How Medical VLMs Underutilize Their Vision Encoders: A Dermatology Perspective
Organizations: Tulane University · Oak Ridge National Laboratory
Abstract
Medical Vision-Language Models (VLMs) show significant promise for clinical image understanding, offering accurate diagnosis with interpretable reasoning. However, a critical performance gap exists between their strong vision encoders and the full multimodal model: in dermatology, the MedSigLIP encoder outperforms MedGemma by an average of 10.26 percentage points even when both use zero target-task labels; few-shot linear probing provides further evidence of strong visual representations. This gap motivates an investigation of how visual information is used in end-to-end diagnosis and why plausible-sounding predictions can lack grounding in image evidence. Using dermatology as our primary testbed, we systematically investigate three hypotheses for this phenomenon. We further provide a mechanistic analysis of the model's internal attention patterns, showing that a simple describe-then-decide prompting strategy increases vision attention by 30-40% during generation. Task-specific fine-tuning improves dermatology classification but reduces cross-domain medical question-answering performance in our evaluation. To address these challenges, we combine label-free prompting with low-label encoder-assisted reranking while keeping the VLM frozen. We validate the interventions across five VLM backbones in dermatology and provide supporting representation and attention analyses across additional medical modalities.
Figures & tables
| Zero target labels | 8-shot | ||||
| Dataset | VLM | MedSigLIP | Image ICL | LP | Reranking |
| Derm7pt | 16.46 | 24.18 | 19.44 | 28.66 | 35.56 |
| eSkinHealth | 13.35 | 26.53 | 18.15 | 38.80 | 42.05 |
| Fitzpatrick17k | 16.73 | 28.37 | 20.72 | 38.43 | 37.82 |
| SD-260 | 10.81 | — | — | 37.12 | 42.33 |
| PAD-UFES-20 | 46.91 | 55.42 | 49.58 | 53.33 | 80.31 |
| Prompt context | Fitzpatrick17k | PAD-UFES-20 |
| Names only | 16.73 | 46.22 |
| Class-aligned descriptions | 24.01 | 52.23 |
| Length-matched generic text | 16.68 | 36.36 |
| Shuffled descriptions | 12.71 | 15.64 |
| Dataset | DA | in-context | DtD | top-5 to top-1 | all combined |
| Derm7pt | 16.46 ( 0.17) | 26.72 ( 0.82) | 30.98 ( 1.37) | 35.10 ( 1.95) | 38.27 ( 0.81) |
| eSkinHealth | 13.35 ( 0.23) | 30.07 ( 1.51) | 29.77 ( 0.92) | 43.94 ( 1.03) | 48.00 ( 0.86) |
| Fitzpatrick17k | 16.73 ( 0.25) | 24.01 ( 2.01) | 24.75 ( 1.53) | 28.32 ( 1.67) | 40.97 ( 1.41) |
| SD-260 (subset) | 24.31 ( 0.15) | 34.29 ( 1.06) | 33.80 ( 1.37) | 40.01 ( 2.18) | 44.90 ( 0.91) |
| PAD-UFES-20 | 46.22 ( 0.17) | 52.23 ( 1.26) | 62.33 ( 1.58) | 75.23 ( 2.07) | 84.68 ( 1.80) |
| Inference Strategy | Derm7pt | eSkinHealth | Fitzpatrick17k |
| Direct Answer (Baseline) | 12.77 ( 0.12) | 23.76 ( 0.21) | 10.05 ( 0.08) |
| + Top-5 Filtering | 29.66 ( 1.45) | 40.25 ( 1.82) | 58.37 ( 1.15) |
| + In-Context Description | 31.19 ( 1.33) | 44.03 ( 2.01) | 62.97 ( 1.28) |
| + DtD (Ours) | 32.56 ( 0.95) | 44.89 ( 1.67) | 63.91 ( 1.05) |
| Model | Dataset | DA | DtD | Top-5 |
| InternVL3-4B | D7 | 5.68 | 6.20 | 14.83 |
| F17 | 10.10 | 12.23 | 19.70 | |
| InternVL3.5-4B | D7 | 7.21 | 7.85 | 18.32 |
| F17 | 9.25 | 13.15 | 22.16 | |
| biomed-Qwen2.5-VL-3B | D7 | 20.93 | 38.50 | 41.24 |
| F17 | 12.14 | 19.96 | 22.35 |
| Linear Probe | VLM | ||||||
| Dataset | Modality | #Cls | 1-shot | 4-shot | 8-shot | 16-shot | 0-shot |
| CXR | Radiology | 5 | 24.6 ( 2.1) | 54.6 ( 1.5) | 59.3 ( 1.2) | 60.9 ( 0.9) | 36.1 ( 0.5) |
| PCam | Pathology | 2 | 58.2 ( 2.4) | 78.9 ( 1.3) | 82.2 ( 0.8) | 81.5 ( 1.0) | 70.9 ( 0.8) |
| PathM | Pathology | 9 | 78.2 ( 1.6) | 90.9 ( 0.9) | 93.5 ( 0.6) | 94.3 ( 0.5) | 40.6 ( 0.6) |
| BloodM | Hematology | 8 | 61.3 ( 2.3) | 78.1 ( 1.4) | 86.3 ( 0.9) | 89.0 ( 0.7) | 26.8 ( 0.4) |
| OrganA | CT | 11 | 49.2 ( 2.5) | 63.9 ( 1.6) | 71.5 ( 1.1) | 76.2 ( 0.8) | 21.4 ( 0.3) |
Appendix figures & tables25 assets
Supplementary material from the paper’s appendix.
Appendix
| Dataset | MedGemma | MedSigLIP | BiomedCLIP | DermLIP |
| Derm7pt | 16.46 | 24.18 | 24.55 | 24.03 |
| eSkinHealth | 13.35 | 26.53 | 28.22 | 29.28 |
| Fitzpatrick17k | 16.73 | 28.37 | 25.71 | 31.55 |
| PAD-UFES-20 | 46.91 | 55.42 | 46.39 | 53.06 |
| Dataset | VLM 0-shot | Image ICL | LP | Reranking |
| Derm7pt | 16.46 | 19.44 | 28.66 | 35.56 |
| eSkinHealth | 13.35 | 18.15 | 38.80 | 42.05 |
| Fitzpatrick17k | 16.73 | 20.72 | 38.43 | 37.82 |
| PAD-UFES-20 | 46.91 | 49.58 | 53.33 | 80.31 |
| Baseline VLM | Linear Probe | Our Pipeline | |||
| Dataset | Zero-Shot | (Vision Encoder Only) | (LP Top-5 VLM Top-1) | ||
| 0-shot | 1-shot | 8-shot | 1-shot | 8-shot | |
| Derm7pt | 16.46 ( 0.01) | 12.96 ( 1.75) | 28.66 ( 1.38) | 20.02 ( 2.39) | 35.56 ( 0.99) |
| eSkinHealth | 13.35 ( 0.23) | 23.51 ( 1.91) | 38.80 ( 1.06) | 30.98 ( 2.85) | 42.05 ( 1.48) |
| Fitzpatrick17k | 16.73 ( 0.19) | 17.63 ( 3.13) | 38.43 ( 1.03) | 25.35 ( 2.41) | 37.82 ( 1.37) |
| SD-260 | 10.81 ( 0.13) | 11.48 ( 2.27) | 37.12 ( 1.46) | 22.31 ( 1.95) | 42.33 ( 0.92) |
| Setting | Fitzpatrick17k | PAD-UFES-20 |
| Names only | 16.73 | 46.22 |
| Class-aligned descriptions | 24.01 | 52.23 |
| Length-matched generic text | 16.68 | 36.36 |
| Shuffled descriptions | 12.71 | 15.64 |
| Top-5-to-Top-1 | 28.32 | 75.23 |
| All combined | 40.97 | 84.68 |
| Data Details | MedGemma-4B | PanDerm | |||||||||
| Datasets | #Class | #Train | #Test | Zero-Shot | Fine-tune | Linear Probe | Linear Probe | ||||
| ACC | F1 | ACC | F1 | ACC | F1 | ACC | F1 | ||||
| Derm7pt | 14 | 413 | 395 | 16.46 ( 0.02) | 17.77 | 39.50 ( 2.15) | 22.49 | 57.22 ( 0.88) | 30.07 | 58.99 ( 0.76) | 57.93 |
| eSkinHealth | 24 | 2,714 | 2,676 | 13.35 ( 0.15) | 16.33 | 60.26 ( 1.42) | 56.17 | 65.35 ( 0.54) | 42.51 | 60.64 ( 0.61) | 59.83 |
| Fitzpatrick17k | 20 | 3,100 | 3,100 | 16.73 ( 0.08) | 11.13 | 47.32 ( 1.10) | 45.16 | 66.32 ( 0.45) | 66.90 | 64.87 ( 0.39) | 64.88 |
| SD-260 | 260 | 10,362 | 10,238 | 10.81 ( 0.05) | 7.94 | 39.45 ( 0.95) | 34.63 | 75.35 ( 0.32) | 60.10 | 72.08 ( 0.28) | 60.24 |
| Model | Dataset | DA | DtD | Top-5-to-Top-1 |
| InternVL3-4B | Derm7pt | 5.68 | 6.20 | 14.83 |
| Fitzpatrick17k | 10.10 | 12.23 | 19.70 | |
| InternVL3.5-4B | Derm7pt | 7.21 | 7.85 | 18.32 |
| Fitzpatrick17k | 9.25 | 13.15 | 22.16 | |
| biomed-Qwen2.5-VL-3B | Derm7pt | 20.93 | 38.50 | 41.24 |
| Fitzpatrick17k | 12.14 | 19.96 | 22.35 |
| Model | Closed-ended | Open-ended | Token recall |
| Base MedGemma-4B | 70.92 | 37.50 | 49.96 |
| Fitzpatrick17k QLoRA | 65.88 | 22.50 | 27.43 |
| Dataset | Modality | DA | DtD | |
| Fitzpatrick17k | Dermatology | 4.81 | 4.67 | 0.14 |
| CheXpert | Radiology | 4.81 | 4.61 | 0.20 |
| PatchCamelyon | Pathology | 4.74 | 4.58 | 0.16 |
| PathMNIST | Pathology | 4.77 | 4.69 | 0.08 |
| BloodMNIST | Hematology | 4.65 | 4.57 | 0.08 |
| OrganAMNIST | CT | 4.88 | 4.67 | 0.21 |
| Dataset | Modality | DA | DtD | (Rel.) |
| Fitz17k | Dermatology | 2.85 | 3.98 | +39.8% |
| CXR | Radiology | 3.02 | 4.24 | +40.2% |
| PCam | Pathology | 2.98 | 3.95 | +32.5% |
| PathM | Pathology | 2.32 | 3.02 | +30.1% |
| BloodM | Hematology | 2.86 | 3.80 | +33.1% |
| OrganA | CT | 2.67 | 3.60 | +34.7% |
| Type | Prompt |
| direct answer (baseline) | You are a helpful medical assistant. Look at the given image and determine the most likely dermatology condition from the options: (A) Granuloma annulare (B) Lupus erythematosus (C) Vitiligo. … … |
| in-context | You are a helpful medical assistant. Look at the given image and determine the most likely dermatology condition from the options: (A) Granuloma annulare, characterized by smooth skin-colored or pink papules arranged in an annular ring with firm ridge. (B) Lupus erythematosus, characterized by scaly plaques with follicular plugging and central scarring on sun-exposed skin; acute malar rash appears as flat red butterfly across cheeks sparing folds. (C) Vitiligo, characterized by sharply bordered milky white macules on face, hands, or genital skin with normal texture and pigment loss. … … |
| DtD | You are a helpful medical assistant. Look at the given image and describe visible lesion attributes (location, lesion type, shape/border, color, texture). Then determine the most likely diagnosis from the options: (A) Granuloma annulare (B) Lupus erythematosus (C) Vitiligo. … … |
| Hyperparameter | Search Space | Selected Value |
| LoRA Rank ( ) | ||
| LoRA Alpha ( ) | ||
| Learning Rate | ||
| LoRA Dropout | - | |
| Target Modules | - | All Linear Layers |
| Precision | - | 4-bit (QLoRA) |
| Rank ( ) | Alpha ( ) | Learning Rate | Accuracy (%) |
| 4 | 8 | 42.15 | |
| 4 | 8 | 46.12 | |
| 4 | 8 | 45.88 | |
| 4 | 16 | 41.80 | |
| 4 | 16 | 45.05 | |
| 4 | 16 | 44.20 |
| Hyperparameter | Value |
| Vision Encoder | MedSigLIP (Frozen) |
| Feature Pooling | Global Average Pooling |
| Precision (Backbone) | bfloat16 |
| Precision (Head) | float32 |
| Optimizer | AdamW |
| Batch Size | 128 |
| Dataset | 0-shot Top-1 | 1-shot | 2-shot | 4-shot | 8-shot | 16-shot | ||||||||||
| Top1 | Top5 | 0-Shot | Top1 | Top5 | 0-Shot | Top1 | Top5 | 0-Shot | Top1 | Top5 | 0-Shot | Top1 | Top5 | 0-Shot | ||
| Derm7pt | 16.46 | 12.96 | 52.25 | 20.02 | 18.53 | 58.03 | 25.73 | 21.06 | 61.42 | 32.80 | 28.66 | 72.35 | 35.56 | 38.53 | 82.68 | 37.95 |
| eSkinHealth | 13.35 | 23.51 | 55.75 | 30.98 | 27.99 | 63.84 | 33.67 | 35.04 | 69.70 | 41.22 | 38.80 | 73.96 | 42.05 | 43.04 | 78.41 | 43.17 |
| Fitzpatrick17k | 16.73 | 17.63 | 50.58 | 25.35 | 23.08 | 59.50 | 27.42 | 31.01 | 67.67 | 33.68 | 38.43 | 75.88 | 37.82 | 45.05 | 80.99 | 38.01 |
| SD-260 | 10.81 | 11.48 | 26.89 | 22.31 | 17.90 | 38.61 | 25.02 | 26.97 | 51.92 | 33.50 | 37.12 | 63.61 | 42.33 | 49.01 | 76.72 | 44.72 |
| PAD-UFES-20 | 46.91 | 34.85 | 93.99 | 58.33 | 38.56 | 96.70 | 67.60 | 45.36 | 98.33 | 77.85 | 53.33 | 98.63 | 80.31 | 59.90 | 98.99 | 91.11 |
| VLM Zero-Shot | Fine-Tuning (FT) | Linear Probe (LP) | ||||
| Dataset | ACC | F1 | ACC | F1 | ACC | F1 |
| Derm7pt | 12.77 | 15.05 | 44.81 | 22.98 | 50.16 | 26.59 |
| eSkinHealth | 13.76 | 10.33 | 57.74 | 39.24 | 62.77 | 42.90 |
| Fitzpatrick17k | 10.05 | 8.27 | 42.84 | 30.49 | 58.88 | 46.22 |
| Skin Condition | Real Training | Real Test | Synthetic |
| Acne (ACN) | 92 | 91 | 93 |
| Actinic Keratosis (AK) | 88 | 87 | 164 |
| Allergic Contact Dermatitis (ACD) | 215 | 215 | 181 |
| Basal Cell Carcinoma (BCC) | 234 | 234 | 154 |
| Eczema (ECZ) | 102 | 102 | 166 |
| Erythema Multiforme (EM) | 118 | 118 | 155 |
| Dataset | # Cls | Train | Test | Class Names |
|---|---|---|---|---|
| Derm7pt | 14 | 413 | 395 | clark nevus, melanoma, reed or spitz nevus, seborrheic keratosis, basal cell carcinoma, vascular lesion, lentigo, blue nevus, dermal nevus, dermatofibroma, combined nevus, congenital nevus, miscellaneous, recurrent nevus |
| eSkinHealth | 24 | 2,714 | 2,676 | buruli ulcer, scabies, yaws, prurigo nodularis, tinea corporis, erysipelas, tinea capitis, leprosy, impetigo, necrotizing fasciitis, contact dermatitis, lichen planus, tinea versicolor, folliculitis, chickenpox, acne, vitiligo, abscess, keratosis, herpes zoster, atopic dermatitis, eczema, lipome, mycetoma |
| Fitzpatrick17k | 20 | 3,100 | 3,100 | psoriasis, squamous cell carcinoma, lichen planus, basal cell carcinoma, allergic contact dermatitis, lupus erythematosus, sarcoidosis, folliculitis, scabies, melanoma, erythema multiforme, granuloma annulare, eczema, pityriasis rosea, mycosis fungoides, acne, actinic keratosis, prurigo nodularis, vitiligo, keloid |
| SD-260 | 260 | 10,362 | 10,238 | abrasion, acne excoriee, acne keloidalis nuchae, acne vulgaris, acrokeratosis verruciformis, actinic solar damage, actinex treatment, actinic cheilitis, actinic keratosis, cutis rhomboidalis nuchae, actinic favre-racouchot, pigmentation, actinic solar elastosis, solar purpura, telangiectasia, actinic wrinkles, acute eczema, allergic contact dermatitis, alopecia areata, anagen effluvium, androgenetic alopecia, angiofibroma, angiokeratoma, angioma, angular cheilitis, aphthous ulcer, apocrine hydrocystoma, arsenical keratosis, atopic dermatitis, balanitis xerotica obliterans, basal cell carcinoma, beaus lines, beckers nevus, behcets syndrome, benign keratosis, blue nevus, bowenoid papulosis, bowens disease, cafe au lait macule, callus, candidiasis, cellulitis, chalazion, cherry angioma, clubbing of fingers, combined nevus, compound nevus, congenital nevus, contact dermatitis, crowes sign, cutanea larva migrans, cutaneous horn, cutaneous leishmaniasis, cutaneous t-cell lymphoma, cutis marmorata, darier-white disease, dermatofibroma, dermatomyositis, dermatosis papulosa nigra, desquamation, digital fibroma, dilated pore of winer, discoid lupus erythematosus, disseminated actinic porokeratosis, drug eruption, dry skin eczema, dyshidrosiform eczema, dysplastic nevus, eccrine poroma, eczema, epidermal nevus, epidermoid cyst, epithelioma adenoides cysticum, erythema ab igne, erythema annulare centrifigum, erythema craquele, erythema multiforme, exfoliative erythroderma, factitial dermatitis, favre-racouchot, fibroma, fibroma molle, fixed drug eruption, follicular mucinosis, follicular retention cyst, fordyce spots, frictional lichenoid dermatitis, ganglion, geographic tongue, granulation tissue, granuloma annulare, green nail, guttate psoriasis, hailey-hailey disease, half and half nail, halo nevus, hand foot mouth disease, herpes gestationis, herpes simplex virus, herpes zoster, hidradenitis suppurativa, hirsutism, histiocytosis x, hyperkeratosis palmaris et plantaris, hypertrichosis, ichthyosis, ichthyosis vulgaris, id reaction, impetigo, infantile atopic dermatitis, insect bite, intradermal nevus, inverse psoriasis, ischemia, junction nevus, keloid, keratoacanthoma, keratolysis exfoliativa of wende, keratosis pilaris, kerion, koilonychia, kyrles disease, leiomyoma, lentigo maligna melanoma, lentigo simplex, leprosy, leukemia cutis, leukocytoclastic vasculitis, leukonychia, lichen planus, lichen sclerosis et atrophicus, lichen simplex chronicus, lichen spinulosis, linear epidermal nevus, lipoma, livedo reticularis, lymphangioma circumscriptum, lymphocytic infiltrate of jessner, lymphocytoma cutis, lymphomatoid papulosis, mal perforans, malignant melanoma, median nail dystrophy, melasma, metastatic carcinoma, milia, molluscum contagiosum, morphea, mucha-habermann disease, mucous membrane psoriasis, myxoid cyst, nail cosmesis, nail dystrophy, nail nevus, nail psoriasis, nail ridging, nail trauma, neurodermatitis, neurofibroma, neurotic excoriations, nevus cell nevus, nevus comedonicus, nevus incipiens, nevus sebaceous of jadassohn, nevus spilus, nummular eczema, onychogryphosis, onycholysis, onychomycosis, onychoschizia, paronychia, pearly penile papules, pediculosis pubis, pemphigus foliaceus, perioral dermatitis, photodermatitis, pilomatrixoma, pincer nail syndrome, pitted keratolysis, pityriasis alba, pityriasis rosea, pityriasis rubra pilaris, pityriasis versicolor, pityrosporum folliculitis, poikiloderma atrophicans vasculare, pomade acne, porokeratosis of mibelli, port wine stain, pseudofolliculitis barbae, pseudorhinophyma, psoriasis, pterygium inversum unguis, pustular psoriasis, pyoderma gangrenosum, pyogenic granuloma, racquet nail, radiodermatitis, rhinophyma, rosacea, scabies, scalp psoriasis, scar, scarring alopecia, schambergs disease, sebaceous gland hyperplasia, seborrheic dermatitis, seborrheic keratosis, skin tag, solar elastosis, solar lentigo, spindle cell nevus, squamous cell carcinoma (scc), stasis dermatitis, stasis edema, stasis ulcer, steroid acne, steroid atrophy, steroid striae, steroid use, stomatitis, strawberry hemangioma, striae, subacute cutaneous lupus erythematosus, subungual hematoma, superficial actinic porokeratosis, syringoma, systemic lupus erythematosus, terrys nails, thermal burn, tick bite, tinea capitis, tinea corporis, tinea cruris, tinea faciale, tinea incognito, tinea manus, tinea pedis, tinea versicolor, toe deformity, traction alopecia, trichilemmal cyst, trichoepithelioma, trichofolliculoma, trichostasis spinulosa, trichotillomania, tuberous sclerosis, twenty nail dystrophy, ulcer, urticaria, uvl burn, varicella, verruca vulgaris, viral exanthem, virilization, vitiligo, von recklinghausens disease, wart, wound infection, xerosis, x-linked ichthyosis |
| PAD-UFES-20 | 6 | 1,134 | 1,164 | actinic keratosis, basal cell carcinoma, melanoma, nevus, seborrheic keratosis, squamous cell carcinoma |
| Condition | Description |
|---|---|
| acne | Face/chest/back comedones and inflamed papules/pustules ±nodules; red or skin-colored with black/white heads; oily, ±crust. |
| actinic keratosis | Sun-exposed rough, scaly flat/slightly raised papule <1 cm; pink/red/brown; gritty sandpaper feel. |
| allergic contact dermatitis | At contact sites, ill-defined pink-red (darker on dark skin) patches/plaques ±vesicles/edema; weepy/crusty/scaly surface. |
| basal cell carcinoma | Sun-exposed pearly/waxy papule or thin scaly patch with rolled edge ±central ulcer; translucent or brown/black; smooth/shiny ±crust. |
| eczema | Flexural dry itchy ill-defined patches/plaques ±tiny vesicles; red/pink or purple/gray on dark skin; flaky ±lichenified. |
| erythema multiforme | Acral target lesions—round 1–3 cm with dark center, pale ring, red outer rim—mostly flat ±blister. |