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PathLang: A Language-Centered Benchmark for Vision-Language Models in Computational Pathology
Fanqi Cheng, Kuo Gong, Shangke Liu +15
Pathology vision-language models (VLMs) have shown strong visual perception ability, but their robustness in the language domain remains poorly characterized. Existing pathology VL…
Benchmarking Active Spot Selection for Cost-Efficient Spatial Transcriptomics
Zheyu Zhu, Junchao Zhu, Fengbei Liu +7
Spatial transcriptomics (ST) measures gene expression in tissue context, but dense capture grids can be costly and may repeatedly sample morphologically similar regions. Most activ…
Seeing Abnormal from Normal: Glomerular Abnormality in Representations of Normal Renal Morphology
Greta Hasko, Rachit Saluja, Tianyu Shi +13
Fine-grained evaluation of glomerular pathology must distinguish normal glomeruli from abnormalities such as global and segmental glomerulosclerosis, obsolescent, ischemic, solidif…
ShapKO: Shapley-Adaptive Modality Knockout for Robust Multimodal Learning
Nusrat Binta Nizam, Fengbei Liu, Sunwoo Kwak +3
Multimodal medical models often degrade when inputs are missing, a common scenario in real-world clinical workflows. Separately, even when all modalities are present, modality domi…
MORI-Seg: Learning Morphological Geometry for Instance Segmentation without Instance Annotations
Leiyue Zhao, Tianyu Shi, Daniel Reisenbuchler +12
Instance-level quantification of kidney functional units is essential for morphometric analysis, yet most publicly available pathology datasets provide only semantic segmentation a…
Prediction of Rectal Cancer Regrowth from Longitudinal Endoscopy
Jorge Tapias Gomez, Despoina Kanata, Aneesh Rangnekar +8
Clinical trial studies indicate benefit of watch-and-wait (WW) surveillance for patients with rectal cancer showing a complete or near clinical response (CR) directly after treatme…
Spectral Vision Transformer for Efficient Tokenization with Limited Data
Alexandra G. Roberts, Maneesh John, Jinwei Zhang +10
We propose a novel spectral vision transformer architecture for efficient tokenization in limited data, with an emphasis on medical imaging. We outline convenient theoretical prope…
NeuroVolve: Evolving Visual Stimuli toward Programmable Neural Objectives
Haomiao Chen, Keith W Jamison, Mert R. Sabuncu +1
What visual information is encoded in individual brain regions, and how do distributed patterns combine to create their neural representations? Prior work has used generative model…
AtlasMorph: Learning conditional deformable templates for brain MRI
Marianne Rakic, Andrew Hoopes, S. Mazdak Abulnaga +3
Deformable templates, or atlases, are images that represent a prototypical anatomy for a population, and are often enhanced with probabilistic anatomical label maps. They are commo…
From Classification to Cross-Modal Understanding: Leveraging Vision-Language Models for Fine-Grained Renal Pathology
Zhenhao Guo, Rachit Saluja, Tianyuan Yao +14
Fine-grained glomerular subtyping is essential for kidney biopsy interpretation, yet it presents a harder setting than the broad organ- or disease-level recognition tasks commonly…
BackSplit: The Importance of Sub-dividing the Background in Biomedical Lesion Segmentation
Rachit Saluja, Asli Cihangir, Ruining Deng +3
Segmenting small lesions in medical images remains notoriously difficult. Most prior work tackles this challenge by either designing better architectures, loss functions, or data a…
M^3-GloDets: Multi-Region and Multi-Scale Analysis of Fine-Grained Diseased Glomerular Detection
Tianyu Shi, Xinzi He, Kenji Ikemura +3
Accurate detection of diseased glomeruli is fundamental to progress in renal pathology and underpins the delivery of reliable clinical diagnoses. Although recent advances in comput…
Glo-VLMs: Leveraging Vision-Language Models for Fine-Grained Diseased Glomerulus Classification
Zhenhao Guo, Rachit Saluja, Tianyuan Yao +8
Vision-language models (VLMs) have shown considerable potential in digital pathology, yet their effectiveness remains limited for fine-grained, disease-specific classification task…
DyMorph-B2I: Dynamic and Morphology-Guided Binary-to-Instance Segmentation for Renal Pathology
Leiyue Zhao, Yuechen Yang, Yanfan Zhu +7
Accurate morphological quantification of renal pathology functional units relies on instance-level segmentation, yet most existing datasets and automated methods provide only binar…
CoFi: A Fast Coarse-to-Fine Few-Shot Pipeline for Glomerular Basement Membrane Segmentation
Hongjin Fang, Daniel Reisenbüchler, Kenji Ikemura +3
Accurate segmentation of the glomerular basement membrane (GBM) in electron microscopy (EM) images is fundamental for quantifying membrane thickness and supporting the diagnosis of…
RealKeyMorph: Keypoints in Real-world Coordinates for Resolution-agnostic Image Registration
Mina C. Moghadam, Alan Q. Wang, Omer Taub +2
Many real-world settings require registration of a pair of medical images that differ in spatial resolution, which may arise from differences in image acquisition parameters like p…
Modality-agnostic, patient-specific digital twins modeling temporally varying digestive motion
Jorge Tapias Gomez, Nishant Nadkarni, Lando S. Bosma +7
Objective: Clinical implementation of deformable image registration (DIR) requires voxel-based spatial accuracy metrics such as manually identified landmarks, which are challenging…
CASC-AI: Consensus-aware Self-corrective Learning for Noise Cell Segmentation
Ruining Deng, Yihe Yang, David J. Pisapia +15
Multi-class cell segmentation in high-resolution gigapixel whole slide images (WSIs) is crucial for various clinical applications. However, training such models typically requires…
Fine-tuning Vision Language Models with Graph-based Knowledge for Explainable Medical Image Analysis
Chenjun Li, Laurin Lux, Alexander H. Berger +3
Accurate staging of Diabetic Retinopathy (DR) is essential for guiding timely interventions and preventing vision loss. However, current staging models are hardly interpretable, an…
The 2024 Brain Tumor Segmentation (BraTS) Challenge: Glioma Segmentation on Post-treatment MRI
Maria Correia de Verdier, Rachit Saluja, Louis Gagnon +82
Gliomas are the most common malignant primary brain tumors in adults and one of the deadliest types of cancer. There are many challenges in treatment and monitoring due to the gene…
BrainMorph: A Foundational Keypoint Model for Robust and Flexible Brain MRI Registration
Alan Q. Wang, Rachit Saluja, Heejong Kim +3
We present a keypoint-based foundation model for general purpose brain MRI registration, based on the recently-proposed KeyMorph framework. Our model, called BrainMorph, serves as…
Zero-shot Learning of Individualized Task Contrast Prediction from Resting-state Functional Connectomes
Minh Nguyen, Gia H. Ngo, Mert R. Sabuncu
Given sufficient pairs of resting-state and task-evoked fMRI scans from subjects, it is possible to train ML models to predict subject-specific task-evoked activity using resting-s…
Characterizing the Features of Mitotic Figures Using a Conditional Diffusion Probabilistic Model
Cagla Deniz Bahadir, Benjamin Liechty, David J. Pisapia +1
Mitotic figure detection in histology images is a hard-to-define, yet clinically significant task, where labels are generated with pathologist interpretations and where there is no…
UniverSeg: Universal Medical Image Segmentation
Victor Ion Butoi, Jose Javier Gonzalez Ortiz, Tianyu Ma +3
While deep learning models have become the predominant method for medical image segmentation, they are typically not capable of generalizing to unseen segmentation tasks involving…