WSI-INR: Implicit Neural Representations for Lesion Segmentation in Whole-Slide Images

Whole-slide images (WSIs) are fundamental for computational pathology, where accurate lesion segmentation is critical for clinical decision making. Existing methods partition WSIs into discrete patches, disrupting spatial continuity and treating multi-resolution views as independent samples, which leads to spatially fragmented segmentation and reduced robustness to resolution variations. To address the issues, we propose WSI-INR, a novel patch-free framework based on Implicit Neural Representations (INRs). WSI-INR models the WSI as a continuous implicit function mapping spatial coordinates directly to tissue semantics features, outputting segmentation results while preserving intrinsic spatial information across the entire slide. In the WSI-INR, we incorporate multi-resolution hash grid encoding to regard different resolution levels as varying sampling densities of the same continuous tissue, achieving a consistent feature representation across resolutions. In addition, by jointly training a shared INR decoder, WSI-INR can capture general priors across different cases. Experimental results showed that WSI-INR maintains robust segmentation performance across resolutions; at Base/4, our resolution-specific optimization improves Dice score by +26.11%, while U-Net and TransUNet decrease by 54.28% and 36.18%, respectively. Crucially, this work enables INRs to segment highly heterogeneous pathological lesions beyond structurally consistent anatomical tissues, offering a fresh perspective for pathological analysis.

Stroke outcome and evolution prediction from CT brain using a spatiotemporal diffusion autoencoder

Stroke is a major cause of death and disability worldwide. Accurate outcome and evolution prediction has the potential to revolutionize stroke care by individualizing clinical decision-making leading to better outcomes. However, despite a plethora of attempts and the rich data provided by neuroimaging, modelling the ultimate fate of brain tissue remains a challenging task. In this work, we apply recent ideas in the field of diffusion probabilistic models to generate a self-supervised semantically meaningful stroke representation from Computed Tomography (CT) images. We then improve this representation by extending the method to accommodate longitudinal images and the time from stroke onset. The effectiveness of our approach is evaluated on a dataset consisting of 5,824 CT images from 3,573 patients across two medical centers with minimal labels. Comparative experiments show that our method achieves the best performance for predicting next-day severity and functional outcome at discharge.

Attachment Anchors: A Novel Framework for Laparoscopic Grasping Point Prediction in Colorectal Surgery

Accurate grasping point prediction is a key challenge for autonomous tissue manipulation in minimally invasive surgery, particularly in complex and variable procedures such as colorectal interventions. Due to their complexity and prolonged duration, colorectal procedures have been underrepresented in current research. At the same time, they pose a particularly interesting learning environment due to repetitive tissue manipulation, making them a promising entry point for autonomous, machine learning-driven support. Therefore, in this work, we introduce attachment anchors, a structured representation that encodes the local geometric and mechanical relationships between tissue and its anatomical attachments in colorectal surgery. This representation reduces uncertainty in grasping point prediction by normalizing surgical scenes into a consistent local reference frame. We demonstrate that attachment anchors can be predicted from laparoscopic images and incorporated into a grasping framework based on machine learning. Experiments on a dataset of 90 colorectal surgeries demonstrate that attachment anchors improve grasping point prediction compared to image-only baselines. There are particularly strong gains in out-of-distribution settings, including unseen procedures and operating surgeons. These results suggest that attachment anchors are an effective intermediate representation for learning-based tissue manipulation in colorectal surgery.

VariViT: A Vision Transformer for Variable Image Sizes

Vision Transformers (ViTs) have emerged as the state-of-the-art architecture in representation learning, leveraging self-attention mechanisms to excel in various tasks. ViTs split images into fixed-size patches, constraining them to a predefined size and necessitating pre-processing steps like resizing, padding, or cropping. This poses challenges in medical imaging, particularly with irregularly shaped structures like tumors. A fixed bounding box crop size produces input images with highly variable foreground-to-background ratios. Resizing medical images can degrade information and introduce artefacts, impacting diagnosis. Hence, tailoring variable-sized crops to regions of interest can enhance feature representation capabilities. Moreover, large images are computationally expensive, and smaller sizes risk information loss, presenting a computation-accuracy tradeoff. We propose VariViT, an improved ViT model crafted to handle variable image sizes while maintaining a consistent patch size. VariViT employs a novel positional embedding resizing scheme for a variable number of patches. We also implement a new batching strategy within VariViT to reduce computational complexity, resulting in faster training and inference times. In our evaluations on two 3D brain MRI datasets, VariViT surpasses vanilla ViTs and ResNet in glioma genotype prediction and brain tumor classification. It achieves F1-scores of 75.5% and 76.3%, respectively, learning more discriminative features. Our proposed batching strategy reduces computation time by up to 30% compared to conventional architectures. These findings underscore the efficacy of VariViT in image representation learning. Our code can be found here: https://github.com/Aswathi-Varma/varivit

Multi-View Stenosis Classification Leveraging Transformer-Based Multiple-Instance Learning Using Real-World Clinical Data

Coronary artery stenosis is a leading cause of cardiovascular disease, diagnosed by analyzing the coronary arteries from multiple angiography views. Although numerous deep-learning models have been proposed for stenosis detection from a single angiography view, their performance heavily relies on expensive view-level annotations, which are often not readily available in hospital systems. Moreover, these models fail to capture the temporal dynamics and dependencies among multiple views, which are crucial for clinical diagnosis. To address this, we propose SegmentMIL, a transformer-based multi-view multiple-instance learning framework for patient-level stenosis classification. Trained on a real-world clinical dataset, using patient-level supervision and without any view-level annotations, SegmentMIL jointly predicts the presence of stenosis and localizes the affected anatomical region, distinguishing between the right and left coronary arteries and their respective segments. SegmentMIL obtains high performance on internal and external evaluations and outperforms both view-level models and classical MIL baselines, underscoring its potential as a clinically viable and scalable solution for coronary stenosis diagnosis. Our code is available at https://github.com/NikolaCenic/mil-stenosis.

A Master Class on Reproducibility: A Student Hackathon on Advanced MRI Reconstruction Methods

We report the design, protocol, and outcomes of a student reproducibility hackathon focused on replicating the results of three influential MRI reconstruction papers: (a) MoDL, an unrolled model-based network with learned denoising; (b) HUMUS-Net, a hybrid unrolled multiscale CNN+Transformer architecture; and (c) an untrained, physics-regularized dynamic MRI method that uses a quantitative MR model for early stopping. We describe the setup of the hackathon and present reproduction outcomes alongside additional experiments, and we detail fundamental practices for building reproducible codebases.

Unintended Memorization of Sensitive Information in Fine-Tuned Language Models

Fine-tuning Large Language Models (LLMs) on sensitive datasets carries a substantial risk of unintended memorization and leakage of Personally Identifiable Information (PII), which can violate privacy regulations and compromise individual safety. In this work, we systematically investigate a critical and underexplored vulnerability: the exposure of PII that appears only in model inputs, not in training targets. Using both synthetic and real-world datasets, we design controlled extraction probes to quantify unintended PII memorization and study how factors such as language, PII frequency, task type, and model size influence memorization behavior. We further benchmark four privacy-preserving approaches including differential privacy, machine unlearning, regularization, and preference alignment, evaluating their trade-offs between privacy and task performance. Our results show that post-training methods generally provide more consistent privacy-utility trade-offs, while differential privacy achieves strong reduction in leakage in specific settings, although it can introduce training instability. These findings highlight the persistent challenge of memorization in fine-tuned LLMs and emphasize the need for robust, scalable privacy-preserving techniques.

VERIDAH: Solving Enumeration Anomaly Aware Vertebra Labeling across Imaging Sequences

The human spine commonly consists of seven cervical, twelve thoracic, and five lumbar vertebrae. However, enumeration anomalies may result in individuals having eleven or thirteen thoracic vertebrae and four or six lumbar vertebrae. Although the identification of enumeration anomalies has potential clinical implications for chronic back pain and operation planning, the thoracolumbar junction is often poorly assessed and rarely described in clinical reports. Additionally, even though multiple deep-learning-based vertebra labeling algorithms exist, there is a lack of methods to automatically label enumeration anomalies. Our work closes that gap by introducing "Vertebra Identification with Anomaly Handling" (VERIDAH), a novel vertebra labeling algorithm based on multiple classification heads combined with a weighted vertebra sequence prediction algorithm. We show that our approach surpasses existing models on T2w TSE sagittal (98.30% vs. 94.24% of subjects with all vertebrae correctly labeled, p < 0.001) and CT imaging (99.18% vs. 77.26% of subjects with all vertebrae correctly labeled, p < 0.001) and works in arbitrary field-of-view images. VERIDAH correctly labeled the presence 2 Möller et al. of thoracic enumeration anomalies in 87.80% and 96.30% of T2w and CT images, respectively, and lumbar enumeration anomalies in 94.48% and 97.22% for T2w and CT, respectively. Our code and models are available at: https://github.com/Hendrik-code/spineps.

Towards a Unified Theoretical Framework for Self-Supervised MRI Reconstruction

The demand for high-resolution, non-invasive imaging continues to drive innovation in magnetic resonance imaging (MRI), yet prolonged acquisition times hinder accessibility and real-time applications. While deep learning-based reconstruction methods have accelerated MRI, their predominant supervised paradigm depends on fully-sampled reference data that are challenging to acquire. Recently, self-supervised learning (SSL) approaches have emerged as promising alternatives, but most are empirically designed and fragmented. Therefore, we introduce UNITS (Unified Theory for Self-supervision), a general framework for self-supervised MRI reconstruction. UNITS unifies prior SSL strategies within a common formalism, enabling consistent interpretation and systematic benchmarking. We prove that SSL can achieve the same expected performance as supervised learning. Under this theoretical guarantee, we introduce sampling stochasticity and flexible data utilization, which improve network generalization under out-of-domain distributions and stabilize training. Together, these contributions establish UNITS as a theoretical foundation and a practical paradigm for interpretable, generalizable, and clinically applicable self-supervised MRI reconstruction.

Stochastic Siamese MAE Pretraining for Longitudinal Medical Images

Temporally aware image representations are crucial for capturing disease progression in 3D volumes of longitudinal medical datasets. However, recent state-of-the-art self-supervised learning approaches like Masked Autoencoding (MAE), despite their strong representation learning capabilities, lack temporal awareness. In this paper, we propose STAMP (Stochastic Temporal Autoencoder with Masked Pretraining), a Siamese MAE framework that encodes temporal information through a stochastic process by conditioning on the time difference between the 2 input volumes. Unlike deterministic Siamese approaches, which compare scans from different time points but fail to account for the inherent uncertainty in disease evolution, STAMP learns temporal dynamics stochastically by reframing the MAE reconstruction loss as a conditional variational inference objective. We evaluated STAMP on two OCT and one MRI datasets with multiple visits per patient. STAMP pretrained ViT models outperformed both existing temporal MAE methods and foundation models on different late stage Age-Related Macular Degeneration and Alzheimer's Disease progression prediction which require models to learn the underlying non-deterministic temporal dynamics of the diseases.