Leakage-safe primary test
Held-out family or pathway
Compare frozen UniPert features with native ridge, ESM2-only, nearest-neighbour and random-embedding controls. Report verified-unseen and unresolved-exposure results separately.
UniPert feasibility
NWLE-10 · partial feasibility audit
Can UniPert add useful perturbation identity features?
NMD-VCell can evaluate UniPert now as a frozen gene-and-compound identity representation. The first release separates verified source and identifier readiness from every encoder, embedding, transfer and DMD-response claim.
No embedding or predictive result. The 21 / 21 identifier preflight only confirms that the governed candidate list can be mapped to reviewed human UniProt primary accessions. It does not show that UniPert encodes them correctly, improves prediction or transfers to DMD.
Genetic cause spaceGene · UniProt · FASTA21/21 identifiers ready
Chemical cause spaceName · SMILESPublic compound inputs supported
Identity bridgeUniPert frozen representationEncoder runs in NMD-VCell: 0
U2Relation retrievalregistered
U3Held-out family G2registered
U4Gene ↔ compound transferregistered
Not encoded directlydirectiondosetimemodalitycell stateDMD contextfunction
Source and implementation audit
Useful immediately as a bounded representation baseline
Open the complete source, implementation and rights audit
| Audit item | Verified state | Operational consequence |
|---|---|---|
| Formal paper | Cell 2026 · DOI 10.1016/j.cell.2026.06.005 | Citable method and reported benchmarks; not DMD validation. |
| Public repository | Audited commit 2f5d46930dcbdeb92073a13e898abe6e363e679a | Frozen model and encoding demos are present. |
| Reproduction surface | Full G2CP training and paper-split reproduction pipeline not found in the audited public tree | Do not label a local encoder run as paper reproduction. |
| Condition semantics | Identity inputs are available; direction, dose, time, modality and DMD state are not direct tokens | Use as an identity feature, not a condition-response simulator. |
| Rights | Article CC BY · code GPL-3.0 · article reports related patent filing | Retain licence provenance and perform separate deployment/FTO review. |
U0–U4 execution ladder
Only U0 and the identifier part of U1 are complete
| Stage | Task | State | Current result |
|---|---|---|---|
| U0 | Paper, code, licence, patent-notice and implementation-surface audit | Available nowEXECUTED | Source and implementation boundaries frozen in this contract. |
| U1 | Candidate identifier and sequence-input preflight | Available nowPARTIAL_IDENTIFIER_PREFLIGHT_EXECUTED_ENCODER_NOT_RUN | 21/21 candidates map to reviewed human UniProt primary accessions. |
| U2 | Cause-space sanity checks and known-relation retrieval | Available nowREGISTERED_NOT_EXECUTED | No result |
| U3 | Leakage-safe G2 incremental benchmark | Available nowREGISTERED_NOT_EXECUTED | No result |
| U4 | Public gene-to-compound cross-domain learning curve | Available nowREGISTERED_NOT_EXECUTED | No result |
Candidate input preflight
21 governed candidates have reviewed human primary accessions
Open all 21 candidate mappings
| Gene | UniProt | Sequence length | State |
|---|---|---|---|
| ADAM10 | O14672 | 748 | No result yetIDENTIFIER_PREFLIGHT_PASS_ENCODER_NOT_RUN |
| CALR | P27797 | 417 | No result yetIDENTIFIER_PREFLIGHT_PASS_ENCODER_NOT_RUN |
| CPEB1 | Q9BZB8 | 566 | No result yetIDENTIFIER_PREFLIGHT_PASS_ENCODER_NOT_RUN |
| DDX19B | Q9UMR2 | 479 | No result yetIDENTIFIER_PREFLIGHT_PASS_ENCODER_NOT_RUN |
| DNAAF3 | Q8N9W5 | 541 | No result yetIDENTIFIER_PREFLIGHT_PASS_ENCODER_NOT_RUN |
| DNM1 | Q05193 | 864 | No result yetIDENTIFIER_PREFLIGHT_PASS_ENCODER_NOT_RUN |
| EHMT2 | Q96KQ7 | 1210 | No result yetIDENTIFIER_PREFLIGHT_PASS_ENCODER_NOT_RUN |
| EPS8L1 | Q8TE68 | 723 | No result yetIDENTIFIER_PREFLIGHT_PASS_ENCODER_NOT_RUN |
| GFOD2 | Q3B7J2 | 385 | No result yetIDENTIFIER_PREFLIGHT_PASS_ENCODER_NOT_RUN |
| INTS13 | Q9NVM9 | 706 | No result yetIDENTIFIER_PREFLIGHT_PASS_ENCODER_NOT_RUN |
| LMO2 | P25791 | 158 | No result yetIDENTIFIER_PREFLIGHT_PASS_ENCODER_NOT_RUN |
| MON1A | Q86VX9 | 652 | No result yetIDENTIFIER_PREFLIGHT_PASS_ENCODER_NOT_RUN |
| MPHOSPH6 | Q99547 | 160 | No result yetIDENTIFIER_PREFLIGHT_PASS_ENCODER_NOT_RUN |
| NAGLU | P54802 | 743 | No result yetIDENTIFIER_PREFLIGHT_PASS_ENCODER_NOT_RUN |
| RAC3 | P60763 | 192 | No result yetIDENTIFIER_PREFLIGHT_PASS_ENCODER_NOT_RUN |
| RNASEH2C | Q8TDP1 | 164 | No result yetIDENTIFIER_PREFLIGHT_PASS_ENCODER_NOT_RUN |
| RNF8 | O76064 | 485 | No result yetIDENTIFIER_PREFLIGHT_PASS_ENCODER_NOT_RUN |
| WDR4 | P57081 | 412 | No result yetIDENTIFIER_PREFLIGHT_PASS_ENCODER_NOT_RUN |
| ZFP69B | Q9UJL9 | 534 | No result yetIDENTIFIER_PREFLIGHT_PASS_ENCODER_NOT_RUN |
| ZNF133 | P52736 | 654 | No result yetIDENTIFIER_PREFLIGHT_PASS_ENCODER_NOT_RUN |
| ZNF236 | Q9UL36 | 1845 | No result yetIDENTIFIER_PREFLIGHT_PASS_ENCODER_NOT_RUN |
Adoption gate
Incremental value, not visual plausibility
Adopt UniPert as a feature only if it improves a predeclared held-out task over simple baselines with uncertainty, survives exposure and leakage audit, and does not degrade worst-group performance.
Hard boundary
An identity embedding is not a simulated perturbation
It does not specify CRISPRi, CRISPRa, KO, overexpression, dose, time, cell state, disease background, mechanism, function or safety. Those variables need explicit conditioning and independently evaluated outcomes.
Boundary. This release verifies sources, implementation limits and 21-candidate identifier readiness. It publishes zero UniPert embeddings, zero UniPert predictive benchmarks and zero DMD functional outcomes.