embeddings/
+raw_data/

paper/nature_neuroscience_revision/auxiliary_task_assessment/PROVENANCE.md

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+# Provenance
+
+## Recovered sources
+
+- Seed-specific CalMS21 decoder scripts and the all-seed plotting script were
+  recovered from `task_ablation_code_collection_dell.tar.gz`.
+- Annotator/bout summary CSVs, final figures and the plotting notebook were
+  recovered from `auxiliary_task_final_collection.tar.gz`.
+
+## Transformations
+
+- The five seed-specific CalMS21 scripts are byte-for-byte copies of their
+  recovered sources.
+- `plot_calms21_posthoc_allseeds.py` preserves the recovered aggregation and
+  plotting logic. Its single historical hard-coded absolute root was replaced
+  with `--root` and optional `--output` arguments.
+- `plot_combined_calms21_mars1_annotator_bias.py` was extracted from the final
+  executed cell of `annotator-bias.ipynb`. Absolute paths were replaced with
+  package-relative paths, and notebook-only `display()` calls were changed to
+  terminal printing. The calculations, panel definitions and plotting
+  parameters were otherwise preserved.
+- The original notebook is not included because it contains many duplicated
+  exploratory cells, embedded outputs and private absolute paths.
+- No scientific result was synthesized, recalculated from prose or manually
+  entered into a new table.
+
+## Known limitation
+
+The original metric-generation script for the CalMS21/MARS1 annotator and bout
+summary CSVs was not found in the supplied code collections. The preserved
+summary tables and final plotting implementation are included transparently.

paper/nature_neuroscience_revision/auxiliary_task_assessment/README.md

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+# Auxiliary-task assessment and annotator/bout analyses
+
+This directory contains code associated with two additions made during the
+LISBET manuscript revision:
+
+1. **CalMS21 leave-one-task-out decoding**: five matched encoder seeds for the
+   full auxiliary-task model and the four leave-one-task-out variants, followed
+   by frozen-embedding k-nearest-neighbor decoding and all-seed aggregation.
+2. **CalMS21 Task 2 and MARS1 annotator/bout characterization**: summary-level
+   agreement, label-prevalence and bout-duration tables together with the code
+   used to reproduce the final six-panel figure.
+
+## CalMS21 leave-one-task-out code
+
+The five `reviewer_2_2_calms21_pipeline_seed*.py` files are exact copies of the
+seed-specific analysis scripts recovered from the Dell code archive. Each
+script accepts `--lisbet-root`; use that argument rather than relying on its
+historical default directory.
+
+Example for seed 0:
+
+```bash
+python scripts/reviewer_2_2_calms21_pipeline_seed0.py all \
+  --lisbet-root /path/to/Lisbet
+```
+
+The all-seed aggregation script was changed only to replace one private,
+hard-coded source path with explicit command-line arguments:
+
+```bash
+python scripts/plot_calms21_posthoc_allseeds.py \
+  --root /path/containing/reviewer_2_2_calms21_posthoc_seed0_to_seed4
+```
+
+The seed-level and aggregate CalMS21 result CSVs were not present in the
+uploaded source archives, so they are not included here. No result table was
+reconstructed from manuscript text.
+
+## Annotator and bout figure
+
+Run from any directory:
+
+```bash
+python annotator_bout_metrics/scripts/plot_combined_calms21_mars1_annotator_bias.py
+```
+
+The script reads the included summary CSVs and writes the PNG, PDF, SVG and
+combined summary CSV to `annotator_bout_metrics/figures/`.
+
+The available source material contained plotting code and derived summary
+CSVs, but not the upstream script that originally calculated all agreement and
+bout tables from raw annotations. Accordingly, this folder supports exact
+figure reproduction from the preserved summary tables but does not claim to
+recreate those tables from raw CalMS21 or MARS1 annotations.
+
+Raw annotations, pose data, embeddings, model weights and private machine paths
+are intentionally excluded.

paper/nature_neuroscience_revision/auxiliary_task_assessment/annotator_bout_metrics/figures/combined_annotator_bias_summary_shared_legend.csv

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+dataset,n_annotators,n_pairwise_comparisons,total_frames_annotated,accuracy_mean,balanced_accuracy_mean,macro_f1_mean,cohen_kappa_mean,mcc_mean
+CalMS21 Task 2,5,10,1722361,0.587981380553702,0.36366716663646165,0.32895675619170517,0.10709882698855706,0.11124012746025029
+MARS1,8,28,1818304,0.906520650902092,0.8035393198111029,0.7709196531952476,0.7987126001605034,0.8032185150286512