Domain-Specific Latent Representations Improve the Fidelity of Diffusion-Based Medical Image Super-Resolution
Authors: Sebastian Cajas, Ashaba Judith, Rahul Gorijavolu, Sahil Kapadia, Hillary Clinton Kasimbazi, Leo Kinyera, Emmanuel Paul Kwesiga, Sri Sri Jaithra Varma Manthena, Luis Filipe Nakayama, Ninsiima Doreen, Leo Anthony Celi
Organizations: MIT Critical Data, Massachusetts Institute of Technology, Cambridge, MA, USA. · Department of Biomedical Engineering, Mbarara University of Science and Technology, Uganda. · School of Medicine, Johns Hopkins University, Baltimore, MD, USA. · Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA. · University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. · Department of Radiology and Radiotherapy, Makerere University, Uganda. · Department of Radiotherapy, Uganda Cancer Institute, Uganda. · Department of Radiology and Radiological Science, School of Medicine, Johns Hopkins University, Baltimore, MD, USA. · Department of Public Health Sciences, Cavendish University, Uganda. · Department of Applied Natural Sciences, Technical University of Applied Sciences Lübeck (TH Lübeck), Lübeck, Germany. · Department of Ophthalmology, Federal University of S˜ao Paulo, Brazil. · Division of Pulmonary, Critical Care and Sleep Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA. · Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
Latent diffusion models for medical image super-resolution universally inherit variational autoencoders designed for natural photographs. We show that this default choice, not the diffusion architecture, is the dominant constraint on reconstruction quality. In a controlled experiment holding all other pipeline components fixed, replacing the generic Stable Diffusion VAE with MedVAE, a domain-specific autoencoder pretrained on more than 1.6 million medical images, yields +2.91 to +3.29 dB PSNR improvement across knee MRI, brain MRI, and chest X-ray (n = 1,820; Cohen's d = 1.37 to 1.86, all p < 10^{-20}, Wilcoxon signed-rank). Wavelet decomposition localises the advantage to the finest spatial frequency bands encoding anatomically relevant fine structure. Ablations across inference schedules, prediction targets, and generative architectures confirm the gap is stable within plus or minus 0.15 dB, while hallucination rates remain comparable between methods (Cohen's h < 0.02 across all datasets), establishing that reconstruction fidelity and generative hallucination are governed by independent pipeline components. These results provide a practical screening criterion: autoencoder reconstruction quality, measurable without diffusion training, predicts downstream SR performance (R^2 = 0.67), suggesting that domain-specific VAE selection should precede diffusion architecture search. Code and trained model weights are publicly available at https://github.com/sebasmos/latent-sr.
Figures & tables
Figure 1: Latent diffusion SR pipeline. Both methods share an identical LDM UNet (purple); only the VAE encoder/decoder differs. Top: SD-VAE SR uses a generic VAE trained on natural images (4-channel, 32×32 latent). Bottom: MedVAE SR (proposed) uses a domain-specific VAE trained on medical images (3-channel, 64×64 latent). The controlled substitution isolates the VAE’s contribution to SR fidelity.
Dataset
Method
PSNR (dB)
MS-SSIM
LPIPS ‡
MRNet †
Bicubic
23.79
0.906
0.541
ESRGAN
23.28
0.897
0.425
SwinIR
22.48
0.882
0.446
SD-VAE SR
22.34
0.870
0.173
MedVAE SR ∗
25.26
0.936
0.135
MedVAE-AE §
27.85
0.966
0.109
Table 1: SR reconstruction quality across three datasets. PSNR (dB), MS-SSIM, and LPIPS for all methods. Bold: best SR method per dataset per metric. † : MRNet is a refinement task (LR = HR = 256 × 256); bicubic copies LR unchanged. ‡ : BraTS/CXR bicubic PSNR exceeds diffusion SR due to MSE minimisation vs. perceptual quality tradeoff. Bicubic interpolation achieves competitive PSNR because it avoids hallucination artifacts, but produces blurry outputs with high LPIPS (low perceptual quality). †† : BraTS results use the validation split ( n=700 ); the flow-matching ablation (Appendix Table S3 ) uses the test split ( n=720 ).
Dataset
n
MedVAE PSNR
SD-VAE PSNR
Δ PSNR
95% CI
Cohen’s d
p -value
MRNet
120
25.26±1.58
22.34±1.55
+2.91
[+2.52,+3.30]
1.86
9.9×10−22
BraTS
700
26.42±2.10
23.51±1.99
+2.91
[+2.69,+3.12]
1.42
7.8×10−120
CXR
1,000
28.87±2.62
25.58±2.17
+3.29
[+3.09,+3.51]
1.37
2.3×10−117
Table 2: Statistical significance of MedVAE vs. SD-VAE SR. Per-image Wilcoxon signed-rank test and bootstrap effect sizes ( nbootstrap=10,000 ).
Figure 2: SR reconstruction quality across three datasets. (a) PSNR (dB) and (b) LPIPS for all methods on MRNet (knee MRI), BraTS (brain MRI), and MIMIC-CXR (chest X-ray). Error bars: ±1 standard deviation across validation images. Improvement brackets (dark blue) show MedVAE SR vs. SD-VAE SR delta: +X dB for PSNR with 95% bootstrap CI, −Δ for LPIPS (lower = better). MedVAE SR achieves better PSNR than SD-VAE SR and lower LPIPS than bicubic interpolation across all three datasets, occupying the Pareto frontier of the quality-perception tradeoff [ 44 ] . The MedVAE-AE ceiling (light blue, hatched) represents encode-then-decode without diffusion and sets the theoretical maximum for each VAE.
Figure 3: AE reconstruction ceiling predicts SR quality ( R2=0.67 ). Scatter plot of VAE autoencoder ceiling PSNR (encode-then-decode without diffusion, x-axis) vs. diffusion SR output PSNR (y-axis) for all method–dataset combinations ( n=6 ). Points: MedVAE SR (blue) and SD-VAE SR (red); shapes: MRNet (circle), BraTS (square), CXR (triangle). Line: OLS regression with 95% confidence band (Pearson r=0.82 , p<0.001 ). The strong linear relationship indicates that AE reconstruction fidelity, computed without training any diffusion model, is a reliable screening criterion for SR quality in any domain-specific LDM pipeline.
Figure 4: Multi-resolution frequency analysis. Rows: MRNet, BraTS, MIMIC-CXR. Left: per-subband PSNR (3-level Haar, 10 bands) for MedVAE SR (blue) vs. SD-VAE SR (red). Right: log radial FFT spectrum (HR: dashed). Gains concentrate at HH 1 (+1.18, +1.41, +0.70 dB), while LL 3 differences ≤ 0.05 dB.
Figure 5: Visual comparison and pixel-level difference maps — BraTS (brain MRI, 4× SR). Top: side-by-side comparison of AE reconstruction, MedVAE SR, SD-VAE SR, and HR ground truth. Bottom: mean absolute pixel difference ∣SR−HR∣ (hot colormap; brighter = larger error). MedVAE SR produces cooler (darker) error maps, indicating better reconstruction of fine anatomical structure. Scale bar in HR panel: 20 mm (pixel spacing ≈ 0.938 mm; 240 mm FOV resized to 256 px). Qualitatively consistent patterns for MRNet (knee MRI) and MIMIC-CXR are shown in Appendix Figs. S5 – S6 .
Figure 6: Multi-resolution latent embedding comparison (all datasets). Rows: MRNet (knee MRI), BraTS (brain MRI), MIMIC-CXR (chest X-ray). (a) PSNR and (b) cosine similarity between SR latents and HR latents at progressively coarser spatial pooling scales ( 64×64 to 1×1 ). MedVAE SR achieves higher SR-to-HR latent fidelity at all scales, confirming that the domain-specific latent space better preserves HR information throughout the spatial hierarchy.
Figure 7: Statistical analysis of SR quality. (a) Cohen’s d forest plot. Each row shows the effect size (Cohen’s d ) for the MedVAE SR vs. SD-VAE SR PSNR gap on one dataset (MRNet, BraTS, CXR), with horizontal error bars indicating 95% bootstrap confidence intervals ( nbootstrap=10,000 ). The vertical dashed line marks d=0.8 (conventional “large” effect threshold). All three datasets show large-to-very-large effect sizes ( d>1.3 ). (b) Per-image PSNR distribution (violin plots). Each violin shows the distribution of per-image PSNR values for MedVAE SR (blue) and SD-VAE SR (red) across the three validation sets; horizontal lines indicate medians. MedVAE SR achieves consistently higher PSNR. (c) Bland-Altman intensity agreement plots. Each panel shows one validation set; x -axis: mean of SR and HR per-image pixel intensities; y -axis: difference SR − HR. Solid lines: mean bias; dashed lines: 95% limits of agreement (LoA). Both methods show near-zero bias; detailed statistics are given in Appendix Table S9 .
Appendix figures & tables19 assets
Supplementary material from the paper’s appendix.
Appendix
T
PSNR (dB)
MS-SSIM
LPIPS
sec/sample
Speedup
50
25.97
0.9317
0.241
0.18
14.6×
100
26.04
0.9355
0.216
0.30
8.7×
250
26.01
0.9410
0.168
0.69
3.8×
500
25.79
0.9405
0.152
1.33
2.0×
1000
25.25
0.9355
0.135
2.62
1.0×
Appendix
Table S1 : Supplementary Table S1. Inference step ablation on MRNet ( T=50 – 1,000 , MedVAE SR, S1 latents). PSNR is essentially flat across all step counts; LPIPS improves with more steps. All main results (Table 1 ) use T=100 unless stated otherwise.
Table S3 : Supplementary Table S3. Flow matching (rectified flow) vs. DDPM. All datasets, T=16 Euler steps vs. T=100 DDPM. Flow matching achieves 16× speedup with 0.7 – 1.2 dB PSNR cost but better LPIPS. Note: BraTS results here use the test split ( n=720 ); Table 1 of the main text uses the validation split ( n=700 ), which accounts for the difference in reported BraTS PSNR (27.13 dB here vs. 26.42 dB in Table 1 ).
Dataset
Scale
Bicubic PSNR (dB)
Bicubic SSIM
MedVAE SR LPIPS
BraTS
2×
34.91±1.80
0.976±0.006
0.088
4×
29.91±1.84
0.980±0.005
8×
26.27±1.76
0.822±0.035
CXR
2×
34.30±2.92
0.953±0.015
0.127
4×
30.47±2.86
0.977±0.008
8×
26.99±2.78
0.774±0.066
Appendix
Table S4 : Supplementary Table S4. Multi-scale bicubic baseline context. PSNR (dB) and SSIM for bicubic interpolation at 2 × , 4 × , 8 × SR on BraTS and CXR.
Dataset
n
Δ PSNR
95% CI
Cohen’s d
Interpretation
MRNet
120
+2.91
[+2.52,+3.30]
1.858
Very large
BraTS
700
+2.91
[+2.69,+3.12]
1.421
Large
CXR
1,000
+3.29
[+3.09,+3.51]
1.370
Large
Appendix
Table S5 : Supplementary Table S5. Effect sizes (Cohen’s d ) and statistical significance for MedVAE vs. SD-VAE SR. Bootstrap 95% confidence intervals, nbootstrap=10,000 .
Subband
Description
MedVAE (MRNet)
SD-VAE (MRNet)
Δ MRNet
Δ BraTS
Δ CXR
(dB)
(dB)
(dB)
(dB)
(dB)
LL 3
Low-low (coarsest approx.)
14.51±3.15
14.46±2.82
+0.05
+0.02
−0.20
LH 3
Low-high level 3
15.78±2.69
15.48±2.08
+0.30
−0.04
−0.54
HL 3
High-low level 3
13.29±2.68
13.13±1.97
+0.16
−0.13
−0.39
HH 3
High-high level 3
14.08±2.40
13.86±1.96
+0.22
−0.07
−0.75
LH 2
Low-high level 2
18.10±1.55
17.83±1.59
+0.27
−0.08
−0.81
Appendix
Table S6 : Supplementary Table S6. Per-frequency-band PSNR from 3-level Haar wavelet decomposition. MedVAE SR vs. SD-VAE SR, mean ± std across validation images. Subbands ordered coarsest (LL 3 ) to finest (HH 1 ). Bold Δ : MedVAE advantage >0.5 dB.
Dataset
Method
Hallucinated % (above noise floor)
Lost % (below noise floor)
MRNet
MedVAE SR
24.71±8.69
27.07±6.56
MRNet
SD-VAE SR
25.18±8.81
26.94±6.37
BraTS
MedVAE SR
12.91±5.78
13.87±5.82
BraTS
SD-VAE SR
13.30±5.82
13.54±5.78
CXR
MedVAE SR
3.30±3.61
3.81±4.65
CXR
SD-VAE SR
3.40±4.03
3.97±5.15
Appendix
Table S7 : Supplementary Table S7. Pixel-level hallucination rates across datasets and methods.
Table S9 : Supplementary Table S9. Bland-Altman intensity agreement statistics. All biases are near-zero ( ∣ bias ∣<0.01 ), indicating no systematic intensity offset.
Method
Tumor PSNR (dB)
Background PSNR (dB)
Tumor SSIM
Background SSIM
MedVAE SR
12.30
17.41
0.142
0.737
SD-VAE SR
12.48
17.39
0.137
0.726
Bicubic
30.41
29.94
0.834
0.922
Appendix
Table S10 : Supplementary Table S10. BraTS ROI analysis — tumor vs. background reconstruction quality ( n=473 images with annotated tumor masks).
Dataset
MedVAE AE (PSNR)
SD-VAE AE (PSNR)
Δ
MRNet
27.85
23.92
+3.93
BraTS
37.87
31.39
+6.48
CXR
36.93
32.02
+4.91
Appendix
Table S11 : Supplementary Table S11. VAE autoencoder reconstruction ceiling. PSNR (dB) for encode-then-decode without any diffusion component. The MedVAE ceiling exceeds the SD-VAE ceiling by +3.93 to +6.48 dB.
Dataset
MedVAE AE
MedVAE SR
SD-VAE SR
ESRGAN
SwinIR
Bicubic
MRNet †
46
76
73
158
221
161
BraTS
9
38
31
111
83
102
CXR
15
59
48
101
74
111
Appendix
Table S12: Supplementary Table S12. Fréchet Inception Distance (FID) across all methods. Lower is better. MRNet FID values are unreliable ( n=120<2,048 minimum).
Figure S1 : Perception-distortion tradeoff across three medical imaging datasets (MRNet, BraTS, MIMIC-CXR). Each point represents one SR method evaluated on one dataset. x -axis: PSNR (dB; higher = less distortion); y -axis: LPIPS (lower = more perceptually faithful). MedVAE SR moves toward the upper-right Pareto frontier relative to SD-VAE SR, achieving simultaneously higher PSNR and lower LPIPS on all three datasets.
Figure S2 : Pixel-level hallucination and content loss — MRNet (knee MRI). Bar chart showing hallucination rate and loss rate (% of pixels) for MedVAE SR and SD-VAE SR.
Figure S3 : Pixel-level hallucination and content loss — BraTS (brain MRI).
Figure S4 : Pixel-level hallucination and content loss — MIMIC-CXR (chest X-ray, 4× SR).
Dataset
T=50
T=100
T=250
T=1,000
Δ
MRNet
0.962
0.975
0.968
0.956
0.019
BraTS
0.971
0.984
0.978
0.963
0.021
CXR
0.967
0.981
0.975
0.961
0.020
Appendix
Table S13 : Supplementary Table S13. Cosine similarity between SR latents and HR latents across diffusion timestep budgets at the global mean ( 1×1 ) scale. The narrow range ( Δ≤0.025 ) confirms that latent fidelity is determined primarily by the VAE architecture.
Figure S5 : Visual comparison and pixel-level difference maps — MRNet (knee MRI). Top: side-by-side comparison of AE reconstruction, MedVAE SR, SD-VAE SR, and HR ground truth. Bottom: mean absolute pixel difference ∣SR−HR∣ (hot colormap; brighter = larger error).
Figure S6 : Visual comparison and pixel-level difference maps — MIMIC-CXR (chest X-ray, 4× SR). Top: side-by-side comparison of AE reconstruction, MedVAE SR, SD-VAE SR, and HR ground truth. Bottom: mean absolute pixel difference ∣SR−HR∣ (hot colormap).
Medical image super-resolution reconstructs fine spatial detail from low-resolution scans to support clearer anatomy and more useful clinical measurements.
Medical image super-resolution (MedSR) is essential for improving diagnostic precision across diverse imaging modalities such as MRI, CT, X-ray, Ultrasound, and Fundus imaging. Despite rapid advances in deep learning, challenges remain in preserving anatomical accuracy, maintaining perceptual quality, and generalizing across medical domains. This paper presents MedSR-Vision, a novel unified deep learning framework for evaluating and comparing super-resolution models across five modalities: Brain MRI, Chest X-ray, Renal Ultrasound, Nephrolithiasis CT, and Spine MRI, at magnification scales of ×2, ×3, and ×4. Three representative models namely SRCNN, SwinIR, and Real-ESRGAN are benchmarked using multiple quantitative metrics encompassing fidelity, perceptual realism, and sharpness. Experimental analysis demonstrates that Real-ESRGAN achieves superior perceptual quality and edge recovery at higher scales, SwinIR excels in preserving structural and diagnostic features, and SRCNN provides efficient and stable performance at lower magnifications. The results establish domain-specific insights and practical guidelines for model selection in clinical imaging workflows, offering a standardized evaluation framework for future medical image super-resolution research and deployment.
Knight Foundation School of Computing and Information Sciences Florida International University Miami, FL 33199, USA · University of Florida Gainesville, FL 32611, USA · Department of Computer Science California State University, East Bay Hayward, CA 94542, USA
Image super-resolution (SR) with large generative models has recently achieved remarkable perceptual quality, yet maintaining fidelity to the LR observation remains challenging. In particular, we observe that diffusion transformers (DiTs) built on latent representations suffer from a critical limitation: the compression bottleneck of the VAE weakens fine-grained spatial information, leading to hallucinated details that are weakly grounded in the input image. In this work, we revisit generative SR from a representation perspective and propose a pixel-grounded super-resolution (PGSR) framework that preserves LR-observed pixel evidence before VAE compression and reuses it throughout restoration. Instead of relying solely on the compressed latent condition, PGSR extracts pre-VAE pixel evidence from the upsampled LR image and reuses it at two stages. First, Condition-Side Trajectory Guidance fuses LR-derived pixel evidence with the latent LR condition to guide the latent restoration trajectory. Second, Decoder-Side Pixel Grounding injects multi-scale pixel features into the frozen VAE decoder to ground the final rendering with LR-observed cues. To efficiently adapt large pretrained DiT models, we keep the latent autoencoder and main flow-matching backbone frozen, and train only lightweight restoration modules. We further study an efficient local-window attention variant for improved high-resolution efficiency and scalability. Extensive experiments demonstrate that PGSR improves the realism--fidelity trade-off and produces more faithful, visually convincing results than existing latent generative SR approaches.
In an image latent space, the embeddings of high-resolution, natural, and sharp images form a manifold. Degradation of high-resolution images pushes their embeddings off this manifold. Real-world super-resolution (SR) then becomes the task of mapping the degraded embedding back onto this manifold --- not anywhere on the manifold, but to the point that preserves what the input still carries, both its semantics and pixel details. Every published method implements this mapping in a reconstruction-oriented latent space or pixel space. We claim these spaces are the wrong substrates for SR. Low-resolution and degraded images are embedded far from the manifold, making the mapping difficult and expensive. The lack of semantic information in these substrates also makes it difficult to navigate to the faithful point on the manifold, causing severe hallucination when degradation is heavy. Thus, restoring in a suitable latent space is crucial to the SR task. We show that the latent space of 23 fused layers of a frozen DINOv3-L is one such space that makes the SR task easier. Degraded images are embedded near the manifold. Moreover, this substrate contains a hierarchy of information, from pixel record to degradation robust semantics, guiding the model to find the faithful point on the manifold. On this substrate, a 415M decoder is trained under reconstruction and adversarial objectives to map the degraded embeddings back and decode to pixel space in one pass. The resulting model, RAESR, attains the best fidelity--perception trade-off among state-of-the-art adversarial and diffusion-based restorers on RealSR, DRealSR, LSDIR and DIV2K-Val, at 37 ms per 512 by 512 image on a single H20 GPU. Swapping the substrate for a VAE latent under an identical recipe loses on every metric.
Wanzhou Lei, Cuifeng Shen, Yanjin He +6
University of California, Berkeley · Alibaba Group · University of Michigan, Ann Arbor +2