Vision-language models (VLMs) are increasingly deployed in high-stakes settings where reliable uncertainty quantification (UQ) is as important as predictive accuracy. Extended reasoning via chain-of-thought (CoT) prompting or reasoning-trained models has become ubiquitous in modern VLM pipelines, yet its effect on UQ reliability remains poorly understood. Our results show that reasoning tends to degrade the quality of many uncertainty estimates, even when it improves task accuracy. We identify implicit answer conditioning as the primary mechanism: as reasoning traces converge on a conclusion before the final answer is generated, token probabilities increasingly reflect consistency with the model's own reasoning trace rather than uncertainty about correctness. In effect, the model becomes overconfident in its answer. In contrast, agreement-based consistency remains robust and often improves under reasoning, making it a practical choice for uncertainty estimation in reasoning-enabled VLMs.
Figures & tables
Figure 1: Example of implicit answer conditioning: intermediate reasoning progressively commits the model to its eventual answer before that answer is explicitly generated. Colour indicates the model’s confidence in its final predicted answer a^ on the same input, without reasoning ( P(a^∣x,θ) ) and at each reasoning token position t with chain-of-thought reasoning ( P(a^∣x,r≤t,θ) ), where x is the input and r≤t is the reasoning trace up to token t . Although the prediction is incorrect in both cases (3 inches; ground truth: 2), confidence rises sharply as the reasoning trace converges on the wrong answer, exceeding the no-CoT confidence.
No CoT
CoT
Δ (CoT − No CoT)
Type
UQ Estimate
AUGRC ↓
PRR ↑
Spear. ↑
AUGRC ↓
PRR ↑
Spear. ↑
AUGRC
PRR
Spear.
Oxford-IIIT Pet
Single-Generation (Acc: 79.3 / 76.2)
MSP
0.056
0.710
0.404
0.110
0.231
0.075
0.053
-0.478
-0.329
PPL
0.057
0.711
0.399
0.111
0.211
0.061
0.054
-0.500
-0.338
MTE
0.053
0.735
0.431
0.112
0.205
0.056
0.059
-0.530
-0.376
SRC
0.060
0.709
0.377
0.100
0.314
0.151
0.041
-0.394
-0.226
Table 1: Selective generation results for Qwen3-VL-8B-IT with and without CoT prompting. Accuracy is reported as (Acc: No CoT / CoT ) for each setting.
Instruct
Thinking
Δ (Thinking − Instruct)
Type
UQ Estimate
AUGRC ↓
PRR ↑
Spear. ↑
AUGRC ↓
PRR ↑
Spear. ↑
AUGRC
PRR
Spear.
Oxford-IIIT Pet
Single-Generation (Acc: 79.3 / 77.2)
MSP
0.056
0.710
0.404
0.110
0.120
0.032
0.054
-0.590
-0.373
PPL
0.057
0.711
0.399
0.112
0.089
0.021
0.055
-0.621
-0.378
MTE
0.053
0.735
0.431
0.112
0.086
0.019
0.059
-0.649
-0.412
SRC
0.060
0.709
0.377
0.075
0.538
0.320
0.016
-0.171
-0.057
Table 2: Selective generation results for Qwen3-VL-8B-IT (Instruct; no CoT) and Qwen3-VL-8B-Thinking (intrinsic reasoning, no CoT prompting). Accuracy is reported as (Acc: Instruct / Thinking) for each setting.
Figure 2: Confidence shifts induced by CoT reasoning. Bars show the percentage of samples whose confidence increases (solid colour), decreases (striped colour), or remains unchanged (gray) when moving from no-CoT to CoT inference, grouped by correctness. ATL-based estimates systematically increase confidence, including samples that become or remain incorrect, indicating confidence inflation unrelated to correctness. Self-reported confidence (SRC) and Consistency do not exhibit systematic inflation.
Figure 3: Evidence for Implicit Answer Conditioning. (a) Aggregated spearman correlations between reasoning length and confidence under CoT (Fisher z-transformed; 95% CI). Longer reasoning traces correspond to lower confidence. (b) Confidence as a function of how often the final answer appears in the reasoning trace. Repeated answer mentions substantially increase answer-token likelihood. (c–d) Across datasets, answer frequency positively correlates with ATL-based uncertainty estimates. This correlation persists even for incorrect predictions, indicating correctness-agnostic confidence inflation. In contrast, Consistency and SRC show little sensitivity to answer frequency.
No CoT (Acc 59.7)
CoT (Acc 57.7)
Masked-CoT (Acc 57.7)
Random Masked-CoT (Acc 57.7)
UQ Method
AUGRC ↓
Spear. ↑
PRR ↑
AUGRC ↓
Spear. ↑
PRR ↑
AUGRC ↓
Spear. ↑
PRR ↑
AUGRC ↓
Spear. ↑
PRR ↑
MSP
0.152
0.375
0.498
0.196
0.115
0.141
0.161
0.378
0.475
0.190
0.161
0.210
MTE
0.154
0.364
0.481
0.204
0.057
0.071
0.181
0.230
0.329
0.198
0.102
0.137
PPL
0.156
0.345
0.469
0.204
0.059
0.075
0.166
0.340
0.436
0.197
0.113
0.146
Table 3: Masking answer mentions in CoT improves uncertainty. Masked-CoT replaces occurrences of the predicted answer in the reasoning trace with [MASK] , while Random Masked-CoT masks an equal number of random reasoning tokens. Masking answer mentions substantially restores the ranking quality of ATL-based uncertainty estimates. Best values between CoT, Masked-CoT, and Random Masked-CoT are bold. Qwen3-VL-8B-IT on OK-VQA shown here, results for MathVista are given in the supp. material (Sec. L).
Appendix figures & tables13 assets
Supplementary material from the paper’s appendix.
Appendix
Non-Reasoning
Reasoning
Model
Dataset
MSP
SRC
Cons.
MSP
SRC
Cons.
Gemma3-4B-IT
Oxford-IIIT Pet
0.301
0.383
0.313
0.161
0.287
0.161
OK-VQA
0.349
0.416
0.450
0.410
0.557
0.352
MMMU-Pro-Vision
0.581
0.497
0.752
0.682
0.366
0.542
MathVista
0.397
0.585
0.521
0.513
0.440
0.268
Qwen3-VL-8B-IT
Oxford-IIIT Pet
0.061
0.198
0.143
0.170
0.260
0.103
Appendix
Table 4: Expected Calibration Error (ECE, 10 bins) across models and datasets. Lower is better; best per setting in bold .
Model
Temperature
Top- p
Top- k
Presence Penalty
Gemma3-4B-IT
1.0
0.95
64
1.0
InternVL3-9B
0.8
0.80
40
0.0
Qwen3-VL-8B-IT
1.0
1.0
40
2.0
Qwen3-VL-8B-Thinking
1.0
0.95
20
1.5
Qwen3-VL-32B-IT
0.7
0.80
20
1.5
Appendix
Table 5: Decoding hyperparameters used for each model family.
Figure 4: Effect of sample size k on uncertainty quality. Lower AUGRC is better, higher PRR is better.
No CoT
CoT
Δ (CoT − No CoT)
Type
UQ Estimate
AUGRC ↓
PRR ↑
Spear. ↑
AUGRC ↓
PRR ↑
Spear. ↑
AUGRC
PRR
Spear.
Gemma3-4B-IT
Single-Generation (Acc: 65.2 / 70.4)
MSP
0.122
0.498
0.380
0.139
0.200
0.068
0.018
-0.297
-0.312
PPL
0.121
0.498
0.384
0.141
0.186
0.054
0.020
-0.312
-0.330
MTE
0.118
0.521
0.404
0.136
0.219
0.090
0.018
-0.302
-0.314
SRC
0.121
0.511
0.388
0.104
0.504
0.333
-0.016
-0.007
-0.055
Appendix
Table 6: Selective Generation Results on Oxford Pets
No CoT
CoT
Δ (CoT − No CoT)
Type
UQ Estimate
AUGRC ↓
PRR ↑
Spear. ↑
AUGRC ↓
PRR ↑
Spear. ↑
AUGRC
PRR
Spear.
Gemma3-4B-IT
Single-Generation (Acc: 38.8 / 35.4)
MSP
0.270
0.333
0.266
0.294
0.244
0.218
0.024
-0.090
-0.048
PPL
0.278
0.291
0.207
0.305
0.188
0.135
0.027
-0.103
-0.072
MTE
0.276
0.297
0.222
0.303
0.192
0.152
0.027
-0.105
-0.071
SRC
0.270
0.328
0.268
0.289
0.304
0.261
0.018
-0.025
-0.007
Appendix
Table 7: Selective Generation Results on OK-VQA
No CoT
CoT
Δ (CoT − No CoT)
Type
UQ Estimate
AUGRC ↓
PRR ↑
Spear. ↑
AUGRC ↓
PRR ↑
Spear. ↑
AUGRC
PRR
Spear.
Gemma3-4B-IT
Single-Generation (Acc: 19.0 / 18.9)
MSP
0.401
0.118
0.037
0.398
0.036
0.069
-0.003
-0.082
0.032
PPL
0.401
0.116
0.035
0.398
0.036
0.069
-0.003
-0.081
0.034
MTE
0.398
0.129
0.059
0.397
0.039
0.075
-0.001
-0.090
0.016
SRC
0.400
0.077
0.047
0.394
0.122
0.108
-0.006
0.045
0.060
Appendix
Table 8: Selective Generation Results on MMMU-Pro-Vision
No CoT
CoT
Δ (CoT − No CoT)
Type
UQ Estimate
AUGRC ↓
PRR ↑
Spear. ↑
AUGRC ↓
PRR ↑
Spear. ↑
AUGRC
PRR
Spear.
Gemma3-4B-IT
Single-Generation (Acc: 34.7 / 41.9)
MSP
0.292
0.317
0.256
0.269
0.202
0.150
-0.022
-0.115
-0.106
PPL
0.300
0.239
0.192
0.275
0.152
0.110
-0.025
-0.087
-0.082
MTE
0.302
0.229
0.182
0.276
0.152
0.107
-0.026
-0.077
-0.074
SRC
0.340
0.022
-0.094
0.289
0.083
0.012
-0.051
0.060
0.106
Appendix
Table 9: Selective Generation Results on MathVista
Figure 5: Sample-level confidence shifts under Chain-of-Thought prompting for Qwen3-VL-32B-Instruct across different datasets. Each subfigure corresponds to a dataset and reports confidence changes conditioned on correctness transitions.
Answer Tokens
Answer Tokens
Reasoning Tokens
Model
Dataset
No Reasoning
Reasoning
Reasoning
Qwen3-VL-32B-IT
MMMU Pro Vision
1.0 ± 0.0
1.0 ± 0.0
521.9 ± 1742.1
MathVista
1.8 ± 1.8
1.4 ± 1.1
206.8 ± 842.9
OK-VQA
2.0 ± 1.0
2.2 ± 1.2
47.8 ± 24.7
Oxford Pets
1.7 ± 0.4
1.7 ± 0.4
60.9 ± 11.3
Qwen3-VL-8B-IT
MMMU Pro Vision
1.0 ± 0.0
1.0 ± 0.0
186.0 ± 439.2
Appendix
Table 10: Average answer and reasoning lengths (number of tokens; mean ± std).
Figure 6: Confidence shift in the final predicted answer’s MSP as a function of reasoning progress. Curves are split by whether the final answer was correct or incorrect. Solid lines show the mean, and shaded regions show the 95% confidence interval estimated via bootstrapping.
Figure 7: Reasoning Trace Analysis on Incorrect Samples. On OK-VQA, reasoning traces that mention the predicted answer more frequently tend to yield higher final-answer MSP, even when the prediction is incorrect.
Figure 8: Sequential Confidence Trajectory. The log-sum-probability of the answer tokens across multiple rounds of reasoning and answering. Qwen3-VL-8B-IT on a random subset (n=200) of MathVista.
No-CoT (Acc 62.9)
CoT (Acc 72.9)
Masked-CoT (Acc 72.9)
Random Mask (Acc 72.9)
UQ Method
AUGRC ↓
Spear. ↑
PRR ↑
AUGRC ↓
Spear. ↑
PRR ↑
AUGRC ↓
Spear. ↑
PRR ↑
AUGRC ↓
Spear. ↑
PRR ↑
MSP
0.142
0.313
0.522
0.130
0.043
0.115
0.129
0.055
0.200
0.147
-0.083
-0.032
MTE
0.143
0.304
0.526
0.134
0.013
0.075
0.119
0.133
0.264
0.144
-0.062
0.010
PPL
0.145
0.289
0.513
0.134
0.017
0.100
0.131
0.038
0.184
0.148
-0.094
-0.050
Appendix
Table 11: Masked-CoT Results on MathVista using Qwen3-VL-8B-IT. Masking answer mentions partially restores uncertainty ranking, while random masking of an equivalent number of reasoning tokens degrades ranking quality. These results are computed solely on the subset of image/question pairs where the reasoning traces include the predicted final answer.
Uncertainty estimation is critical for deploying reasoning language models, yet remains poorly understood under extended chain-of-thought reasoning. We study parallel sampling as a fully black-box approach using verbalized confidence and self-consistency. Across three reasoning models and 17 tasks spanning mathematics, STEM, and humanities, we characterize how these signals scale. Both self-consistency and verbalized confidence scale in reasoning models, but self-consistency exhibits lower initial discrimination and lags behind verbalized confidence under moderate sampling. Most uncertainty gains, however, arise from signal combination: with just two samples, a hybrid estimator improves AUROC by up to +12 on average and already outperforms either signal alone even when scaled to much larger budgets, after which returns diminish. These effects are domain-dependent: in mathematics, the native domain of RLVR-style post-training, reasoning models achieve higher uncertainty quality and exhibit both stronger complementarity and faster scaling than in STEM or humanities.
Maksym Del, Markus Kängsepp, Marharyta Domnich +4
Institute of Computer Science, University of Tartu
Recent advances in vision language models (VLMs) offer reasoning capabilities, yet how these unfold and integrate visual and textual information remains unclear. We analyze reasoning dynamics in 18 VLMs covering instruction-tuned and reasoning-trained models from two different model families. We track confidence over Chain-of-Thought (CoT), measure the corrective effect of reasoning, and evaluate the contribution of intermediate reasoning steps. We find that models are prone to answer inertia, in which early commitments to a prediction are reinforced, rather than revised during reasoning steps. While reasoning-trained models show stronger corrective behavior, their gains depend on modality conditions, from text-dominant to vision-only settings. Using controlled interventions with misleading textual cues, we show that models are consistently influenced by these cues even when visual evidence is sufficient, and assess whether this influence is recoverable from CoT. Although this influence can appear in the CoT, its detectability varies across models and depends on what is being monitored. Reasoning-trained models are more likely to explicitly refer to the cues, but their longer and fluent CoTs can still appear visually grounded while actually following textual cues, obscuring modality reliance. In contrast, instruction-tuned models refer to the cues less explicitly, but their shorter traces reveal inconsistencies with the visual input. Taken together, these findings indicate that CoT provides only a partial view of how different modalities drive VLM decisions, with important implications for the transparency and safety of multimodal systems.
Danae Sánchez Villegas, Samuel Lewis-Lim, Nikolaos Aletras +1
University of Copenhagen, Department of Computer Science · University of Sheffield, School of Computer Science
Vision-language models (VLMs) can answer simple visual questions, but often struggle when one question requires several visual judgments. We study this gap with controlled tasks for feature binding, numerosity, spatial relations, and amodal completion, together with a Composite task that combines them. Matched counterfactual image pairs isolate changes in the visual evidence needed to answer. Across four models, direct answers, hidden-state readouts, and state interventions show that the individual judgments can be made without explicit reasoning and that intervening on the corresponding states can affect the answer. During reasoning, the Composite answer becomes decodable from hidden states and usable from shortened traces, often before the model stops on its own. We train a small detector to predict this readiness and stop reasoning at that point. On MMStar and RealWorldQA, this reduces mean reasoning tokens by 79.1% and 74.5%, while average accuracy rises by 3.13 and 3.30 percentage points, respectively. These findings connect the internal development of answer readiness to a practical rule for allocating reasoning computation.
Rong Yu Xu, Prayag Tiwari, Shaolei Zhang
Shenzhen College of International Education · Halmstad University, Sweden · Renmin University of China