From patterns to patients: Advances in clinical machine learning for cancer diagnosis, prognosis, and treatment

K Swanson, E Wu, A Zhang, AA Alizadeh, J Zou - Cell, 2023 - cell.com
Machine learning (ML) is increasingly used in clinical oncology to diagnose cancers, predict
patient outcomes, and inform treatment planning. Here, we review recent applications of ML …

Deep learning in cancer diagnosis, prognosis and treatment selection

KA Tran, O Kondrashova, A Bradley, ED Williams… - Genome Medicine, 2021 - Springer
Deep learning is a subdiscipline of artificial intelligence that uses a machine learning
technique called artificial neural networks to extract patterns and make predictions from …

Scaling vision transformers to gigapixel images via hierarchical self-supervised learning

RJ Chen, C Chen, Y Li, TY Chen… - Proceedings of the …, 2022 - openaccess.thecvf.com
Abstract Vision Transformers (ViTs) and their multi-scale and hierarchical variations have
been successful at capturing image representations but their use has been generally …

Towards a general-purpose foundation model for computational pathology

RJ Chen, T Ding, MY Lu, DFK Williamson, G Jaume… - Nature Medicine, 2024 - nature.com
Quantitative evaluation of tissue images is crucial for computational pathology (CPath) tasks,
requiring the objective characterization of histopathological entities from whole-slide images …

Cell type and gene expression deconvolution with BayesPrism enables Bayesian integrative analysis across bulk and single-cell RNA sequencing in oncology

T Chu, Z Wang, D Pe'er, CG Danko - Nature Cancer, 2022 - nature.com
Inferring single-cell compositions and their contributions to global gene expression changes
from bulk RNA sequencing (RNA-seq) datasets is a major challenge in oncology. Here we …

Multistain deep learning for prediction of prognosis and therapy response in colorectal cancer

S Foersch, C Glasner, AC Woerl, M Eckstein… - Nature medicine, 2023 - nature.com
Although it has long been known that the immune cell composition has a strong prognostic
and predictive value in colorectal cancer (CRC), scoring systems such as the immunoscore …

Machine learning in drug discovery: a review

S Dara, S Dhamercherla, SS Jadav, CHM Babu… - Artificial intelligence …, 2022 - Springer
This review provides the feasible literature on drug discovery through ML tools and
techniques that are enforced in every phase of drug development to accelerate the research …

Harnessing multimodal data integration to advance precision oncology

KM Boehm, P Khosravi, R Vanguri, J Gao… - Nature Reviews …, 2022 - nature.com
Advances in quantitative biomarker development have accelerated new forms of data-driven
insights for patients with cancer. However, most approaches are limited to a single mode of …

[HTML][HTML] Conserved pan-cancer microenvironment subtypes predict response to immunotherapy

A Bagaev, N Kotlov, K Nomie, V Svekolkin, A Gafurov… - Cancer cell, 2021 - cell.com
The clinical use of molecular targeted therapy is rapidly evolving but has primarily focused
on genomic alterations. Transcriptomic analysis offers an opportunity to dissect the …

Federated learning for predicting histological response to neoadjuvant chemotherapy in triple-negative breast cancer

J Ogier du Terrail, A Leopold, C Joly, C Béguier… - Nature medicine, 2023 - nature.com
Triple-negative breast cancer (TNBC) is a rare cancer, characterized by high metastatic
potential and poor prognosis, and has limited treatment options. The current standard of …