Organizations: Fudan University, China · Shanghai Innovation Institute, China · Stanford University School of Medicine, United States · Ant Healthcare, Ant Group, China · Shanghai Artificial Intelligence Laboratory, China · Shanghai Jiao Tong University, China · Monash University, Australia
Multimodal medical AI requires a common visual interface for encoding heterogeneous imaging evidence for patient condition modeling. However, existing medical visual tokenizers are often tied to a specific dimension and imaging modality, forcing multimodal systems to rely on fragmented and poorly reusable representations. We introduce MedVTok, a general-purpose visual tokenizer that maps 2D images and 3D volumes from diverse imaging modalities into a unified token space. Building such a tokenizer poses two key challenges: preserving anatomical structure across dimensions and capturing clinical semantics across modalities. To this end, MedVTok introduces (i) slice differential regularization, which explicitly models inter-slice anatomical coherence missing in previous per-pixel/per-voxel supervision, and (ii) multi-expert representation alignment, which integrates knowledge from multiple medical expert encoders while retaining modality-specific complementary knowledge. Trained on 28M images and 70K volumes across 9 imaging modalities, MedVTok supports classification, retrieval, segmentation, synthesis, visual question answering, and medical report generation through a single tokenizer. Across 24 benchmarks, MedVTok achieves state-of-the-art performance, demonstrating a scalable token interface that unifies medical image dimension, modality, and task usage.
Figures & tables
Figure 1: MedVTok provides a unified token interface for multimodal modeling with medical imaging data. Trained on 28M images and 70K volumes, MedVTok achieves state-of-the-art performance across a broad range of downstream tasks covering 24 2D/3D benchmarks.
Figure 2: Overview of the MedVTok training framework. MedVTok learns both (1) structural fidelity across 2D and 3D inputs under the reconstruction loss LR plus the slice differential regularization LSliDR , and (2) clinical semantics across modalities driven by LMERA=Lshared+Lexpert .
Metrics
Method
CFP
CT
Derm.
Endo.
MRI
OCT
Path.
US
X-ray
Avg.
3D-MRI
3D-CT
PSNR ( ↑ )
SDVAE [ 29 ]
37.62
36.38
34.68
33.57
34.31
29.17
24.43
32.13
35.29
33.06
–
–
TokenFlow [ 4 ]
30.57
25.45
29.54
25.75
24.51
24.79
20.17
22.82
26.48
25.56
–
–
MingTok [ 32 ]
35.58
31.23
32.43
29.85
29.37
26.92
21.87
26.42
31.25
29.43
–
–
UniTok [ 10 ]
34.02
31.32
31.89
30.34
30.82
28.00
24.40
29.48
31.57
30.21
–
–
AToken [ 9 ]
41.08
41.60
39.00
39.69
41.64
32.94
28.57
39.41
40.02
38.22
31.46
35.68
PUMIT [ 8 ]
32.03
32.86
27.05
28.73
32.88
27.06
19.43
23.26
26.69
27.78
29.96
31.87
Table 1: Token fidelity evaluation via autoencoding reconstruction [PSNR (dB) ↑ , SSIM (%) ↑ ]. 3D columns are excluded from the 2D average. MedVAE uses separate models for 2D and 3D inputs. The best result is marked in bold and the second-best is underlined .
Figure 3: Qualitative reconstruction for token fidelity evaluation. For each example, we show per-tokenizer absolute error maps with PSNR/SSIM values reported per panel.
Table 4: Image synthesis evaluation (FID ↓ ). A latent diffusion model is trained from scratch in each frozen tokenizer’s latent space with identical architecture and data.
Figure 4: Image synthesis examples. A latent diffusion model trained from scratch on MedVTok’s tokens produces samples with sharper anatomical structure and fewer artifacts than competing tokenizers across modalities, including fundus, X-ray, and dermoscopy.
Method
FundusMM
MM-Skin
Kvasir
PathVQA
SLAKE
GMAI-MM
Avg.
PUMIT [ 8 ]
29.84 ± 0.42
34.74 ± 0.38
69.50 ± 0.51
52.97 ± 0.63
36.44 ± 0.55
28.16 ± 0.47
41.94 ± 0.33
MedVAE [ 5 ]
28.39 ± 0.56
34.21 ± 0.44
66.64 ± 0.72
51.15 ± 0.58
31.57 ± 0.67
27.61 ± 0.53
39.93 ± 0.41
MedITok [ 6 ]
31.29 ± 0.35
36.18 ± 0.41
70.63 ± 0.29
58.46 ± 0.52
45.61 ± 0.38
30.15 ± 0.26
45.39 ± 0.28
MedVTok
33.39 ± 0.31
37.49 ± 0.28
72.98 ± 0.34
57.24 ± 0.45
45.94 ± 0.37
31.81 ± 0.29
46.48 ± 0.22
Table 5: Visual question answering evaluation [Accuracy (%) ↑ ]. Each frozen tokenizer is plugged into the LLaVA-Med [ 58 ] framework for evaluation.
Metrics
Method
Abdomen
Chest
Pelvis
Avg.
BLEU-2 ( ↑ )
PUMIT [ 8 ]
0.289 ± 0.008
0.193 ± 0.003
0.164 ± 0.007
0.215 ± 0.005
MedVAE-3D [ 5 ]
0.249 ± 0.038
0.185 ± 0.020
0.152 ± 0.010
0.195 ± 0.013
MedITok [ 6 ]
0.256 ± 0.013
0.219 ± 0.020
0.294 ± 0.017
0.257 ± 0.012
MedVTok
0.272 ± 0.005
0.263 ± 0.045
0.288 ± 0.017
0.274 ± 0.009
RaTEScore ( ↑ )
PUMIT [ 8 ]
0.604 ± 0.005
0.511 ± 0.035
0.201 ± 0.015
0.439 ± 0.006
MedVAE-3D [ 5 ]
0.613 ± 0.022
0.497 ± 0.053
0.187 ± 0.003
0.432 ± 0.011
Table 6: Medical report generation evaluation. Each frozen tokenizer is integrated into the LaMed [ 59 ] framework for evaluation, generating findings in abdomen, chest, and pelvis regions.
Figure 8: Qualitative comparison on the image segmentation task. Segmentation powered by MedVTok achieves the best performance, while other tokenizers lead to false segmentation in the background. In each image, the mask is highlighted in cyan; the Dice score is shown in the lower right corner.
Model
CFP
CT
Derm.
Endo.
MRI
OCT
Path.
US
X-ray
RetCLIP
91.95 ± 1.05
–
–
–
–
–
–
–
–
DermLIP
–
–
79.72 ± 0.66
–
–
–
–
–
–
PeskaVLP
–
–
–
48.64 ± 2.29
–
–
–
–
–
Conch
–
–
–
–
–
–
93.08 ± 2.44
–
–
MedImageInsight
75.64 ± 2.12
75.32 ± 2.83
85.87 ± 0.38
44.65 ± 0.74
95.47 ± 0.29
90.79 ± 1.18
71.79 ± 2.92
50.18 ± 2.67
96.21 ± 0.83
MedVTok
90.54 ± 1.05
87.03 ± 1.64
75.27 ± 0.99
51.00 ± 1.85
95.03 ± 0.52
94.00 ± 1.18
78.97 ± 1.65
52.92 ± 1.68
97.22 ± 0.61
Appendix
Table 10: Classification accuracy (%) compared with MERA experts. Specialized experts are evaluated on their respective modalities. Values are means ± 95% confidence intervals.
Model
CFP
CT
Derm.
Endo.
MRI
Path.
US
X-ray
RetCLIP
92.46 ± 1.69
–
–
–
–
–
–
–
DermLIP
–
–
89.05 ± 1.86
–
–
–
–
–
PeskaVLP
–
–
–
65.06 ± 1.51
–
–
–
–
Conch
–
–
–
–
–
83.77 ± 1.39
–
–
MedImageInsight
92.34 ± 1.39
25.60 ± 1.35
85.45 ± 2.10
66.96 ± 1.32
55.81 ± 1.31
42.93 ± 1.86
95.80 ± 2.07
50.16 ± 1.48
MedVTok
97.44 ± 1.59
42.91 ± 1.80
90.25 ± 0.77
72.52 ± 1.15
69.62 ± 1.07
77.74 ± 1.56
96.91 ± 1.80
61.13 ± 1.17
Appendix
Table 11: Segmentation Dice (%) compared with MERA experts. Specialized experts are evaluated on their respective modalities. Values are means ± 95% confidence intervals.
AMOS-MM CT
MRISegmenter MRI
Organ
PUMIT
MedVAE 3D
AToken
MedVTok
PUMIT
MedVAE 3D
AToken
MedVTok
Overall
28.67
29.71
36.89
50.13
44.57 ± 0.76
43.70 ± 0.80
54.63 ± 0.68
57.20 ± 0.76
Spleen
63.68 ± 1.58
42.94 ± 2.64
55.76 ± 2.46
70.61 ± 2.30
40.83 ± 2.12
40.68 ± 2.14
63.28 ± 2.71
70.60 ± 2.85
Kidney
48.94 ± 1.96
45.95 ± 2.36
59.56 ± 2.44
74.93 ± 1.74
81.60 ± 1.29
77.46 ± 1.77
83.96 ± 0.67
86.48 ± 0.95
Liver
76.63 ± 2.68
73.73 ± 2.23
80.50 ± 1.72
86.31 ± 1.00
58.11 ± 1.32
59.11 ± 1.23
85.71 ± 0.94
85.83 ± 0.70
Pancreas
13.42 ± 1.99
23.51 ± 2.60
31.64 ± 2.72
41.90 ± 2.36
49.43 ± 2.22
43.98 ± 2.08
49.23 ± 1.92
49.49 ± 2.71
Appendix
Table 12: 3D segmentation Dice (%). Each tokenizer is frozen while a lightweight 3D convolutional head is trained. Values include reported 95% confidence intervals.
Model
MRISegmenter
AMOS-MM MRI
PUMIT
44.57 ± 0.76
31.44 ± 1.52
MedVAE-3D
43.70 ± 0.80
33.52 ± 3.82
AToken
54.63 ± 0.68
44.39 ± 1.75
MedVTok
57.20 ± 0.76
47.24 ± 1.47
Appendix
Table 13: Cross-dataset 3D segmentation Dice (%). Models trained on MRISegmenter are evaluated directly on AMOS-MM MRI. Values are means ± 95% confidence intervals.
Metrics
Method
CFP
CT
Derm.
Endo.
MRI
Path.
X-ray
Avg.
KID ( ↓ )
PUMIT [ 8 ]
0.098
0.110
0.096
0.110
0.067
0.296
0.080
0.123
MedVAE [ 5 ]
0.116
0.084
0.135
0.154
0.077
0.288
0.068
0.132
MedITok [ 6 ]
0.256
0.099
0.078
0.024
0.054
0.055
0.055
0.089
MedVTok
0.027
0.076
0.077
0.035
0.048
0.139
0.019
0.060
FID ( ↓ )
PUMIT [ 8 ]
140.40
183.49
272.26
191.49
227.64
377.12
200.14
227.51
MedVAE [ 5 ]
118.13
154.42
202.09
170.29
145.25
325.87
88.55
172.08
Appendix
Table 14: Additional results on image synthesis evaluation.
Model
Connector only Qwen3 judge
Standard Qwen3 judge
Standard GPT-5 judge
PUMIT
23.05 ± 0.44
41.94 ± 0.33
41.83 ± 0.33
MedVAE
17.88 ± 0.48
39.93 ± 0.41
39.58 ± 0.42
MedITok
24.76 ± 0.39
45.39 ± 0.28
44.82 ± 0.26
MedVTok
29.86 ± 0.36
46.48 ± 0.22
46.02 ± 0.24
Appendix
Table 15: VQA accuracy (%) under training and judge controls. Connector-only training freezes the language model and uses Qwen3-235B-A22B for grading. Standard training updates the connector and language-model LoRA adapters. Values are means ± 95% confidence intervals.
Metrics
Method
Abdomen
Chest
Pelvis
Avg.
BLEU ( ↑ )
PUMIT [ 8 ]
0.289 ± 0.008
0.193 ± 0.003
0.164 ± 0.007
0.215 ± 0.005
MedVAE-3D [ 5 ]
0.249 ± 0.038
0.185 ± 0.020
0.152 ± 0.010
0.195 ± 0.013
MedITok [ 6 ]
0.256 ± 0.013
0.219 ± 0.020
0.294 ± 0.017
0.257 ± 0.012
MedVTok
0.272 ± 0.005
0.263 ± 0.045
0.288 ± 0.017
0.274 ± 0.009
ROUGE-L ( ↑ )
PUMIT [ 8 ]
0.415 ± 0.005
0.277 ± 0.005
0.207 ± 0.007
0.300 ± 0.003
MedVAE-3D [ 5 ]
0.398 ± 0.004
0.266 ± 0.003
0.183 ± 0.004
0.282 ± 0.000
Appendix
Table 16: Additional results on medical report generation evaluation.
Figure 9: Ablation study of λMERA . Classification accuracy and segmentation Dice improve with increasing MERA weight, while reconstruction fidelity (PSNR, SSIM) gradually degrades. λMERA=1 balances semantic quality and reconstruction.
Figure 10: Ablation study of λSliDR . SliDR improves 3D reconstruction without affecting 2D fidelity. λSliDR=0.1 provides the best trade-off, as larger values degrade classification (left).
AMOS-MM CT
MRISegmenter MRI
Objective
PSNR (dB)
SSIM (%)
PSNR (dB)
SSIM (%)
Direct gradient
33.24 ± 0.22
93.01 ± 0.25
26.11 ± 0.14
78.62 ± 0.44
TV
33.05 ± 0.21
93.08 ± 0.24
26.04 ± 0.14
78.00 ± 0.45
Laplacian
32.99 ± 0.21
93.08 ± 0.24
26.20 ± 0.15
77.86 ± 0.45
SliDR
33.46 ± 0.22
93.21 ± 0.25
26.23 ± 0.15
78.70 ± 0.44
Appendix
Table 17: Comparison of depth regularization objectives. All variants use the same 2D-trained checkpoint and a controlled 10K-volume training subset. Higher PSNR and SSIM indicate better reconstruction. The best mean in each column is marked in bold .
Model
k -NN
Linear probe
MedVAE
40.47 ± 0.15
79.47 ± 1.35
PUMIT
36.98 ± 0.55
83.25 ± 0.84
MedITok
90.73 ± 0.62
94.62 ± 0.76
AToken
92.00 ± 2.07
92.84 ± 0.87
MedVTok
94.78 ± 1.81
96.84 ± 0.59
Appendix
Table 18: Classification accuracy (%) on the unseen PBC modality. Both protocols use frozen tokenizer features. Values are means ± 95% confidence intervals.
Model
PSNR (dB)
Accuracy (%)
Dice (%)
AToken
39.35
63.65
69.57
MedITok
36.83
66.59
67.01
MedVTok
39.71
71.70
73.21
Appendix
Table 19: Comparison on the same 2M training images.
Figure 11: t -SNE visualization of frozen tokenizer representations. (a) Out-of-distribution microscopy blood cell dataset. (b) JSIEC fundus dataset (showing the top 16 retinal conditions). MedVTok produces the most clearly separated and coherent clusters in both settings.
Figure 12: Representative responses from the LLaVA-Med model integrating MedVTok as the visual backbone.
Figure 13: Representative medical reports generated by the LaMed model integrating MedVTok as the visual backbone.
Figure 14: Training data distribution across imaging modalities (2D corpus). 2D corpus comprising 28.7M images across 9 modalities and 115 datasets. The colored mid-ring encodes modality with arc length proportional to its sample count; outer spokes correspond to source datasets, with spoke length scaled by log10(count) . Cross-modality datasets ( e.g. , RadImageNet, BIOMEDICA, GLIS-RT) are split equally across their constituent modalities. Long dataset names are abbreviated for layout; full names are listed in Table 20 .
Figure 15: Training data distribution across imaging modalities (3D corpus). 3D corpus comprising 70K volumes across 2 modalities and 37 datasets. The colored mid-ring encodes modality with arc length proportional to its sample count; outer spokes correspond to source datasets, with spoke length scaled by log10(count) . Cross-modality datasets are split equally across their constituent modalities. Long dataset names are abbreviated for layout; full names are listed in Table 21 .
Modern multimodal large language models (MLLMs) typically keep the language model fixed and train a visual projector that maps the pixels into a sequence of tokens in its embedding space, so that images can be presented in essentially the same form as text. However, the language model has been optimized to operate on discrete, semantically meaningful tokens, while prevailing visual projectors transform an image into a long stream of continuous and highly correlated embeddings. This causes the visual tokens to behave differently from the word-like units that LLMs are originally trained to understand. We propose a novel Disentangled Visual Tokenization (DiVT) that clusters patch embeddings into coherent semantic units, so each token corresponds to a distinct visual concept instead of a rigid grid cell. DiVT further adapts its token budget to image complexity, providing an explicit accuracy-compute trade-off modifying neither the vision encoder nor the language model. Across diverse multimodal benchmarks, DiVT matches or surpasses baselines with significantly fewer visual tokens, demonstrating robustness under limited token budgets, significantly reducing memory cost and latency while making visual inputs more compatible with LLMs. Our code is available at https://github.com/snuviplab/DiVT.
Hyun Lee, Hyemin Jeong, Yejin Kim +4
Seoul National University · Ewha Womans University
Vision-language models (VLMs) combining reinforcement learning (RL) ignite remarkable progress in multimodal reasoning, yet still struggle with medical images, which typically exhibit extremely sparse visual evidence to inform clinical decision-making. We recognize that pruning visual tokens outside the grounding region greatly enhances medical reasoning. However, a united RL framework for active visual token pruning (VTP) and medical multimodal reasoning remains unestablished. Here, we propose a dual-stream RL framework, ViToS, to fulfill token pruning and question answering. ViToS trains one policy model with two task branches, where one focuses on grounding while the other conducts token-sparse reasoning after VTP. Furthermore, we solve the coupled policy learning problem by introducing the cross-feedback sequential optimization, avoiding gradient conflict and facilitating convergence of the shared policy model. Evaluated on seven medical benchmarks, our method reduces visual tokens to 77% of the original sequence length while achieving a 108.27% relative performance on Lingshu-7B and 104.16% relative performance on HuatuoGPT-Vision-7B. Overall, ViToS delivers superior performance and inference speedup, establishing an efficient paradigm for medical multimodal reasoning.
Kaitao Chen, Weiqian Zhao, Jiamin Wu +6
1Fudan University · 2Shanghai Artificial Intelligence Laboratory · 3Shanghai Jiao Tong University +1
Latent diffusion models now dominate medical image generation, and every such pipeline rests on a tokenizer that compresses images into the latent codes for image generation to operate on. Thereby, the tokenizer choice bounds every downstream task from reconstruction fidelity and generation quality to the representations available for downstream analysis. Yet, medical imaging pipelines routinely utilize tokenizers from natural imaging on the hypothesis that their behavior carries over. However, this is an assumption never tested in the medical imaging regime, where datasets are orders of magnitude smaller and images exhibit far lower inter-sample variance. We present a systematic evaluation of medical image tokenizers evaluating thirty configurations across ten model families on twelve datasets at three compression factors, spanning reconstruction, generation, latent geometry, downstream classification, and memorization. We find that (1) performance on image reconstruction and generation strongly correlate, unlike prior reports on natural images; (2) modern tokenizers use nearly all of their codebook entries, but still leave most of the latent space unused; (3) training-set memorization is mild and is further suppressed by stronger latent space compression; and (4) discrete quantization can largely preserve downstream classification, with lookup-free schemes being the main exception.
School of Computation, Information and Technology, Technical University of Munich, Germany · Munich Center for Machine Learning, Technical University of Munich, Germany · School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Germany +3