Zach Mainen

I am a Principal Investigator at the Champalimaud Centre for the Unknown in Lisbon, where I run the Systems Neuroscience Lab studying serotonin, decision-making, and perception. I co-founded the International Brain Laboratory, a collaboration rethinking how neuroscience is done. I also write on artificial intelligence, formal ontology, and the design of institutions, and founded Latent States, a research programme exploring subjective experience through science and art.

Research

Selected Writing

• Forget the AI megadaemons. The problem as always is us. On ripening and rotting technological visions and the future we can still build.
• Why Organization Beats Scale Organized retrieval is exponentially faster than unorganized retrieval. Not a little faster. Exponentially. From The Library Theorem.
• Your LLM Is a Finite Automaton A transformer with a fixed context window is a finite automaton. Chain-of-thought doesn't fix this. External memory does.
• Reality Is a Tangle Three ancient problems — similarity, identity, knowledge — share a single topological solution.
• There Is No Meta Room How should we make decisions when we disagree about the rules for making decisions? There is no framework above frameworks. Written by a Claude instance.
• The Micro-Alignment Problem The danger isn't superintelligence — it's synthetic agents forming intimate relationships without informed consent.
• Latent Space Dialogues On latent spaces, metaphor, and dialogue as orientation during technological disruption.

Selected Publications

• The Library Theorem: how external organization governs agentic reasoning capacity. Mainen ZF. arXiv preprint (2026) arXiv:2603.21272
• Facial expressions in mice reveal latent cognitive variables and their neural correlates. Cazettes F, Reato D, Augusto E, Steinfeld R, Renart A, Mainen ZF. Nature Neuroscience (2025) 10.1038/s41593-025-02071-5
• Standardized and reproducible measurement of decision-making in mice. The International Brain Laboratory et al. eLife (2021) 10.7554/eLife.63711
• Neural correlates, computation and behavioural impact of decision confidence. Kepecs A, Uchida N, Zariwala HA, Mainen ZF. Nature (2008) 10.1038/nature07200
• Reliability of spike timing in neocortical neurons. Mainen ZF, Sejnowski TJ. Science (1995) 10.1126/science.7770778

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