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Giorgio Gilestro ab3dc10587 Restructure: descriptive tier and experiment names, paper/manuscript 
- 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
2026-09-13 17:00:40 +01:00
..
bridge docs: accessible figure legends (README.md) for all figures 2026-07-05 08:43:04 +01:00
collapse docs: accessible figure legends (README.md) for all figures 2026-07-05 08:43:04 +01:00
collapse_null Restructure: descriptive tier and experiment names, paper/manuscript 2026-09-13 17:00:40 +01:00
fig2_grounding_sweep Restructure: descriptive tier and experiment names, paper/manuscript 2026-09-13 17:00:40 +01:00
fig2_mnist_collapse Restructure: descriptive tier and experiment names, paper/manuscript 2026-09-13 17:00:40 +01:00
fig4_society_ablation Restructure: descriptive tier and experiment names, paper/manuscript 2026-09-13 17:00:40 +01:00
fig5_speciation_bdm Restructure: descriptive tier and experiment names, paper/manuscript 2026-09-13 17:00:40 +01:00
figS1_architectures Restructure: descriptive tier and experiment names, paper/manuscript 2026-09-13 17:00:40 +01:00
figS2_kernel_sharpen Restructure: descriptive tier and experiment names, paper/manuscript 2026-09-13 17:00:40 +01:00
figS2_kernel_smooth Restructure: descriptive tier and experiment names, paper/manuscript 2026-09-13 17:00:40 +01:00
figS3_rebaselining Restructure: descriptive tier and experiment names, paper/manuscript 2026-09-13 17:00:40 +01:00
figS5_aimed_grounding Restructure: descriptive tier and experiment names, paper/manuscript 2026-09-13 17:00:40 +01:00
figS6_grounding_rnn Restructure: descriptive tier and experiment names, paper/manuscript 2026-09-13 17:00:40 +01:00
figS8_multiparent_union Restructure: descriptive tier and experiment names, paper/manuscript 2026-09-13 17:00:40 +01:00
figS9_specialist_superparent Restructure: descriptive tier and experiment names, paper/manuscript 2026-09-13 17:00:40 +01:00
figS10_rugged_landscapes Restructure: descriptive tier and experiment names, paper/manuscript 2026-09-13 17:00:40 +01:00
figS11_directed_recombination Restructure: descriptive tier and experiment names, paper/manuscript 2026-09-13 17:00:40 +01:00
figS12_quality_diversity Restructure: descriptive tier and experiment names, paper/manuscript 2026-09-13 17:00:40 +01:00
figS13_mating_breadth Restructure: descriptive tier and experiment names, paper/manuscript 2026-09-13 17:00:40 +01:00
llm_compose Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
llm_compose_all Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
llm_compose_gate Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
llm_compose_gate_math500 Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
llm_curriculum_g2 Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
llm_curriculum_gate Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
llm_curriculum_v5 Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
llm_curriculum_v5_calib Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
llm_curriculum_v5_calib_b Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
llm_curriculum_v5_cull Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
llm_curriculum_v5_decor Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
llm_curriculum_v5_early Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
llm_curriculum_v5_early_obl Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
llm_curriculum_v5_g2 Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
llm_curriculum_v5_late Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
llm_curriculum_v5_late_obl Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
llm_curriculum_v5_stop3 Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
llm_curriculum_v5_veto Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
llm_directed llm_directed: directed sex (breed offspring + select on verifier) — E10 in real weights 2026-07-05 18:35:04 +01:00
llm_directed_hard_hpc Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
llm_directed_hard_seeds Phase 3: LLM-tier speciation + multi-seed firm-up of the recombination claims 2026-09-06 15:39:15 +01:00
llm_directed_hpc llm_directed: directed sex (breed offspring + select on verifier) — E10 in real weights 2026-07-05 18:35:04 +01:00
llm_epistasis second review round: tempered claims, robust statistics, corrected technical statements 2026-09-06 17:55:46 +01:00
llm_epistasis_compat epistasis_predicts: functional conflict, not weight geometry, predicts merge failure pre-merge 2026-09-06 17:19:46 +01:00
llm_merge llm_merge_hpc: the 7B firm-up makes the Fisher-Muller sign decisive 2026-07-05 17:32:51 +01:00
llm_merge_hpc Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
llm_merge_seeds second review round: tempered claims, robust statistics, corrected technical statements 2026-09-06 17:55:46 +01:00
llm_merge_seeds_smol Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
llm_moe llm_directed: directed sex (breed offspring + select on verifier) — E10 in real weights 2026-07-05 18:35:04 +01:00
llm_moe_hard Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
llm_moe_hard_hpc Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
llm_moe_hard_seeds second review round: tempered claims, robust statistics, corrected technical statements 2026-09-06 17:55:46 +01:00
llm_moe_hard_seeds_smol Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
llm_moe_hpc llm_moe: the union operator (route/max-merge) vs fusion — and the regime flips at scale 2026-07-05 17:53:47 +01:00
llm_society Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
llm_society_campaign Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
llm_society_pilot1 Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
llm_society_smoke Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
llm_society_v2_calib_a Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
llm_society_v2_calib_a2 Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
llm_society_v2_calib_b Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
llm_society_v2_calib_b_consensus Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
llm_society_v2_calib_b_cross Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
llm_society_v2_calib_b_cross_gated Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
llm_society_v2_calib_b_transmission_conf Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
llm_society_v2_calib_c3b_e6 Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
llm_society_v2_calib_c3b_r64 Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
llm_society_v2_calib_c3b_r64e6 Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
llm_society_v2_calib_c3c_t85e3 Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
llm_society_v2_calib_c3c_t85e6 Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
llm_society_v2_smoke Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
llm_speciation Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
llm_speciation_add Phase 3: LLM-tier speciation + multi-seed firm-up of the recombination claims 2026-09-06 15:39:15 +01:00
recombination docs: accessible figure legends (README.md) for all figures 2026-07-05 08:43:04 +01:00
sexual_vs_asexual_lineage Restructure: descriptive tier and experiment names, paper/manuscript 2026-09-13 17:00:40 +01:00
speciation_bdm_nk Restructure: descriptive tier and experiment names, paper/manuscript 2026-09-13 17:00:40 +01:00
speciation_real third review round: mathematical corrections + operator separation + headline calibration 2026-09-06 19:29:09 +01:00
speciation_real_cliff E13b/c: harden real-weight speciation — full symmetry group + emergent-divergence null 2026-09-06 12:35:14 +01:00
speciation_real_emergent E13b/c: harden real-weight speciation — full symmetry group + emergent-divergence null 2026-09-06 12:35:14 +01:00