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
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1 OK 10.48550/arXiv.2508.06811 Anatomy of a Machine Learning Ecosystem: 2 Million Models on Hug in manuscript
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2 OK 10.48550/arXiv.2405.18432 Unsupervised Model Tree Heritage Recovery in manuscript
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3 OK 10.48550/arXiv.2402.00699 PeaTMOSS: A Dataset and Initial Analysis of Pre-Trained Models i in manuscript
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4 OK 10.48550/arXiv.2306.01708 TIES-Merging: Resolving Interference When Merging Models in manuscript
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5 OK 10.1038/s42256-024-00975-8 Evolutionary optimization of model merging recipes crossref (matched: Evolutionary optimization of model merging recipes)
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6 OK 10.48550/arXiv.2403.13257 Arcee's MergeKit: A Toolkit for Merging Large Language Models in manuscript
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7 OK 10.48550/arXiv.2408.07666 Model Merging in LLMs, MLLMs, and Beyond: Methods, Theories, App in manuscript
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8 OK 10.48550/arXiv.2503.01155 Nature-Inspired Population-Based Evolution of Large Language Mod in manuscript
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9 OK 10.48550/arXiv.2508.16204 Competition and Attraction Improve Model Fusion in manuscript
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10 OK 10.48550/arXiv.2501.05707 Multiagent Finetuning: Self Improvement with Diverse Reasoning C in manuscript
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11 OK 10.48550/arXiv.2406.11704 Nemotron-4 340B Technical Report in manuscript
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12 OK 10.48550/arXiv.2412.08905 Phi-4 Technical Report in manuscript
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13 OK 10.48550/arXiv.2212.10560 Self-Instruct: Aligning Language Models with Self-Generated Inst in manuscript
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14 OK 10.48550/arXiv.2401.05749 A Shocking Amount of the Web is Machine Translated: Insights fro in manuscript
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15 OK 10.48550/arXiv.2403.07183 Monitoring AI-Modified Content at Scale: A Case Study on the Imp in manuscript
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16 OK 10.48550/arXiv.2211.04325 Will we run out of data? Limits of LLM scaling based on human-ge in manuscript
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17 OK 10.1038/s41562-023-01742-2 Machine culture verified by hand
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18 OK 10.48550/arXiv.2304.03442 Generative Agents: Interactive Simulacra of Human Behavior in manuscript
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19 OK 10.48550/arXiv.2402.01680 Large Language Model based Multi-Agents: A Survey of Progress an in manuscript
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20 OK 10.48550/arXiv.2509.10147 Virtual Agent Economies in manuscript
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21 OK 10.1038/s41586-024-07566-y AI models collapse when trained on recursively generated data crossref (matched: AI models collapse when trained on recursively generated data)
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22 OK 10.1371/journal.pcbi.1002510 Structural Drift: The Population Dynamics of Sequential Learning crossref (matched: Structural Drift: The Population Dynamics of Sequential Learning)
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23 OK 10.48550/arXiv.2604.08554 Drift and selection in LLM text ecosystems in manuscript
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24 OK 10.48550/arXiv.2509.20101 First-Extinction Law for Resampling Processes in manuscript
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25 OK 10.48550/arXiv.2407.17493 Model Collapse in the Self-Consuming Chain of Diffusion Finetuni in manuscript
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26 OK 10.1016/s0079-7421(08)60536-8 Catastrophic Interference in Connectionist Networks: The Sequent crossref (matched: Catastrophic Interference in Connectionist Networks: The Sequential Le)
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27 OK 10.1016/s1364-6613(99)01294-2 Catastrophic forgetting in connectionist networks crossref (matched: Catastrophic forgetting in connectionist networks)
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28 OK 10.1016/0027-5107(64)90047-8 The relation of recombination to mutational advance crossref (matched: The relation of recombination to mutational advance)
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29 OK 10.48550/arXiv.2510.16657 Escaping Model Collapse via Synthetic Data Verification: Near-te in manuscript
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30 OK 10.48550/arXiv.2404.01413 Is Model Collapse Inevitable? Breaking the Curse of Recursion by in manuscript
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31 OK 10.1093/genetics/16.2.97 EVOLUTION IN MENDELIAN POPULATIONS crossref (matched: EVOLUTION IN MENDELIAN POPULATIONS)
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32 OK 10.1046/j.1523-1739.1996.10061509.x The One‐Migrant‐per‐Generation Rule in Conservation and Manageme crossref (matched: The One‐Migrant‐per‐Generation Rule in Conservation and Management)
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33 HAND (pre-DOI source) [Review of] The Origin of Species written by hand
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34 OK 10.48550/arXiv.2411.02207 Collective Model Intelligence Requires Compatible Specialization in manuscript
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35 HAND (pre-DOI source) The Genetical Theory of Natural Selection written by hand
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36 OK 10.1086/280418 Some Genetic Aspects of Sex crossref (matched: Some Genetic Aspects of Sex)
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37 OK 10.48550/arXiv.2106.09685 LoRA: Low-Rank Adaptation of Large Language Models in manuscript
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38 OK 10.1016/s0022-5193(87)80029-2 Towards a general theory of adaptive walks on rugged landscapes crossref (matched: Towards a general theory of adaptive walks on rugged landscapes)
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39 HAND (pre-DOI source) Coadaptation and outbreeding depression written by hand
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40 OK 10.1162/evco_a_00025 Abandoning Objectives: Evolution Through the Search for Novelty crossref (matched: Abandoning Objectives: Evolution Through the Search for Novelty Alone)
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41 OK 10.48550/arXiv.2503.05683 WikiBigEdit: Understanding the Limits of Lifelong Knowledge Edit in manuscript
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42 OK 10.48550/arXiv.2502.04390 In Praise of Stubbornness: An Empirical Case for Cognitive-Disso in manuscript
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43 OK 10.48550/arXiv.2607.09202 Interference and Retention in Continual Learning in manuscript
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44 OK 10.1017/s0016672300033140 A general model for the evolution of recombination crossref (matched: A general model for the evolution of recombination)
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45 OK 10.1006/tpbi.1997.1301 Deleterious Mutations, Variable Epistatic Interactions, and the crossref (matched: Deleterious Mutations, Variable Epistatic Interactions, and the Evolut)
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46 OK 10.1038/nrg761 Resolving the paradox of sex and recombination crossref (matched: Resolving the paradox of sex and recombination)
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47 OK 10.1093/genetics/117.3.559 Selection, Generalized Transmission and the Evolution of Modifie crossref (matched: Selection, Generalized Transmission and the Evolution of Modifier Gene)
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48 OK 10.1093/genetics/139.4.1805 The population genetics of speciation: the evolution of hybrid i crossref (matched: The population genetics of speciation: the evolution of hybrid incompa)
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49 OK 10.1111/j.0014-3820.2001.tb00628.x THE EVOLUTION OF POSTZYGOTIC ISOLATION: ACCUMULATING DOBZHANSKY- crossref (matched: THE EVOLUTION OF POSTZYGOTIC ISOLATION: ACCUMULATING DOBZHANSKY-MULLER)
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50 OK 10.48550/arXiv.2209.04836 Git Re-Basin: Merging Models modulo Permutation Symmetries in manuscript
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51 OK 10.48550/arXiv.2606.23607 Scaling Linear Mode Connectivity and Merging to Billion Paramete in manuscript
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52 OK 10.48550/arXiv.2410.12766 The Non-Local Model Merging Problem: Permutation Symmetries and in manuscript
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53 OK 10.48550/arXiv.2607.11997 Are we Merging the Right Models? Impact of Expert Training Durat in manuscript
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54 OK 10.48550/arXiv.2601.22285 Demystifying Mergeability: Interpretable Properties to Predict M in manuscript
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55 OK 10.48550/arXiv.2205.12393 Fine-tuned Language Models are Continual Learners in manuscript
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56 OK 10.48550/arXiv.2403.08763 Simple and Scalable Strategies to Continually Pre-train Large La in manuscript
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57 OK 10.1080/09540099550039318 Catastrophic Forgetting, Rehearsal and Pseudorehearsal crossref (matched: Catastrophic Forgetting, Rehearsal and Pseudorehearsal)
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58 OK 10.48550/arXiv.1705.08690 Continual Learning with Deep Generative Replay in manuscript
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59 OK 10.48550/arXiv.2406.07515 Beyond Model Collapse: Scaling Up with Synthesized Data Requires in manuscript
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60 OK 10.48550/arXiv.1606.04671 Progressive Neural Networks in manuscript
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61 OK 10.48550/arXiv.2405.09673 LoRA Learns Less and Forgets Less in manuscript
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62 OK 10.1037/0033-295x.102.3.419 Why there are complementary learning systems in the hippocampus crossref (matched: Why there are complementary learning systems in the hippocampus and ne)
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63 OK 10.1016/j.tics.2016.05.004 What Learning Systems do Intelligent Agents Need? Complementary crossref (matched: What Learning Systems do Intelligent Agents Need? Complementary Learni)
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64 OK 10.48550/arXiv.1805.06370 Progress & Compress: A scalable framework for continual lear verified by hand
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65 OK 10.48550/arXiv.2212.04089 Editing Models with Task Arithmetic in manuscript
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66 OK 10.48550/arXiv.2407.06322 MagMax: Leveraging Model Merging for Seamless Continual Learning in manuscript
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67 OK 10.48550/arXiv.2407.08699 Mitigating Catastrophic Forgetting in Language Transfer via Mode in manuscript
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68 OK 10.48550/arXiv.2412.06712 How to Merge Your Multimodal Models Over Time? in manuscript
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69 OK 10.48550/arXiv.1812.05159 An Empirical Study of Example Forgetting during Deep Neural Netw in manuscript
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70 OK 10.48550/arXiv.2211.08411 Large Language Models Struggle to Learn Long-Tail Knowledge in manuscript
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71 OK 10.48550/arXiv.2210.00266 Long-Tailed Class Incremental Learning in manuscript
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72 OK 10.48550/arXiv.2309.10105 Understanding Catastrophic Forgetting in Language Models via Imp in manuscript
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73 OK 10.48550/arXiv.2311.03099 Language Models are Super Mario: Absorbing Abilities from Homolo in manuscript
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74 OK 10.48550/arXiv.2203.05482 Model soups: averaging weights of multiple fine-tuned models imp in manuscript
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75 OK 10.48550/arXiv.2603.09463 An Empirical Study and Theoretical Explanation on Task-Level Mod in manuscript
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76 OK 10.48550/arXiv.2506.14126 From Memorization to Parameter Interference: How Overtraining Ex in manuscript
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77 OK 10.1145/2934662 Sex as an algorithm crossref (matched: Sex as an algorithm)
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78 OK 10.48550/arXiv.2311.09807 The Curious Decline of Linguistic Diversity: Training Language M in manuscript
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79 OK 10.48550/arXiv.2309.05196 Does Writing with Language Models Reduce Content Diversity? in manuscript
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80 OK 10.1126/sciadv.adn5290 Generative AI enhances individual creativity but reduces the col crossref (matched: Generative AI enhances individual creativity but reduces the collectiv)
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