We are an interdisciplinary group from UC Berkeley and UCSF working in computational pathology. A major focus of the group is on the vast 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 data. The scale and complexity of these data (e.g. whole slide images are typically 100,000 x 100,000 pixels and take years of medical training to interpret) mean new statistical/machine learning 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 and electronic health record information presents significant opportunities for discovery, but poses major statistical and computational challenges. The computational arm of our work weaves together high-dimensional statistics, network analysis, deep learning, computer vision, and open-source software to solve these challenging biomedical data analysis problems. The scientific arm of our work aims to improve clinical practice through the use of data-driven methods to understand disease development, discover biomarkers, improve diagnosis, and predict response to therapeutics.

Team

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

Huong
Huong Vu
PhD student in Statistics
UC Berkeley

Huong
Neo Yin
PhD student in Statistics
UC Berkeley

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

Kaitlin
Kaitlin Smith
Masters student in Statistics
UC Berkeley

Reya
Reya Vir
Undergraduate student in EECS
UC Berkeley

Jerri
Jerry Li
Undergraduate student in Computer Science and Statistics
UC Berkeley

Kevin
Kevin Zhou
Undergraduate student in Computer Science and Applied Math
UC Berkeley

Kanish
Kanish Mirchia
Neuropathology Fellow
UCSF

Dan
Daniel Qazi
Cytopathology Fellow
UCSF

Michael
Michael Sharpnack
Resident in Pathology
UCSF