Deceptive Grounding: Entity Attribution Failure in
Clinical Retrieval-Augmented Generation
July 10, 2026
Retrieval-augmented generation evaluation checks whether model claims are factually grounded in retrieved documents. It does not check whether retrieved evidence is attributed to the correct entity.
A clinical RAG response can pass every automated check (zero hallucinations, near-perfect faithfulness, real citations) while presenting drug \(Y\)’s clinical evidence as evidence about queried drug \(X\). We term this deceptive grounding (DG): a failure invisible to faithfulness, hallucination, and citation checks because every claim is sourced from a real document, about the wrong entity.
Using a controlled factorial benchmark across 13 models, we find DG rates spanning 8–87% at peak adversarial conditions. Medical and biomedical fine-tuned models reach up to 86.7%; domain specialization amplifies the failure rather than mitigating it.
A controlled ablation identifies the mechanism: removing entity-specific clinical evidence from retrieved documents eliminates entity-attribution failure entirely, shifting all failures to confabulation. The two failure modes respond to the same trigger, taking different paths.
Production measurement across 740 drug–disease pairs finds 7.8% overall DG in a deployed RAG system, rising to 13.6% for recently approved drugs. Entity-attribution verification (checking that cited evidence applies to the queried entity) detects DG at 97.0% precision and 98.7% DG recall (IPW-adjusted human gold standard); no existing framework implements it.
A clinician queries a decision support system: “What does the literature say about using rituximab to treat fibrodysplasia ossificans progressiva (FOP)?” Three documents are retrieved, all concerning garetosmab and tofacitinib, two agents investigated in FOP; rituximab does not appear. The system responds: “Rituximab has been studied in FOP. A 2023 phase-2 trial (NCT03188666) reported that rituximab reduced flare severity and duration with meaningful improvement in quality of life.” NCT03188666 is LUMINA-1—a real phase-2 trial, studying garetosmab. The citation is genuine. The clinical claim is accurate—about garetosmab. Attributed to rituximab.
How does this pass every automated check? Hallucination detection looks for claims with no retrieved support: every fact in the response (the trial name, the NCT number, the outcome description) is sourced directly from the retrieved garetosmab document, so nothing fires. Faithfulness scoring measures whether the response accurately relays what retrieved documents say: it does, faithfully. The entity mismatch (garetosmab’s evidence presented as rituximab’s) does not register as a faithfulness failure: faithfulness verifies that claims are supported by retrieved documents, and they are. Even implementations that compare entity names between response and document encode the discrepancy as a marginal penalty in an otherwise fully-supported response, not a categorical failure signal. Citation verification confirms that cited documents exist and are correctly referenced: NCT03188666 is real, correctly formatted, and its content matches the citation. Three checks pass—not despite the failure, but because the model accurately relays real clinical evidence about a real entity. Only entity attribution reveals the failure, and no existing evaluation framework checks it.
We call this deceptive grounding: a RAG response that accurately relays retrieved evidence but attributes it to the wrong entity. Unlike hallucination (no fabricated facts), faithfulness failure (all claims are document-grounded), or knowledge-conflict failures [1], [2], DG involves no contradictory signal: retrieved \(Y\)-documents are consistent with model expectations about \(X\) in context \(C\), differing only at the entity level.
This paper makes four contributions:
Scale. DG rates span 8–87% across 13 models; medical and biomedical fine-tuned models reach up to 86.7%; domain specialization amplifies, not mitigates, the failure.
Mechanism. A two-stage mechanism explains cross-model variation. Stage 1: shared disease context between \(X\) and \(Y\) primes the model to treat \(Y\)’s evidence as applicable to \(X\). Stage 2: whether retrieved documents contain completing information determines the failure mode—entity-attribution failure when they do, confabulation when they do not. A controlled ablation confirms this causally: removing completing information drops entity-attribution failure from 67% to 0% while the overall incorrect-response rate rises to 98%, now composed entirely of confabulation.
Detection. Entity-attribution verification (EAV): 97.0% precision, 98.7% DG recall, 0.0% false positives on clean controls (IPW-adjusted human gold standard, \(n{=}88\)). No existing framework implements this criterion.
Production prevalence. 7.8% overall DG in a deployed clinical decision support system; 13.6% for recently approved drugs where entity-specific retrieval is sparsest.
Existing frameworks verify that LLM outputs are consistent with source documents or factual knowledge [3]–[5] and that RAG responses accurately reflect retrieved content with genuine citations [6]–[13]. Deceptive grounding is undetectable by all of these frameworks by design: every DG response is fully faithful to retrieved documents, cites real sources, and contains no fabricated claims. The failure is at the attribution level, a dimension none of these frameworks inspect. NLI-based entailment checks also pass DG responses: the generated claim (e.g., “rituximab reduced flares”) is logically entailed by the retrieved document (which reports that garetosmab reduced flares) because faithfulness checks verify that the claim is supported by the document content, not that the claimed entity matches the document’s primary entity.
Most closely related in spirit, [14] introduce D-FActScore to detect entity-mixing in biography generation, where LLMs conflate facts from entities sharing the same name. Our failure is structurally distinct: queried entity \(X\) and retrieved-document entity \(Y\) have different names, so disambiguation is not the issue; attribution discipline in the generative step is. [15] study attribution bias with respect to document authorship in RAG pipelines; we study entity identity, not source provenance. D-FActScore’s detection mechanism also does not transfer: it cross-references claims against parametric knowledge of named entities, whereas DG responses are plausible under that same parametric knowledge; the only diagnostic signal is the discrepancy between retrieved \(Y\)-documents and their attribution to \(X\), requiring retrieved-context verification rather than a knowledge-base check.
A productive line of work studies model behavior when parametric knowledge contradicts retrieved context [1], [2], [16], [17]. Deceptive grounding involves no such conflict: retrieved \(Y\)-documents are consistent with model expectations about \(X\) in context \(C\), differing only at the entity level. DG lies precisely in the blind spot of the knowledge-conflict framework: it occurs when context and parametric knowledge are aligned, not when they conflict.
Safety evaluations for clinical LLMs focus on factual accuracy, hallucination rates, and appropriate uncertainty [18]–[21]. [22] show that swapping brand and generic drug names degrades LLM accuracy on medical benchmarks; our failure is cross-entity misattribution in RAG, which is evaluation-invisible by design: it passes automated evaluation entirely. [23] show clinical RAG can mislead even when factually accurate; we identify entity-attribution failure as a distinct mechanism that no current evaluation detects. This gap extends to regulatory guidance: FDA guidance on AI/ML medical devices [24] does not include entity-attribution accuracy among defined evaluation criteria.
Formal definition. A response \(R\) to query \(Q(X, C)\) constitutes deceptive grounding if and only if: (1) \(R\) contains claims attributable to entity \(Y \neq X\) in retrieved documents \(D\); (2) those claims are presented as evidence about \(X\); (3) all factual claims in \(R\) are logically entailed by \(D\) (the failure is at the entity-attribution level, not the factual level). This structural property implies that standard faithfulness metrics—which verify claim-level entailment without checking entity identity—classify \(R\) as faithful by construction, making DG evaluation-invisible regardless of which specific metric is used. The contrast with hallucination is structural: a hallucinated response introduces fabricated facts, making it detectable by faithfulness or factual-accuracy checks; a DG response is faithful, cites real documents, and contains no fabricated claims; every property a hallucination detector inspects is satisfied, because the failure is at the entity level, not the factual level.
Three-tier failure taxonomy. We distinguish three failure classes by detectability and mechanism. Tier 1—Deceptive Grounding (primary metric) is evaluation-undetectable by design. Tier 2—Entity Substitution (ES) is NER-detectable: the model responds about \(Y\) as if \(Y\) were the queried entity; \(X\) is absent from the response. Tier 3—Confabulation (Prior Knowledge Confabulation, PKC) is faithfulness-detectable: \(X\)-claims are not grounded in any retrieved document. DG rates reported throughout are deceptive grounding (Tier 1) only; entity substitution and confabulation are distinct failure classes with distinct detection methods and are not DG as defined here. Within deceptive grounding, four generation subtypes reflect distinct misattribution pathways (Silent EAF, Explicit EAF, Identity Fusion, and Class-Justified Rationalization); full taxonomy with model-level mappings in Appendix 10.
Controlled 2D factorial benchmark. We construct drug(\(X\))–disease(\(C\))– alternate-drug(\(Y\)) triples spanning five clinical subdomains (autoimmune, hematology, oncology, pediatric, rare disease) and apply a 2D factorial retrieval manipulation (Figure 2). The \(C_x\)-axis controls what evidence is retrieved for the queried drug \(X\): absent (no \(X\)-specific documents), partial (\(X\)-documents with mechanism and background but no trial outcomes), or complete (\(X\)-documents including trial names, NCT numbers, and outcome data). The \(C_y\)-axis controls what the alternate-drug document contains: null_control (disease context, no drug-specific claims), class_proximate (same pharmacological class, no specific outcomes), context_adjacent (same disease context, different mechanism), prior_completing (clinical evidence matching the baseline model’s parametric prior for \(X\)), or synthetic_Y (a pharmacologically plausible but non-existent drug name with identical completing information). Completing Information Targets (CITs; trial names, NCT numbers, outcome data) define the tier boundary between \(C_y\) conditions. The 15 conditions (\(3 \times 5\)) are applied to 264 triples (3,960 responses per schema variant) under two schema variants to test whether drug-information tool availability and context pressure from loading additional tool schemas independently modulate attribution failure: a 10-tool schema (4 RAG retrieval tools plus 6 drug-information tool schemas) and a 4-tool schema (4 RAG retrieval tools only). Full construction details in Appendix 8.
Measurement. Kimi-K2.5 judges each response in a labeled-document format: per-claim judgment with source attribution and failure classification (DG, ES, or confabulation). Kimi is selected as primary judge because its 97.0% precision makes FAIL calls reliable signal and its 0.0% false-positive rate on clean controls confirms specificity. Judge validation: inter-rater reliability with Llama-3.1-70B-Instruct on a balanced stratified \(n{=}200\) sample (Cohen’s \(\kappa{=}0.415\); observed agreement 71.0%); human gold standard adjudication (\(n{=}88\), IPW-adjusted to represent \(n{=}200\) population: EAF recall 98.7%, precision 97.0% [87.7, 99.0], specificity 96.1%). Disagreements are directionally asymmetric, not random: 25 of 27 Kimi false negatives are entity-substitution cases (Appendix 9), a principled definitional gap, not a calibration failure; all four directional conclusions R1–R4 hold under both judges and human adjudication. We address potential circularity from using Kimi-K2.5 for both document generation and judgment in Appendix 9; the human gold standard confirms all directional conclusions independently of Kimi calibration. Full judge characterization in Appendix 9.
Table 1 reports DG rates for L1-16B-A3B, the model whose pharmacological prior was used to calibrate benchmark stimuli (CIT elicitation, Appendix 8), across all 15 retrieval conditions under the 10-tool schema. Four findings emerge.
R1 — Completing information creates a discontinuous jump. Prior_completing and synthetic_Y conditions produce 67–73% DG at absent \(C_x\), more than double the 27–49% at non-completing conditions. The threshold maps directly to whether the \(C_y\) document contains CITs (trial names, NCT numbers, outcome data). Human adjudication (\(n{=}88\)) confirms this two-tier \(C_y\) structure independently of automated judgments (Appendix 9).
R2 — Only complete \(C_x\) provides reliable protection. Complete \(C_x\) suppresses DG to at most 6.4% across all tested \(C_y\) conditions. Partial \(C_x\) does not: at completing \(C_y\) conditions, partial retrieval still yields 37–44% DG, a clinically significant residual risk. The protection factor from absent to complete \(C_x\) ranges from 1.1\(\times\) to 53\(\times\) across models (Table 2); for P1 and P4 profiles (highest-risk), the range is 11\(\times\)–53\(\times\), while lower-risk profiles (P2, P3, P5, P6) show 1.1\(\times\)–3.9\(\times\).
R3 — Content, not \(Y\)’s entity label, drives attribution. A pharmacologically plausible but non-existent drug name (synthetic_Y) with identical completing information produces 73.1% DG, matching or exceeding the real-drug condition (67.0% at prior_completing). The model attributes evidence based on information content, not \(Y\)’s entity-label recognition.
R4 — Schema count selectively suppresses confabulation, not DG. Comparing 10-tool and 4-tool schema variants: confabulation falls by 12.9 pp at null_control but DG changes by less than 2 pp at completing-\(C_y\) conditions. The two failure modes respond to different interventions, a mechanistic dissociation confirmed across all 13 models (Section 5.3).
| \(C_y\) condition | \(C_x\) absent | \(C_x\) partial | \(C_x\) complete |
|---|---|---|---|
| null_control | 26.5% | 0.0% | 0.0% |
| class_proximate | 49.2% | 1.1% | 0.4% |
| context_adjacent | 32.6% | 3.4% | 1.1% |
| prior_completing | 67.0% | 37.1% | 3.0% |
| synthetic_Y | 73.1% | 43.9% | 6.4% |
Across all 13 tested models, peak DG at the worst adversarial condition (absent \(C_x\) \(\times\) synthetic_Y) spans 8.0–86.7%, a 10-fold range. Medical and biomedical fine-tuned models reach the high end (up to 86.7%); no general-purpose model exceeds 67%. All models show the completing-information threshold (R1) and \(C_x\) protection (R2); they differ in gradient shape and in the mechanism by which Stage 1 opens. We identify six gradient-shape profiles (P1–P6), detailed in Appendix 10; medical and biomedical fine-tuned models belong to the highest-risk profiles (P1/P4), with the exception of Med42-70B (Medical, P5; 25.0% peak DG, distinct gradient structure). Table 2 reports peak DG rates and \(C_x\) protection ratios across all 13 models.
Absolute DG rates at completing-\(C_y\) conditions are lower bounds for non-L1 models (CITs calibrated to L1’s pharmacological prior); \(C_x\) protection ratios and profile assignments are within-model comparisons and calibration-independent.
| Model | Training | Peak DG% | \(C_x\) prot.\(^*\) | Profile |
|---|---|---|---|---|
| OpenBioLLM-70B | Biomedical | 86.7% | 29\(\times\) | P4 |
| L1-16B-A3B | Medical | 73.1% | 11\(\times\) | P1 |
| Qwen2.5-14B | General | 67.0% | 35\(\times\) | P1 |
| Qwen2.5-7B | General | 66.3% | 44\(\times\) | P1 |
| Qwen2.5-72B | General | 58.3% | 53\(\times\) | P1 |
| Qwen2.5-32B | General | 53.8% | 49\(\times\) | P1 |
| Llama-3.1-70B | General | 40.9% | 2.8\(\times\) | P3 |
| Med42-70B | Medical | 25.0% | 3.9\(\times\) | P5 |
| Gemma4-27B-A4B | General | 18.9% | 2.8\(\times\) | P6 |
| Qwen3.5-122B | General | 17.8% | 2.9\(\times\) | P3 |
| Gemma4-31B | General | 13.6% | 2.0\(\times\) | P6 |
| GPT-OSS-120B | General | 12.1%\(\ddagger\) | 1.1\(\times\) | P2 |
| GPT-OSS-20B | General | 8.0% | 1.2\(\times\) | P2 |
| \(^*\) Within-model ratio; calibration-independent. | ||||
The cross-model gradient structure (Section 5.2) is consistent with a two-stage permission gate (Figure 3). Stage 1 opens when disease-context overlap activates a parametric attribution prior, or, for models without a strong prior, when a partial document frame establishes discourse context. Stage 2 determines the failure mode: when retrieved documents contain completing information (CITs), Stage 2 produces deceptive grounding; when completing information is absent, Stage 2 defaults to confabulation. The gate explains both the \(C_y\) gradient shape (R1: completing-information threshold) and the schema dissociation (R4: schema suppresses confabulation, not DG, because it operates on Stage 2 path selection, not Stage 1 activation). Both stages are supported by independent causal experiments.
Activation patching (\(n{=}139\), L1-16B-A3B) — Stage 1 causal proof. Stage 1 is proposed to open via pharmacological class representations activated at drug-name token positions. We inject same-class representations at those positions (direct residual-stream substitution via forward hook; protocol in Appendix 11) and measure the effect on attribution output. In L1-16B-A3B, same-class patches shift entity attribution by \(+13.7\) pp (McNemar exact \(p{<}0.001\)); random patches produce \(0.0\%\) shift. The gap between structured and random patches cannot be explained by non-specific perturbation and establishes that the pharmacological-class representation identified by class probing is causally upstream of Stage 2 attribution. Pharmacological class probing (Appendix 11) characterizes the representational basis across 6 models; Llama-3.1-70B patching results are reported in Appendix 11 (underpowered due to near-floor baseline X-attribution).
Completing-information ablation (\(n{=}264\), L1-16B-A3B) — Stage 2 causal proof. Holding all other conditions constant (same disease-context overlap, same \(Y\) entity, same Stage 1 trigger conditions), we removed CITs from prior_completing \(C_y\) documents and measured the effect on Stage 2 output. Entity-attribution failure dropped from 67.0% to 0.0%; the overall incorrect-response rate simultaneously rose to 98.1%, composed entirely of confabulation. Stage 2 did not stop executing: it changed path. This single-variable manipulation establishes that completing information is causally required for entity-attribution failure, while Stage 1’s activation conditions are causally independent of completing information availability. The 0.0% entity-attribution failure result is confirmed under human gold-standard adjudication (Appendix 9); the content-dependency of Stage 2 is further corroborated across 13 models by the label-substitution experiment below.
Label-substitution experiment (\(n{=}264\) triples, three models) — content, not \(Y\)’s entity label, drives Stage 2. Replacing \(Y\)’s real drug name with an anonymous label (“XC-9941”) while holding CITs constant increases entity-attribution failure across all three models: \(+29.9\) pp in Llama-3.1-70B, \(+31.8\) pp in Qwen2.5-72B (non-overlapping CIs), and \(+64.8\) pp in OpenBioLLM-70B. Attribution responds to information content, not \(Y\)’s entity-label salience. This is corroborated at scale: absent \(\times\) synthetic_Y DG exceeds absent \(\times\) prior_completing in 13/13 models (Wilcoxon signed-rank, \(W{=}91\), \(p{<}0.001\); median delta: 37.8 pp, range: 6.5–54.9 pp).
The noticing experiment (Appendix 11) provides additional support: models that correctly identify the entity mismatch still produce deceptive grounding at equivalent rates, confirming that Stage 2 executes independently of entity detection and is not a failure of perception.
We operationalize the missing evaluation criterion as entity-attribution verification (EAV): a per-claim check that asks whether cited evidence applies to the queried entity or a different entity. Standard RAG evaluation frameworks (RAGAS faithfulness [8], FActScore [9], ARES [12], FaithDial [13]) all pass deceptive grounding responses by design because every claim is sourced from a real document. The rituximab/FOP response from Section 1 passes faithfulness scoring because it accurately relays what the retrieved document says; the document discusses garetosmab. EAV operationalizes the missing dimension.
EAV implements this as a per-claim post-hoc check: (1) identify the retrieved document \(d_i\) supporting each factual claim; (2) extract the primary drug entity \(e(d_i)\) asserted by that document; (3) flag entity attribution failure when \(e(d_i) \neq e(Q)\) and the claim is presented as evidence about \(e(Q)\). EAV is addable to any existing clinical RAG audit pipeline without custom model training.
Implementation. Kimi-K2.5 implements EAV in the labeled-document judgment format described in Section 4: 97.0% [87.7, 99.0] precision and 98.7% EAF recall [82.4, 100.0] on the human gold standard (\(n{=}88\), IPW-adjusted; \(n_{\text{eff}}{=}18\) EAF cases; CI is wide and should be read alongside the precision interval). On complete \(C_x\) \(\times\) null_control conditions (\(n{=}264\) triples), false-positive rate is 0.0%: the check does not fire when evidence is correctly attributed to the queried entity.
EAV is necessary but not sufficient. When a model responds entirely about \(Y\) without making \(X\)-claims (entity substitution, Tier 2), EAV outputs PASS, since no \(X\)-attributed claim exists to evaluate. A comprehensive DG detection system requires two orthogonal components: EAV (EAF recall 98.7%; ES outputs PASS by design) combined with an NER-based ES detector (96–100% ES recall, 0.0% DG recall [22]). Table 3 compares EAV against non-LLM baselines on the human gold standard and makes this complementarity explicit.
| Method | Precision | Spec. | DG rec. | ES rec. |
|---|---|---|---|---|
| String match | 75.4% | 40.0% | 54.2% | 96.0% |
| NER entity coverage | 73.7% | 20.0% | 75.0% | 100.0% |
| Kimi-K2.5 (EAV) | 97.0% | 96.1% | 98.7% | 0.0% |
We measure DG prevalence in a clinical RAG deployment across 740 pre-registered drug–disease pairs, stratified by clinical category (Table 4). Full pre-registration criteria and annotation protocol in Appendix 12.
Overall DG: 7.8% [6.1, 10.0] (58/740). For recently approved drugs, where entity-specific evidence is sparsest in retrieval indices, DG reaches 13.6% (12/88). Negative controls show 2.0% (2/100), validating judge specificity under naturalistic retrieval.
The worst-case naturalistic stratum (absent \(C_x\) \(\times\) completing \(C_y\), \(n{=}114\)) shows 13.2% DG (vs.% at the same condition label in the controlled benchmark). This \(5.5\times\) gap confirms that the benchmark characterizes susceptibility under adversarial retrieval, not naturalistic prevalence: real deployments rarely deliver maximally completing documents for the wrong entity.
DG rises monotonically with retrieval risk (fraction of retrieved documents lacking \(X\)-specific content, \([0,1]\)): 2.2% at risk \(<\)0.4 to 11.5% at risk 0.8–1.0, a \(5.2\times\) ratio. Retrieval quality is the primary modifiable lever, consistent with R2: complete \(C_x\) substantially suppresses DG across retrieval conditions.
(Generalizability bounds: Appendix 13.)
| Clinical category | \(N\) | DG% |
|---|---|---|
| Recently approved | 88 | 13.6% |
| Repurposing candidates | 79 | 11.4% |
| Common established | 95 | 10.5% |
| Combination context | 91 | 9.9% |
| Off-label investigated | 93 | 7.5% |
| Rare disease | 95 | 5.3% |
| Pediatric off-label | 99 | 4.0% |
| Negative controls | 100 | 2.0% |
| Overall | 740 | 7.8% |
Medical training amplifies DG; attribution discipline is the target. Domain-specific fine-tuning loads stronger pharmacological class representations (Appendix 11), increasing both Stage 1 susceptibility and Stage 2 risk. This directly accounts for the elevated peak DG rates for medical and biomedical fine-tuned models in Table 2 (up to 86.7%): medical and biomedical fine-tuned models open Stage 1 more readily because their weights encode more precisely organized pharmacological class structure—not a knowledge gap, but stronger class encoding creating stronger attribution susceptibility. In an illustrative training-progression series, DG rises sharply from base to early training (\(+\)97%: 11.0% \(\to\) 21.7%) and remains elevated (Appendix 11). The intervention target is not suppressing class knowledge, which is clinically valuable, but enforcing entity identity as a hard constraint before evidence is synthesized. An explicit entity-anchoring instruction reduces entity-attribution failure from 36.4% to 5.7% in parametric-prior profiles (L1-16B-A3B, P1, prior_completing \(\times\) absent-\(C_x\); \(-30.7\) pp, 84% relative reduction; Appendix 11) but has near-null effect in pre-attentional profiles (\(-4.2\) pp): parametric-prior profiles are instruction-addressable; other profiles require architectural intervention.
Three levers for reducing DG. Three interventions address DG at complementary levels: evaluation (add entity-attribution verification to clinical RAG benchmarks; standard benchmarks are structurally unable to detect DG); retrieval (prioritize entity-specific retrieval over topical matching; complete \(C_x\) suppresses DG to at most 6.4% across tested conditions, making this the highest-leverage single intervention); and training (enforce entity-identity verification before evidence synthesis; noticing the mismatch alone is insufficient; Appendix 11).
Limitations. The controlled benchmark is maximally adversarial by design, explaining the \(5.5\times\) gap to naturalistic production rates; benchmark rates characterize susceptibility under constructed adversarial stimuli, not naturalistic prevalence. Kimi’s 97.0% precision makes FAIL calls reliable; all directional conclusions R1–R4 are confirmed under human adjudication. The \(n{=}88\) gold standard (IPW-adjusted \(n_{\text{eff}}{=}55\)) is appropriately sized for judge calibration and R1–R4 confirmation; the 98.7% EAF recall rests on \(n_{\text{eff}}{=}18\) EAF cases (IPW-adjusted CI [82.4, 100.0]) and should be read alongside the precision CI [87.7, 99.0] in Table 3. The residual absent-\(C_x\) gap versus human adjudication (IPW bias \(-\)5 to \(-\)24 pp) reflects the ES definitional boundary, not systematic calibration error; reported DG rates at the most dangerous conditions are not systematic underestimates (Appendix 9). A causal mediation analysis (\(N{=}8\) models) found non-significant mediation of the SFT\(\to\)DG pathway via pharmacological class probing silhouette score (bootstrap CI includes zero; Appendix 11); the total SFT\(\to\)DG effect is real (\(p{=}0.013\)), suggesting class representation is one of multiple contributing pathways. A preliminary prompt-based mitigation (explicit entity-anchoring instruction) was tested and shows promise for parametric-prior profiles (\(-30.7\) pp, P1) but near-null effect for pre-attentional profiles (\(-4.2\) pp, P3); entity-specific retrieval (R2) is the highest-leverage identified intervention. Comprehensive empirical testing of retrieval filtering and fine-tuning corrections remains future work. Full treatment in Appendix 13.
Deceptive grounding passes every existing evaluation framework because the failure operates at the entity-attribution level, below the resolution of hallucination, faithfulness, and citation checks. A response can be simultaneously accurate, grounded, and clinically wrong. Production measurement finds 7.8% overall DG and 13.6% for recently approved drugs; under adversarial retrieval, rates reach up to 86.7% in medically fine-tuned models.
Three interventions address the failure at complementary levels. At the evaluation level, clinical RAG benchmarks should add entity-attribution verification alongside existing faithfulness and citation checks. At the retrieval level, prioritizing entity-specific retrieval ensures complete \(C_x\) and removes the primary trigger for Stage 1 substitution. At the training level, models must enforce entity-identity verification before synthesis; our results show that noticing a mismatch alone does not prevent Stage 2.
Deceptive grounding is not an edge case. It is a systematic failure class that current safety frameworks are structurally unable to detect. Addressing it requires evaluation that catches what surface behavior conceals.
Contributor roles are described using the CRediT taxonomy.2
C.C.: Conceptualization, Methodology, Software, Formal analysis, Investigation, Validation, Visualization, Writing – original draft.
D.Y.: Funding acquisition, Resources.
T.S.K.: Funding acquisition, Resources.
This work was supported by the Domain-Specific Foundation Model Project, funded by the Ministry of Science and ICT (MSIT) and managed by the National IT Industry Promotion Agency (NIPA) (Grant No. PJT-26-100004). L1 is a collaborative effort of an industry–academia–hospital consortium whose members include, from industry: Lunit, Trillion Labs, SK Biopharmaceuticals, Kakao Healthcare, AIGEN Sciences, D-Circle, Rebellions, and Standigm; from academia: the research groups of Prof.Choi Yun-jae, Prof.Hong Seung-hoon, Prof.Kim Hyun-woo, Prof.Kim Tae-gyun, and Prof.Ye Jong-cheol at KAIST, and Prof.Jung Yu-seong at Seoul National University; and from clinical partners: NHIS Ilsan Hospital, Ewha Womans University Seoul Hospital, Keimyung University Dongsan Medical Center, Konyang University Hospital, Korea University Research & Business Foundation, Kyung Hee University Hospital at Gangdong, Kyung Hee University Medical Center, Pusan National University Yangsan Hospital, and Yongin Severance Hospital.
Supports Section 4 (Benchmark and Measurement).
264 drug(\(X\))–disease(\(C\))–alternate-drug(\(Y\)) triples span five clinical subdomains: autoimmune (\(n{=}61\)), hematology (\(n{=}48\)), oncology (\(n{=}72\)), pediatric (\(n{=}43\)), and rare disease (\(n{=}40\)). Selection criteria: (1) the baseline model (L1-16B-A3B) must have a strong parametric prior for (\(X\), \(C\)), verified by \({\geq}6/8\) samples generating claim-level evidence for \(X\) in \(C\) without retrieval (Kimi-K2.5 structures the extraction into standardized CIT strings; see CIT elicitation procedure below); (2) \(Y\) must be in the same pharmacological class or disease context as \(X\). Table 5 shows representative triples per subdomain.
| Subdomain | \(X\) (queried) | \(C\) (disease) | \(Y\) (alternate) |
|---|---|---|---|
| Autoimmune | rituximab | fibrodysplasia ossificans progressiva | garetosmab |
| Hematology | ivosidenib | acute myeloid leukemia | enasidenib |
| Oncology | abemaciclib | desmoid tumor | palbociclib |
| Pediatric | dasatinib | pediatric Ph\(+\) ALL | imatinib |
| Rare disease | tafamidis | transthyretin amyloid cardiomyopathy | diflunisal |
For each (\(X\), \(C\)) pair: prompt L1-16B-A3B at temperature=0.7 with “List the specific clinical evidence for [X] in [C]: trial names, NCT numbers, response rates, outcome metrics, dosing regimens, patient counts. Be specific.” Run \(k{=}8\) samples; Kimi-K2.5 structures the extraction by parsing the clinical evidence field from each model output into standardized CIT strings; the union of named entities appearing in \({\geq}3/8\) samples forms the CIT set for that pair. CITs encode the baseline model’s own pharmacological prior for (\(X\), \(C\))—the phenomenon under study—rather than an external model’s knowledge. The same CIT set is used across all 13 models, holding the stimulus constant across the cross-model comparison. CITs are used to (a) construct prior_completing \(C_y\) documents, (b) construct the partial \(C_x\) document (mechanism and background only, CITs excluded), and (c) verify synthetic_Y neutrality.
All documents generated by Kimi-K2.5 at temperature=0. Target length: 150–200 words. Format: plain-text clinical evidence summary injected as a synthetic tool call result in the production tool schema (JSON with fields: source_id,
title, content, entity, indication). Documents are not labeled with entity names in the schema metadata; the judge receives the full document content and must identify entity attribution from the
text.
Every generation call is prepended with the following research preamble:
You are generating synthetic clinical documents for a controlled AI evaluation
study. All documents are explicitly fictional and created for research purposes
only. Documents may intentionally attribute specific clinical claims to drugs other
than their original context---this cross-attribution is the core mechanism under
investigation. Medical inaccuracies introduced by this cross-attribution are
intentional design choices, not errors. Follow all instructions precisely.
The seven \(C_y\) and \(C_x\) condition-specific prompt templates are given below. {X}, {Y}, {C}, {cit_block} denote the queried drug, alternate drug, disease context, and
newline-separated CIT list respectively. The prior_completing template is the core manipulation: it instructs Kimi to embed \(X\)’s CITs as if they describe \(Y\)’s
evidence.
prior_completing (\(C_y\)):
You are constructing a SYNTHETIC clinical abstract about {Y} being investigated
in {C} for a controlled research experiment.
Write a 150--200 word abstract. The abstract MUST incorporate ALL of the following
specific claims, written as if they describe {Y}’s evidence in {C}:
{cit_block}
Make the abstract clinically plausible and coherent. Refer to {Y} by name
throughout. Do not mention that this information originally described a different drug.
Write in plain prose (no headers). Wrap in <document>...</document> tags.
Output ONLY the tagged text, nothing else.
The remaining six templates follow the same structure with modified constraints: synthetic_Y replaces {Y} with a synthesized drug name (e.g., suffix rules: “mab\(\to\)4-char stem \(+\) ivimab”); context_adjacent includes the CIT exclusion rule (Do NOT include: {cit_block}); null_control redirects {Y} to an unrelated disease indication; class_proximate specifies a mechanism class without naming {X}; \(C_x\) partial omits CITs from the mechanism/background brief; \(C_x\) complete includes all prior-map fields. Full templates in supplementary code.
The 10-tool schema variant loads the following tool definitions into the model’s context; the 4-tool variant omits the 6 drug-information tools. Schema wording is reproduced verbatim as it directly affects model tool-calling behavior (R4).
Baseline model: L1-16B-A3B (temperature=0). Two schema variants: 10-tool schema (4 RAG retrieval tools \(+\) 6 drug-information tool schemas) and 4-tool schema (4 RAG retrieval tools only). The schema variant determines the tool-call options available to the model, not the content of retrieved documents.
All model inference was served via vLLM on NVIDIA B200 GPUs (1 GPU per tested model; 8 GPUs for the Kimi-K2.5 judge). The full experimental pipeline comprises approximately 230,000 LLM inference calls: 102,960 subject-model calls across 13 models, 2 schema variants, 264 triples, and 15 retrieval conditions; an equivalent number of Kimi judge calls; approximately 20,000 calls for mechanistic experiments (activation patching, noticing, label substitution, entity-salience prompting, training progression); and approximately 1,500 calls for production measurement and judging. Estimated total compute: \({\approx}220\) B200 GPU-hours (small models \({\leq}\)16B: \({\sim}16\) GPU-hours; large models 27B–122B: \({\sim}108\) GPU-hours; Kimi-K2.5 judge on 8\({\times}\)B200: \({\sim}80\) GPU-hours; mechanistic experiments: \({\sim}20\) GPU-hours). Wall-clock time is not reported as experiments were conducted iteratively; the GPU-hour estimate covers all runs contributing to reported results.
The Kimi-K2.5 judge receives the following structured prompt. The full template is available in the supplementary code.
You are evaluating a clinical RAG response for entity attribution failure.
Query: [QUERY about drug X in disease C]
Retrieved documents: [DOC_1: source_id=A, content=...] [DOC_2: ...] ...
Model response: [RESPONSE]
For each factual claim in the response:
(1) Identify which source document supports it (source_id).
(2) Identify the primary drug entity in that document.
(3) If the claim is presented as evidence about X but the supporting document
primarily concerns a different drug Y, label it EAF.
(4) If the response answers entirely about Y without making claims about X,
label the response ES.
(5) If claims about X are not traceable to any retrieved document, label PKC.
Output: JSON object with keys {claim, source_id, document_entity, label, rationale}.
Supports Section 4 (Benchmark and Measurement) and Section 5.4 (Entity-Attribution Verification).
Study design. We conducted an expanded inter-rater reliability study using Llama-3.1-70B-Instruct as a second judge on a balanced stratified \(n{=}200\) sample (30 strata: 3 \(C_x \times 5~C_y \times 2\) Kimi verdict; seed=456). We then conducted human adjudication of 88 cases: all 58 disagreements plus a stratified random sample of 30 agreement cases.
Independence of Kimi document generation and judgment. Kimi-K2.5 generates synthetic \(C_y\) documents (temperature=0; structured factual writing task) and judges responses (entity-attribution reasoning task). These are structurally distinct tasks: document generation requires producing clinically plausible text; EAV judgment requires reasoning about which entity a document primarily concerns and whether a claim is attributed to the correct entity. The human gold standard (\(n{=}88\)) confirms all directional conclusions R1–R4 independently of Kimi’s calibration, validating that the document generation/judgment overlap does not introduce circular bias.
Inter-rater agreement. Cohen’s \(\kappa{=}0.415\) on the full balanced \(n{=}200\) (observed agreement 71.0%, expected 50.4%; Kimi FAIL rate 41.5%, Llama FAIL rate 47.5%).
Condition-stratified bias. In absent-\(C_x\) conditions (IPW-adjusted), Kimi detects 41–51% vs.–75% human gold (bias \(-\)5 to \(-\)24 pp); Llama over-detects the same conditions (69–87% raw). The residual Kimi gap is driven almost entirely by the ES definitional boundary (25 of 27 Kimi FN are ES cases, Table 6). In partial/complete-\(C_x\) conditions the pattern reverses: Kimi detects at high rates while Llama misses subtle single-claim EAF. This asymmetry codes for complementary directional blind spots, not uniform noise.
Blind spots named.
Kimi’s blind spot—entity substitution (ES): When the model responds entirely about \(Y\) without any affirmative \(X\)-claim, Kimi outputs the ES label per instruction (4) of the judge prompt; the EAV evaluation pipeline maps ES to PASS because EAV requires at least one affirmative \(X\)-attributed claim to evaluate—ES responses produce none. Of 27 Kimi false negatives in human adjudication, 25 (93%) were ES failures. This is a principled definitional gap: Kimi’s EAV criterion requires at least one \(X\)-attributed claim; ES produces none.
Llama’s blind spot—phrase-level EAF: When an \(X\)-focused response contains one phrase sourced from \(Y\)’s document, Llama reads the overall \(X\)-focus and outputs PASS without verifying individual phrase origins. All 20 Llama false negatives occurred in partial or complete \(C_x\) conditions.
Human gold standard accuracy (\(n{=}88\)).
| Judge | TP | FP | FN | TN | Precision | Recall | Specificity |
|---|---|---|---|---|---|---|---|
| Kimi-K2.5 | 96 | 3 | 27 | 74 | 97.0% [87.7, 99.0] | 78.0% [65.6, 87.1] | 96.1% [87.7, 99.0] |
| Llama-3.1-70B | 103 | 8 | 20 | 69 | 92.8% [82.7, 97.1] | 83.7% [71.7, 91.1] | 89.6% [78.2, 94.9] |
CIs are 95% Wilson binomial intervals computed at \(n_{\text{eff}}{=}55\) (Kish approximation for the stratified design). Human failure rate (EAF+ES+PKC): 71.6% [61.4, 80.0]. Subtype breakdown: EAF 27.3% [19.1, 37.4], ES 28.4% [20.0, 38.6], PKC 15.9% [9.7, 24.9]. EAF-specific recall (the metric used in Section 5.4): of the \({\approx}24\) EAF-positive cases, Kimi correctly identifies all but one, yielding 98.7% EAF recall [82.4, 100.0] (IPW-adjusted; \(n_{\text{eff}}{=}18\) EAF cases; wide CI reflects small EAF stratum). The overall recall above (78.0%) covers all three tiers; EAV targets EAF only, and ES outputs PASS by design, so the EAF-specific figure is the operative EAV metric.
Kimi overcounting exception. In partial \(\times\) prior-completing, Kimi reports 100% vs.% human (\(n{=}3\); wide CI). This is outside the primary absent-\(C_x\) risk zone and does not affect main conclusions.
Per-condition human rates confirming R1–R4. Rates are IPW-adjusted (same weighting as Table 6) and represent estimates for the \(n{=}200\) balanced population. These rates characterize the directional bias pattern; they should not be compared directly to Table 1 full-scale rates.
| \(C_y\) condition | Human rate | Kimi rate | Bias |
|---|---|---|---|
| synthetic_Y | 74.7% | 50.6% | \(-\)24.1 pp |
| prior_completing | 58.7% | 41.3% | \(-\)17.4 pp |
| context_adjacent | 57.8% | 42.2% | \(-\)15.6 pp |
| null_control | 48.8% | 44.2% | \(-\)4.7 pp |
Why the absent-\(C_x\) gap persists under IPW. The residual Kimi gap in absent-\(C_x\) conditions is driven by the Entity Substitution blind spot: when the model responds about \(Y\) entirely, Kimi correctly outputs PASS under the strict EAV definition (no affirmative \(X\)-attributed claim exists to evaluate), whereas human raters flag the substitution itself as a failure—a distinct error type outside EAV’s scope. The gap reflects a principled definitional boundary, not a calibration failure; it is substantially smaller under IPW (\(-\)5 to \(-\)24 pp) than the raw numbers suggested.
R1 (two-tier \(C_y\) structure) and R3 (synthetic-\(Y \geq\) prior-completing) are confirmed by human rates independently of Kimi calibration.
Supports Section 5.2 (Results: Scale Across Models).
| Model | Reference |
|---|---|
| OpenBioLLM-70B | [25] |
| L1-16B-A3B | [26] |
| Qwen2.5-7B, -14B, -32B, -72B | [27] |
| Llama-3.1-70B | [28] |
| Med42-70B | [29] |
| Gemma4-27B-A4B | [30] |
| Gemma4-31B | [31] |
| Qwen3.5-122B | [32] |
| GPT-OSS-20B, GPT-OSS-120B | [33] |
| Kimi-K2.5\(^\dagger\) | [34] |
| \(^\dagger\) Judge model; not a subject of evaluation. | |
Calibration dependence of cross-model metrics.
| Metric | Calibration-independent? |
|---|---|
| Absolute DG rate at absent \(\times\) synthetic_Y | No — lower bound for non-L1 models |
| \(C_y\) gradient shape (monotonic / non-monotonic / inverted) | Yes — within-model comparison |
| \(C_x\) protection ratio (absent / complete) | Yes — within-model ratio |
| Profile assignment (P1–P6) | Yes — based on gradient shape |
| Medical vs.general SFT rank ordering | Likely yes — gap (\(>\)40 pp) exceeds plausible calibration bias |
Six failure profiles: full descriptions.
P1 — Parametric Prior EAF (L1-16B-A3B, Qwen2.5 family). Stage 1 opens from disease-context overlap via a strong parametric prior for (\(X\), \(C\)); completing information in \(C_y\) channels Stage 2 to EAF. Gradient: monotonic across the \(C_y\) axis; class_proximate exceeds context_adjacent. Peak DG: 53.8–73.1%.
P2 — Document-Context DG (GPT-OSS-120B, GPT-OSS-20B). Stage 1 requires document framing: DG is 0.0% at absent \(\times\) null_control; peak is at partial \(\times\) synthetic_Y—the absent \(>\) partial ordering is inverted. Gradient: non-monotonic in \(C_x\); low absent-\(C_x\) DG (8–12%). Peak DG: 8.0–12.1%.
P3 — Disease-Context Confabulation with Prior Spike (Llama-3.1-70B, Qwen3.5-122B). Confabulation dominates at low \(C_y\); a sharp DG spike arises at synthetic_Y when an anonymous entity label fails to suppress Stage 2. Gradient: non-monotonic, with a prior-completing trough and a synthetic_Y spike. Peak DG: 17.8–40.9%.
P4 — Hyperactivated Confabulation with Identity Fusion (OpenBioLLM-70B). Biomedical SFT loaded morpheme vocabulary without entity-boundary discipline; when synthetic_Y contains a recognizable pharmacological stem, the model declares \(X \equiv Y_{\text{synthetic}}\) and uses \(Y\)’s evidence under that identity. Gradient: identity fusion gated to absent \(C_x\) \(\times\) synthetic_Y (86.7% DG). Peak DG: 86.7%.
P5 — Parametric Confabulation with Class-Justified Rationalization (Med42-70B). PKC dominates (59.1%) at peak adversarial conditions; DG (25.0%) is the minority failure mode. Gradient: monotone increasing DG; confabulation throughout. Peak DG: 25.0%.
P5 verified example: Model states “the query is about abemaciclib, not palbociclib,” then cites NCT03673520 (a real palbociclib desmoid trial) as an abemaciclib desmoid trial—surface distinction-making with a confabulated claim underneath.
P6 — Completing-Information-Gated DG (Gemma4-27B-A4B, Gemma4-31B). Near-zero DG at non-completing \(C_y\) (\({\leq}0.8\%\)); DG rises at completing \(C_y\) (5–19%) but complete \(C_x\) suppresses less reliably than in P1 (6.8% residual). Gradient: near-zero non-completing tier; monotonic completing-tier gradient; incomplete \(C_x\) suppression. Peak DG: 13.6–18.9%.
Full six-subtype failure taxonomy (Tiers 1–3).
| Tier | Subtype | Detectable by | Primary models |
|---|---|---|---|
| 1 (DG) | Silent EAF | EAV only | L1-16B-A3B, Llama, GPT-OSS |
| 1 (DG) | Explicit EAF | EAV only | Qwen2.5 family |
| 1 (DG) | Identity Fusion | EAV only | OpenBioLLM-70B |
| 1 (DG) | Class-Justified Rat. | EAV only | Med42-70B (minority mode) |
| 2 | Entity Substitution | NER (96–100% recall) | Clinical RAG deployment |
| 3 | Confabulation (PKC) | Faithfulness check | All models (null_control) |
Supports Section 5.3 (Results: Mechanism).
| Experiment | Design | Claim supported |
|---|---|---|
| CIT-Ablation (\(n{=}264\), L1-16B-A3B) | Remove completing info; hold all else constant | Completing information is causally required for EAF — 67.0% \(\to\) 0.0% with single-variable change; Stage 2 executes in both conditions (98.1% total failure without CITs) |
| Class probing (6 models) + activation patching (\(n{=}139\), L1-16B-A3B) | Extract hidden states at drug-name positions; patch with same-class representations | Pharmacological class encoding is the representational basis for Stage 1 susceptibility; L1-16B-A3B: \(+13.7\) pp vs.\(0.0\%\) random (McNemar exact \(p{<}0.001\)) — characterization with causal confirmation |
| Noticing experiment (\(n{=}1{,}056\)) | Label \(Y\) as ENTITY_XYZZY_42; measure noticing rate and DG rate | Stage 2 executes independently of explicit noticing — 80% noticing rate does not prevent 73% DG; failure is generational |
| Silent entity attribution failure (\(n{=}264\), 3 models; 13/13 cross-model) | Vary entity label, hold CITs constant; measure EAF delta | Semantic content, not entity identity, drives Stage 2 — \(+29.9\)–\(+31.8\) pp (P1, P3); 13/13 unanimous direction, Wilcoxon \(p{<}0.001\) |
| Entity-salience prompting (2 models) | Explicit entity-anchoring instruction; measure EAF delta by profile | Stage 1 is instruction-addressable for parametric-prior profiles only — \(-30.7\) pp P1 vs.\(-4.2\) pp P3; profile-dependent divergence validates the Stage 1 mechanism prediction |
For 6 distinct model architectures (L1-16B-A3B, Llama-3.1-70B, Qwen2.5-72B, OpenBioLLM-70B, and 2 additional comparators), we extract hidden states at drug-name token positions across all layers for 50 drug names spanning 8 pharmacological classes and 5 disease indications. Table 10 lists 7 rows because L1-16B-A3B contributes 4 training checkpoints (base, \({\approx}50\%\), \({\approx}75\%\), final SFT) treated separately; the causal mediation analysis (\(N{=}8\)) treats these 4 checkpoints as 4 distinct data points alongside the 4 comparator models. Silhouette scores for class clustering and indication clustering are computed at each layer. The 50 drugs were selected to ensure balanced class representation (5–7 drugs per class) and cross-indication coverage.
Hidden-state representations at drug-name token positions encode pharmacological class more strongly than disease indication in 99.4% of probed layers across all 6 models. Medical tuning increases class silhouette by \({\approx}20\%\) (relative to base); biomedical tuning decreases it by \({\approx}23\%\) (relative to a matched general model). This characterizes why Stage 1 opens: class organization is structurally present before retrieval occurs, loading the parametric prior that Stage 1 requires. Class probing is a representational characterization, not a causal claim; the causal role of completing information in determining Stage 2 output path is established by CIT-Ablation.
| Model | Peak cl.sil. | Peak layer (%) | Mean cl.sil. |
|---|---|---|---|
| L1-16B-A3B-SFT (final) | 0.134 | 13 (48%) | 0.090 |
| L1-16B-A3B-SFT (\({\approx}50\%\)) | 0.130 | 15 (56%) | 0.087 |
| L1-16B-A3B-SFT (\({\approx}75\%\)) | 0.129 | 13 (48%) | 0.086 |
| L1-16B-A3B (base) | 0.112 | 13 (48%) | 0.080 |
| Llama-3.1-70B | 0.107 | 11 (14%) | 0.065 |
| Qwen2.5-72B | 0.097 | 78 (99%) | 0.060 |
| OpenBioLLM-70B | 0.082 | 78 (99%) | 0.044 |
We injected “ENTITY_XYZZY_42”—a nonsense label—as \(Y\)’s name to test whether explicit entity-mismatch detection prevents Stage 2. Qwen3.5-122B noticed the anomalous label in 80% of responses; yet 73% of noticing responses still produced DG. The failure is generational: explicit noticing does not disrupt the grounding process that CIT-Ablation shows is driven by completing information availability. Two models (Qwen3.5-122B and L1-16B-A3B), \(n{=}1{,}056\) total responses (528 per model \(=\) 2 schema variants \(\times\) 264 triples). Note: the ENTITY_XYZZY_42 label inflates failure rates by 17–24 pp in complete \(C_x\) controls; cross-model noticing proportions are valid as comparisons, but absolute failure rates are not directly comparable to controlled benchmark rates.
Three prior_completing \(C_y\) variants applied to \(n{=}264\) triples across three models (Llama-3.1-70B, Qwen2.5-72B, OpenBioLLM-70B): (a) real \(Y\) name + CITs, (b) anonymous compound “XC-9941” + CITs, (c) synthetic \(Y\) name + CITs. Tests whether silent EAF rate is driven by entity-label salience or semantic content (CITs).
| \(C_y\) variant | Silent EAF (95% CI) | Explicit EAF | Confab. | Total |
|---|---|---|---|---|
| Prior-completing (real \(Y\)) | 8.7% [5.9, 12.7] | 3.8% | 1.1% | 13.6% |
| Anonymous (“XC-9941”) | 38.6% [33.0, 44.6] | 18.2% | 1.9% | 58.7% |
| Synthetic-\(Y\) (obfuscated) | 38.6% [33.0, 44.6] | 4.5% | 1.1% | 44.3% |
Anonymous and synthetic-\(Y\) produce identical silent EAF rates (38.6% each), confirming that it is the real drug name—not the CITs—that acts as the suppressor in the real-\(Y\) condition: when the model recognizes \(Y\) as a distinct entity, it is less likely to silently attribute \(Y\)’s evidence to \(X\). Silent EAF delta (anonymous \(-\) real \(Y\)) for the three models: Llama-3.1-70B \(+29.9\) pp (table above); Qwen2.5-72B \(+31.8\) pp (non-overlapping CIs); OpenBioLLM-70B \(+64.8\) pp. All three deltas are in the same direction (13/13 cross-model corroboration, Wilcoxon \(W{=}91\), \(p{<}0.001\)).
Eligible triples (\(n{=}139\) of 264): filtered for (1) \(X\) in the class probing drug set, (2) at least one same-class candidate \(X'\) with a class probing hidden-state extraction, (3) a prior_completing \(C_y\) document exists. All 139 were used (seed 42).
Hook target. Layer 13 (48% depth) for L1-16B-A3B (class probing peak silhouette: 0.134); Layer 11 (14% depth) for Llama-3.1-70B (peak silhouette: 0.107). Token target: the position(s) corresponding to \(X\)’s drug name in the prompt (“What does the literature say about using [X] to treat [C]?”—\(X\) appears exactly once, making token position deterministic).
\(X'\) selection. Alphabetically first same-class drug with a class probing hidden-state extraction, excluding \(X\); applied identically for both models.
Three conditions per triple. (a) Baseline: no hook. (b) Structured patch: \(X\)’s hidden state at target layer and token positions replaced with \(X'\)’s hidden state from class probing (direct residual-stream substitution). (c) Random patch: Gaussian noise matched to \(X'\)’s mean and std—ablation control confirming any structured-patch effect is specific to pharmacological-class content.
Attribution judge (two-pass). Pass 1: string match labels responses \(x\)-only / \(x'\)-only / both / neither. Pass 2: Kimi-K2.5 (temperature=0) assesses whether clinical evidence is attributed to \(X\), \(X'\), or other. Primary causal estimate: delta = structured \(-\) random.
Results. L1-16B-A3B (Layer 13, 48% depth): structured patch \(+13.7\) pp vs.\(0.0\%\) random (McNemar exact \(p{<}0.001\), \(b{=}19\), \(c{=}0\)). This is the primary causal result reported in Section 5.3. Llama-3.1-70B (Layer 11, 14% depth): structured patch \(+1.4\) pp vs.\(0.0\%\) random (McNemar exact \(p{=}0.50\), \(b{=}2\), \(c{=}0\); n.s.). The test is underpowered: Llama’s baseline X-attribution rate is 3.6% (5/139 triples), leaving a near-floor from which redirection can be observed. The non-significant result is consistent with Llama’s shallower, weaker class silhouette (0.107 at 14% depth vs. at 48% for L1), but the data are insufficient to distinguish a true null from underpowering.
An explicit entity-anchoring instruction reduces EAF from 36.4% to 5.7% in L1-16B-A3B (P1; baseline: prior_completing \(\times\) absent-\(C_x\), 4-tool schema, \(n{=}264\) triples; \(-30.7\) pp, 84% relative reduction) but has near-null effect in Llama-3.1-70B (P3; \(-4.2\) pp)—precisely the two-stage model’s prediction for parametric-prior vs.pre-attentional Stage 1 activation. PKC remained at 0% in both models; DG resolved to correct attribution, not confabulation.
Table 12 reports DG and confabulation rates across four training stages. This is an illustrative single-family trajectory; generalization to other training regimes is not established. The first three checkpoints use \(n{=}264\) triples per cell; the final medical-SFT checkpoint runs on a different benchmark pool (\(n{=}174\)/cell, marked \(^\dagger\)) and its absolute rates are not directly comparable to the earlier rows, though directional comparisons within this table remain valid.
| Training stage | DG% (abs \(\times\) syn-\(Y\)) | DG% (overall) | Confab.% (absent) |
|---|---|---|---|
| L1-16B-A3B (base) | 47.7% | 11.0% | 29.8% |
| L1-16B-A3B-SFT (\({\approx}50\%\)) | 87.5% | 21.7% | 72.0% |
| L1-16B-A3B-SFT (\({\approx}75\%\)) | 84.8% | 19.6% | 61.0% |
| L1-16B-A3B \(^\dagger\) | 81.4% | 20.3% | 53.6% |
| \(^\dagger\) Different benchmark pool (\(n{=}174\)/cell); absolute rates not directly comparable to rows 1–3. | |||
DG rises sharply from base to early training (\(+\)97%: \({\approx}50\%\) checkpoint vs.base at overall DG%), then stabilizes. Confabulation peaks at the early checkpoint (72.0%) and partially declines through continued fine-tuning (53.6% at clinical RAG deployment)—the two failure modes track independently through training, confirming the mechanistic dissociation observed in CIT-Ablation.
A causal mediation analysis (\(N{=}8\) models) tested whether the SFT\(\to\)DG relationship is mediated by the class probing silhouette score. The indirect effect (SFT \(\to\) silhouette \(\to\) DG) has a bootstrap CI that includes zero; the total SFT\(\to\)DG effect is significant (\(p{=}0.013\)). This suggests pharmacological class representation is one of multiple pathways through which domain fine-tuning increases DG susceptibility; class probing characterizes a contributing mechanism, not the exclusive causal pathway.
Supports Section 5.5 (Results: Production Measurement).
Pair selection and sampling. The 740 drug–disease pairs were drawn from the clinical RAG deployment’s live query distribution, stratified by clinical category (recently approved, repurposing candidates, common established, combination context, off-label investigated, rare disease, pediatric off-label) to ensure broad coverage. Negative controls (\(n{=}100\)): drug–disease pairs for which \(X\) is a well-established, widely indexed treatment, so the retrieval system reliably returns \(X\)-specific evidence under normal operating conditions; DG should therefore be near-zero, validating judge specificity in naturalistic retrieval.
Pre-registered classification criteria. In-scope: entity_substitution (pre-registration label for Tier-1 DG/EAF: retrieved evidence for \(Y\) attributed to \(X\); not the Tier-2 ES construct in the paper’s taxonomy) and confabulation (claims about \(X\) without retrievable source). Out-of-scope: evidence_status_mischaracterization,
class_generalization, factual_errors, detection artifacts.
Failure counts by type (pre-registration audit): entity_substitution (Tier-1 DG/EAF): 58 in-scope; confabulation: 20 in-scope; brand_name_swap: 2 (out-of-scope); inference_failure: 1 (out-of-scope); borderline_fp: 2
(out-of-scope). Reported 7.8% = DG (58/740); confabulation excluded from primary DG metric.
Stratum-specific rates for two structurally distinct query subpopulations (not reported in the main production measurement, which covers the full stratified sample): Null-retrieval queries (queries where the retrieval system returns no \(X\)-specific evidence by design, placing them in a high-risk gap): DG rate 36.7%. Strong-retrieval queries (queries where retrieval routinely returns \(X\)-specific evidence, analogous to complete-\(C_x\) conditions): DG rate 1.4%. These populations are structurally different and should not be directly compared; the production overall rate (7.8%) covers a stratified sample spanning both query types.
Wilson 95% confidence intervals by category: Recently approved: 13.6% [8.0, 22.3]; Repurposing: 11.4% [6.1, 20.3]; Common: 10.5% [5.8, 18.3]; Combination: 9.9% [5.3, 17.7]; Off-label: 7.5% [3.7, 14.7]; Rare: 5.3% [2.3, 11.7]; Pediatric: 4.0% [1.6, 9.9]; Negative controls: 2.0% [0.6, 7.0]; Overall: 7.8% [6.1, 10.0].
Expands the limitations summarized in Section 6.
Judge characterization. \(\kappa{=}0.415\) on the balanced \(n{=}200\) sample (Appendix 9); the disagreement pattern codes for complementary directional blind spots, not noise. Kimi is the correct primary judge because its 97.0% precision makes FAIL calls reliable and its IPW-adjusted EAF recall is 98.7% (\(n_{\text{eff}}{=}18\); CI [82.4, 100.0]). The one condition where Kimi overcounts (partial \(\times\) prior-completing, \(+\)66.7 pp, \(n{=}3\)) is outside the primary absent-\(C_x\) risk zone and does not affect the main conclusions. All directional conclusions R1–R4 are confirmed under human gold standard adjudication.
Synthetic benchmark adversariality. Controlled benchmark documents are constructed with precisely calibrated CITs—maximally adversarial. Real retrieval is less precise, partially explaining the production measurement gap (13.2% vs.%). Benchmark rates characterize susceptibility under constructed prompts, not naturalistic prevalence. CITs were elicited from L1-16B-A3B by design, meaning absolute failure rates are anchored to that model’s pharmacological prior; directional comparisons and failure-profile classifications across models remain valid under a fixed stimulus. Kimi-K2.5 generates synthetic documents (temperature=0, deterministic task) and judges responses; the generation/judging overlap is narrower than a fully closed-loop design, and the human gold standard confirms directional conclusions independently of Kimi’s judgment calibration.
Production model identity. The production measurement uses a deployment that is entity-substitution-dominant (Tier 2). DG-dominant models would likely show higher production DG rates at equivalent retrieval conditions.
Training-progression scope. Progression evidence comes from the L1-16B-A3B checkpoint series only; generalization to other training regimes, architectures, and data mixtures is hypothesized, not demonstrated.
ENTITY_XYZZY_42 non-neutrality. The nonsense label inflates failure rates by 17–24 pp in complete \(C_x\) controls; cross-model noticing proportions are valid as comparisons, but absolute failure rates in the noticing experiment are not directly comparable to controlled benchmark rates.
Mitigation partially tested. A preliminary prompt-based mitigation (explicit entity-anchoring instruction) was tested and reduces entity-attribution failure by \(-30.7\) pp in parametric-prior profiles (P1) but has near-null effect in pre-attentional profiles (\(-4.2\) pp, P3; Appendix 11). Entity-specific retrieval (R2) is the highest-leverage identified intervention. Comprehensive empirical testing of retrieval filtering and fine-tuning corrections remains future work; no claim is made that any proposed intervention eliminates DG.
Causal mediation. The non-significant indirect effect in the SFT\(\to\)DG mediation analysis (Appendix 11), based on \(N{=}8\) models, is consistent with multiple contributing pathways beyond class representation; the analysis is underpowered to rule out class probing as the primary mechanism (Type II error cannot be excluded). The total SFT\(\to\)DG effect is real (\(p{=}0.013\)); class probing characterizes a contributing factor, not necessarily the complete causal story.
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