Implement hybrid TRM-ERS-PMLL model with documentation and fixes. #65

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drqsatoshi wants to merge 73 commits intoSamsungSAILMontreal:mainfrom

drqsatoshi:main

Commits on Jan 30, 2026

Commits on Jan 31, 2026

Implement agent infrastructure for ARC-AGI-3 games

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drqsatoshi
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Merge pull request #2 from drqsatoshi/copilot/create-custom-agent
Dr Q. Josef Kurk Edwards
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Initial plan
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Add ARC-AGI-3 Benchmarking Tooling documentation

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Update README with benchmarking documentation link

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Fix parallel structure in benchmarking documentation

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Merge pull request #3 from drqsatoshi/copilot/add-benchmarking-tool
Dr Q. Josef Kurk Edwards
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Initial plan
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Add TRM agent for ARC-AGI-3 integration with tests and documentation

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Add ARC-AGI-3 integration summary and final verification

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Address code review feedback: improve test assertions and add coordinate range documentation

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Merge pull request #4 from drqsatoshi/copilot/run-arc-agi-3-experiment
Dr Q. Josef Kurk Edwards
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Initial plan
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Initial plan for RNA structure pipeline integration

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Add RNA structure prediction integration with TRM

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Complete RNA integration with tests and documentation

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Fix padding index and label grouping issues from code review

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Address remaining documentation and clarity issues

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Add Kaggle competition submission support

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Add comprehensive RNA implementation summary

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Merge pull request #5 from drqsatoshi/copilot/add-dataset-description-documentation
Dr Q. Josef Kurk Edwards
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Kaggle Notebook | notebook2c58d98f8d | Version 4
Dr Q. Josef Kurk Edwards
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Initial plan
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Add pretrain_rna.py code to notebook2c58d98f8d.ipynb

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Fix code review issues - remove unused imports and add notebook usage notes

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Merge pull request #8 from drqsatoshi/copilot/add-pretrain-rna-to-notebook
Dr Q. Josef Kurk Edwards
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Initial plan
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Add self-contained submission notebook for RNA structure prediction

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Merge pull request #10 from drqsatoshi/copilot/generate-submission-csv-notebook
Dr Q. Josef Kurk Edwards
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Kaggle Notebook | notebook2c58d98f8d | Version 6
Dr Q. Josef Kurk Edwards
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Initial plan
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Fix IndexError for sequences longer than max_length in kaggle_submission.py

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Merge pull request #11 from drqsatoshi/copilot/test-run-session
Dr Q. Josef Kurk Edwards
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Initial plan
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Fix index error for sequences longer than 500 nucleotides

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Add documentation and testing for index error fix

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Add inline comments to explain seq_len limiting

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Merge pull request #13 from drqsatoshi/copilot/fix-index-error-in-notebook
Dr Q. Josef Kurk Edwards
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Kaggle Notebook | notebook2c58d98f8d | Trm
Dr Q. Josef Kurk Edwards
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Kaggle Notebook | notebook2c58d98f8d | Version 7
Dr Q. Josef Kurk Edwards
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Kaggle Notebook | notebook2c58d98f8d | Version 9
Dr Q. Josef Kurk Edwards
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Add BibTeX citation for Rtmtrm
Dr Q. Josef Kurk Edwards
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Initial plan
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Add chain and copy columns to submission format

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Update test to expect 20 columns with chain and copy

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Add chain and copy columns to all submission files

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Merge pull request #14 from drqsatoshi/copilot/fix-submission-scoring-error
Dr Q. Josef Kurk Edwards
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Commits on Feb 13, 2026

Kaggle Notebook | notebook55e6af31b605e5e56d38 | Version 12
Dr Q. Josef Kurk Edwards
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Kaggle Notebook | notebook55e6af31b605e5e56d38 | Version 14
Dr Q. Josef Kurk Edwards
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Commits on Feb 26, 2026

Initial plan
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Add FloJsonOutputCollector memory schema and MCP tool integration

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Merge pull request #15 from drqsatoshi/copilot/add-memory-schema-integration
Dr Q. Josef Kurk Edwards
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Delete kaggle_submission.py
Dr Q. Josef Kurk Edwards
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Delete dataset/build_rna_dataset.py
Dr Q. Josef Kurk Edwards
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Delete experiments/run_trm_arc_agi_3.py
Dr Q. Josef Kurk Edwards
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Delete ARC_AGI_3_SUMMARY.md
Dr Q. Josef Kurk Edwards
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Delete kaggle directory
Dr Q. Josef Kurk Edwards
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Delete agents/templates/random_agent.py
Dr Q. Josef Kurk Edwards
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Delete agents/my_awesome_agent.py
Dr Q. Josef Kurk Edwards
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Delete docs/ARC_AGI_3_INTEGRATION.md
Dr Q. Josef Kurk Edwards
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Delete docs/KAGGLE_SUBMISSION.md
Dr Q. Josef Kurk Edwards
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Delete tests/test_kaggle_submission.py
Dr Q. Josef Kurk Edwards
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Initial plan
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Remove Kaggle/RNA-related files unrelated to memory tooling

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Merge pull request #16 from drqsatoshi/copilot/prune-unviewed-files
Dr Q. Josef Kurk Edwards
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