@article{milo2002network,
  title={Network motifs: simple building blocks of complex networks},
  author={Milo, Ron and Shen-Orr, Shai and Itzkovitz, Shalev and Kashtan, Nadav and Chklovskii, Dmitri and Alon, Uri},
  journal={Science},
  volume={298},
  number={5594},
  pages={824--827},
  year={2002},
  publisher={American Association for the Advancement of Science}
}

@article{alon2007network,
  title={Network motifs: theory and experimental approaches},
  author={Alon, Uri},
  journal={Nature Reviews Genetics},
  volume={8},
  number={6},
  pages={450--461},
  year={2007},
  publisher={Nature Publishing Group}
}

@article{spivak2021learners,
  title={Learners' Languages},
  author={Spivak, David I},
  journal={Compositionality},
  volume={3},
  number={4},
  year={2021}
}

@article{vagner2015algebras,
  title={Algebras of open dynamical systems on the operad of wiring diagrams},
  author={Vagner, Dmitry and Spivak, David I and Lerman, Eugene},
  journal={Theory and Applications of Categories},
  volume={30},
  number={51},
  pages={1793--1822},
  year={2015}
}

@book{fong2019seven,
  title={Seven sketches in compositionality: An invitation to applied category theory},
  author={Fong, Brendan and Spivak, David I},
  year={2019},
  publisher={Cambridge University Press}
}

@book{maturana1980autopoiesis,
  title={Autopoiesis and cognition: The realization of the living},
  author={Maturana, Humberto R and Varela, Francisco J},
  year={1980},
  publisher={Reidel}
}

@article{wei2022chain,
  author = {Wei, Jason and Yi, Xuezhi and Zhang, Maarten and Liu, Yiming and Li, Xinyu and Wang, Xing and Zhou, Yujia and Li, Yiming and Wang, Yuyang and Li, Zhi and others},
  title = {Chain-of-Thought Prompting Elicits Reasoning in Large Language Models},
  year = {2022},
  journal = {arXiv preprint arXiv:2201.11903},
  note = {Available at: \url{https://arxiv.org/abs/2201.11903}},
  doi = {10.48550/arXiv.2201.11903}
}

% --- BIOLOGY: The Cost of Computation ---
@article{lynch2015bioenergetic,
  title={The bioenergetic costs of a gene},
  author={Lynch, Michael and Marinov, Georgi K},
  journal={Proceedings of the National Academy of Sciences},
  volume={112},
  number={51},
  pages={15690--15695},
  year={2015},
  publisher={National Acad Sciences}
}

@article{kempes2017thermodynamic,
  title={The thermodynamic efficiency of computations made in cells across the range of life},
  author={Kempes, Christopher P and Wolpert, David H and Cohen, Zachary and P{\'e}rez-Mercader, Juan},
  journal={Philosophical Transactions of the Royal Society A},
  volume={375},
  number={2109},
  year={2017}
}

@article{aubrey2018p53,
  title={How does p53 induce apoptosis and how does this relate to p53-mediated tumour suppression?},
  author={Aubrey, B.J. and Strasser, A. and Kelly, G.L.},
  journal={Cell Death \& Differentiation},
  volume={25},
  pages={104--113},
  year={2018},
  publisher={Nature Publishing Group}
}

% --- MATH: Resource Co-algebras ---
@inproceedings{nakov2021quantitative,
  title={Quantitative Polynomial Functors},
  author={Nakov, Georgi and Forsberg, Fredrik Nordvall},
  booktitle={Conference on Algebra and Coalgebra in Computer Science (CALCO)},
  year={2021},
  organization={Schloss Dagstuhl-Leibniz-Zentrum f{\"u}r Informatik}
}

@article{niu2023polynomial,
  title={Polynomial Functors: A Mathematical Theory of Interaction},
  author={Niu, Nelson and Spivak, David I},
  journal={arXiv preprint arXiv:2312.00990},
  year={2023}
}

@article{boreale2023weighted,
  title={Coalgebras for Bisimulation of Weighted Automata},
  author={Boreale, Michele},
  journal={Logical Methods in Computer Science},
  volume={19},
  year={2023}
}

% --- BIOLOGY: Mitochondrial Information Processing ---
@article{picard2022mips,
  title={The Mitochondrial Information Processing System: A New Model of Mitochondrial-Nuclear Communication},
  author={Picard, Martin and Shirihai, Orian S},
  journal={Trends in Neurosciences},
  volume={41},
  number={4},
  pages={206--208},
  year={2018},
  note={Revisited and expanded in 2022-2024 work},
  publisher={Elsevier}
}

@article{allen2022energy,
  title={Energy transduction and the mind: mitochondria in brain function},
  author={Allen, John F},
  journal={The Biochemist},
  volume={44},
  number={4},
  pages={8--13},
  year={2022},
  publisher={Portland Press}
}

@article{picard2022signaling,
  title={Mitochondria as multifaceted regulators of cell death},
  author={Picard, Martin and Shirihai, Orian S},
  journal={Cell Metabolism},
  volume={34},
  number={11},
  pages={1607--1627},
  year={2022},
  publisher={Elsevier}
}

@article{chandel2024mitochondria,
  title={Mitochondria as signaling organelles},
  author={Chandel, Navdeep S},
  journal={BMC Biology},
  volume={12},
  pages={34},
  year={2014},
  note={Revisited in 2024 work on metabolic-epigenetic coupling},
  publisher={BioMed Central}
}

% --- THEORETICAL BIOLOGY: Information and Energy ---
@article{friston2010,
  title={The free-energy principle: a unified brain theory?},
  author={Friston, Karl},
  journal={Nature Reviews Neuroscience},
  volume={11},
  number={2},
  pages={127--138},
  year={2010},
  publisher={Nature Publishing Group}
}

@book{waddington1957,
  title={The Strategy of the Genes},
  author={Waddington, Conrad H},
  year={1957},
  publisher={Allen \& Unwin},
  note={Introduced the concept of the ``epigenetic landscape''}
}

% --- EVOLUTION: Power and Complexity ---
@book{vermeij2023power,
  title={The Evolution of Power: A New Understanding of the History of Life},
  author={Vermeij, Geerat J},
  year={2023},
  publisher={Princeton University Press}
}

% --- BENCHMARKS ---
@article{patil2023gorilla,
  title={Gorilla: Large Language Model Connected with Massive APIs},
  author={Patil, Shishir G. and Zhang, Tianjun and Wang, Xin and Gonzalez, Joseph E.},
  journal={arXiv preprint arXiv:2305.15334},
  year={2023}
}

@inproceedings{debenedetti2024agentdojo,
  title={AgentDojo: A Dynamic Environment to Evaluate Prompt Injection Attacks and Defenses for LLM Agents},
  author={Debenedetti, Edoardo and Severi, Giorgio and Carlini, Nicholas and Coull, Scott and Tram\`{e}r, Florian},
  booktitle={NeurIPS},
  year={2024}
}

% --- CATEGORICAL OPTIMIZATION ---
@article{abbott2023neural,
  title={Neural Circuit Diagrams: Robust Diagrams for the Communication, Implementation, and Analysis of Deep Learning Architectures},
  author={Abbott, Vincent},
  journal={arXiv preprint arXiv:2402.05424},
  year={2023},
  note={Foundation for the diagrammatic scheme used in FlashAttention on a Napkin}
}

@misc{abbott2025flashattention,
  title={FlashAttention on a Napkin: A Diagrammatic Approach to Deep Learning IO-Awareness},
  author={Abbott, Vincent and Zardini, Gioele},
  year={2025},
  url={https://openreview.net/forum?id=pF2ukh7HxA},
  eprint={2412.03317},
  archivePrefix={arXiv},
  note={Derives FlashAttention via Neural Circuit Diagrams with IO-aware performance model}
}

% --- EPISTEMIC LOGIC ---
@book{fagin1995reasoning,
  title={Reasoning About Knowledge},
  author={Fagin, Ronald and Halpern, Joseph Y and Moses, Yoram and Vardi, Moshe Y},
  year={1995},
  publisher={MIT Press}
}

@article{halpern1990knowledge,
  title={Knowledge and Common Knowledge in a Distributed Environment},
  author={Halpern, Joseph Y and Moses, Yoram},
  journal={Journal of the ACM},
  volume={37},
  number={3},
  pages={549--587},
  year={1990},
  publisher={ACM}
}

% --- AGENT SCALING ---
@article{kim2025scaling,
  title={Towards a Science of Scaling Agent Systems},
  author={Kim, Yubin and Gu, Ken and Park, Chanwoo and Park, Chunjong and Schmidgall, Samuel and Heydari, A. Ali and Yan, Yao and Zhang, Zhihan and Zhuang, Yuchen and Liu, Yun and Malhotra, Mark and Liang, Paul Pu and Park, Hae Won and Yang, Yuzhe and Xu, Xuhai and Du, Yilun and Patel, Shwetak and Althoff, Tim and McDuff, Daniel and Liu, Xin},
  year={2025},
  journal={arXiv preprint arXiv:2512.08296},
  note={Google Research, Google DeepMind, and MIT}
}

% --- EPISTEMIC LOGIC IN DISTRIBUTED SYSTEMS ---
@misc{davis2026reasoning,
  title={Reasoning About Knowledge in {TLA+}},
  author={Davis, Jesse Jiryu},
  year={2026},
  note={UCLA CS 201-A Seminar, MongoDB Distributed Systems Research Group}
}

% --- TEMPORAL DATABASES ---
@book{snodgrass2000temporal,
  title={Developing Time-Oriented Database Applications in {SQL}},
  author={Snodgrass, Richard T.},
  year={2000},
  publisher={Morgan Kaufmann},
  note={Foundational treatment of valid time, transaction time, and bi-temporal data models}
}

@article{kulkarni2012temporal,
  title={Temporal features in {SQL:2011}},
  author={Kulkarni, Krishna and Michels, Jan-Eike},
  journal={ACM SIGMOD Record},
  volume={41},
  number={3},
  pages={34--43},
  year={2012},
  publisher={ACM}
}

@article{dupoux2026learning,
  title={Why {AI} Systems Don't Learn and What to Do About It},
  author={Dupoux, Emmanuel and LeCun, Yann and Malik, Jitendra},
  journal={arXiv preprint arXiv:2603.15381},
  year={2026}
}

@article{hao2026bigmas,
  title={Brain-Inspired Graph Multi-Agent Systems for {LLM} Reasoning},
  author={Hao, Jie and Dai, Xu and Qin, Yuhang and Yu, Philip S.},
  journal={arXiv preprint arXiv:2603.15371},
  year={2026}
}
