We are an interdisciplinary group from UC Berkeley and UCSF working in computational pathology. We build data driven, computational systems to analyze high-resolution histology images of diseased tissue and other clinical data sources. Artificial intelligence aided diagnosis in Pathology has the potential to improve clinical practice for treating cancer and other diseases by increasing diagnostic precision, reducing the costs of care, speeding up clinical workflows, and making diagnostic expertise accessible to more patients. Computational approaches also have the potential to advance the state of care by facilitating the discovery of novel biomarkers for disease prognosis and therapeutic response as well as streamlining basic scientific investigation of disease processes.

The major focus of our research is analysis of the large amounts of high-resolution spatial-omics data that are starting to be generated in Pathology laboratories such as digitized H&E stained slides, multiplex immunofluorescence, spatially resolved transcriptomics, and 3D histology images. The scale and complexity of these data (e.g. whole slide images are typically 10s-100s of thousands of pixels in dimension and take years of medical training to interpret) often mean new algorithms need to be developed to fully harness the promise of these emerging tissue measurement technologies. Linking these different tissue-based data modalities together with other molecular, radiology, and electronic health record information presents significant opportunities for discovery, but also poses statistical and computational challenges. We work to solve these difficult biomedical data analysis problems by weaving together domain expertise, deep-learning, computer vision, statistical inference, and open-source software.

Team

Iain Carmichael
Neyman Visiting Assistant Professor, Department of Statistics, UC Berkeley
Adjunct Visiting Assistant Professor, Department of Pathology, UCSF


Huong Vu
PhD student in Statistics
UC Berkeley


Neo Yin
PhD student in Statistics
UC Berkeley


Shenghuan (Harry) Sun
PhD student in the Biological and Medical Informatics Program
UCSF


Van Hovenga
PhD student in Statistics
UC Berkeley


Maggie Keying Kuang
PhD student in Biostatistics
UC Berkeley


Florica Constantine
PhD student in Statistics
UC Berkeley


Rodrigo Palmaka
Masters student in Statistics
UC Berkeley


Carolyn Dunlap
Masters student in the Information and Data Science program
UC Berkeley


Reya Vir
Undergraduate student in EECS
UC Berkeley


Sharan Shu
Undergraduate student in EECS and Applied Math
UC Berkeley


Sasmit Agarwal
Undergraduate student in EECS
UC Berkeley


Kanish Mirchia
Neuropathology Fellow
UCSF


Daniel Qazi
Cytopathology Fellow
UCSF


Alexander Craig
Pathology Resident
UCSF

Alumni

Kaitlin Smith
2023
Data scientist at AstraZeneca

Jerri Li
2023
Citadel

Michael Sharpnack
2023
Director, Pathologist, Department of Pathobiology at Gilead Sciences

Kevin Zhou
2023
Masters program at UIUC