calyr.aí
YAML source of truth content/books.yamlBinding method_catalog

Research system

calyr.aí method catalog

A growing collection of reusable scientific-AI, numerical, inference, validation, and closed-loop experimental method contracts developed within the calyr.aí research system.

03published05structures defined

Catalog index

Designed to grow by method family and domain
Research practiceWorking contract

CALYR-METHOD-EVIDENCE-WORKFLOW-001

Evidence Reading Workflow

Capture sources in Safari, preserve them in Zotero, extract page-bound evidence, and publish curated claims to the calyr.aí knowledge catalog.

literature reviewscientific writingknowledge extractionSafariZoteroannotationscitationsevidence graphYAML
Open method contract →
Scientific AIWorking contract

CALYR-METHOD-NR-AI-001

Scientific AI and Numerical Methods

Trustworthy surrogate prediction through numerical baselines, uncertainty, applicability limits, and validation.

SAXSSPRcryo-EMnumericssurrogate predictionprobabilistic inferencevalidation
Open method contract →
ReproducibilityStructure defined

CALYR-METHOD-REP-001

Reproducible Baseline and Delta Analysis

Freeze sources, environments, datasets, metrics, and random states before extending a scientific baseline; explain every deviation from the reference result.

scientific softwaremodel reproductionsource freezeenvironment lockbaselinedelta analysis
Contract structure in development
Data governanceStructure defined

CALYR-METHOD-DATA-001

Traceable Scientific Data and Reuse

Move observations through immutable raw, staging, curated, feature, and registry layers with ownership, source, license, version, checksum, schema, and quality status.

experimental datascientific MLprovenanceintegritydataset cardsreuse
Contract structure in development
ValidationStructure defined

CALYR-METHOD-EVID-001

Evidence Levels and Acceptance Gates

Separate hypothesis, reproduced baseline, retrospective validation, prospective validation, and repeated closed-loop evidence; attach an explicit gate to every claim and release.

scientific claimsmodel lifecycleevidence levelsacceptance gateslimitationsrelease criteria
Contract structure in development
Experimental learningStructure defined

CALYR-METHOD-LOOP-001

Closed-Loop Experimental Learning

Connect constrained design, informative candidate selection, multi-modal observation, surrogate updates, experimental validation, and selection of the next batch.

design of experimentsactive learningclosed loopassayacquisition policybatch update
Contract structure in development
Decision systemsWorking contract

CALYR-METHOD-ORACLE-001

Oracling

Turn evidence, predictions, uncertainty, constraints, and trade-offs into traceable decision proposals and explicit next actions.

multi-objective designoracle systemstrait modelsconstraintsdiversityPareto ranking
Open method contract →
Scientific governanceStructure defined

CALYR-METHOD-GOV-001

Reusable Method and Project-Result Boundary

Classify reusable platform methods, project-specific results, mixed artifacts, licenses, and approval requirements before knowledge moves between repositories or products.

IPknowledge transferbackground methodsproject resultsclassificationapproval
Contract structure in development