Solutions/For AI builders/Encoded Reasoning

Capture how your best scientists weigh evidence and resolve contradictions, and compile it into versioned reasoning your agents apply consistently, not prompts that drift.

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EXPERT JUDGMENTENCODED REASONINGCOMPILEv3.0

Program the reasoning behind every scientific call

Judgment, not prompt text

Encode frameworks, thresholds, and trade-offs as structured reasoning you can inspect, test, and version.

Runs the same way every time

The same evidence yields the same call, so your standards hold across every agent, team, and model.

An asset that compounds

Reasoning lives as something you own and refine, getting sharper instead of walking out the door.

REASONING SYSTEM · RANKING & PRIORITIZATIONSingle-object profileTarget PrioritizationRANK IN FIELD#6 of 178PERCENTILE97th0.86/1.0View Model·ANCHOR OBJECT5 WEIGHTED CRITERIA · OPEN ONE FOR EVIDENCEEVIDENCE SCORE−1+1Genetic associationw 0.300.00Differential expressionw 0.250.00Cross-dataset replicationw 0.200.00Multi-omic supportw 0.150.00Druggabilityw 0.100.00
01Capture

Start from how your experts actually reason

BioBox captures how your best scientists weigh evidence: their frameworks, thresholds, and the calls they trust. It becomes a structured model you can inspect.

Evidence Updates (3)3 appliedPathway Enrichment Score0.670.67QueryFormulaOldNewWeight0.150.15(+47% increase)Literature Citation Score0.720.72QueryFormulaOldNewWeight0.180.18(no change)Clinical Trial Evidence0.850.85QueryFormulaOldNewWeight0.250.25(+12% increase)
02Compile

Reasoning you version, not prompts you babysit

Adjudication rules and trade-offs become executable modules that run consistently, far past the point where brittle prompt text falls apart.

Decision TracerLive312traced today298matched14flaggedRECENT TRACESAllFlaggedSafety Reviewjust nowAdvance hepatotox-flagged case CASE-204?dili.risk v3.0✓ matchedTarget Triage12s agoIs KRAS-G12D tractable enough to advance?target.rank v2.1✓ matchedIndication Fit30s agoBest lead indication for the asset?indication.fit v1.4✓ matchedPortfolio Review1m agoHold or kill Program Atlas?portfolio.gate v2.0⚑ flaggedQUESTIONHold or kill Program Atlas?REASONING TRACEReasoning ModuleReasoning ModuleReasoning ModuleReasoning ModuleReasoning ModuleReasoning Module
03Test

Prove it reasons the way you would

Replay past decisions and hard edge cases to confirm the encoded reasoning matches your experts before it ever reaches an agent.

04Own

Expertise that stays with you

Every refinement is kept and versioned, so institutional judgment becomes a durable asset instead of tribal knowledge.

Programmable scientific reasoning

Score associations from a perspective you define.

BioBox turns how your experts weigh evidence into a quantifiable, traceable score of association, grounded in your own ontology and data.

Grounded in your ontology and data

Reasoning runs over a custom ontology and the real-world evidence already in your graph: your entities, your relationships, your results, never a foundation model's generic priors.

A scientific perspective, encoded

Experts define which lines of evidence count and how much they weigh. The same perspective is applied the same way to every question, and can be revised without unpicking the rest.

A quantified, defensible score

Every module returns one signed score of association that decomposes back into the evidence behind it. Defensible to a scientist, not just plausible to a reader.

Association score

Target Prioritization

GeneDisease
+0.86Net-supported
−1 · contradicted0+1 · supported

Lines of evidence

Genetic association
Differential expression
Pathway centrality
Tissue specificity

Every score decomposes into the evidence, supporting and contradicting, that produced it.

Powering Agentic Science

Your knowledge stays sovereign, and unmistakably yours.

Your scientists' judgment lives in reasoning modules grounded in your own ontology and data, and any AI co-scientist reasons against those instead of raw context. So your differentiated knowledge never dissolves into someone else's model. It stays sovereign, governed, and yours to compound.

The model navigates. The science adjudicates.

Ontology-licensed path

Agent queryGROUNDDisease contextENRICHMechanismREFINESafety signalGrounded answer

An agent composes reasoning modules along a path the ontology licenses. Each one adds a layer of grounded evidence, so the answer is built up, never guessed.

Modules, not raw context

Each reasoning module anchors two concepts in your ontology, carries rich descriptions of what it means and when it applies, and traces to the curated evidence that justifies it. It captures not just what something is, but why it reads that way.

Agents do what they are good at

The agent reads intent and decides which modules to activate and in what order. Adjudication stays inside the modules, so swapping models, or rerunning the same one, returns the same grounded answer.

Composed for the question

Modules chain along paths the ontology licenses. Broad questions recruit complementary modules from related domains; a safety read narrows through tightly scoped, reinforcing ones. The composition adapts while the grounding stays fixed.

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See BioBox on your hardest decision

A working session with our team, mapped to one of your active discovery programs.

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