{"id":90,"date":"2026-08-23T08:45:20","date_gmt":"2026-08-23T08:45:20","guid":{"rendered":"https:\/\/genetec.io\/?page_id=90"},"modified":"2026-08-23T12:04:58","modified_gmt":"2026-08-23T12:04:58","slug":"cognimed","status":"publish","type":"page","link":"https:\/\/genetec.io\/?page_id=90","title":{"rendered":"Cognimed"},"content":{"rendered":"\r\n

Cognimed is the research program of this site: computing the body from the genome. It treats development as a cognitive process — the genome read as a large model, the tissue as a neural cellular automaton, and the bioelectric field as the latent space in which anatomy is specified. The themes covered on these pages — the TERRA RNAs<\/a>, the HOX clusters<\/a>, the Polycomb complex<\/a>, and the bioelectric layer — are its working parts.<\/p>\r\n\r\n\r\n\r\n

The papers<\/h2>\r\n\r\n\r\n\r\n

Nine papers are published open-access on Zenodo (CC-BY 4.0). Author: Miles Bradford Jacobs, genetec.io.<\/p>\r\n\r\n\r\n\r\n

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  1. Cognitive Biology: From Systems to Somatic Networks, Tissue Cognition, Cognitive Morphogenesis, and Tissue Emotions<\/em> — DOI 10.5281\/zenodo.20722139<\/a><\/li>\r\n
  2. Cognitive Biology: Perceptrons and Morphogen Primordia<\/em> — DOI 10.5281\/zenodo.21143761<\/a><\/li>\r\n
  3. Cognitive Biology Across Phyla: One Bioelectric Operator and a Substrate Reader That Sets the Boundary<\/em> — DOI 10.5281\/zenodo.20746637<\/a><\/li>\r\n
  4. Cognitive Biology and Organ Formation: Organs as Master-Transcription-Factor Heads Read From an Accessibility Code<\/em> — DOI 10.5281\/zenodo.20925727<\/a><\/li>\r\n
  5. Cognitive Biology: The Inner Perceptron versus the Outer Perceptron<\/em> — DOI 10.5281\/zenodo.21143016<\/a><\/li>\r\n
  6. Cognitive Biology: Computing the Embryo<\/em> — DOI 10.5281\/zenodo.21221930<\/a><\/li>\r\n
  7. Cognitive Biology: The Human Model and the GWAS Scaffold<\/em> — DOI 10.5281\/zenodo.21796907<\/a><\/li>\r\n
  8. Cognitive Biology: Differentiation Clocks, Organ Formation and the MLP<\/em> — DOI 10.5281\/zenodo.21322049<\/a><\/li>\r\n
  9. Cognitive Biology: The Mouse Model and the Attention-Head Manifold<\/em> — DOI 10.5281\/zenodo.21791849<\/a><\/li>\r\n
  10. Cognitive Biology: Assembling the Body by Relational Attractors<\/em> — in preparation<\/li>\r\n<\/ol>\r\n\r\n\r\n\r\n

    Code and data<\/h2>\r\n\r\n\r\n\r\n

    Every published result is reproducible from the open series repository: github.com\/AlphaFanX\/cognitive-biology<\/a> (MIT for code, CC-BY for the papers). The model is trained on public spatial transcriptomic atlases (MOSTA, ZESTA, HESTA<\/a>) and grounded in public regulatory databases (AlphaGenome, SEdb, ABC<\/a>).<\/p>\r\n\r\n\r\n\r\n

    The model itself is published on Hugging Face: huggingface.co\/jacobsme\/cognimed-nca-lgm<\/a><\/strong> — the complete NCA+LGM parameter set: the W0<\/sub> kernel modules, the genome kernel\/adapter partition, the per-allele adapter tables, the head maps and conductances, every derived result table, and our dense 3D atlas reconstructions. The whole model is 37 MB — its parameters are read from the genome through public databases, not fitted at scale: a glass box, small enough to audit line by line.<\/p>\r\n\r\n\r\n\r\n

    Why it matters<\/h2>\r\n\r\n\r\n\r\n

    A computational model of development faithful enough to be interrogated is the precondition for in-silico medicine: designing and validating interventions against the model before the wet lab. The long-range targets are partial epigenetic reprogramming and aging, regenerative medicine, and gene therapy on the now-open AAV platform.<\/p>\r\n\r\n","protected":false},"excerpt":{"rendered":"

    Cognimed is the research program of this site: computing the body from the genome. It treats development as a cognitive process — the genome read as a large model, the tissue as a neural cellular automaton, and the bioelectric field as the latent space in which anatomy is specified. The themes covered on these pages […]<\/p>\n","protected":false},"author":0,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-90","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/genetec.io\/index.php?rest_route=\/wp\/v2\/pages\/90","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/genetec.io\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/genetec.io\/index.php?rest_route=\/wp\/v2\/types\/page"}],"replies":[{"embeddable":true,"href":"https:\/\/genetec.io\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=90"}],"version-history":[{"count":4,"href":"https:\/\/genetec.io\/index.php?rest_route=\/wp\/v2\/pages\/90\/revisions"}],"predecessor-version":[{"id":144,"href":"https:\/\/genetec.io\/index.php?rest_route=\/wp\/v2\/pages\/90\/revisions\/144"}],"wp:attachment":[{"href":"https:\/\/genetec.io\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=90"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}