bijux-proteomics-intelligence

bijux-proteomics-intelligence owns decision policy in bijux-proteomics. It turns evidence and program constraints into scores, rankings, scenarios, counterfactuals, and explanations that remain inspectable instead of pretending to be upstream fact. This is where the system stops only describing the world and starts making bounded judgments about what should happen next.

This package is more concrete now than older docs suggested. It is not a vague "decision layer." It owns recommendation posture, benchmark-backed challenge routes, confidence and regret surfaces, interpretation summaries, and learning-facing judgment that stays visibly separate from scientific truth.

flowchart LR
    foundation["foundation<br/>shared meaning"]
    core["core<br/>durable rules"]
    knowledge["knowledge<br/>evidence state"]
    intelligence["intelligence<br/>scores, scenarios, explanations"]
    lab["lab<br/>plans and outcomes"]
    runtime["runtime<br/>execution"]

    foundation --> intelligence
    core --> intelligence
    knowledge --> intelligence
    intelligence --> lab
    intelligence --> runtime

What Makes This Package Different

• it does not claim to be raw truth
• it turns evidence plus constraints into choices
• it must explain itself because recommendation without explanation is only opaque force

What It Owns

• candidate scoring and ranking policy
• scenario evaluation and recommendation logic
• explanation and reporting surfaces for those decisions
• challenge, confidence, regret, and downgrade routes that show where the analytical posture narrows before the lab or operator is asked to act

Concrete Analytical Families

owner band	visible package substance	why it matters
candidates and claims	ranking pressure, shortlist logic, recommendation-facing claims	analytical posture starts from explicit competitive pressure
interpretation	run summaries, differential-abundance readings, PTM and review synthesis	scientific outputs become typed analytical narratives
judgment and posture	review-board decisions, readiness, downgrade, regret, refusal	recommendation strength is challengeable as policy
reviews and learning	benchmark-backed review packets and outcome-aware refinement	the package can improve or narrow because of later evidence

Why This Package Matters More Now

• the repository now has enough benchmark, runtime, and grounding depth that recommendation posture can no longer hide behind generic prose
• stronger workflow families create stronger overconfidence risk, which this package must expose rather than smooth away
• the repository now ships blinded and counterfactual pressure surfaces instead of only confidence-sounding summaries
• lab consequence now depends on explicit analytical judgment instead of an implied handoff

Shared Reader Routes

• Use Decision Support when the question is still about grounding, recommendation posture, or public artifact roles rather than one intelligence-owner module.
• Use Workflow Consequence Maps when the question is whether current recommendation language already outruns the weakest downstream boundary.
• Use What Changed The Recommendation when the question is which contradiction, comparator, or lab burden actually moved the recommendation.
• Use Workflow Families when the family trust sentence is still the main question.

Start Inside This Package

• Open Foundation for the package role and boundary.
• Open Workflow Recommendation Confidence when the question is where overconfidence, underconfidence, or regret already shows up in public artifacts.
• Open Workflow Recommendation Challenges when the question is whether one family still survives hidden reveal or counterfactual pressure.
• Open Architecture when the question is how scoring, scenarios, and explanations are arranged.
• Open Interfaces when the issue is a policy-facing surface or explanation output.

Reader Questions This Package Can Answer

• why the current recommendation moved instead of staying at an earlier, seemingly safer posture
• which workflow families still carry bounded recommendation posture even when their benchmark and runtime routes look strong
• whether overconfidence, underconfidence, or regret pressure is already visible in the shipped analytical artifacts
• how recommendation language changes when contradiction, comparator pressure, or lab burden is reintroduced

What Changed Since v0.3.7

• analytical judgment is no longer hidden inside one confidence-sounding layer
• challenge, downgrade, and regret surfaces now make overclaiming easier to detect from public docs
• the package now looks like a real analytical owner instead of a soft bridge between evidence and lab follow-up

Analytical Proof Surfaces

• decision-support pages for repository-wide recommendation posture before the question narrows to one policy surface
• workflow recommendation confidence for overconfidence, underconfidence, and regret-facing evidence
• workflow recommendation challenges for blinded and counterfactual pressure on each family
• architecture and interface pages for how scoring, scenarios, and explanation outputs stay separated from evidence truth

What It Refuses

• evidence truth and contradiction handling
• durable program contracts and shared payload meaning
• execution and operator-facing runtime behavior
• assay-worth claims that belong to lab consequence

Strongest Proof Route

• start at Decision Support when the question is still repository-wide
• continue to Workflow Recommendation Confidence when the dispute is already about recommendation pressure
• open the challenge and counterfactual routes once the question is no longer whether a recommendation exists, but whether it survives scrutiny

First Proof Check

• packages/bijux-proteomics-intelligence/src/bijux_proteomics_intelligence
• packages/bijux-proteomics-intelligence/tests
• challenge, confidence, counterfactual, and regret artifacts
• explainability and reporting modules once a claim narrows to one surface