@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{abbott2024neural,
  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={2024},
  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}
}

% --- 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}
}

@article{jiang2026anatomy,
  title={Anatomy of Agentic Memory: Taxonomy and Empirical Analysis of Evaluation and System Limitations},
  author={Jiang, Dongming and Li, Yi and Wei, Songtao and Yang, Jinxin and Kang, Dingyi and Hu, Xu and Kishore, Ayushi and Li, Qiannan and Zhao, Alysa and Chen, Feng and Li, Bingzhe},
  journal={arXiv preprint arXiv:2602.19320},
  year={2026}
}

@article{lin2026memma,
  title={{MemMA}: Coordinating the Memory Cycle through Multi-Agent Reasoning and In-Situ Self-Evolution},
  author={Lin, Minhua and Zhang, Zhiwei and Lu, Hanqing and Liu, Hui and Tang, Xianfeng and He, Qi and Zhang, Xiang and Wang, Suhang},
  journal={arXiv preprint arXiv:2603.18718},
  year={2026}
}

@article{feng2026selfevolving,
  title={Self-evolving Embodied {AI}},
  author={Feng, Tongtong and Wang, Xin and Zhu, Wenwu},
  journal={National Science Review},
  year={2026}
}

% --- CONVERGENCE INVESTIGATION ---
@misc{animaworks,
  title={AnimaWorks: Autonomous Agent Runtime with Priming and Heartbeat Consolidation},
  author={{AnimaWorks Contributors}},
  year={2025},
  howpublished={\url{https://github.com/xuiltul/animaworks}},
  note={Operational runtime for autonomous agents with developmental priming}
}

@misc{swarms,
  title={Swarms: The Enterprise-Grade Production-Ready Multi-Agent Orchestration Framework},
  author={Osagie, Kye Gomez},
  year={2024},
  howpublished={\url{https://github.com/kyegomez/swarms}},
  note={Multi-agent orchestration with sequential, concurrent, and graph workflows}
}

@misc{deerflow,
  title={DeerFlow: Deep Exploration and Efficient Research Flow},
  author={{ByteDance Research}},
  year={2025},
  howpublished={\url{https://github.com/bytedance/deer-flow}},
  note={Community-driven AI research workflow framework}
}

@misc{ralph,
  title={Ralph: An Event-Driven Agent Orchestrator with Hat-Based Role Composition},
  author={O'Brien, Mikey},
  year={2025},
  howpublished={\url{https://github.com/mikeyobrien/ralph-orchestrator}},
  note={Hat-based agent orchestration with backpressure and iteration limits}
}

@misc{aevolve,
  title={A-Evolve: Autonomous LLM Agent Evolution Framework},
  author={{A-EVO-Lab}},
  year={2025},
  howpublished={\url{https://github.com/A-EVO-Lab/a-evolve}},
  note={Evolutionary framework for LLM agent skill optimization}
}

@phdthesis{zardini2023codesign,
  title={Co-Design of Complex Systems: From Compositionality to Monotone Theory},
  author={Zardini, Gioele},
  year={2023},
  school={ETH Zurich},
  note={Monotone co-design theory for compositional system design}
}

@article{evans2026plural,
  title={Agentic {AI} and the Next Intelligence Explosion},
  author={Evans, Richard and Bratton, Benjamin H. and Ag{\"u}era y Arcas, Blaise},
  journal={arXiv preprint arXiv:2603.20639},
  year={2026},
  note={Position paper arguing intelligence is fundamentally plural and social}
}

@article{yue2026acg,
  title={From Static Templates to Dynamic Runtime Graphs: A Survey of Workflow Optimization for {LLM} Agents},
  author={Yue, Xiang and Bhandari, Anil and Ko, Youngwon and Patel, Rishi and Lin, Zhuoer and Zhou, Shuaichen and Gao, Jiacheng and Chen, Wenhu and Pan, Xinyu},
  journal={arXiv preprint arXiv:2603.22386},
  year={2026},
  note={Comprehensive taxonomy of agent workflow optimization methods}
}

@article{chi2025asyncthink,
  title={{AsyncThink}: Asynchronous Thinking for Language Model Agents},
  author={Chi, Yihang and Lin, Zhuoer and Yue, Xiang},
  journal={arXiv preprint},
  year={2025},
  note={Intra-stage parallel reasoning with Fork/Join execution}
}

@article{ao2026delegation,
  title={Delegation in Multi-Agent Systems: When and How Can Delegating to Networked Agents Beat the Single Best Agent?},
  author={Ao, Shuangning and Gao, Zhengyuan and Simchi-Levi, David},
  journal={arXiv preprint arXiv:2603.26993},
  year={2026},
  note={Proves that without exogenous signals, delegated multi-agent networks are dominated by centralized baselines}
}

@article{delosriscos2026categorical,
  title={Working Paper: Towards a Category-theoretic Comparative Framework for Artificial General Intelligence},
  author={de los Riscos, Pablo and Corbacho, Fernando and Arbib, Michael A.},
  journal={arXiv preprint arXiv:2603.28906},
  year={2026},
  note={Category-theoretic framework (ArchAgents) for comparing agent architectures}
}

@misc{banu2026operon,
  title={Operon: Biomimetic Wiring Diagrams for Robust Agentic Systems},
  author={Banu, Bogdan},
  year={2026},
  howpublished={\url{https://github.com/coredipper/operon}},
  note={Open-source framework for biology-inspired agent control patterns}
}

@article{lee2026metaharness,
  title={Meta-Harness: Searching Over Agent Harness Code with Full Filesystem Access},
  author={Lee, Kensen and Nair, Suraj and Zhang, Yichen and Khattab, Omar and Finn, Chelsea},
  journal={arXiv preprint arXiv:2603.28052},
  year={2026},
  note={Shows that filesystem access to all prior candidates outperforms compressed-feedback optimizers}
}

@article{hofmeyr2000architecture,
  title={Architecture for an artificial immune system},
  author={Hofmeyr, Steven A and Forrest, Stephanie},
  journal={Evolutionary Computation},
  volume={8},
  number={4},
  pages={443--473},
  year={2000},
  publisher={MIT Press}
}

@article{dasgupta2006advances,
  title={Advances in artificial immune systems},
  author={Dasgupta, Dipankar and Yu, Senhua and Nino, Fernando},
  journal={IEEE Computational Intelligence Magazine},
  volume={1},
  number={4},
  pages={40--49},
  year={2006},
  publisher={IEEE}
}

@book{bonabeau1999swarm,
  title={Swarm Intelligence: From Natural to Artificial Systems},
  author={Bonabeau, Eric and Dorigo, Marco and Theraulaz, Guy},
  year={1999},
  publisher={Oxford University Press}
}

@article{wellman2001auction,
  title={Auction protocols for decentralized scheduling},
  author={Wellman, Michael P and Walsh, William E and Wurman, Peter R and MacKie-Mason, Jeffrey K},
  journal={Games and Economic Behavior},
  volume={35},
  number={1--2},
  pages={271--303},
  year={2001},
  publisher={Elsevier}
}

@misc{banu2026convergence,
  title={Convergence by Composition: A Structured Adapter Architecture for Multi-Agent System Integration},
  author={Banu, Bogdan},
  year={2026},
  note={Preprint}
}

@article{banu2026benchmarks,
  title={Do Biological Structural Guarantees Earn Their Complexity? Empirical Benchmarks for Biologically-Inspired Agent Reliability},
  author={Banu, Bogdan},
  year={2026},
  journal={arXiv preprint arXiv:2605.15225},
  eprint={2605.15225},
  archivePrefix={arXiv},
  primaryClass={cs.LG},
  note={Empirical companion to \texttt{banu2026harness}. Tests three biologically-grounded reliability features against naive non-biological alternatives and ablated controls across 10M+ data points (1{,}000 trials $\times$ 10 seeds), plus a real-sentence-embedding follow-up and a Gemma~4 27B end-to-end run. Findings: metabolic priority gating serves 100\% of critical operations under bursty load vs 39.8\% for a flat budget counter ($\Delta=+0.602$, $p<0.001$); autoinducer quorum sensing reaches 0\% false-positive rate with 71--87\% true-positive rate at 40\% agent compromise, an operating point unreachable by majority voting or independent detection; Bayesian two-signal stagnation detection wins on convergence discrimination only with real embeddings (96\% vs 2--40\% naive), a conditional guarantee gated on embedding quality. The cross-benchmark pattern: biological design earns its complexity through \emph{mechanism-level structural guarantees}, not algorithmic sophistication --- state-integrity guarantees (DNA repair) are deterministic, while behavioral/output-layer guarantees show honest limitations with capable models. This is the empirical grounding for which $\mathrm{Know}$-level certificates of \texttt{banu2026harness} actually deliver; cited by operon-langgraph-gates v0.1.0 (\S4.1 integrity, \S4.3 real-embedding stagnation).}
}

@article{zhou2026externalization,
  title={Externalization in {LLM} Agents: A Unified Review of Memory, Skills, Protocols and Harness Engineering},
  author={Zhou, Chenyu and Chai, Huacan and Chen, Wenteng and others},
  journal={arXiv preprint arXiv:2604.08224},
  year={2026}
}

@article{ma2026atomic,
  title={Scaling Coding Agents via Atomic Skills},
  author={Ma, Yingwei and Liu, Yue and Yang, Xinlong and others},
  journal={arXiv preprint arXiv:2604.05013},
  year={2026}
}

@article{liu2026lambda,
  title={$\lambda_A$: A Typed Lambda Calculus for {LLM} Agent Composition},
  author={Liu, Qin},
  journal={arXiv preprint arXiv:2604.11767},
  year={2026},
  note={Formal semantics for agent composition; shows 94.1\% of GitHub agent configs are structurally incomplete}
}

@article{willstro2026nlah,
  title={Natural-Language Agent Harnesses},
  author={Willstr{\"o}m, Erik and others},
  journal={arXiv preprint arXiv:2603.25723},
  year={2026},
  note={Harness behavior as portable, editable natural-language artifacts with explicit contracts}
}

@article{chen2026skilltester,
  title={{SkillTester}: Benchmarking Utility and Security of Agent Skills},
  author={Chen, Zhiyu and others},
  journal={arXiv preprint arXiv:2603.28815},
  year={2026},
  note={Comparative quality-assurance harness for agent skills}
}

@misc{agrawal2025gepa,
  title={{GEPA}: Reflective Prompt Evolution Can Outperform Reinforcement Learning},
  author={Agrawal, Lakshya A. and Tan, Shangyin and Soylu, Dilara and Ziems, Noah and others},
  year={2025},
  howpublished={\url{https://github.com/gepa-ai/gepa}},
  note={Open-source reflective prompt optimizer, v0.1.1}
}

@misc{yang2024opro,
  title={Large Language Models as Optimizers},
  author={Yang, Chengrun and Wang, Xuezhi and Lu, Yifeng and Liu, Hanxiao and Le, Quoc V. and Zhou, Denny and Chen, Xinyun},
  year={2024},
  eprint={2309.03409},
  archivePrefix={arXiv},
  note={OPRO: prompt optimization via LLM-generated gradient-like updates}
}

@misc{zhou2022ape,
  title={Large Language Models Are Human-Level Prompt Engineers},
  author={Zhou, Yongchao and Muresanu, Andrei Ioan and Han, Ziwen and Paster, Keiran and Pitis, Silviu and Chan, Harris and Ba, Jimmy},
  year={2022},
  eprint={2211.01910},
  archivePrefix={arXiv},
  note={APE: automatic prompt generation via LLM candidate pool + scoring}
}

@misc{khattab2024dspy,
  title={{DSPy}: Compiling Declarative Language Model Calls into Self-Improving Pipelines},
  author={Khattab, Omar and Singhvi, Arnav and Maheshwari, Paridhi and Zhang, Zhiyuan and Santhanam, Keshav and Vardhamanan, Sri and Haq, Saiful and Sharma, Ashutosh and Joshi, Thomas T. and Moazam, Hanna and Miller, Heather and Zaharia, Matei and Potts, Christopher},
  year={2024},
  howpublished={\url{https://github.com/stanfordnlp/dspy}},
  note={Programming-not-prompting framework for LM pipelines}
}

@misc{a2a2025,
  title={Agent2Agent ({A2A}) Protocol},
  author={{A2A Project}},
  year={2025},
  howpublished={\url{https://github.com/a2aproject/A2A}},
  note={Open cross-vendor agent-communication protocol; JSON-RPC 2.0 over HTTP+SSE}
}

@misc{autocontext2025,
  title={Autocontext: Multi-Agent Knowledge-Accumulation Runtime},
  author={{greyhaven-ai}},
  year={2025},
  howpublished={\url{https://github.com/greyhaven-ai/autocontext}},
  note={Staged-validation agent loops with persistent playbooks across generations}
}

@book{dellaert2017factor,
  title={Factor Graphs for Robot Perception},
  author={Dellaert, Frank and Kaess, Michael},
  year={2017},
  series={Foundations and Trends in Robotics},
  volume={6},
  number={1-2},
  pages={1--139},
  publisher={now Publishers},
  note={Standard reference for factor-graph formulations of SLAM, smoothing, and MAP estimation}
}

@article{kaess2012isam2,
  title={i{SAM2}: Incremental Smoothing and Mapping Using the {B}ayes Tree},
  author={Kaess, Michael and Johannsson, Hordur and Roberts, Richard and Ila, Viorela and Leonard, John J. and Dellaert, Frank},
  journal={International Journal of Robotics Research},
  volume={31},
  number={2},
  pages={216--235},
  year={2012},
  note={Incremental fixed-lag smoothing over factor graphs; production state-estimation baseline}
}

@misc{dellaert2026stag,
  title={Factor Graphs and World Models},
  author={Dellaert, Frank},
  year={2026},
  howpublished={\url{https://gtsam.org/2026/04/21/factor-graphs-and-world-models.html}},
  note={Frames factor graphs as a concrete structured instance of energy-based world models; introduces the STAG past-graph / future-graph rolling loop}
}

@article{marom2026category,
  title={A Category-Theoretic Framework from Biological Mechanics to Engineered Stimulus-Response Systems},
  author={Marom, Lee and Tibbits, Skylar and Zardini, Gioele and Buehler, Markus J.},
  journal={arXiv preprint arXiv:2604.26367},
  year={2026},
  eprint={2604.26367},
  archivePrefix={arXiv},
  primaryClass={cond-mat.soft},
  note={Defines category Dyn of stimulus-response dynamical systems with subcategories Nat/Art, implementation functor F: Nat to Art, specification space Spec with projection pi, compilation functor E: Spec to Comp; instantiated on hygromorphic pinecone to 4D-printed bilayer pipeline}
}

@inproceedings{nielsen2025conductor,
  title={Learning to Orchestrate Agents in Natural Language with the Conductor},
  author={Nielsen, Stefan and Cetin, Edoardo and Schwendeman, Peter and Sun, Qi and Xu, Jinglue and Tang, Yujin},
  booktitle={The Fourteenth International Conference on Learning Representations (ICLR)},
  year={2026},
  eprint={2512.04388},
  archivePrefix={arXiv},
  primaryClass={cs.LG},
  note={Sakana AI. RL-trained Conductor model that designs targeted communication topologies and prompt-engineers focused instructions for specialized LLMs; recursive topology support enables dynamic test-time scaling. SOTA on LiveCodeBench and GPQA. Parallel work to operon's Theorem 3 GEPA conjecture on the topology axis.}
}

@article{ta2026reinforced,
  title={Reinforced Agent: Inference-Time Feedback for Tool-Calling Agents},
  author={Ta, Anh and Zhu, Junjie and Shayandeh, Shahin},
  year={2026},
  journal={arXiv preprint arXiv:2604.27233},
  eprint={2604.27233},
  archivePrefix={arXiv},
  primaryClass={cs.AI},
  note={Inference-time reviewer agent that evaluates provisional tool calls before execution, shifting tool-call assessment from post-hoc trajectory analysis to proactive evaluation. Introduces Helpfulness/Harmfulness metrics quantifying the reviewer-injects-its-own-errors tradeoff (o3-mini 3:1, GPT-4o 2.1:1 on BFCL irrelevance detection). GEPA prompt optimization adds +1.5-2.8\%. Published validation of the runtime-gating wedge claim that operon-langgraph-gates rests on.}
}

@article{liu2026memorycurse,
  title={The Memory Curse: How Expanded Recall Erodes Cooperative Intent in LLM Agents},
  author={Liu, Jiayuan and Li, Tianqin and Du, Shiyi and Luo, Xin and Zeng, Haoxuan and Tewolde, Emanuel and Lee, Tai Sing and Wang, Tonghan and Kingsford, Carl and Conitzer, Vincent},
  year={2026},
  journal={arXiv preprint arXiv:2605.08060},
  eprint={2605.08060},
  archivePrefix={arXiv},
  primaryClass={cs.CL},
  note={Across 7 LLMs x 4 social-dilemma games x 500 rounds, expanded context windows degrade cooperation in 18 of 28 model-game settings via erosion of forward-looking intent. Memory sanitization (replacing visible history with synthetic cooperative records, holding prompt length fixed) restores cooperation, proving the trigger is content not length. Ablating Chain-of-Thought reasoning often reduces the collapse, so deliberation amplifies the memory curse. Defines the empirical scope-line for any multi-agent operon topology.}
}

@article{singh2026agenticimodels,
  title={Agentic-imodels: Evolving agentic interpretability tools via autoresearch},
  author={Singh, Chandan and Tan, Yan Shuo and Xu, Weijia and Gero, Zelalem and Yang, Weiwei and Galley, Michel and Gao, Jianfeng},
  year={2026},
  journal={arXiv preprint arXiv:2605.03808},
  eprint={2605.03808},
  archivePrefix={arXiv},
  primaryClass={cs.LG},
  note={Autoresearch loop evolves scikit-learn-compatible regressors over tabular data, jointly optimizing predictive accuracy and a novel LLM-based simulatability metric (whether an LLM can predict model behavior from its string representation). Evolved models generalize across datasets and lift BLADE downstream agentic-data-science performance by up to 73\% for Copilot CLI and Claude Code. First positive evidence in the operon corpus for evolution-as-optimization yielding generalizing, agent-readable artefacts; in productive tension with operon's internal C8 finding that optimization does not generalize across structural types.}
}

@misc{meng2026agentharness,
  title={Agent Harness for Large Language Model Agents: A Survey},
  author={Meng, Qianyu and Wang, Yanan and Chen, Liyi and Wu, Wei and Li, Yihang and Jiang, Wenyuan and Wang, Qimeng and Lu, Chengqiang and Gao, Yan and Wu, Yi and Hu, Yao},
  year={2026},
  howpublished={\url{https://www.preprints.org/manuscript/202604.0428/v2}},
  doi={10.20944/preprints202604.0428.v2},
  note={Preprints DOI 10.20944/preprints202604.0428.v2. Formalizes the agent harness as a six-component tuple H=(E,T,C,S,L,V); 110+ papers and 23 systems surveyed on a Harness Completeness Matrix; identifies compositional verification as one of nine open challenges. Companion repository: https://github.com/Gloriaameng/Awesome-Agent-Harness}
}

@article{banu2026harness,
  title={Harness Engineering as Categorical Architecture},
  author={Banu, Bogdan},
  year={2026},
  journal={arXiv preprint arXiv:2605.12239},
  eprint={2605.12239},
  archivePrefix={arXiv},
  primaryClass={cs.LG},
  note={Frames agent harness engineering through the categorical Architecture triple $(G, \mathrm{Know}, \Phi)$ from the ArchAgents framework. The four pillars of agent externalization (Memory, Skills, Protocols, Harness) map onto the triple's components: Memory as coalgebraic state, Skills as operad-composed objects, Protocols as syntactic wiring $G$, and the full Harness as the Architecture itself. Structural guarantees---integrity gates, quality-based escalation, supported convergence checks---are $\mathrm{Know}$-level certificates whose preservation is structural replay: compiler functors targeting Swarms, DeerFlow, Ralph, Scion, and LangGraph preserve three named certificate types by identity/replay. Companion to the operon-langgraph-gates v0.1.0 wedge and the L1/L2 cert hooks in operon-ai v0.38+.}
}
