Prompts Without Evidence: How Neuroimaging Mentions Shift Clinical Vision-Language Model Predictions
Organizations: Natural Language Processing for Expert Domains (ExpNLP), Technical University of Darmstadt
Abstract
Trustworthy clinical AI must use real evidence and avoid relying on surface-level artifacts. We evaluate 12 open-weight vision-language models (VLMs) on two clinical neuroimaging cohorts for binary classification of affective disorders and cognitive decline. Both cohorts include structural magnetic resonance imaging (MRI) acquired under their original research protocols. Prior work does not establish the included neuroimaging inputs as reliable stand-alone diagnostic evidence for the present tasks. Nevertheless, when neuroimaging context is introduced, smaller VLMs gain up to 0.66 F1 under the evaluated augmented conditions, becoming competitive with models an order of magnitude larger. Confidence estimation shows that most of the calibration improvement for the analyzed smaller models occurs after the MRI reference is added to the prompt, before any image is supplied. Our preliminary expert case study finds that faithfulness remains low in every condition examined, with the reviewed model introducing unverified clinical details. Finally, in our single-model intervention, preference alignment suppresses MRI-referencing behavior but reduces the augmented-condition advantage, leaving the underlying issue unresolved. These results caution against reading surface metric gains as evidence of true multimodal integration, with direct implications for clinical VLM deployment.
Figures & tables
| Cond. | Input | CSV | Prompt(MRI) | Parcel. | Image | Image Type |
|---|---|---|---|---|---|---|
| C1 | text(csv) | ✓ | ||||
| C2 | text(csv) prompt(mri) | ✓ | ✓ | |||
| C3 | text(csv) prompt(mri) plot(MRI) | ✓ | ✓ | ✓ | nilearn brain plot | |
| C4 | text(csv, parcel) prompt(mri) plot(MRI) | ✓ | ✓ | ✓ | ✓ | nilearn brain plot |
| C5 | text(csv, parcel) prompt(mri) plot(swap) | ✓ | ✓ | ✓ | ✓ | OOD image (ablation) |
| Dataset | Group / Status | # Samples |
| FOR2107 | Active MDD | 701 |
| Control | 1,071 | |
| OASIS-3 | Cognitive Decline | 487 |
| Cognitive Normal | 849 |
| Cond. | Qwen2.5-VL-3B | Ministral-3-3B | ||
|---|---|---|---|---|
| ECE | Brier | ECE | Brier | |
| C1 | ||||
| C2 | ||||
| C4 | ||||
| Grp. | Cond., Class | Faith. | Clin. Acc. | Reasoning |
|---|---|---|---|---|
| 0 | C1, Control | |||
| 1 | C1, MDD | |||
| 2 | C4, Control | |||
| 3 | C4, MDD |
| Cond. | Input | FOR2107 | OASIS-3 | ||
|---|---|---|---|---|---|
| Qwen2.5-VL-3B | Ministral-3-3B | Qwen2.5-VL-3B | Ministral-3-3B | ||
| C1 | text(csv) | 0.153 | 0.064 | 0.262 | 0.504 |
| C2 | text(csv) prompt(mri) | 0.728 | 0.480 | 0.589 | 0.541 |
| C2 † | text(csv) prompt(fmri) | 0.702 | 0.361 | 0.379 | 0.569 |
| C2 ‡ | text(csv) prompt(weather) | 0.056 | 0.031 | 0.148 | 0.425 |
| Cond. | Before MPO | After MPO |
|---|---|---|
| C1 | 0.153 | 0.459 |
| C2 | 0.728 | 0.496 |
| C4 | 0.723 | 0.477 |
Appendix figures & tables29 assets
Supplementary material from the paper’s appendix.
Appendix
| Model | Prefix token IDs | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| GLM-4.1V-9B | 73022 | 2236 | 198 | 515 | 220 | 330 | 5471 | 788 | 330 | |
| GLM-4.6V-Flash | 73022 | 2236 | 198 | 515 | 220 | 330 | 5471 | 788 | 330 | |
| LLaVA-OV-1.5-4B | 73594 | 2236 | 198 | 515 | 220 | 330 | 5471 | 788 | 330 | |
| Ministral-3-3B | 1975 | 8353 | 1010 | 2030 | 1032 | 1429 | 17278 | 2811 | 1429 | |
| Ministral-3-14B | 1975 | 8353 | 1010 | 2030 | 1032 | 1429 | 17278 | 2811 | 1429 | |
| Qwen2.5-VL-3B | 73594 | 2236 | 198 | 515 | 220 | 330 | 5471 | 788 | 330 | |
| Abbreviation | Checkpoint (Link to HF) |
|---|---|
| GLM-4.1V-9B | zai-org/GLM-4.1V-9B-Thinking |
| GLM-4.6V-Flash | zai-org/GLM-4.6V-Flash |
| LLaVA-OV-1.5-4B | lmms-lab/LLaVA-OneVision-1.5-4B-Instruct |
| Ministral-3-3B | mistralai/Ministral-3-3B-Instruct-2512-BF16 |
| Ministral-3-14B | mistralai/Ministral-3-14B-Instruct-2512-BF16 |
| Qwen2.5-VL-3B | Qwen/Qwen2.5-VL-3B-Instruct |
| Model | F1 (C2 C1) | F1 (C4 C2) | F1 (C5 C4) |
|---|---|---|---|
| Qwen2.5-VL-3B | +0.575 [+0.531, +0.620] | 0.005 [ 0.039, +0.030] | +0.005 [ 0.024, +0.035] |
| Ministral-3-3B | +0.416 [+0.370, +0.461] | +0.197 [+0.148, +0.247] | 0.002 [ 0.045, +0.040] |
| InternVL3.5-4B | +0.255 [+0.215, +0.295] | 0.003 [ 0.059, +0.053] | +0.147 [+0.090, +0.205] |
| GLM-4.1V-9B | +0.119 [+0.068, +0.170] | +0.080 [+0.035, +0.125] | +0.012 [ 0.030, +0.052] |
| Model | F1 (C2 C1) | F1 (C4 C2) | F1 (C5 C4) |
|---|---|---|---|
| Qwen2.5-VL-3B | +0.327 [+0.262, +0.391] | +0.006 [ 0.053, +0.066] | +0.024 [ 0.033, +0.081] |
| Ministral-3-3B | +0.037 [ 0.010, +0.087] | +0.022 [ 0.019, +0.061] | +0.005 [ 0.041, +0.052] |
| InternVL3.5-4B | +0.020 [ 0.008, +0.047] | +0.019 [ 0.014, +0.053] | +0.020 [ 0.017, +0.055] |
| GLM-4.1V-9B | +0.118 [+0.051, +0.184] | +0.059 [ 0.008, +0.125] | +0.067 [+0.002, +0.132] |
| Model | F1 | P | R | ACC |
|---|---|---|---|---|
| C1: text(csv) | ||||
| InternVL3.5-4B | 0.000 | 0.000 | 0.000 | 0.604 |
| InternVL3.5-14B | 0.559 | 0.946 | 0.397 | 0.752 |
| GLM-4.1V-9B | 0.521 | 0.958 | 0.358 | 0.740 |
| GLM-4.6V-Flash | 0.795 | 0.896 | 0.715 | 0.854 |
| LLaVA-OV-1.5-4B | 0.663 | 0.954 | 0.508 | 0.796 |
| Model | F1 | P | R | ACC |
|---|---|---|---|---|
| C1: text(csv) | ||||
| InternVL3.5-4B | 0.616 | 0.470 | 0.893 | 0.594 |
| InternVL3.5-14B | 0.773 | 0.865 | 0.698 | 0.850 |
| GLM-4.1V-9B | 0.278 | 0.909 | 0.164 | 0.689 |
| GLM-4.6V-Flash | 0.359 | 0.901 | 0.224 | 0.708 |
| LLaVA-OV-1.5-4B | 0.679 | 0.591 | 0.799 | 0.725 |
| Dataset | Cond. | medgemma-4b-it | medgemma-27b-it | ||||||
|---|---|---|---|---|---|---|---|---|---|
| F1 | P | R | ACC | F1 | P | R | ACC | ||
| FOR2107 | C1 | 0.130 | 0.891 | 0.070 | 0.629 | 0.467 | 0.982 | 0.307 | 0.724 |
| C2 | 0.100 | 0.902 | 0.053 | 0.623 | 0.582 | 0.914 | 0.427 | 0.757 | |
| C3 | 0.003 | 1.000 | 0.001 | 0.605 | 0.625 | 0.925 | 0.472 | 0.776 | |
| C4 | 0.014 | 1.000 | 0.007 | 0.607 | 0.386 | 0.966 | 0.241 | 0.696 | |
| C5 | 0.003 | 1.000 | 0.001 | 0.605 | 0.322 | 0.951 | 0.194 | 0.677 | |
| Model | Cond. | ECE 15 | Brier |
|---|---|---|---|
| InternVL3.5-4B | C1 | 0.382 | 0.371 |
| C2 | 0.289 | 0.283 | |
| C4 | 0.265 | 0.264 | |
| GLM-4.1V-9B | C1 | 0.265 | 0.265 |
| C2 | 0.196 | 0.196 | |
| C4 | 0.204 | 0.204 |
| # | Category | Phrase | ||
|---|---|---|---|---|
| 1 | • MRI / neuroimaging | Brain MRI findings are available. | +0.43 | +0.02 |
| 2 | • General clinical | Diagnostic results are available. | +0.24 | +0.02 |
| 3 | • MRI / neuroimaging | Brain scans have been performed. | +0.23 | -0.01 |
| 4 | • Structural / format | Classification result: | +0.00 | -0.02 |
| 5 | • General clinical | A clinical diagnosis has been established. | -0.07 | -0.01 |
| 6 | • Structural / format | The answer is: | -0.25 | -0.09 |
| Cond. | Input | FOR2107 | OASIS-3 | ||
|---|---|---|---|---|---|
| InternVL3.5-4B | GLM-4.1V-9B | InternVL3.5-4B | GLM-4.1V-9B | ||
| C1 | text(csv) | 0.000 | 0.521 | 0.616 | 0.278 |
| C2 | text(csv) prompt(mri) | 0.255 | 0.640 | 0.636 | 0.396 |
| C2 † | text(csv) prompt(fmri) | 0.186 | 0.661 | 0.652 | 0.527 |
| C2 ‡ | text(csv) prompt(weather) | 0.000 | 0.512 | 0.594 | 0.339 |
| Hyperparameter | Value |
|---|---|
| Rank ( ) | 64 |
| Alpha ( ) | 128 |
| Dropout | 0.05 |
| Bias | none |
| Target modules | q, k, v, o, gate, up, down_proj |
| Hyperparameter | Value |
|---|---|
| MPO losses | |
| Loss types | sigmoid, bco_pair, sft |
| Loss weights | 0.8, 0.2, 1.0 |
| KL penalty ( ) | 0.1 |
| Optimization | |
| Learning rate | |
| Name | Description |
|---|---|
| Proband | Test subject |
| Datum_Interview | Date interview as stated on the interview form |
| Datum_Fragebogen | Date of the questionnaire |
| Geburtsjahr | Year of birth |
| Alter | Age |
| Geschlecht | Gender |
| Name | Description |
|---|---|
| RS-25: Resilience Scale | |
| RS251 | If I have plans, I follow them through. |
| RS252 | I usually manage everything somehow. |
| RS253 | I can rely on myself rather than on others. |
| RS254 | It is important for me to stay interested in many things. |
| RS255 | If I have to, I can be alone. |
| Name | Description |
|---|---|
| FSozU1 | I have people who can look after my home (flowers, pets) when I’m not there. |
| FSozU2 | There are people who accept me for who I am. |
| FSozU3 | It is important for my friends/relatives to know my opinion on certain things. |
| FSozU4 | I would like more understanding and care from others. |
| FSozU5 | I have a very trusted person whose help I can always count on. |
| FSozU6 | I can borrow tools and food if necessary. |
| Name | Description |
|---|---|
| LEQ_pn1 / LEQ1 | Health: Serious illness of one’s own (Type of influence / Influence on life) |
| LEQ_pn2 / LEQ2 | Health: Major change in eating habits |
| LEQ_pn3 / LEQ3 | Health: Major change in sleeping habits |
| LEQ_pn4 / LEQ4 | Health: Significant change in the type or amount of leisure activities |
| LEQ_pn5 / LEQ5 | Health: Major dental procedure |
| LEQ_pn6 / LEQ6 | Health: Pregnancy |
| Name | Description |
|---|---|
| LEQ_pn29 / LEQ29 | Love/Partnership: Entering into an engagement |
| LEQ_pn30 / LEQ30 | Love/Partnership: Problems with boyfriend or girlfriend |
| LEQ_pn31 / LEQ31 | Love/Partnership: Separation from boyfriend/girlfriend or breaking engagement |
| LEQ_pn32 / LEQ32 | Love/Partnership: Pregnancy of wife or girlfriend |
| LEQ_pn33 / LEQ33 | Love/Partnership: Miscarriage or abortion of wife or girlfriend |
| LEQ_pn34 / LEQ34 | Love/Partnership: Marriage or domestic partnership |
| Name | Description |
|---|---|
| LEQ_pn56 / LEQ56 | Personal/Social: Greater personal achievement |
| LEQ_pn57 / LEQ57 | Personal/Social: Important decision regarding your immediate future |
| LEQ_pn58 / LEQ58 | Personal/Social: Changes in your personal habits (clothing, lifestyle, hobbies) |
| LEQ_pn59 / LEQ59 | Personal/Social: Changes in your religious beliefs |
| LEQ_pn60 / LEQ60 | Personal/Social: Changes in your political views |
| LEQ_pn61 / LEQ61 | Personal/Social: Loss or damage to your personal property |
| Name | Description |
|---|---|
| SozDemo1 – SozDemo5 | Current living, work situation, occupation, social contacts |
| Haushaltu14 / Haushaltab14 | People in the household under/over 14 years |
| Haushaltsnetto | Household net income |
| Schulabschluss | Highest educational qualification achieved by subject |
| Schule_Vater / Schule_Mutter | Highest educational qualification achieved by father / mother |
| GebJahr_Mutter / GebJahr_Vater | Mother’s / Father’s year of birth |
| Name | Description |
|---|---|
| FzT: Drinking Habits | |
| FzT1 – FzT5 | Questions on frequency and quantity of alcohol consumption (now/past). |
| FzT6 – FzT9 | Questions on binge drinking (6+ drinks) and inability to stop (now/past). |
| FzT10 – FzT13 | Failing expectations due to alcohol; morning drinking (now/past). |
| FzT14 – FzT17 | Guilt, remorse, and memory loss due to alcohol (now/past). |
| FzT18 – FzT20 | Injuries, advice to reduce, and professional help sought for alcohol. |
| Name | Description |
|---|---|
| Subject Demographics & Family | |
| OASISID | OASIS subject ID |
| GENDER | Subject’s gender |
| RACE | Subject’s race |
| HAND | Subject’s Handedness |
| TWIN | Is this a new informant? (Note: Label suggests ’Twin’ but description asks about new informant status) |
| Name | Description |
|---|---|
| INSEX | Informant’s sex |
| INHISP | Does informant report being of Hispanic/Latino ethnicity? |
| INHISPOR | If yes, what are the informant’s reported origins? |
| INRACE | What does informant report as his/her race? |
| INRASEC | What additional race does informant report? |
| INRATER | What additional race, beyond what was indicated above, does informant report? |
| Name | Description |
|---|---|
| General Medical History | |
| HYPERTEN | Hypertension |
| HYPERCHO | Hypercholesterolemia |
| DIABETES | Diabetes |
| B12DEF | B12 deficiency |
| THYROID | Thyroid Disease |
| Name | Description |
|---|---|
| Lifestyle, Sleep & Trauma | |
| TOBAC100 | Smoked more than 100 cigarettes in life? |
| SMOKYRS | Total years smoked |
| ALCOHOL | Substance abuse - alcohol (clinically significant over a 12 month period) |
| TRAUMEXT | Traumatic brain injury with extended loss of consciousness ( 5 minutes) |
| TRAUMCHR | Traumatic brain injury with chronic deficit or dysfunction |