214 citations · 378 across the 9 of their papers we have counts for
9 papers
Tissue Classification and Whole-Slide Images Analysis via Modeling of the Tumor Microenvironment and Biological Pathways
Junzhuo Liu, Xuemei Du, Daniel Reisenbuchler +5
Automatic integration of whole slide images (WSIs) and gene expression profiles has demonstrated substantial potential in precision clinical diagnosis and cancer progression studie…
A Multicenter Benchmark of Multiple Instance Learning Models for Lymphoma Subtyping from HE-stained Whole Slide Images
Rao Muhammad Umer, Daniel Sens, Jonathan Noll +12
Timely and accurate lymphoma diagnosis is essential for guiding cancer treatment. Standard diagnostic practice combines hematoxylin and eosin (HE)-stained whole slide images with i…
Domain-incremental White Blood Cell Classification with Privacy-aware Continual Learning
Pratibha Kumari, Afshin Bozorgpour, Daniel Reisenbüchler +4
White blood cell (WBC) classification plays a vital role in hematology for diagnosing various medical conditions. However, it faces significant challenges due to domain shifts caus…
B-Cos Aligned Transformers Learn Human-Interpretable Features
Manuel Tran, Amal Lahiani, Yashin Dicente Cid +7
Vision Transformers (ViTs) and Swin Transformers (Swin) are currently state-of-the-art in computational pathology. However, domain experts are still reluctant to use these models d…
Data Models for Dataset Drift Controls in Machine Learning With Optical Images
Luis Oala, Marco Aversa, Gabriel Nobis +10
Camera images are ubiquitous in machine learning research. They also play a central role in the delivery of important services spanning medicine and environmental surveying. Howeve…
Coarse-grained modelling of supercoiled RNA
Christian Matek, Petr Šulc, Ferdinando Randisi +2
We study the behaviour of double-stranded RNA under twist and tension using oxRNA, a recently developed coarse-grained model of RNA. Introducing explicit salt-dependence into the m…
Plectoneme tip bubbles: Coupled denaturation and writhing in supercoiled DNA
Christian Matek, Thomas E. Ouldridge, Jonathan P. K. Doye +1
Biological information is not only stored in the digital chemical sequence of double helical DNA, but is also encoded in the mechanical properties of the DNA strands, which can inf…
Coarse-graining DNA for simulations of DNA nanotechnology
Jonathan P. K. Doye, Thomas E. Ouldridge, Ard A. Louis +8
To simulate long time and length scale processes involving DNA it is necessary to use a coarse-grained description. Here we provide an overview of different approaches to such coar…
DNA cruciform arms nucleate through a correlated but non-synchronous cooperative mechanism
Christian Matek, Thomas E. Ouldridge, Adam Levy +2
Inverted repeat (IR) sequences in DNA can form non-canonical cruciform structures to relieve torsional stress. We use Monte Carlo simulations of a recently developed coarse-grained…