Encoded but Not Decoded: Layer-Localized Evidence for a Three-Level Gap in LLM Syntax

Zhenyan Lu; He Wang; Xiaohui Huang

cs.CLSep 24, 2026

Encoded but Not Decoded: Layer-Localized Evidence for a Three-Level Gap in LLM Syntax

Authors: Zhenyan Lu, He Wang, Xiaohui Huang

Organizations: College of International Studies, National University of Defense Technology, Nanjing, China

Abstract

A language model can fail a syntactic test in two distinct ways: by not encoding the relevant structure, or by encoding it but failing to use it at the output. Behavioral evaluation alone cannot tell these apart. We propose a three-level evaluation framework (behavioral deployment, LM-head readout, and probe recoverability) measured on the same items under the same binary decision. Using a compact trilingual (English, Chinese, German) control-dependency benchmark, we find that probe recoverability exceeds or equals LM-head readout, which in turn exceeds or equals behavioral deployment, across seven models and all three languages in the aggregate. The recoverability surplus is never negative across all 14 (model, task) conditions. The disconnect concentrates in subject-control, where a nearest-noun heuristic gives the wrong answer. The single largest gap (0.653) appears on Qwen3-0.6B Instruct in question answering. The gap persists at Qwen3-14B Instruct. Instruction tuning degrades deployment more than encoding in percentage terms. We rule out option-position bias, late-layer erasure, output-formatting artifacts, and probe-training variance. The pattern is consistent with decoding that favors surface shortcuts, and the behavior-probe gap measures the strength of that preference. Activation patching shows the gap is layer-localized. Under instruction tuning, the LM-head-decoded layer shifts approximately ten layers later than the probe-decoded layer. These findings argue that behavioral evaluation understates what models encode, while probing alone overstates what they deploy.

Figures & tables

Model	QA	Paraphrase	Mean Behavior	Best LM-head	Best Probe	Surplus	B/R Ratio
Qwen3-0.6B Base	0.542	0.646	0.594	0.708	0.938	0.344	0.633
Qwen3-0.6B Instruct	0.417	0.604	0.510	0.667	0.833	0.323	0.612
Qwen3-14B Instruct	0.812	0.771	0.792	0.792	1.000	0.208	0.792
Llama-3.2-1B Base	0.521	0.625	0.573	0.688	0.812	0.240	0.705
Llama-3.2-1B Instruct	0.479	0.542	0.510	0.583	0.625	0.115	0.817
Gemma-4 E4B	0.521	0.604	0.562	0.604	0.604	0.042	0.931

Table 1: Main trilingual model comparison across behavioral deployment, LM-head readout, and probe recoverability.

Figure 1: Three-level gap across all seven models (right: recoverability surplus).

Figure 2: Three-level framework on the hardest case (Qwen3-0.6B Instruct, QA, subject-control), where behavioral deployment (0.250) falls far below LM-head readout (0.667), which falls far below probe recoverability (0.903).

Figure 3: Probe accuracy by relative layer depth across Qwen3 models.

Figure 4: Three-level separation for Qwen3-0.6B base and instruct, by task, on the same items.

Figure 5: Subject-control deployment gap (probe

-

behavior) across scale.

Appendix figures & tables12 assets

Supplementary material from the paper’s appendix.

Appendix

QA Format	Paraphrase Format
Sentence: “John promised Mary to leave early.”	Sentence: “John promised Mary to leave early.”
Prompt: Q: Who is understood to leave early? A: John $\leftarrow$ log-prob scored A: Mary $\leftarrow$ log-prob scored	Prompt: Which sentence better describes the situation? (A) John is understood to leave early. $\leftarrow$ scored (B) Mary is understood to leave early. $\leftarrow$ scored
Decision: $\arg\max\log P(\text{continuation}\mid\text{sentence}+\text{Q})$	Decision: $\arg\max\log P(\text{interpretation}\mid\text{sentence}+\text{prompt})$
Gold controller: John ( promise = subject-control)

Appendix

Table 2: The two behavioral evaluation formats, both using pairwise log-probability scoring over the same candidate controller nouns and differing only in prompt structure.

Mode	Qwen3-0.6B Base	Qwen3-0.6B Instruct	Qwen3- 14B Instruct
ab	0.924	0.847	0.958
bv	0.889	0.792	0.979
av	0.618	0.458	0.931
abv	0.847	0.701	0.944
v	0.757	0.521	0.986

Appendix

Table 3: Best per-mode probe accuracy across layers, mean over three seeds.

Model	Seed 1729	Seed 2718	Seed 3141	Mean	Std
Qwen3-0.6B Base	0.938	0.938	0.896	0.924	0.020
Qwen3-0.6B Instruct	0.833	0.812	0.896	0.847	0.035
Qwen3-14B Instruct	1.000	0.979	0.979	0.986	0.010
Llama-3.2-1B Base	0.812	0.833	0.833	0.826	0.010
Llama-3.2-1B Instruct	0.625	0.625	0.625	0.625	0.000
Gemma-4 E4B Base	0.604	0.479	0.625	0.569	0.064

Appendix

Table 4: Probe accuracy across three training seeds at the globally-best (layer, feature mode) selected by three-seed mean.

Model	Language	Behavior	LM-head	Probe	Surplus
Qwen3-0.6B Base	English	0.656	0.875	0.938	+0.281
	Chinese	0.656	0.625	1.000	+0.344
	German	0.469	0.625	0.875	+0.406
Qwen3-0.6B Instruct	English	0.688	0.875	0.812	+0.125
	Chinese	0.469	0.562	1.000	+0.531
	German	0.375	0.562	0.688	+0.312

Appendix

Table 5: Per-language breakdown for all seven models.

Model	Variant	Summary	Accuracy	Object	Subject	Order Gap
Qwen3-0.6B Base	debiased_forced_choice_ab	debiased	0.531	0.604	0.458	0.062
Qwen3-0.6B Base	debiased_label_choice	debiased	0.552	0.542	0.562	0.021
Qwen3-0.6B Base	contrastive_scoring	single	0.479	0.667	0.292	nan
Qwen3-0.6B Instruct	debiased_forced_choice_ab	debiased	0.500	0.500	0.500	0.000
Qwen3-0.6B Instruct	debiased_label_choice	debiased	0.562	0.479	0.646	0.083
Qwen3-0.6B Instruct	contrastive_scoring	single	0.500	0.708	0.292	nan

Appendix

Table 6: Readout-cleaning results after counterbalancing option order and label order.

Figure 6: Raw accuracy under both option orders and the debiased result, per model.

Figure 7: Patching causal lift versus relative layer depth on QA subject-control (vertical dotted lines mark probe peaks).

Figure 8: Patching causal lift across all four cells per model.

Model	Task	Type	Behavior	Best Probe	Gap	Probe Layer	Probe Mode
Qwen3-0.6B Base	qa	object-control	0.375	0.917	0.542	18	ab
Qwen3-0.6B Base	qa	subject-control	0.708	0.931	0.222	18	ab
Qwen3-0.6B Base	paraphrase	object-control	0.750	0.917	0.167	18	ab
Qwen3-0.6B Base	paraphrase	subject-control	0.542	0.931	0.389	18	ab
Qwen3-0.6B Instruct	qa	object-control	0.583	0.847	0.264	16	ab
Qwen3-0.6B Instruct	qa	subject-control	0.250	0.903	0.653	19	bv

Appendix

Table 7: Type-level behavior-versus-probe comparison for the most relevant models.

Mode	Type	Item-out	Verb-out	Gap
ab	subj	$0.819\pm 0.05$	$0.681\pm 0.13$	$+0.139$
bv	subj	$0.958\pm 0.04$	$0.944\pm 0.06$	$+0.014$
av	subj	$0.972\pm 0.02$	$0.889\pm 0.09$	$+0.083$
abv	subj	$0.903\pm 0.05$	$0.889\pm 0.10$	$+0.014$
v	subj	$1.000\pm 0.00$	$0.889\pm 0.05$	$+0.111$
ab	obj	$0.806\pm 0.02$	$0.792\pm 0.00$	$+0.014$

Appendix

Table 8: Item-out LOOCV vs. verb-out CV at the Qwen3-14B Instruct v -mode probe peak (layer 17, mean

\pm

SD across three seeds).

Figure 9: Subject-control verb-out gap (item-out LOOCV

-

verb-out CV) across the full layer trajectory in bv mode.

Model	Layer	Item-out	Verb-out	Gap	Verdict
Qwen3-0.6B Base	18	$0.917\pm 0.00$	$0.500\pm 0.04$	$+0.417$	LEAK
Qwen3-0.6B Instruct	19	$0.903\pm 0.02$	$0.472\pm 0.06$	$+0.431$	LEAK
Llama-3.2-1B Base	7	$0.917\pm 0.00$	$0.250\pm 0.00$	$+0.667$	LEAK
Llama-3.2-1B Instruct	2	$0.625\pm 0.00$	$0.083\pm 0.00$	$+0.542$	LEAK
Gemma-4 E4B	2	$0.611\pm 0.06$	$0.153\pm 0.02$	$+0.458$	LEAK
Gemma-4 E4B Instruct	4	$0.750\pm 0.00$	$0.306\pm 0.06$	$+0.444$	LEAK

Appendix

Table 9: Subject-control full-trajectory probe peak in bv mode across all seven models, with verb-out CV at the same layer (mean

\pm

standard deviation across three seeds; gap criterion as in Figure 9 ).

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