Foundation¶

The foundation section explains the durable role of bijux-proteomics-intelligence before it explains implementation detail. Use it to resolve why decision policy belongs here without pretending to own evidence truth or execution.

That boundary needs more explicit language now because the repository has enough benchmark, workflow, and grounding depth that analytical judgment can no longer hide behind vague prose. This section exists to show where recommendation posture begins, how challenge evidence disciplines that posture, and why explanation must stay visibly downstream from scientific truth.

Why Readers Should Stay Here Longer¶

this is where the repository shows that recommendation language is not a vague afterthought layered on top of benchmarks
blinded challenges, counterfactual collapses, regret, and downgrade posture now make analytical judgment inspectable instead of merely assertive
the package exposes real public routes for how one family sentence survives, weakens, or collapses under withheld evidence

flowchart LR
    evidence["evidence input"]
    constraints["program constraints"]
    policy["scoring and scenario policy"]
    explanation["explanations"]
    intelligence["intelligence foundation"]
    action["downstream action"]

    evidence --> intelligence
    constraints --> intelligence
    policy --> intelligence
    intelligence --> explanation
    intelligence --> action

What This Section Protects¶

a visible seam between fact and judgment
recommendation logic that can be argued about instead of merely obeyed
explanation surfaces that stay tied to policy rather than pretending to be raw evidence

What This Section Now Carries¶

recommendation posture that remains separate from evidence truth
challenge and confidence routes that expose overconfidence, underconfidence, and regret instead of smoothing them away
explanation surfaces that justify analytical judgment without pretending to be upstream fact

Start With¶

Open Package Overview for the shortest statement of the package role.
Open Ownership Boundary when the question is whether a change belongs here or in a neighbor.
Open Scope and Non-Goals when a proposed change risks broadening the package.
Open Capability Map when you need the concrete work the package is allowed to do.
Open This Package Does Not Own when a proposal is trying to recast recommendation policy as scientific truth or runtime control.
Open Workflow Recommendation Challenges when you need the current blinded recommendation record rather than summary language.
Open Workflow Recommendation Confidence when you need the current counterfactual, overconfidence, underconfidence, and regret surfaces.

Section Pages¶

What This Section Settles¶

when a rule is a judgment policy rather than a knowledge claim
which recommendation behavior belongs here before runtime or lab acts on it
when a proposed change is really about evidence truth or workflow rules and should leave this package

Reader Questions This Section Can Answer Well¶

why one workflow family still stops at a downgrade even when its benchmark packet looks strong
which hidden evidence pattern would make the current recommendation regretful
where overconfidence is already measurable instead of only suspected
how recommendation pressure differs from scientific truth and downstream lab consequence

Strongest Intelligence Proof¶

start with Workflow Recommendation Challenges when the dispute is whether recommendation posture survives blinded pressure
continue to Workflow Recommendation Confidence when the question is where confidence, regret, and counterfactual weakness still remain
open This Package Does Not Own when someone is trying to rename scientific truth or runtime control as intelligence policy

First Proof Check¶

packages/bijux-proteomics-intelligence/src/bijux_proteomics_intelligence
packages/bijux-proteomics-intelligence/tests
neighboring handbooks once the change crosses the local boundary

Neighbors¶

Open bijux-proteomics-knowledge when the question leaves scoring, ranking, scenarios, and explanations.
Open bijux-proteomics-core when the issue is clearly outside this package's local role.