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Restructure: descriptive tier and experiment names, paper/manuscript

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- paper/pnas -> paper/manuscript (venue-neutral)
- configs/layer1 -> configs/inheritance, src/knowledge -> src/inheritance
  (imported as `inheritance`), make layer1 -> make inheritance; layer2 alias dropped
- inheritance and trained-network bundles named after the manuscript figure
  they feed (fig2_grounding_sweep, figS3_rebaselining, ...), or descriptively
  where they feed none; configs keep their `experiment:` value so parquet
  hashes are unchanged, only output.dir moves
- figure scripts, SI figure sources, notebooks, REPRODUCING.md, README and the
  SI Methods/tables updated; make clean no longer deletes tracked manifests;
  reproduce.sh hashes the s{seed}/ layouts too

Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Y64o8FKP7rCuXzC48pxpMm
This commit is contained in:
Giorgio Gilestro 2026-09-13 17:00:40 +01:00
parent 84124de143
commit ab3dc10587
240 changed files with 477 additions and 476 deletions
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184
results/figS3_rebaselining/resolved_config.yaml Normal file
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experiment: E6_remint_gate
seed: 20260704
n_replicates: 100
source_config:
experiment: E6_remint_gate
seed: 20260704
n_replicates: 100
generations: 400
truth:
K: 500
R: 1
tail: zipf
zipf_s: 1.1
tail_frac: 0.5
tail_threshold: 0.001
init: truth
dynamics:
n: 200
teachers:
K_T: 1
rho: 0.0
q: 1.0
grounding:
m: 3
policy: proportional
selection:
mode: none
novelty_alpha: 0.0
remint:
enabled: false
period: 150
H_gate: null
metrics:
kl_floor: 1.0e-09
support_eps: 1.0e-09
sweep:
- param: arm
values:
- name: healthy_remint
set:
dynamics.grounding.m: 60
dynamics.remint.enabled: true
dynamics.remint.H_gate: null
- name: collapsed_remint
set:
dynamics.grounding.m: 1
dynamics.remint.enabled: true
dynamics.remint.H_gate: null
- name: collapsed_gated
set:
dynamics.grounding.m: 1
dynamics.remint.enabled: true
dynamics.remint.H_gate: 0.75
- name: collapsed_noremint
set:
dynamics.grounding.m: 1
dynamics.remint.enabled: false
output:
dir: results/figS3_rebaselining
grid:
- label:
arm: healthy_remint
lineage_cfg:
truth:
K: 500
R: 1
tail: zipf
zipf_s: 1.1
tail_frac: 0.5
tail_threshold: 0.001
init: truth
dynamics:
n: 200
teachers:
K_T: 1
rho: 0.0
q: 1.0
grounding:
m: 60
policy: proportional
selection:
mode: none
novelty_alpha: 0.0
remint:
enabled: true
period: 150
H_gate: null
generations: 400
metrics:
kl_floor: 1.0e-09
support_eps: 1.0e-09
- label:
arm: collapsed_remint
lineage_cfg:
truth:
K: 500
R: 1
tail: zipf
zipf_s: 1.1
tail_frac: 0.5
tail_threshold: 0.001
init: truth
dynamics:
n: 200
teachers:
K_T: 1
rho: 0.0
q: 1.0
grounding:
m: 1
policy: proportional
selection:
mode: none
novelty_alpha: 0.0
remint:
enabled: true
period: 150
H_gate: null
generations: 400
metrics:
kl_floor: 1.0e-09
support_eps: 1.0e-09
- label:
arm: collapsed_gated
lineage_cfg:
truth:
K: 500
R: 1
tail: zipf
zipf_s: 1.1
tail_frac: 0.5
tail_threshold: 0.001
init: truth
dynamics:
n: 200
teachers:
K_T: 1
rho: 0.0
q: 1.0
grounding:
m: 1
policy: proportional
selection:
mode: none
novelty_alpha: 0.0
remint:
enabled: true
period: 150
H_gate: 0.75
generations: 400
metrics:
kl_floor: 1.0e-09
support_eps: 1.0e-09
- label:
arm: collapsed_noremint
lineage_cfg:
truth:
K: 500
R: 1
tail: zipf
zipf_s: 1.1
tail_frac: 0.5
tail_threshold: 0.001
init: truth
dynamics:
n: 200
teachers:
K_T: 1
rho: 0.0
q: 1.0
grounding:
m: 1
policy: proportional
selection:
mode: none
novelty_alpha: 0.0
remint:
enabled: false
period: 150
H_gate: null
generations: 400
metrics:
kl_floor: 1.0e-09
support_eps: 1.0e-09