How Good are Foundation Models in
Longitudinal MRI Disease Progression Reasoning?

Time-Aware Multi-View MRI Benchmark

MICCAI 2026 Early Accept · Top 9% Spotlight Presentation
Wafa Al Ghallabi1, Ritesh Thawkar1, Sara Ghaboura1, Omkar Thawakar1, Numan Saeed1, Dana Al Nuaimi2, Ajnas Alkatheeri3, Salman Khan1, Fahad Shahbaz Khan1,4
1 MBZUAI   ·   2 Department of Health Abu Dhabi   ·   3 Fatima College of Health Sciences   ·   4 Linköping University

Abstract

Real-world radiology is comparative and longitudinal: disease progression is assessed by comparing current and prior MRI scans across multiple anatomical views and sequences. The Time-Aware Multi-View MRI Benchmark evaluates whether foundation models can reason over these longitudinal changes rather than interpret isolated images. It brings together 3,920 expert-verified question-answer pairs from 890 patients and more than 3,200 MRI timepoints across seven longitudinal cohorts, spanning glioblastoma, brain metastases, neurodegeneration, and vestibular schwannoma. Across 16 vision-language models, the benchmark reveals persistent limitations in clinically important change characterization, temporal reasoning, and quantitative assessment.

At a Glance

3,920Expert-verified QA pairs
890Patients
3,200+MRI timepoints
7Longitudinal cohorts
5Evaluation tasks
16VLMs evaluated
Longitudinal reasoning

Models must identify what changed, where it changed, and how that change evolves across timepoints.

Multi-view MRI

Axial, coronal, and sagittal evidence is evaluated together rather than treating scans as isolated 2D images.

Clinically grounded evaluation

The benchmark spans multiple diseases and uses expert-reviewed question-answer pairs.

Time-Aware Multi-View MRI Benchmark

Benchmark pipeline

Benchmark construction pipeline. Longitudinal MRI cohorts are harmonized through multi-view extraction and preprocessing, followed by expert-guided QA generation and radiologist verification.

Overview

The benchmark evaluates foundation models on five complementary tasks designed around longitudinal MRI interpretation and disease progression reasoning.

Benchmark Coverage

Temporal Reasoning · Disease Progression · Structured Localization Guidance · Temporal Sequence Ordering · Change Localization Over Time

Benchmark coverage comparison

Comparison with existing MRI benchmarks. Time-Aware MRI provides full coverage across all five reasoning dimensions.

Five Evaluation Tasks

Temporal Reasoning

Interpret interval changes across sequential scans, planes, and contrasts.

Disease Progression

Characterize growth, regression, or stability over time.

Structured Localization Guidance

Identify changed anatomy, boundaries, features, and confounders.

Temporal Sequence Ordering

Arrange scans chronologically from visible progression patterns.

Change Localization Over Time

Identify the timepoint and spatial region showing maximal change.

Representative Benchmark Samples

Representative benchmark samples

Representative longitudinal MRI reasoning samples across metastatic lesions, glioblastoma, and neurodegenerative progression.

Main Findings

Across 16 vision-language models, current systems achieve moderate temporal alignment but remain limited in clinically important change characterization and quantitative reasoning.

0.800Best TAC

InternVL3.5-Inst

35.15%Best Final Accuracy

InternVL3.5-Inst

97.3%Progression Localization

Peak result in the multi-view analysis

<16%Change Segmentation & Quantification

Across evaluated models

Key observation. Strong spatial localization does not translate into reliable geometric or quantitative reasoning, highlighting an important gap for longitudinal MRI foundation models.

Data Access & Reproducibility

Source MRI images are not redistributed through this project page or repository. Researchers should obtain the source datasets from their official providers and follow the corresponding licenses and data-use agreements. The repository provides preprocessing and evaluation code for reproducing the benchmark workflow.

BibTeX

@inproceedings{alghallabi2026timeaware,
  title={How Good are Foundation Models in Longitudinal MRI Disease Progression Reasoning?},
  author={Al Ghallabi, Wafa and Thawkar, Ritesh and Ghaboura, Sara and Thawakar, Omkar and Saeed, Numan and Al Nuaimi, Dana and Alkatheeri, Ajnas and Khan, Salman and Khan, Fahad Shahbaz},
  booktitle={Medical Image Computing and Computer Assisted Intervention -- MICCAI 2026},
  year={2026}
}