Microbial density is clinically important for tumor assessment and treatment decision-making, and recent advances in deep learning suggest that it can be non-invasively inferred from multimodal MRI. In this work, MRI-based Microbial Density Stratification (MRI-MDS) is first investigated as a patient-level representation learning task, and Center Heatmap-driven Macro-micro modeling Network (CHM-Net) is introduced for this task. CHM-Net first establishes the link between imaging phenotypes and microbial states through center heatmap-guided small-lesion response localization. Building upon this, it constructs patient-level macro-micro evidence from localized heatmap responses for microbial density prediction. Experiments on the novel GBNPC 2026 dataset constructed for MRI-MDS demonstrate the effectiveness of CHM-Net, achieving superior performance over representative baselines with a 12.06% absolute ACC gain over the strongest competing result. Additionally, auxiliary validation on two 3D medical image datasets further verifies its robustness across volumetric medical image classification scenarios. The project is available at https://anonymous.4open.science/r/CHM-Net-942E/.
Jiaming Liang, Haolin Chen, Tingting Li et al.· 0 citations
This paper presents FairNVT, a lightweight debiasing framework for pretrained transformer-based encoders that improves prediction fairness while preserving task performance. FairNVT is motivated by the intuition that reducing sensitive-attribute information in the representation used by the downstream classifier can facilitate fairer predictions. Our approach learns task-relevant and sensitive embeddings via lightweight adapters, applies calibrated Gaussian noise to the sensitive embedding, and fuses it with the task representation. Together with orthogonality constraints and fairness regularization, these components jointly reduce sensitive-attribute leakage in the learned embeddings and encourage fairer downstream predictions. Across three datasets spanning vision and language, FairNVT reduces sensitive-attribute attacker accuracy, improves fairness metrics such as demographic parity difference and equalized odds, and maintains competitive task performance.
Qiaoyue Tang, Sepidehsadat Hosseini, Mengyao Zhai et al.· 0 citations
Reliable uncertainty estimation is critical for medical image segmentation, where automated contours feed downstream quantification and clinical decision support. Many strong uncertainty methods require repeated inference, while efficient single-forward-pass alternatives often provide weaker failure ranking or rely on restrictive feature-space assumptions. We present $\textbf{SegWithU}$, a post-hoc framework that augments a frozen pretrained segmentation backbone with a lightweight uncertainty head. SegWithU taps intermediate backbone features and models uncertainty as perturbation energy in a compact probe space using rank-1 posterior probes. It produces two voxel-wise uncertainty maps: a calibration-oriented map for probability tempering and a ranking-oriented map for error detection and selective prediction. Across ACDC, BraTS2024, and LiTS, SegWithU is the strongest and most consistent single-forward-pass baseline, achieving AUROC/AURC of $0.9838/2.4885$, $0.9946/0.2660$, and $0.9925/0.8193$, respectively, while preserving segmentation quality. These results suggest that perturbation-based uncertainty modeling is an effective and practical route to reliability-aware medical segmentation.
Source code is available at https://github.com/ProjectNeura/SegWithU.
Tianhao Fu, Austin Wang, Charles Chen et al.· 0 citations
Recent text-driven motion generation methods span both discrete token-based approaches and continuous-latent formulations. MotionGPT3 exemplifies the latter paradigm, combining a learned continuous motion latent space with a diffusion-based prior for text-conditioned synthesis. While rectified flow objectives have recently demonstrated favorable convergence and inference-time properties relative to diffusion in image and audio generation, it remains unclear whether these advantages transfer cleanly to the motion generation setting. In this work, we conduct a controlled empirical study comparing diffusion and rectified flow objectives within the MotionGPT3 framework. By holding the model architecture, training protocol, and evaluation setup fixed, we isolate the effect of the generative objective on training dynamics, final performance, and inference efficiency. Experiments on the HumanML3D dataset show that rectified flow converges in fewer training epochs, reaches strong test performance earlier, and matches or exceeds diffusion-based motion quality under identical conditions. Moreover, flow-based priors exhibit stable behavior across a wide range of inference step counts and achieve competitive quality with fewer sampling steps, yielding improved efficiency-quality trade-offs. Overall, our results suggest that several known benefits of rectified flow objectives do extend to continuous-latent text-to-motion generation, highlighting the importance of the training objective choice in motion priors.
Spiking Neural Networks (SNNs), known for their biologically plausible architecture, face the challenge of limited performance. The self-attention mechanism, which is the cornerstone of the high-performance Transformer and also a biologically inspired structure, is absent in existing SNNs. To this end, we explore the potential of leveraging both self-attention capability and biological properties of SNNs, and propose a novel Spiking Self-Attention (SSA) and Spiking Transformer (Spikformer). The SSA mechanism eliminates the need for softmax and captures the sparse visual feature employing spike-based Query, Key, and Value. This sparse computation without multiplication makes SSA efficient and energy-saving. Further, we develop a Spiking Convolutional Stem (SCS) with supplementary convolutional layers to enhance the architecture of Spikformer. The Spikformer enhanced with the SCS is referred to as Spikformer V2. To train larger and deeper Spikformer V2, we introduce a pioneering exploration of Self-Supervised Learning (SSL) within the SNN. Specifically, we pre-train Spikformer V2 with masking and reconstruction style inspired by the mainstream self-supervised Transformer, and then finetune the Spikformer V2 on the image classification on ImageNet. Extensive experiments show that Spikformer V2 outperforms other previous surrogate training and ANN2SNN methods. An 8-layer Spikformer V2 achieves an accuracy of 80.38% using 4 time steps, and after SSL, a 172M 16-layer Spikformer V2 reaches an accuracy of 81.10% with just 1 time step. To the best of our knowledge, this is the first time that the SNN achieves 80+% accuracy on ImageNet. The code will be available at Spikformer V2.
Zhaokun Zhou, Yijie Lu, Kaiwei Che et al.· 0 citations
This study addresses critical gaps in automated lymphoma segmentation from PET/CT images, focusing on issues often overlooked in existing literature. While deep learning has been applied for lymphoma lesion segmentation, few studies incorporate out-of-distribution testing, raising concerns about model generalizability across diverse imaging conditions and patient populations. We highlight the need to compare model performance with expert human annotators, including intra- and inter-observer variability, to understand task difficulty better. Most approaches focus on overall segmentation accuracy but overlook lesion-specific measures important for precise lesion detection and disease quantification. To address these gaps, we propose a clinically relevant framework for evaluating deep segmentation networks. Using this lesion measure-specific evaluation, we assess the performance of four deep networks (ResUNet, SegResNet, DynUNet, and SwinUNETR) across 611 cases from multi-institutional datasets, covering various lymphoma subtypes and lesion characteristics. Beyond standard metrics like the Dice similarity coefficient, we evaluate clinical lesion measures and their prediction errors. We also introduce detection criteria for lesion localization and propose a new detection Criterion 3 based on metabolic characteristics. We show that networks perform better on large, intense lesions with higher metabolic activity. Finally, we compare network performance to physicians via intra- and inter-observer variability analyses, demonstrating that network errors closely resemble those made by experts, i.e., the small and faint lesions remain challenging for both humans and networks. This study aims to improve automated lesion segmentation's clinical relevance, supporting better treatment decisions for lymphoma patients. The code is available at: https://github.com/microsoft/lymphoma-segmentation-dnn.
Shadab Ahamed, Yixi Xu, Sara Kurkowska et al.· 0 citations
Despite comprising over 70% of its surface, the world's oceans are critically underobserved compared to the land surface or the atmosphere. Understanding the global ocean requires jointly observing its surface and subsurface structure, yet no standardized, high-resolution dataset couples satellite surface fields to co-located in situ depth profiles in an AI-ready format. Existing resources either consist of model-reconstructed gridded products rather than observations, cover only a single variable or basin, or operate at resolutions too coarse for mesoscale dynamics. We introduce OceanDepths, the first open, global, regridded AI-ready dataset that pairs satellite-derived sea surface temperature (SST), sea surface salinity (SSS), and sea surface height (SSH) L4 products with co-located EN4 subsurface temperature and salinity profiles, complemented by matched GLORYS12 ocean reanalysis data to support comparisons or multi-stage learning. The dataset spans 2000-2024 at 0.1 degrees x 0.1 degrees spatial resolution and at weekly temporal resolution, covering the entire globe's sea surface and with over 9.5 million paired profiles interpolated to 50 standardized depth levels. We provide a configurable system to split the globe in equally sized spatial patches. The 4D multivariate structure, high resolution, long temporal extent, and extreme sparsity of subsurface observations (approximately 0.01% per depth level) make OceanDepths a challenging testbed for novel AI methods. We demonstrate subsurface state reconstruction as an example task with simple baseline models, but also envision OceanDepths to support the development of observation-based forecast methods and other related tasks. Available at: https://huggingface.co/datasets/ESA-philab/OceanDepths.
Simon Donike, Ruben Cartuyvels, Antonino Ian Ferola et al.· 0 citations
Can neural networks learn algebraic rules from visual inputs, or do they merely fit observed patterns? We study this question using MNIST (or EMNIST letters) as states and modular arithmetic operations as actions in a JEPA-style world model. Standard supervised and JEPA baselines with operation embeddings achieve high accuracy on seen operations but fail to extrapolate reliably to unseen operations. We propose BRo-JEPA, a world model with a block-rotation predictor that represents arithmetic operations as rotations, resulting in the cyclic structure of modular arithmetic in latent space. By applying actions as rotations, the BRo-JEPA predictor learns the rotation angles to align the latent representations with the underlying modular structure which enables strict zero-shot operation generalization. While our best block-rotation supervised baseline reaches only 54.54% zero-shot accuracy on MNIST and 25.13% on EMNIST, BRo-JEPA with a ResNet-18 encoder achieves 99.44% and 94.35% respectively, despite being trained only on the primitive operations $\pm$1. Our results suggest that world models can learn algebraic rules when the latent transformations encode the underlying modular structure. Code is available \href{https://github.com/DL-World-Models/brojepa}{here}.
Divyansh Jha, Yuanfang Xie, Brennen Yu et al.· 0 citations
Reliable quantitative analysis of dynamic contrast-enhanced MRI requires high-quality spatiotemporal reconstructions at high undersampling rates. Scan-specific reconstructions using Gaussian and Gabor primitives have shown promising results without the need for large training datasets, but have not addressed the additional dimension of dynamic contrast. We propose a multi-dimensional, primitive based framework for dynamic contrast-enhanced MRI reconstruction that disentangles the underlying anatomy, the dynamic contrast enhancement, and residual motion into separate temporal basis functions, thereby enabling a geometrical interpretation of the representation. We show that this architecture achieves performance competitive with conventional reconstruction methods, both in reconstruction quality and in the accuracy of extracted aorta and kidney enhancement curves. The modular tier design extends naturally to additional dynamic factors and higher acceleration rates. Code available at https://github.com/compai-lab/2026-GaborDCE-spieker.
Veronika Spieker, Wenqi Huang, Cemre Ariyurek et al.· 0 citations
MRI reconstruction methods for undersampled k-space data naturally utilize complex-valued measurements. Parallel developments in sparse phase retrieval have shown that magnitude-only measurements may provide complementary information for signal recovery. However, their use in MRI reconstruction remains largely unexplored, due to lack of practical settings where informative magnitude measurements can be obtained without additional scan time. In this work, we investigate the use of auxiliary k-space magnitude information for accelerated steady-state dynamic MRI reconstruction, and demonstrate strong consistency of k-space magnitudes across time-frames. Building on this observation, we propose $\mathbb{C}+\text{Mag}$, a magnitude-informed physics-driven deep learning reconstruction method. The proposed method employs an ADMM-based unrolling framework with a novel magnitude-aware data-fidelity formulation, where quadratically smoothed optimization and momentum-based updates are introduced to address the non-differentiability and non-convexity of the magnitude constraints. Experiments on retrospectively undersampled cine MRI and phase-contrast flow MRI datasets, as well as prospectively undersampled real-time cine MRI acquisitions, demonstrate improved artifact suppression, sharper anatomical recovery, and better preservation of phase information compared to conventional PD-DL methods, which is further supported through blinded expert reader evaluations.
Appendicitis is one of the most common abdominal emergencies worldwide and requires prompt diagnosis and treatment to prevent life-threatening conditions. However, accurately differentiating complicated cases, such as perforation or abscess formation, from uncomplicated appendicitis remains a significant clinical challenge. Among other methods, ultrasound is a safer and more cost-efficient diagnostic technique because of the lack of radiation exposure. In this research, an advanced system capable of automatically detecting complicated appendicitis from ultrasound images was developed. A dataset consisting of 4679 ultrasound images with 5 classes, namely perforated, abscess, acute, appendicolith, and normal, was used for the proposed model training and testing. Four pretrained deep learning models, DenseNet201, InceptionV3, ConvNextTiny, and VGG19, have been employed for detecting and classifying complicated appendicitis. In the initial configuration, InceptionV3 achieved the second highest accuracy, with a value of 69.21%. Owing to suboptimal performance with raw images, further optimization techniques, including image preprocessing, hyperparameter tuning, model fine-tuning, and image sharpening, were applied. These enhancements significantly improved the model's performance, with an accuracy of 95.58% for InceptionV3. The model performance is then explained with gradient-weighted class activation mapping (Grad-CAM), which creates a heatmap of the regions responsible for the model's prediction of the infected areas. This could make crosschecking with experts much easier.
Fahad Ahammed, Omar Faruq Shikdar, Navid Zaman et al.· 0 citations
The health of marine ecosystems is a critical indicator of global environmental change, yet the physical constraints of underwater observation and the intrinsic challenges of processing marine imagery severely limit the scalability of systematic monitoring. While recent visual foundation models such as the Segment Anything Model (SAM) series show great promise, they still struggle with the fine-grained recognition required in these complex scenarios and still require expert supervision. Our work addresses this gap by bridging state-of-the-art foundation models with existing sparse supervision. Because historical benthic surveys are typically annotated with only a few sparse expert points per image, we utilize these legacy point-labels as visual prompts for SAM2. Our primary contribution is a novel mechanism to automatically identify which of these points are suitable, and which are actively harmful, when used for propagation. By filtering out unreliable points, we extract high-quality pseudo-ground-truth masks capable of training more accurate, fine-grained semantic segmentation models. We demonstrate the effectiveness of our approach on public benthic data and introduce a new, challenging benchmark featuring real-world sparse expert annotations, paving the way for scalable ecological analysis.
Cesar Borja, Breck A. McCollum, Jarret E. Byrnes et al.· 0 citations