26 citations · 97 across the 18 of their papers we have counts for
21 papers
A general-purpose System One decision model for clinical records
Andrew Zhang, Trinh T. L. Vuong, Sophia J. Wagner +14
Clinical care, health-system operations and biomedical discovery depend on extracting reliable answers from patient records, yet applying diverse clinical questions across entire p…
Discrete Neural Interlingua for Ontology-Agnostic EHR Modeling
Tong Ding, Caiwei Tian, Dongmin Bang +6
EHR foundation models promise scalable clinical prediction across health systems, yet their deployment is constrained by a tokenization bottleneck. The same clinical concept can ap…
Beyond Sparse Captions: Aligning Slide-Level Text and Patch-Level Vision in Pathology
Daniel Shao, Dongmin Bang, Luca L. Weishaupt +6
Contrastive vision-language (VL) pretraining in computational pathology has generally relied on curated image-caption datasets sourced from social media, educational videos, and re…
VIPER: An Expert-Curated Benchmark for Vision-Language Models in Veterinary Pathology
Luca L. Weishaupt, Simone de Brot, Javier Asin +9
Pathology vision-language models are advancing rapidly, yet existing benchmarks remain focused on human tissue, particularly oncology, leaving non-human pathology largely unaddress…
A multimodal and temporal foundation model for virtual patient representations at healthcare system scale
Andrew Zhang, Tong Ding, Sophia J. Wagner +8
Modern medicine generates vast multimodal data across siloed systems, yet no existing model integrates the full breadth and temporal depth of the clinical record into a unified pat…
Mixture of Mini Experts: Overcoming the Linear Layer Bottleneck in Multiple Instance Learning
Daniel Shao, Joel Runevic, Richard J. Chen +4
Multiple Instance Learning (MIL) is the predominant framework for classifying gigapixel whole-slide images in computational pathology. MIL follows a sequence of 1) extracting patch…
Towards Spatial Transcriptomics-driven Pathology Foundation Models
Konstantin Hemker, Andrew H. Song, Cristina Almagro-Pérez +6
Spatial transcriptomics (ST) provides spatially resolved measurements of gene expression, enabling characterization of the molecular landscape of human tissue beyond histological a…
NOVA: An Agentic Framework for Automated Histopathology Analysis and Discovery
Anurag J. Vaidya, Felix Meissen, Daniel C. Castro +7
Digitized histopathology analysis involves complex, time-intensive workflows and specialized expertise, limiting its accessibility. We introduce NOVA, an agentic framework that tra…
Do Multiple Instance Learning Models Transfer?
Daniel Shao, Richard J. Chen, Andrew H. Song +4
Multiple Instance Learning (MIL) is a cornerstone approach in computational pathology (CPath) for generating clinically meaningful slide-level embeddings from gigapixel tissue imag…
A Foundation Model for Spatial Proteomics
Muhammad Shaban, Yuzhou Chang, Huaying Qiu +57
Foundation models have begun to transform image analysis by acting as pretrained generalist backbones that can be adapted to many tasks even when post-training data are limited, ye…
Evidence-based diagnostic reasoning with multi-agent copilot for human pathology
Luca L. Weishaupt, Chengkuan Chen, Drew F. K. Williamson +8
Pathology is experiencing rapid digital transformation driven by whole-slide imaging and artificial intelligence (AI). While deep learning-based computational pathology has achieve…
AI-driven 3D Spatial Transcriptomics
Cristina Almagro-Pérez, Andrew H. Song, Luca Weishaupt +13
A comprehensive three-dimensional (3D) map of tissue architecture and gene expression is crucial for illuminating the complexity and heterogeneity of tissues across diverse biomedi…
Accelerating Data Processing and Benchmarking of AI Models for Pathology
Andrew Zhang, Guillaume Jaume, Anurag Vaidya +2
Advances in foundation modeling have reshaped computational pathology. However, the increasing number of available models and lack of standardized benchmarks make it increasingly c…
Molecular-driven Foundation Model for Oncologic Pathology
Anurag Vaidya, Andrew Zhang, Guillaume Jaume +15
Foundation models are reshaping computational pathology by enabling transfer learning, where models pre-trained on vast datasets can be adapted for downstream diagnostic, prognosti…
Multimodal Whole Slide Foundation Model for Pathology
Tong Ding, Sophia J. Wagner, Andrew H. Song +20
The field of computational pathology has been transformed with recent advances in foundation models that encode histopathology region-of-interests (ROIs) into versatile and transfe…
Multistain Pretraining for Slide Representation Learning in Pathology
Guillaume Jaume, Anurag Vaidya, Andrew Zhang +7
Developing self-supervised learning (SSL) models that can learn universal and transferable representations of H&E gigapixel whole-slide images (WSIs) is becoming increasingly valua…
Multimodal Prototyping for cancer survival prediction
Andrew H. Song, Richard J. Chen, Guillaume Jaume +3
Multimodal survival methods combining gigapixel histology whole-slide images (WSIs) and transcriptomic profiles are particularly promising for patient prognostication and stratific…
Triage of 3D pathology data via 2.5D multiple-instance learning to guide pathologist assessments
Gan Gao, Andrew H. Song, Fiona Wang +7
Accurate patient diagnoses based on human tissue biopsies are hindered by current clinical practice, where pathologists assess only a limited number of thin 2D tissue slices sectio…
HEST-1k: A Dataset for Spatial Transcriptomics and Histology Image Analysis
Guillaume Jaume, Paul Doucet, Andrew H. Song +8
Spatial transcriptomics enables interrogating the molecular composition of tissue with ever-increasing resolution and sensitivity. However, costs, rapidly evolving technology, and…
Morphological Prototyping for Unsupervised Slide Representation Learning in Computational Pathology
Andrew H. Song, Richard J. Chen, Tong Ding +3
Representation learning of pathology whole-slide images (WSIs) has been has primarily relied on weak supervision with Multiple Instance Learning (MIL). However, the slide represent…
Transcriptomics-guided Slide Representation Learning in Computational Pathology
Guillaume Jaume, Lukas Oldenburg, Anurag Vaidya +5
Self-supervised learning (SSL) has been successful in building patch embeddings of small histology images (e.g., 224x224 pixels), but scaling these models to learn slide embeddings…