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Restructure: descriptive tier and experiment names, paper/manuscript

Browse source 
- 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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379
results/grounding/resolved_config.yaml
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@ -1,379 +0,0 @@
experiment: grounding_phase_boundary
seed: 20260704
n_replicates: 18
source_config:
experiment: grounding_phase_boundary
kind: gen_lineage
seed: 20260704
n_replicates: 18
generations: 30
synthetic:
K: 256
R: 1
tail: zipf
zipf_s: 1.3
tail_frac: 0.5
tail_threshold: 0.001
init: truth
style_len: 3
style_vocab: 5
id_base: 2
model:
kind: rnn
hidden: 128
embed: 24
epochs: 25
lr: 0.002
batch_size: 256
n_eval: 15000
dynamics:
n: 200
grounding:
m: 0
policy: proportional
remint:
enabled: false
period: null
H_gate: null
metrics:
kl_floor: 1.0e-09
support_eps: 1.0e-09
sweep:
- param: g
values:
- 0.0
- 0.005
- 0.01
- 0.02
- 0.035
- 0.05
- 0.075
- 0.1
- 0.2
output:
dir: results/grounding
grid:
- label:
g: 0.0
m: 0
neural_cfg:
synthetic:
K: 256
R: 1
tail: zipf
zipf_s: 1.3
tail_frac: 0.5
tail_threshold: 0.001
init: truth
style_len: 3
style_vocab: 5
id_base: 2
model:
kind: rnn
hidden: 128
embed: 24
epochs: 25
lr: 0.002
batch_size: 256
n_eval: 15000
dynamics:
n: 200
grounding:
m: 0
policy: proportional
remint:
enabled: false
period: null
H_gate: null
generations: 30
metrics:
kl_floor: 1.0e-09
support_eps: 1.0e-09
- label:
g: 0.005
m: 1
neural_cfg:
synthetic:
K: 256
R: 1
tail: zipf
zipf_s: 1.3
tail_frac: 0.5
tail_threshold: 0.001
init: truth
style_len: 3
style_vocab: 5
id_base: 2
model:
kind: rnn
hidden: 128
embed: 24
epochs: 25
lr: 0.002
batch_size: 256
n_eval: 15000
dynamics:
n: 200
grounding:
m: 1
policy: proportional
remint:
enabled: false
period: null
H_gate: null
generations: 30
metrics:
kl_floor: 1.0e-09
support_eps: 1.0e-09
- label:
g: 0.01
m: 2
neural_cfg:
synthetic:
K: 256
R: 1
tail: zipf
zipf_s: 1.3
tail_frac: 0.5
tail_threshold: 0.001
init: truth
style_len: 3
style_vocab: 5
id_base: 2
model:
kind: rnn
hidden: 128
embed: 24
epochs: 25
lr: 0.002
batch_size: 256
n_eval: 15000
dynamics:
n: 200
grounding:
m: 2
policy: proportional
remint:
enabled: false
period: null
H_gate: null
generations: 30
metrics:
kl_floor: 1.0e-09
support_eps: 1.0e-09
- label:
g: 0.02
m: 4
neural_cfg:
synthetic:
K: 256
R: 1
tail: zipf
zipf_s: 1.3
tail_frac: 0.5
tail_threshold: 0.001
init: truth
style_len: 3
style_vocab: 5
id_base: 2
model:
kind: rnn
hidden: 128
embed: 24
epochs: 25
lr: 0.002
batch_size: 256
n_eval: 15000
dynamics:
n: 200
grounding:
m: 4
policy: proportional
remint:
enabled: false
period: null
H_gate: null
generations: 30
metrics:
kl_floor: 1.0e-09
support_eps: 1.0e-09
- label:
g: 0.035
m: 7
neural_cfg:
synthetic:
K: 256
R: 1
tail: zipf
zipf_s: 1.3
tail_frac: 0.5
tail_threshold: 0.001
init: truth
style_len: 3
style_vocab: 5
id_base: 2
model:
kind: rnn
hidden: 128
embed: 24
epochs: 25
lr: 0.002
batch_size: 256
n_eval: 15000
dynamics:
n: 200
grounding:
m: 7
policy: proportional
remint:
enabled: false
period: null
H_gate: null
generations: 30
metrics:
kl_floor: 1.0e-09
support_eps: 1.0e-09
- label:
g: 0.05
m: 11
neural_cfg:
synthetic:
K: 256
R: 1
tail: zipf
zipf_s: 1.3
tail_frac: 0.5
tail_threshold: 0.001
init: truth
style_len: 3
style_vocab: 5
id_base: 2
model:
kind: rnn
hidden: 128
embed: 24
epochs: 25
lr: 0.002
batch_size: 256
n_eval: 15000
dynamics:
n: 200
grounding:
m: 11
policy: proportional
remint:
enabled: false
period: null
H_gate: null
generations: 30
metrics:
kl_floor: 1.0e-09
support_eps: 1.0e-09
- label:
g: 0.075
m: 16
neural_cfg:
synthetic:
K: 256
R: 1
tail: zipf
zipf_s: 1.3
tail_frac: 0.5
tail_threshold: 0.001
init: truth
style_len: 3
style_vocab: 5
id_base: 2
model:
kind: rnn
hidden: 128
embed: 24
epochs: 25
lr: 0.002
batch_size: 256
n_eval: 15000
dynamics:
n: 200
grounding:
m: 16
policy: proportional
remint:
enabled: false
period: null
H_gate: null
generations: 30
metrics:
kl_floor: 1.0e-09
support_eps: 1.0e-09
- label:
g: 0.1
m: 22
neural_cfg:
synthetic:
K: 256
R: 1
tail: zipf
zipf_s: 1.3
tail_frac: 0.5
tail_threshold: 0.001
init: truth
style_len: 3
style_vocab: 5
id_base: 2
model:
kind: rnn
hidden: 128
embed: 24
epochs: 25
lr: 0.002
batch_size: 256
n_eval: 15000
dynamics:
n: 200
grounding:
m: 22
policy: proportional
remint:
enabled: false
period: null
H_gate: null
generations: 30
metrics:
kl_floor: 1.0e-09
support_eps: 1.0e-09
- label:
g: 0.2
m: 50
neural_cfg:
synthetic:
K: 256
R: 1
tail: zipf
zipf_s: 1.3
tail_frac: 0.5
tail_threshold: 0.001
init: truth
style_len: 3
style_vocab: 5
id_base: 2
model:
kind: rnn
hidden: 128
embed: 24
epochs: 25
lr: 0.002
batch_size: 256
n_eval: 15000
dynamics:
n: 200
grounding:
m: 50
policy: proportional
remint:
enabled: false
period: null
H_gate: null
generations: 30
metrics:
kl_floor: 1.0e-09
support_eps: 1.0e-09