Outcome Learning Loops¶
These loops record how requested-versus-observed follow-up should tighten or weaken the next recommendation.
They exist because downstream consequence should not be memoryless. Once the repository has asked for assays, observed only part of them, or learned that the information gain was weaker than expected, the next recommendation should change in public.
What One Loop Tells You¶
Each workflow-family loop keeps the same questions visible:
- what the recommendation posture was before follow-up
- what assays were requested
- what assays actually happened
- whether the loop was worth the assay spend
- how the observed result should narrow or strengthen the next recommendation
Cross-Family Snapshot¶
| workflow family | initial posture | revised posture | worth the assay spend | current lesson |
|---|---|---|---|---|
dda |
recommend_with_downgrade |
recommend_with_downgrade |
yes | matched assays preserved the intended closure loop without widening public language |
dia |
recommend_with_downgrade |
do_not_recommend |
no | requested assay loss should block any attempt to treat DIA follow-up as laboratory closure |
lfq |
do_not_recommend |
do_not_recommend |
no | low-information repeats should stay refused when the biological conclusion is still design-limited |
multiplex |
do_not_recommend |
do_not_recommend |
no | no shipped requested-versus-observed outcome loop exists for this family yet |
ptm |
do_not_recommend |
recommend_with_downgrade |
yes | site-level ambiguity can still repay follow-up when the closure question is narrow and explicitly targetable |
targeted |
do_not_recommend |
recommend_with_downgrade |
yes | fast calibration-facing loops can be worth it even when broader targeted authority remains bounded |
dda¶
- initial posture:
recommend_with_downgrade - revised posture after outcome:
recommend_with_downgrade - worth the assay spend: yes
- requested assays:
dda-repeat-digest,dda-pooled-reference,dda-carryover-blank - observed assays:
dda-repeat-digest,dda-pooled-reference,dda-carryover-blank - matched assays:
dda-repeat-digest,dda-pooled-reference,dda-carryover-blank - blocked assays: none
- weakened assays: none
- learning points: matched assays preserved the intended closure loop without widening public language, the follow-up repaid cost because it stabilized the contaminant and pooled-reference boundary
- next adjustments: matched assays preserved the intended closure loop without widening public language, the follow-up repaid cost because it stabilized the contaminant and pooled-reference boundary
- evidence paths:
artifacts/lab/flagship-follow-up-outcomes/dda.json,claim:dda_target_decoy_stability
dia¶
- initial posture:
recommend_with_downgrade - revised posture after outcome:
do_not_recommend - worth the assay spend: no
- requested assays:
dia-library-bridge,dia-matrix-shift-repeat - observed assays:
dia-matrix-shift-repeat - matched assays:
dia-matrix-shift-repeat - blocked assays:
dia-library-bridge - weakened assays:
dia-matrix-shift-repeat - learning points: requested assay loss should block any attempt to treat DIA follow-up as laboratory closure, strong import-backed review does not rescue a loop that fails its own library bridge
- next adjustments: requested assay loss should block any attempt to treat DIA follow-up as laboratory closure, strong import-backed review does not rescue a loop that fails its own library bridge, feed the revised follow-up result back into future recommendation posture instead of keeping the original recommendation sentence unchanged, treat blocked assays as explicit evidence for narrower or slower future follow-up, carry weakened assays forward as downgrade evidence rather than as partial confirmation
- evidence paths:
artifacts/lab/flagship-follow-up-outcomes/dia.json
lfq¶
- initial posture:
do_not_recommend - revised posture after outcome:
do_not_recommend - worth the assay spend: no
- requested assays:
lfq-extra-replicate-block,lfq-randomized-repeat - observed assays:
lfq-extra-replicate-block - matched assays:
lfq-extra-replicate-block - blocked assays:
lfq-randomized-repeat - weakened assays:
lfq-extra-replicate-block - learning points: low-information repeats should stay refused when the biological conclusion is still design-limited
- next adjustments: low-information repeats should stay refused when the biological conclusion is still design-limited, treat blocked assays as explicit evidence for narrower or slower future follow-up, carry weakened assays forward as downgrade evidence rather than as partial confirmation
- evidence paths:
artifacts/lab/flagship-follow-up-outcomes/lfq.json
multiplex¶
- initial posture:
do_not_recommend - revised posture after outcome:
do_not_recommend - worth the assay spend: no
- requested assays:
- observed assays:
- matched assays: none
- blocked assays: none
- weakened assays: none
- learning points: no shipped requested-versus-observed outcome loop exists for this family yet
- next adjustments: publish a dedicated downstream lab consequence and observed outcome loop before strengthening recommendation posture
- evidence paths:
artifacts/intelligence/recommendation-packets/multiplex.json
ptm¶
- initial posture:
do_not_recommend - revised posture after outcome:
recommend_with_downgrade - worth the assay spend: yes
- requested assays:
ptm-site-targetability,ptm-orthogonal-validation - observed assays:
ptm-site-targetability,ptm-orthogonal-validation - matched assays:
ptm-site-targetability,ptm-orthogonal-validation - blocked assays: none
- weakened assays:
ptm-site-targetability - learning points: site-level ambiguity can still repay follow-up when the closure question is narrow and explicitly targetable, useful PTM follow-up should strengthen a bounded claim rather than erase the wider ambiguity warning
- next adjustments: site-level ambiguity can still repay follow-up when the closure question is narrow and explicitly targetable, useful PTM follow-up should strengthen a bounded claim rather than erase the wider ambiguity warning, feed the revised follow-up result back into future recommendation posture instead of keeping the original recommendation sentence unchanged, carry weakened assays forward as downgrade evidence rather than as partial confirmation
- evidence paths:
artifacts/lab/flagship-follow-up-outcomes/ptm.json,claim:ptm_site_resolution_boundary
targeted¶
- initial posture:
do_not_recommend - revised posture after outcome:
recommend_with_downgrade - worth the assay spend: yes
- requested assays:
prm-assay,orthogonal-assay - observed assays:
prm-assay,orthogonal-assay - matched assays:
prm-assay,orthogonal-assay - blocked assays: none
- weakened assays: none
- learning points: fast calibration-facing loops can be worth it even when broader targeted authority remains bounded, follow-up value here comes from interference clarification, not from pretending vendor-parity authority exists
- next adjustments: fast calibration-facing loops can be worth it even when broader targeted authority remains bounded, follow-up value here comes from interference clarification, not from pretending vendor-parity authority exists, feed the revised follow-up result back into future recommendation posture instead of keeping the original recommendation sentence unchanged
- evidence paths:
artifacts/lab/flagship-follow-up-outcomes/targeted.json,claim:targeted_transition_consistency,claim:targeted_interference_boundary
Boundary¶
A recommendation that changes after one shipped follow-up loop should not keep its old public sentence by inertia.