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Notes from building an AI co-scientist.
Research, method and engineering writing from the team building the co-scientist.
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View all →Sep 1, 2026Codon resolution at metagenomic scale: why we built OILCodon corpora stop at reference organisms. Metagenomic corpora throw the codons away by storing coding sequence as protein. OIL is 2.35 trillion nucleotides that keep both, with provenance on every record and nothing back-translated.Research
5 min readAug 14, 2026Codon-level equivariance: what it fixes, and what it does notThe genetic code is degenerate, and most mRNA models learn that the expensive way. Equi-mRNA encodes it in the representation instead. The mechanism, the numbers, and the thing people get wrong about synonymous codons.Research
2 min readAug 4, 2026Introducing Equi-mRNA: the first codon-level equivariant mRNA language modelMost sequence models treat the genetic code as text and relearn its geometry from scratch. Equi-mRNA builds that geometry in: a 15M-parameter model that outperforms baselines 3-5x its size, peer-reviewed at NeurIPS 2025.Research
8 min readJul 24, 2026What we keep in the knowledge graph, including the things that did not workMost biomedical graphs remember hits. Ours keeps curated negatives alongside them, types every edge by how it was established, and refuses to settle a disagreement by deleting one side of it.Engineering
2 min read
5 min readAug 14, 2026Codon-level equivariance: what it fixes, and what it does notThe genetic code is degenerate, and most mRNA models learn that the expensive way. Equi-mRNA encodes it in the representation instead. The mechanism, the numbers, and the thing people get wrong about synonymous codons.Research
2 min readAug 4, 2026Introducing Equi-mRNA: the first codon-level equivariant mRNA language modelMost sequence models treat the genetic code as text and relearn its geometry from scratch. Equi-mRNA builds that geometry in: a 15M-parameter model that outperforms baselines 3-5x its size, peer-reviewed at NeurIPS 2025.Research
8 min readJul 24, 2026What we keep in the knowledge graph, including the things that did not workMost biomedical graphs remember hits. Ours keeps curated negatives alongside them, types every edge by how it was established, and refuses to settle a disagreement by deleting one side of it.Engineering
2 min read
News
Releases, milestones and announcements.
ProductSep 11, 2026
Early access to Helixir opens to research teams
Research and biotech teams can apply for early access to the Co-Scientist and run hypothesis discovery, de novo design and literature review on their own targets.
ResearchSep 6, 2026
MIRAGE: a benchmark for protein-family generalization in affinity prediction
Our preprint treats historical public protein-family support as an explicit experimental variable, for affinity and for pose, and reports what happens to frontier co-folders on families they have not seen.
ResearchSep 1, 2026
OIL: an open codon-resolved nucleotide framework, presented at MoML 2026
The Omics Integrated Library assembles 2.35 trillion nucleotides across fifteen sources, codon-resolved and with provenance on every record. Scripts and the automated procedure follow later this year.
ResearchDec 1, 2025
First equivariant foundation model for mRNA design at NeurIPS 2025
Our foundation model learns biology in a geometry-aware representation: the technical core the co-scientist platform is built on.
ResearchAug 21, 2025
Equi-mRNA: the first codon-level equivariant mRNA language model
Our paper encodes synonymous-codon symmetry directly into the representation as SO(2) cyclic subgroups, rather than leaving a language model to infer it from data.
Most read
01Codon resolution at metagenomic scale: why we built OILResearch · 5 min02Codon-level equivariance: what it fixes, and what it does notResearch · 2 min03Introducing Equi-mRNA: the first codon-level equivariant mRNA language modelResearch · 8 min04What we keep in the knowledge graph, including the things that did not workEngineering · 2 min
