# Cortex — Bibliography

The 97-reference bibliography behind Cortex's 36 neuroscience-grounded
mechanisms and its information-retrieval pipeline. Every mechanism in the
codebase traces to one or more of these published sources — see the
per-module docstrings under `mcp_server/core/`. The two research papers in
`docs/arxiv-thermodynamic/` and `docs/arxiv-context-assembly/` draw their
focused reference lists from this consolidated set.

This file is the canonical home of the "97-reference bibliography" cited in
the README and the MCP bundle manifest.

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## References

Abraham, W. C. & Bear, M. F. (1996). Metaplasticity: The plasticity of synaptic plasticity. *Trends in Neurosciences*, 19(4), 126--130.

Adcock, R. A., Thangavel, A., Whitfield-Gabrieli, S., Knutson, B., & Gabrieli, J. D. E. (2006). Reward-motivated learning: Mesolimbic activation precedes memory formation. *Neuron*, 50(3), 507--517.

Anderson, J. R. & Lebiere, C. (1998). *The Atomic Components of Thought*. Mahwah, NJ: Lawrence Erlbaum Associates.

Anderson, M. C. & Neely, J. H. (1996). Interference and inhibition in memory retrieval. In *Memory: Handbook of Perception and Cognition* (2nd ed.), 237--313.

Baddeley, A. D. (2003). Working memory: Looking back and looking forward. *Nature Reviews Neuroscience*, 4(10), 829--839.

Bahrick, H. P. (1984). Semantic memory content in permastore: Fifty years of memory for Spanish learned in school. *Journal of Experimental Psychology: General*, 113(1), 1--29.

Bar, M. (2007). The proactive brain: Using analogies and associations to generate predictions. *Trends in Cognitive Sciences*, 11(7), 280--289.

Bastos, A. M., Usrey, W. M., Adams, R. A., Mangun, G. R., Fink, P., & Friston, K. J. (2012). Canonical microcircuits for predictive coding. *Neuron*, 76(4), 695--711.

Behrouz, A., Hashemi, M., Srinivasa, S., Kang, M., & Leskovec, J. (2025). Titans: Learning to memorize at test time. *Advances in Neural Information Processing Systems* (NeurIPS 2025).

Beyer, K., Goldstein, J., Ramakrishnan, R., & Shaft, U. (1999). When is "nearest neighbor" meaningful? In *International Conference on Database Theory* (ICDT), 217--235.

Bi, G.-Q. & Poo, M.-M. (1998). Synaptic modifications in cultured hippocampal neurons: Dependence on spike timing, synaptic strength, and postsynaptic cell type. *Journal of Neuroscience*, 18(24), 10464--10472.

Bienenstock, E. L., Cooper, L. N., & Munro, P. W. (1982). Theory for the development of neuron selectivity: Orientation specificity and binocular interaction in visual cortex. *Journal of Neuroscience*, 2(1), 32--48.

Borbely, A. A. (1982). A two process model of sleep regulation. *Human Neurobiology*, 1(3), 195--204.

Botvinick, M. M., Braver, T. S., Barch, D. M., Carter, C. S., & Cohen, J. D. (2001). Conflict monitoring and cognitive control. *Psychological Review*, 108(3), 624--652.

Bouton, M. E. (2004). Context and behavioral processes in extinction. *Learning & Memory*, 11(5), 485--494.

Bruch, S., Lucchese, C., & Nardini, F. M. (2023). Efficient and effective tree-based and neural learning to rank. *Foundations and Trends in Information Retrieval*, 17(1), 1--123. (ACM TOIS context for WRRF formulation.)

Buzsaki, G. (2015). Hippocampal sharp wave-ripple: A cognitive biomarker for episodic memory and planning. *Hippocampus*, 25(10), 1073--1188.

Collins, A. M. & Loftus, E. F. (1975). A spreading-activation theory of semantic processing. *Psychological Review*, 82(6), 407--428.

Cowan, N. (2001). The magical number 4 in short-term memory: A reconsideration of mental storage capacity. *Behavioral and Brain Sciences*, 24(1), 87--114.

Davidson, T. J., Kloosterman, F., & Wilson, M. A. (2009). Hippocampal replay of extended experience. *Neuron*, 63(4), 497--507.

De Pitta, M., Volman, V., Berry, H., & Ben-Jacob, E. (2012). A tale of two stories: Astrocyte regulation of synaptic depression and facilitation. *PLOS Computational Biology*, 7(12), e1002293.

Diana, R. A., Yonelinas, A. P., & Ranganath, C. (2007). Imaging recollection and familiarity in the medial temporal lobe: A three-component model. *Trends in Cognitive Sciences*, 11(9), 379--386.

Diba, K. & Buzsaki, G. (2007). Forward and reverse hippocampal place-cell sequences during ripples. *Nature Neuroscience*, 10, 1241--1242.

Diekelmann, S. & Born, J. (2010). The memory function of sleep. *Nature Reviews Neuroscience*, 11(2), 114--126.

Doya, K. (2000). Complementary roles of basal ganglia and cerebellum in learning and motor control. *Current Opinion in Neurobiology*, 10(6), 732--739.

Doya, K. (2002). Metalearning and neuromodulation. *Neural Networks*, 15(4--6), 495--506.

Dudai, Y. (2012). The restless engram: Consolidations never end. *Annual Review of Neuroscience*, 35, 227--247.

Ebbinghaus, H. (1885). *Uber das Gedachtnis: Untersuchungen zur experimentellen Psychologie*. Leipzig: Duncker & Humblot.

Foster, D. J. & Wilson, M. A. (2006). Reverse replay of behavioural sequences in hippocampal place cells during the awake state. *Nature*, 440, 680--683.

Frey, U. & Morris, R. G. M. (1997). Synaptic tagging and long-term potentiation. *Nature*, 385, 533--536.

Friston, K. (2005). A theory of cortical responses. *Philosophical Transactions of the Royal Society B*, 360(1456), 815--836.

Gilboa, A. & Marlatte, H. (2017). Neurobiology of schemas and schema-mediated memory. *Trends in Cognitive Sciences*, 21(8), 618--631.

Graybiel, A. M. (2008). Habits, rituals, and the evaluative brain. *Annual Review of Neuroscience*, 31, 359--387.

Gutierrez, B. J., McNeal, N., Washington, C., Chen, Y., Li, L., Sun, H., & Su, Y. (2024). HippoRAG: Neurobiologically inspired long-term memory for large language models. *Advances in Neural Information Processing Systems* (NeurIPS 2024).

Hasselmo, M. E. (2005). What is the function of hippocampal theta rhythm? Linking behavioral data to phasic properties of field potential and unit recording data. *Hippocampus*, 15(7), 936--949.

Hebb, D. O. (1949). *The Organization of Behavior: A Neuropsychological Theory*. New York: Wiley.

Hebb, D. O. (1955). Drives and the C.N.S. (conceptual nervous system). *Psychological Review*, 62(4), 243--254. [source of the arousal--performance inverted-U, "Hebb's curve"]

Ito, M. (2008). Control of mental activities by internal models in the cerebellum. *Nature Reviews Neuroscience*, 9(4), 304--313.

Johnson, M. K. & Raye, C. L. (1981). Reality monitoring. *Psychological Review*, 88(1), 67--85.

Johnson, M. K., Hashtroudi, S., & Lindsay, D. S. (1993). Source monitoring. *Psychological Bulletin*, 114(1), 3--28.

Joren, D., Coster, T. D., & Moens, M.-F. (2025). Sufficient context: A new lens on retrieval augmented generation systems. *International Conference on Learning Representations* (ICLR 2025).

Josselyn, S. A. & Frankland, P. W. (2007). Memory allocation: Mechanisms and function. *Annual Review of Neuroscience*, 41, 389--413.

Josselyn, S. A. & Tonegawa, S. (2020). Memory engrams: Recalling the past and imagining the future. *Science*, 367(6473), eaaw4325.

Kandel, E. R. (2001). The molecular biology of memory storage: A dialogue between genes and synapses. *Science*, 294(5544), 1030--1038.

Kanerva, P. (2009). Hyperdimensional computing: An introduction to computing in distributed representation with high-dimensional random vectors. *Cognitive Computation*, 1(2), 139--159.

Kastellakis, G., Cai, D. J., Mednick, S. C., Silva, A. J., & Poirazi, P. (2015). Synaptic clustering within dendrites: An emerging theory of memory formation. *Progress in Neurobiology*, 126, 19--35.

Ketz, N. A., Morkonda, S. G., & O'Reilly, R. C. (2023). C-HORSE: A comprehensive model of hippocampal function. *Hippocampus*, 33(4), 340--368.

Krause, A. & Guestrin, C. (2008). Near-optimal observation selection using submodular functions. *Journal of Machine Learning Research*, 9, 2761--2801.

Larsen, K. G. & Nelson, J. (2017). Optimality of the Johnson-Lindenstrauss lemma. In *IEEE Symposium on Foundations of Computer Science* (FOCS), 633--644.

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Lisman, J. E. & Jensen, O. (2013). The theta-gamma neural code. *Neuron*, 77(6), 1002--1016.

Luboeinski, J. & Tetzlaff, C. (2021). Memory consolidation and improvement by synaptic tagging and capture in recurrent neural networks. *Communications Biology*, 4, 275.

Maharana, A., Lee, D., Tulyakov, S., Bansal, M., Barbieri, F., & Fang, Y. (2024). Evaluating very long-term conversational memory of LLM agents. *Annual Meeting of the Association for Computational Linguistics* (ACL 2024).

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McGaugh, J. L. (2004). The amygdala modulates the consolidation of memories of emotionally arousing experiences. *Annual Review of Neuroscience*, 27, 1--28.

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Mnih, V., Kavukcuoglu, K., Silver, D., Rusu, A. A., Veness, J., Bellemare, M. G., ... & Hassabis, D. (2015). Human-level control through deep reinforcement learning. *Nature*, 518(7540), 529--533.

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Oudiette, D. & Paller, K. A. (2013). Upgrading the sleeping brain with targeted memory reactivation. *Trends in Cognitive Sciences*, 17(3), 142--149.

Packer, C., Wooders, S., Lin, K., Fang, V., Patil, S. G., Stoica, I., & Gonzalez, J. E. (2023). MemGPT: Towards LLMs as operating systems. *arXiv preprint arXiv:2310.08560*.

Perea, G., Navarrete, M., & Araque, A. (2009). Tripartite synapses: Astrocytes process and control synaptic information. *Trends in Neurosciences*, 32(8), 421--431.

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Rankin, C. H., Abrams, T. W., Barry, R. J., Bhatnagar, S., Clayton, D. F., Colombo, J., ... & Thompson, R. F. (2009). Habituation revisited: An updated and revised description of the behavioral characteristics of habituation. *Neurobiology of Learning and Memory*, 92(2), 135--138.

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