% ---------------------------------------------------------------
% References for "Thermodynamic Memory vs. Flat-Importance Stores"
% Keys reused from docs/arxiv/references.bib where the same paper
% is cited; new entries added for thermodynamics/neuro citations.
% ---------------------------------------------------------------

% --- Reused from docs/arxiv/references.bib ---

@article{Radovanovic2010,
  author    = {Radovanovi\'{c}, Milo\v{s} and Nanopoulos, Alexandros and Ivanovi\'{c}, Mirjana},
  title     = {Hubs in Space: Popular Nearest Neighbors in High-Dimensional Data},
  journal   = {Journal of Machine Learning Research},
  volume    = {11},
  pages     = {2487--2531},
  year      = {2010}
}

@inproceedings{Beyer1999,
  author    = {Beyer, Kevin and Goldstein, Jonathan and Ramakrishnan, Raghu and Shaft, Uri},
  title     = {When Is ``Nearest Neighbor'' Meaningful?},
  booktitle = {Proceedings of the 7th International Conference on Database Theory (ICDT)},
  pages     = {217--235},
  year      = {1999}
}

@inproceedings{Cormack2009,
  author    = {Cormack, Gordon V. and Clarke, Charles L. A. and Buettcher, Stefan},
  title     = {Reciprocal Rank Fusion Outperforms {C}ondorcet and Individual Rank Learning Methods},
  booktitle = {Proceedings of the 32nd International ACM SIGIR Conference},
  pages     = {758--759},
  year      = {2009},
  doi       = {10.1145/1571941.1572114}
}

% Verified against Crossref (10.1145/3596512): authors, title, journal,
% volume 42, issue 1, page range 1--35, and 2023 all confirmed. arXiv
% preprint id 2210.11934. (Crossref returns page range only, no ACM
% article number; do not add articleno without confirming it.)
@article{Bruch2023,
  author    = {Bruch, Sebastian and Gai, Siyu and Ingber, Amir},
  title     = {An Analysis of Fusion Functions for Hybrid Retrieval},
  journal   = {ACM Transactions on Information Systems},
  volume    = {42},
  number    = {1},
  pages     = {1--35},
  year      = {2023},
  doi       = {10.1145/3596512},
  eprint    = {2210.11934},
  archivePrefix = {arXiv}
}

@inproceedings{Karpukhin2020,
  author    = {Karpukhin, Vladimir and Oguz, Barlas and Min, Sewon and Lewis, Patrick and Wu, Ledell and Edunov, Sergey and Chen, Danqi and Yih, Wen-tau},
  title     = {Dense Passage Retrieval for Open-Domain Question Answering},
  booktitle = {Proceedings of the 2020 Conference on Empirical Methods in Natural Language Processing (EMNLP)},
  pages     = {6769--6781},
  year      = {2020},
  doi       = {10.18653/v1/2020.emnlp-main.550}
}

@inproceedings{Reimers2019,
  author    = {Reimers, Nils and Gurevych, Iryna},
  title     = {Sentence-{BERT}: Sentence Embeddings Using {S}iamese {BERT}-Networks},
  booktitle = {Proceedings of the 2019 Conference on Empirical Methods in Natural Language Processing (EMNLP)},
  pages     = {3982--3992},
  year      = {2019},
  doi       = {10.18653/v1/D19-1410}
}

@inproceedings{Maharana2024,
  author    = {Maharana, Adyasha and Lee, Dong-Ho and Tulyakov, Sergey and Bansal, Mohit and Barbieri, Francesco and Fang, Yuwei},
  title     = {Evaluating Very Long-Term Conversational Memory of {LLM} Agents},
  booktitle = {Proceedings of the 62nd Annual Meeting of the Association for Computational Linguistics (ACL)},
  year      = {2024},
  note      = {LoCoMo dataset; arXiv:2402.17753}
}

@inproceedings{Wu2025,
  author    = {Wu, Di and Wang, Hongwei and Yu, Wenhao and Zhang, Yuwei and Chang, Kai-Wei and Yu, Dong},
  title     = {{LongMemEval}: Benchmarking Chat Assistants on Long-Term Interactive Memory},
  booktitle = {Proceedings of the International Conference on Learning Representations (ICLR)},
  year      = {2025},
  note      = {arXiv:2410.10813}
}

@inproceedings{Tavakoli2026,
  author    = {Tavakoli, Arash and others},
  title     = {{BEAM}: Beyond a Million Tokens --- Benchmarking Long-Term Memory in {AI} Agents},
  booktitle = {Proceedings of the International Conference on Learning Representations (ICLR)},
  year      = {2026},
  note      = {arXiv:2510.27246}
}

@article{McClelland1995,
  author    = {McClelland, James L. and McNaughton, Bruce L. and O'Reilly, Randall C.},
  title     = {Why There Are Complementary Learning Systems in the Hippocampus and Neocortex},
  journal   = {Psychological Review},
  volume    = {102},
  number    = {3},
  pages     = {419--457},
  year      = {1995},
  doi       = {10.1037/0033-295X.102.3.419}
}

@article{Packer2024,
  author    = {Packer, Charles and others},
  title     = {{MemGPT}: Towards {LLMs} as Operating Systems},
  journal   = {Conference on Language Modeling (COLM)},
  year      = {2024}
}

% --- New entries for thermodynamic-memory paper ---

@article{Friston2010,
  author    = {Friston, Karl},
  title     = {The Free-Energy Principle: A Unified Brain Theory?},
  journal   = {Nature Reviews Neuroscience},
  volume    = {11},
  number    = {2},
  pages     = {127--138},
  year      = {2010},
  doi       = {10.1038/nrn2787}
}

@book{Ebbinghaus1885,
  author    = {Ebbinghaus, Hermann},
  title     = {{\"U}ber das Ged{\"a}chtnis: Untersuchungen zur experimentellen Psychologie},
  publisher = {Duncker \& Humblot},
  address   = {Leipzig},
  year      = {1885}
}

@article{Hopfield1982,
  author    = {Hopfield, John J.},
  title     = {Neural Networks and Physical Systems with Emergent Collective Computational Abilities},
  journal   = {Proceedings of the National Academy of Sciences},
  volume    = {79},
  number    = {8},
  pages     = {2554--2558},
  year      = {1982},
  doi       = {10.1073/pnas.79.8.2554}
}

@article{Tonegawa2015,
  author    = {Tonegawa, Susumu and Liu, Xu and Ramirez, Steve and Redondo, Roger},
  title     = {Memory Engram Cells Have Come of Age},
  journal   = {Neuron},
  volume    = {87},
  number    = {5},
  pages     = {918--931},
  year      = {2015},
  doi       = {10.1016/j.neuron.2015.08.002}
}

@article{Doya2002,
  author    = {Doya, Kenji},
  title     = {Metalearning and Neuromodulation},
  journal   = {Neural Networks},
  volume    = {15},
  number    = {4--6},
  pages     = {495--506},
  year      = {2002},
  doi       = {10.1016/S0893-6080(02)00044-8}
}

@article{Schultz1997,
  author    = {Schultz, Wolfram and Dayan, Peter and Montague, P. Read},
  title     = {A Neural Substrate of Prediction and Reward},
  journal   = {Science},
  volume    = {275},
  number    = {5306},
  pages     = {1593--1599},
  year      = {1997},
  doi       = {10.1126/science.275.5306.1593}
}

@article{Kandel2001,
  author    = {Kandel, Eric R.},
  title     = {The Molecular Biology of Memory Storage: A Dialogue Between Genes and Synapses},
  journal   = {Science},
  volume    = {294},
  number    = {5544},
  pages     = {1030--1038},
  year      = {2001},
  doi       = {10.1126/science.1067020}
}

@article{Frey1997,
  author    = {Frey, Uwe and Morris, Richard G. M.},
  title     = {Synaptic Tagging and Long-Term Potentiation},
  journal   = {Nature},
  volume    = {385},
  number    = {6616},
  pages     = {533--536},
  year      = {1997},
  doi       = {10.1038/385533a0}
}

@article{Buzsaki2015,
  author    = {Buzs\'{a}ki, Gy{\"o}rgy},
  title     = {Hippocampal Sharp Wave-Ripple: A Cognitive Biomarker for Episodic Memory and Planning},
  journal   = {Hippocampus},
  volume    = {25},
  number    = {10},
  pages     = {1073--1188},
  year      = {2015},
  doi       = {10.1002/hipo.22488}
}

@article{Hasselmo2005,
  author    = {Hasselmo, Michael E.},
  title     = {What is the Function of Hippocampal Theta Rhythm?---Linking Behavioral Data to Phasic Properties of Field Potential and Unit Recording Data},
  journal   = {Trends in Cognitive Sciences},
  volume    = {9},
  number    = {7},
  pages     = {351--359},
  year      = {2005},
  doi       = {10.1016/j.tics.2005.05.001}
}

@article{Leutgeb2007,
  author    = {Leutgeb, Jill K. and Leutgeb, Stefan and Moser, May-Britt and Moser, Edvard I.},
  title     = {Pattern Separation in the Dentate Gyrus and {CA3} of the Hippocampus},
  journal   = {Science},
  volume    = {315},
  number    = {5814},
  pages     = {961--966},
  year      = {2007},
  doi       = {10.1126/science.1135801}
}

@article{Yassa2011,
  author    = {Yassa, Michael A. and Stark, Craig E. L.},
  title     = {Pattern Separation in the Hippocampus},
  journal   = {Trends in Neurosciences},
  volume    = {34},
  number    = {10},
  pages     = {515--525},
  year      = {2011},
  doi       = {10.1016/j.tins.2011.06.006}
}

@article{Wang2020,
  author    = {Wang, Chao and Yue, Hairong and Hu, Zhicai and Shen, Yuwen and others},
  title     = {Microglia Mediate Forgetting via Complement-Dependent Synaptic Elimination},
  journal   = {Science},
  volume    = {367},
  number    = {6478},
  pages     = {688--694},
  year      = {2020},
  doi       = {10.1126/science.aaz2288}
}

% Verified against Crossref (10.1037/h0041823). The arousal-performance
% inverted-U ("Hebb's curve") is Hebb 1955, not Yerkes-Dodson 1908 --- the
% latter measured stimulus strength vs. habit-formation, never plotting
% performance against arousal. The code docstring (emotional_tagging.py)
% already makes this distinction; the paper now matches it.
@article{Hebb1955,
  author    = {Hebb, Donald O.},
  title     = {Drives and the {C.N.S.} (Conceptual Nervous System)},
  journal   = {Psychological Review},
  volume    = {62},
  number    = {4},
  pages     = {243--254},
  year      = {1955},
  doi       = {10.1037/h0041823}
}

@article{Yerkes1908,
  author    = {Yerkes, Robert M. and Dodson, John D.},
  title     = {The Relation of Strength of Stimulus to Rapidity of Habit-Formation},
  journal   = {Journal of Comparative Neurology and Psychology},
  volume    = {18},
  pages     = {459--482},
  year      = {1908}
}

% Verified against Crossref (10.1038/s41562-022-01502-8) and PubMed
% (36646837). Replaces a fabricated "Wang & Bhatt 2024, Cell Reports"
% placeholder that described this mechanism (amygdala-hippocampal HFA
% prioritising emotionally salient encoding) but had no matching record.
@article{Qasim2023,
  author    = {Qasim, Salman E. and Mohan, Uma R. and Stein, Joel M. and Jacobs, Joshua},
  title     = {Neuronal Activity in the Human Amygdala and Hippocampus Enhances Emotional Memory Encoding},
  journal   = {Nature Human Behaviour},
  volume    = {7},
  number    = {5},
  pages     = {754--764},
  year      = {2023},
  doi       = {10.1038/s41562-022-01502-8}
}

@article{Yonelinas2015,
  author    = {Yonelinas, Andrew P. and Ritchey, Maureen},
  title     = {The Slow Forgetting of Emotional Episodic Memories: An Emotional Binding Account},
  journal   = {Trends in Cognitive Sciences},
  volume    = {19},
  number    = {5},
  pages     = {259--267},
  year      = {2015},
  doi       = {10.1016/j.tics.2015.02.009}
}

@article{Kleinsmith1963,
  author    = {Kleinsmith, Lewis J. and Kaplan, Stephen},
  title     = {Paired-Associate Learning as a Function of Arousal and Interpolated Interval},
  journal   = {Journal of Experimental Psychology},
  volume    = {65},
  number    = {2},
  pages     = {190--193},
  year      = {1963},
  doi       = {10.1037/h0040288}
}

@article{Liu2023,
  author    = {Liu, Nelson F. and Lin, Kevin and Hewitt, John and Paranjape, Ashwin and Bevilacqua, Michele and Petroni, Fabio and Liang, Percy},
  title     = {Lost in the Middle: How Language Models Use Long Contexts},
  journal   = {Transactions of the Association for Computational Linguistics (TACL)},
  year      = {2023}
}

@inproceedings{Lewis2020,
  author    = {Lewis, Patrick and Perez, Ethan and Piktus, Aleksandra and Petroni, Fabio and Karpukhin, Vladimir and Goyal, Naman and K{\"u}ttler, Heinrich and Lewis, Mike and Yih, Wen-tau and Rockt{\"a}schel, Tim and Riedel, Sebastian and Kiela, Douwe},
  title     = {Retrieval-Augmented Generation for Knowledge-Intensive {NLP} Tasks},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year      = {2020}
}

@inproceedings{Park2023,
  author    = {Park, Joon Sung and O'Brien, Joseph C. and Cai, Carrie J. and Morris, Meredith Ringel and Liang, Percy and Bernstein, Michael S.},
  title     = {Generative Agents: Interactive Simulacra of Human Behavior},
  booktitle = {Proceedings of the 36th Annual ACM Symposium on User Interface Software and Technology (UIST)},
  year      = {2023}
}

@inproceedings{Aggarwal2001,
  author    = {Aggarwal, Charu C. and Hinneburg, Alexander and Keim, Daniel A.},
  title     = {On the Surprising Behavior of Distance Metrics in High Dimensional Space},
  booktitle = {Proceedings of the 8th International Conference on Database Theory (ICDT)},
  pages     = {420--434},
  year      = {2001},
  doi       = {10.1007/3-540-44503-X_27}
}

@article{Anderson1991,
  author    = {Anderson, John R. and Schooler, Lael J.},
  title     = {Reflections of the Environment in Memory},
  journal   = {Psychological Science},
  volume    = {2},
  number    = {6},
  pages     = {396--408},
  year      = {1991},
  doi       = {10.1111/j.1467-9280.1991.tb00174.x}
}

@incollection{Anderson1989,
  author    = {Anderson, John R.},
  title     = {A Rational Analysis of Human Memory},
  booktitle = {Varieties of Memory and Consciousness},
  pages     = {195--210},
  year      = {1989},
  publisher = {Lawrence Erlbaum}
}

@article{Wixted1991,
  author    = {Wixted, John T. and Ebbesen, Ebbe B.},
  title     = {On the Form of Forgetting},
  journal   = {Psychological Science},
  volume    = {2},
  number    = {6},
  pages     = {409--415},
  year      = {1991}
}

@incollection{Mandelbrot1953,
  author    = {Mandelbrot, Benoit},
  title     = {An Informational Theory of the Statistical Structure of Language},
  booktitle = {Communication Theory},
  pages     = {486--502},
  year      = {1953},
  publisher = {Butterworths}
}

@article{Shannon1948,
  author    = {Shannon, Claude E.},
  title     = {A Mathematical Theory of Communication},
  journal   = {Bell System Technical Journal},
  volume    = {27},
  pages     = {379--423, 623--656},
  year      = {1948}
}

@book{ErdosSpencer1974,
  author    = {Erd{\H o}s, Paul and Spencer, Joel},
  title     = {Probabilistic Methods in Combinatorics},
  publisher = {Academic Press},
  year      = {1974}
}

@book{David2003,
  author    = {David, Herbert A. and Nagaraja, Haikady N.},
  title     = {Order Statistics},
  edition   = {3rd},
  publisher = {Wiley},
  year      = {2003}
}

@book{Bickel1976,
  author    = {Bickel, Peter J. and Doksum, Kjell A.},
  title     = {Mathematical Statistics: Basic Ideas and Selected Topics},
  publisher = {Holden-Day},
  year      = {1976}
}

@inproceedings{Ethayarajh2019,
  author    = {Ethayarajh, Kawin},
  title     = {How Contextual are Contextualized Word Representations? Comparing the Geometry of {BERT}, {ELMo}, and {GPT}-2 Embeddings},
  booktitle = {Proceedings of the 2019 Conference on Empirical Methods in Natural Language Processing (EMNLP)},
  year      = {2019}
}

@misc{Deust2026a,
  author    = {Deust, Cl{\'e}ment},
  title     = {cortex-beam-abstain --- A Learned Retrieval-Abstention Model for {BEAM}},
  year      = {2026},
  howpublished = {\url{https://github.com/cdeust/cortex-know-when-to-stop-training-model}}
}

@misc{Deust2026b,
  author    = {Deust, Cl{\'e}ment},
  title     = {automatised-pipeline --- Codebase Intelligence as an {MCP} Server},
  year      = {2026},
  howpublished = {\url{https://github.com/cdeust/automatised-pipeline}}
}

@misc{Deust2026c,
  author    = {Deust, Cl{\'e}ment},
  title     = {prd-spec-generator --- Stateless Reducer Turning Feature Descriptions into Multi-Judge-Verified {PRDs}},
  year      = {2026},
  howpublished = {\url{https://github.com/cdeust/prd-spec-generator}}
}

@misc{Deust2026d,
  author    = {Deust, Cl{\'e}ment},
  title     = {zetetic-team-subagents --- 116 Reasoning Agents with Commit-Time Source-Citation Enforcement},
  year      = {2026},
  howpublished = {\url{https://github.com/cdeust/zetetic-team-subagents}}
}

@misc{Deust2026e,
  author    = {Deust, Cl{\'e}ment},
  title     = {Cortex-cowork --- {SQLite} Variant of Cortex for Sandboxed Environments},
  year      = {2026},
  howpublished = {\url{https://github.com/cdeust/Cortex-cowork}}
}
