LLM-as-a-Judge: Reassessing the Performance of LLMs in Extractive QA

Extractive reading comprehension question answering (QA) datasets are typically evaluated using Exact Match (EM) and F1-score, but these metrics often fail to fully capture model performance. With the success of large language models (LLMs), they have been employed in various tasks, including serving as judges (LLM-as-a-judge). In this paper, we reassess the performance of QA models using LLM-as-a-judge across four reading comprehension QA datasets. We examine different families of LLMs and various answer types to evaluate the effectiveness of LLM-as-a-judge in these tasks. Our results show that LLM-as-a-judge is highly correlated with human judgments and can replace traditional EM/F1 metrics. By using LLM-as-a-judge, the correlation with human judgments improves significantly, from 0.17 (EM) and 0.36 (F1-score) to 0.85. These findings confirm that EM and F1 metrics underestimate the true performance of the QA models. While LLM-as-a-judge is not perfect for more difficult answer types (e.g., job), it still outperforms EM/F1, and we observe no bias issues, such as self-preference, when the same model is used for both the QA and judgment tasks.

Is fitting error a reliable metric for assessing deformable motion correction in quantitative MRI?

Quantitative MR (qMR) can provide numerical values representing the physical and chemical properties of the tissues. To collect a series of frames under varying settings, retrospective motion correction is essential to align the corresponding anatomical points or features. Under the assumption that the misalignment makes the discrepancy between the corresponding features larger, fitting error is a commonly used evaluation metric for motion correction in qMR. This study evaluates the reliability of the fitting error metric in cardiac diffusion tensor imaging (cDTI) after deformable registration. We found that while fitting error correlates with the negative eigenvalues, the negative Jacobian Determinant increases with broken cardiomyocytes, indicated by helix angle gradient line profiles. Since fitting error measures the distance between moved points and their re-rendered counterparts, the fitting parameter itself may be adjusted due to poor registration. Therefore, fitting error in deformable registration itself is a necessary but not sufficient metric and should be combined with other metrics.

Lightweight Hypercomplex MRI Reconstruction: A Generalized Kronecker-Parameterized Approach

Magnetic Resonance Imaging (MRI) is crucial for clinical diagnostics but is hindered by prolonged scan times. Current deep learning models enhance MRI reconstruction but are often memory-intensive and unsuitable for resource-limited systems. This paper introduces a lightweight MRI reconstruction model leveraging Kronecker-Parameterized Hypercomplex Neural Networks to achieve high performance with reduced parameters. By integrating Kronecker-based modules, including Kronecker MLP, Kronecker Window Attention, and Kronecker Convolution, the proposed model efficiently extracts spatial features while preserving representational power. We introduce Kronecker U-Net and Kronecker SwinMR, which maintain high reconstruction quality with approximately 50% fewer parameters compared to existing models. Experimental evaluation on the FastMRI dataset demonstrates competitive PSNR, SSIM, and LPIPS metrics, even at high acceleration factors (8x and 16x), with no significant performance drop. Additionally, Kronecker variants exhibit superior generalization and reduced overfitting on limited datasets, facilitating efficient MRI reconstruction on hardware-constrained systems. This approach sets a new benchmark for parameter-efficient medical imaging models.

Pretext Task Adversarial Learning for Unpaired Low-field to Ultra High-field MRI Synthesis

Given the scarcity and cost of high-field MRI, the synthesis of high-field MRI from low-field MRI holds significant potential when there is limited data for training downstream tasks (e.g. segmentation). Low-field MRI often suffers from a reduced signal-to-noise ratio (SNR) and spatial resolution compared to high-field MRI. However, synthesizing high-field MRI data presents challenges. These involve aligning image features across domains while preserving anatomical accuracy and enhancing fine details. To address these challenges, we propose a Pretext Task Adversarial (PTA) learning framework for high-field MRI synthesis from low-field MRI data. The framework comprises three processes: (1) The slice-wise gap perception (SGP) network aligns the slice inconsistencies of low-field and high-field datasets based on contrastive learning. (2) The local structure correction (LSC) network extracts local structures by restoring the locally rotated and masked images. (3) The pretext task-guided adversarial training process introduces additional supervision and incorporates a discriminator to improve image realism. Extensive experiments on low-field to ultra high-field task demonstrate the effectiveness of our method, achieving state-of-the-art performance (16.892 in FID, 1.933 in IS, and 0.324 in MS-SSIM). This enables the generation of high-quality high-field-like MRI data from low-field MRI data to augment training datasets for downstream tasks. The code is available at: https://github.com/Zhenxuan-Zhang/PTA4Unpaired_HF_MRI_SYN.

Task-oriented Uncertainty Collaborative Learning for Label-Efficient Brain Tumor Segmentation

Multi-contrast magnetic resonance imaging (MRI) plays a vital role in brain tumor segmentation and diagnosis by leveraging complementary information from different contrasts. Each contrast highlights specific tumor characteristics, enabling a comprehensive understanding of tumor morphology, edema, and pathological heterogeneity. However, existing methods still face the challenges of multi-level specificity perception across different contrasts, especially with limited annotations. These challenges include data heterogeneity, granularity differences, and interference from redundant information. To address these limitations, we propose a Task-oriented Uncertainty Collaborative Learning (TUCL) framework for multi-contrast MRI segmentation. TUCL introduces a task-oriented prompt attention (TPA) module with intra-prompt and cross-prompt attention mechanisms to dynamically model feature interactions across contrasts and tasks. Additionally, a cyclic process is designed to map the predictions back to the prompt to ensure that the prompts are effectively utilized. In the decoding stage, the TUCL framework proposes a dual-path uncertainty refinement (DUR) strategy which ensures robust segmentation by refining predictions iteratively. Extensive experimental results on limited labeled data demonstrate that TUCL significantly improves segmentation accuracy (88.2\% in Dice and 10.853 mm in HD95). It shows that TUCL has the potential to extract multi-contrast information and reduce the reliance on extensive annotations. The code is available at: https://github.com/Zhenxuan-Zhang/TUCL_BrainSeg.

GEMA-Score: Granular Explainable Multi-Agent Score for Radiology Report Evaluation

Automatic medical report generation supports clinical diagnosis, reduces the workload of radiologists, and holds the promise of improving diagnosis consistency. However, existing evaluation metrics primarily assess the accuracy of key medical information coverage in generated reports compared to human-written reports, while overlooking crucial details such as the location and certainty of reported abnormalities. These limitations hinder the comprehensive assessment of the reliability of generated reports and pose risks in their selection for clinical use. Therefore, we propose a Granular Explainable Multi-Agent Score (GEMA-Score) in this paper, which conducts both objective quantification and subjective evaluation through a large language model-based multi-agent workflow. Our GEMA-Score parses structured reports and employs NER-F1 calculations through interactive exchanges of information among agents to assess disease diagnosis, location, severity, and uncertainty. Additionally, an LLM-based scoring agent evaluates completeness, readability, and clinical terminology while providing explanatory feedback. Extensive experiments validate that GEMA-Score achieves the highest correlation with human expert evaluations on a public dataset, demonstrating its effectiveness in clinical scoring (Kendall coefficient = 0.70 for Rexval dataset and Kendall coefficient = 0.54 for RadEvalX dataset). The anonymous project demo is available at: https://github.com/Zhenxuan-Zhang/GEMA_score.

Towards Universal Learning-based Model for Cardiac Image Reconstruction: Summary of the CMRxRecon2024 Challenge

Cardiovascular magnetic resonance (CMR) offers diverse imaging contrasts for assessment of cardiac function and tissue characterization. However, acquiring each single CMR modality is often time-consuming, and comprehensive clinical protocols require multiple modalities with various sampling patterns, further extending the overall acquisition time and increasing susceptibility to motion artifacts. Existing deep learning-based reconstruction methods are often designed for specific acquisition parameters, which limits their ability to generalize across a variety of scan scenarios. As part of the CMRxRecon Series, the CMRxRecon2024 challenge provides diverse datasets encompassing multi-modality multi-view imaging with various sampling patterns, and a platform for the international community to develop and benchmark reconstruction solutions in two well-crafted tasks. Task 1 is a modality-universal setting, evaluating the out-of-distribution generalization of the reconstructed model, while Task 2 follows sampling-universal setting assessing the one-for-all adaptability of the universal model. Main contributions include providing the first and largest publicly available multi-modality, multi-view cardiac k-space dataset; developing a benchmarking platform that simulates clinical acceleration protocols, with a shared code library and tutorial for various k-t undersampling patterns and data processing; giving technical insights of enhanced data consistency based on physic-informed networks and adaptive prompt-learning embedding to be versatile to different clinical settings; additional finding on evaluation metrics to address the limitations of conventional ground-truth references in universal reconstruction tasks.

Mamba Neural Operator: Who Wins? Transformers vs. State-Space Models for PDEs

Partial differential equations (PDEs) are widely used to model complex physical systems, but solving them efficiently remains a significant challenge. Recently, Transformers have emerged as the preferred architecture for PDEs due to their ability to capture intricate dependencies. However, they struggle with representing continuous dynamics and long-range interactions. To overcome these limitations, we introduce the Mamba Neural Operator (MNO), a novel framework that enhances neural operator-based techniques for solving PDEs. MNO establishes a formal theoretical connection between structured state-space models (SSMs) and neural operators, offering a unified structure that can adapt to diverse architectures, including Transformer-based models. By leveraging the structured design of SSMs, MNO captures long-range dependencies and continuous dynamics more effectively than traditional Transformers. Through extensive analysis, we show that MNO significantly boosts the expressive power and accuracy of neural operators, making it not just a complement but a superior framework for PDE-related tasks, bridging the gap between efficient representation and accurate solution approximation.

Explicit Differentiable Slicing and Global Deformation for Cardiac Mesh Reconstruction

Mesh reconstruction of the cardiac anatomy from medical images is useful for shape and motion measurements and biophysics simulations to facilitate the assessment of cardiac function and health. However, 3D medical images are often acquired as 2D slices that are sparsely sampled and noisy, and mesh reconstruction on such data is a challenging task. Traditional voxel-based approaches rely on pre- and post-processing that compromises image fidelity, while mesh-level deep learning approaches require mesh annotations that are difficult to get. Therefore, direct cross-domain supervision from 2D images to meshes is a key technique for advancing 3D learning in medical imaging, but it has not been well-developed. While there have been attempts to approximate the optimized meshes' slicing, few existing methods directly use 2D slices to supervise mesh reconstruction in a differentiable manner. Here, we propose a novel explicit differentiable voxelization and slicing (DVS) algorithm that allows gradient backpropagation to a mesh from its slices, facilitating refined mesh optimization directly supervised by the losses defined on 2D images. Further, we propose an innovative framework for extracting patient-specific left ventricle (LV) meshes from medical images by coupling DVS with a graph harmonic deformation (GHD) mesh morphing descriptor of cardiac shape that naturally preserves mesh quality and smoothness during optimization. Experimental results demonstrate that our method achieves state-of-the-art performance in cardiac mesh reconstruction tasks from CT and MRI, with an overall Dice score of 90% on multi-datasets, outperforming existing approaches. The proposed method can further quantify clinically useful parameters such as ejection fraction and global myocardial strains, closely matching the ground truth and surpassing the traditional voxel-based approach in sparse images.

Learning Task-Specific Sampling Strategy for Sparse-View CT Reconstruction

Sparse-View Computed Tomography (SVCT) offers low-dose and fast imaging but suffers from severe artifacts. Optimizing the sampling strategy is an essential approach to improving the imaging quality of SVCT. However, current methods typically optimize a universal sampling strategy for all types of scans, overlooking the fact that the optimal strategy may vary depending on the specific scanning task, whether it involves particular body scans (e.g., chest CT scans) or downstream clinical applications (e.g., disease diagnosis). The optimal strategy for one scanning task may not perform as well when applied to other tasks. To address this problem, we propose a deep learning framework that learns task-specific sampling strategies with a multi-task approach to train a unified reconstruction network while tailoring optimal sampling strategies for each individual task. Thus, a task-specific sampling strategy can be applied for each type of scans to improve the quality of SVCT imaging and further assist in performance of downstream clinical usage. Extensive experiments across different scanning types provide validation for the effectiveness of task-specific sampling strategies in enhancing imaging quality. Experiments involving downstream tasks verify the clinical value of learned sampling strategies, as evidenced by notable improvements in downstream task performance. Furthermore, the utilization of a multi-task framework with a shared reconstruction network facilitates deployment on current imaging devices with switchable task-specific modules, and allows for easily integrate new tasks without retraining the entire model.