Cognitive Model Organism: The Unboxing of Thinking Process (Data and Reproduction Workflow)
Year: 2026
Type: preprint
Abstract: This repository contains the revised preprint manuscript (Version 3, revision 1), Supporting Information, and the complete frozen reproduction and analysis archive for "Cognitive Model Organism: The Unboxing of Thinking Process." We establish the Hortus Regis Alti (HRA) Experimental and Observational Protocol for studying a frozen language model (DeepSeek-R1-Distill-Qwen-7B, revision 916b56a44061fd5cd7d6a8fb632557ed4f724f60, INT8 linear layers with BF16 elsewhere) as a cognitive model organism. Across two experimental stages (18 Stage 1 conditions and 26 Stage 2 conditions across four observation configurations of one Bayesian decision problem), the archived corpus comprises 176 complete native-token trajectories containing 2,205,963 generated tokens. Eight paired 16K/32K baseline executions regenerate identical overlapping prefixes across 93,016 native-token positions. Complete mechanical extraction and contextual reading cover all 176 trajectories, with 1,926 location-verified evidence anchors mapped to character offsets and native-token coordinates. Included files:- Preprint_Not_Peer_Reviewed.pdf & Supporting_Information.pdf: Version 3, revision 1 manuscript and supplement (use these top-level PDFs for the latest text and figures; the internal docs/ folder inside the sealed reproduction ZIP retains the original frozen v3 PDFs to preserve archive byte identity).- CMO_Reproduction_v3_HRA_20261030.zip (SHA-256: 9daf88aab04b312a880b50811ea77227c086705763477bce094c3402a2e8b9d9): Outer reproduction distribution with integrity-checked launchers and embedded sealed scientific supplement CMO_FullCorpus_Analysis_Supplement_20261030_r2.zip (SHA-256: fcdf7e11a83e8c088fe23a8cde6fd940c299c0a1f22bbac30d16435c6fd475fd), containing all 176 raw JSONL records, native tokenizer, semantic ledgers, and a zero-dependency Python 3.11+ deterministic CPU recomputation pipeline.
Authors: Jia, Yuncheng, Qin, Bo, Phanumartwiwath, Anuchit
Language: English
Topic: Topic Modeling
Subfield: Artificial Intelligence
Field: Computer Science
Domain: Physical Sciences
Open Access status: green
OpenAlex ID: W7224087790