4.7 Review

Harnessing multimodal data integration to advance precision oncology

Related references

Note: Only part of the references are listed.
Article Computer Science, Interdisciplinary Applications

Pathomic Fusion: An Integrated Framework for Fusing Histopathology and Genomic Features for Cancer Diagnosis and Prognosis

Richard J. Chen et al.

Summary: This study proposes an interpretable strategy for multimodal fusion of histology image and genomic features for survival outcome prediction. The results on glioma and clear cell renal cell carcinoma datasets demonstrate that this approach improves the prognostic determinations.

IEEE TRANSACTIONS ON MEDICAL IMAGING (2022)

Review Medicine, Research & Experimental

Artificial intelligence and computational pathology

Miao Cui et al.

Summary: Computational pathology, driven by data processing and clinical informatics, offers innovative solutions for patient care. However, challenges such as data integration, hardware limitations, and talent development need to be addressed for the field to advance further.

LABORATORY INVESTIGATION (2021)

Article Computer Science, Artificial Intelligence

Deep neural network models for computational histopathology: A survey

Chetan L. Srinidhi et al.

Summary: This paper presents a comprehensive review of state-of-the-art deep learning approaches used in histopathological image analysis. Through a survey of over 130 papers, the progress in the field based on different machine learning strategies is reviewed. Additionally, the paper discusses the application of deep learning in survival models and highlights the challenges and limitations of current deep learning methods, as well as potential directions for future research.

MEDICAL IMAGE ANALYSIS (2021)

Article Multidisciplinary Sciences

Benchmarking joint multi-omics dimensionality reduction approaches for the study of cancer

Laura Cantini et al.

Summary: High-dimensional multi-omics data are common in biology and can enhance our understanding of biological systems. A systematic evaluation of nine jDR methods found intNMF is best for clustering and MCIA is effective in many contexts.

NATURE COMMUNICATIONS (2021)

Article Biochemistry & Molecular Biology

Synthetic lethality-mediated precision oncology via the tumor transcriptome

Joo Sang Lee et al.

Summary: Precision oncology has advanced significantly by targeting actionable mutations in cancer driver genes and exploring the utility of tumor transcriptome to guide patient treatment. SELECT, a precision oncology framework harnessing genetic interactions, has shown predictive accuracy in 80% of tested clinical trials and is publicly available for academic use, providing a foundation for future prospective clinical studies.
Review Multidisciplinary Sciences

Exploring tissue architecture using spatial transcriptomics

Anjali Rao et al.

Summary: Spatial transcriptomic technologies have revolutionized the field of biological research by systematically measuring gene expression levels throughout tissue space. In addition to generating biological insights, these technologies can be used for exploratory data analysis, hypothesis testing, and integration with other data modalities, providing a framework for understanding tissue organization.

NATURE (2021)

Review Biochemical Research Methods

Spatial omics and multiplexed imaging to explore cancer biology

Sabrina M. Lewis et al.

Summary: Understanding intratumoral heterogeneity through single-cell analyses has revealed new biomarkers, but lacks information on cellular location within the tumor microenvironment. New technologies enabling detection of cancer subclones in their native spatial context promise to drive the next generation of cancer research, diagnosis, and therapeutic strategies.

NATURE METHODS (2021)

Article Multidisciplinary Sciences

Learning mutational signatures and their multidimensional genomic properties with TensorSignatures

Harald Vohringer et al.

Summary: TensorSignatures algorithm can learn mutational signatures across different variant categories and their genomic properties. By analyzing multiple genomic variables, it elucidates complex mutational footprints and their underlying processes.

NATURE COMMUNICATIONS (2021)

Proceedings Paper Engineering, Biomedical

Generalizing Convolution Neural Networks on Stain Color Heterogeneous Data for Computational Pathology

Amjad Khan et al.

Summary: The study compares methods for dealing with stain color heterogeneity in histopathology slides to improve machine learning-based computational analysis in normal versus tumor tissue classification. Through systematic experimentation, stain color normalization and augmentation techniques are used to train CNNs to generalize on unseen data from multiple centers, resulting in improved performance metrics on external test sets.

MEDICAL IMAGING 2020: DIGITAL PATHOLOGY (2021)

Article Multidisciplinary Sciences

In situ genome sequencing resolves DNA sequence and structure in intact biological samples

Andrew C. Payne et al.

Summary: In situ genome sequencing (IGS) allows for sequencing and imaging of genomes within intact biological samples, providing spatial localization of genomic loci and revealing parent-specific changes in genome structure across embryonic stages, single-cell chromatin domains in zygotes, and epigenetic memory of global chromosome positioning within individual embryos. These results demonstrate the capability of IGS to directly connect sequence and structure across length scales from single base pairs to whole organisms.

SCIENCE (2021)

Review Oncology

Designing deep learning studies in cancer diagnostics

Andreas Kleppe et al.

Summary: The number of publications on deep learning for cancer diagnostics is increasing rapidly, but clinical translation progress is slow. It is advocated to estimate performance in external cohorts, define a primary analysis in a standardized protocol stored online, and establish recommended protocol items in the field to facilitate transition to the clinic.

NATURE REVIEWS CANCER (2021)

Editorial Material Medicine, General & Internal

Should Health Care Demand Interpretable Artificial Intelligence or Accept Black Box Medicine?

Fei Wang et al.

ANNALS OF INTERNAL MEDICINE (2020)

Article Computer Science, Information Systems

Hybrid context enriched deep learning model for fine-grained sentiment analysis in textual and visual semiotic modality social data

Akshi Kumar et al.

INFORMATION PROCESSING & MANAGEMENT (2020)

Article Multidisciplinary Sciences

Studies on the mechanism of general anesthesia

Mahmud Arif Pavel et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Article Genetics & Heredity

Unraveling tumor-immune heterogeneity in advanced ovarian cancer uncovers immunogenic effect of chemotherapy

Alejandro Jimenez-Sanchez et al.

NATURE GENETICS (2020)

Article Biochemistry & Molecular Biology

Geospatial immune variability illuminates differential evolution of lung adenocarcinoma

Khalid AbdulJabbar et al.

NATURE MEDICINE (2020)

Article Medicine, General & Internal

Olaparib for Metastatic Castration-Resistant Prostate Cancer

J. de Bono et al.

NEW ENGLAND JOURNAL OF MEDICINE (2020)

Article Gastroenterology & Hepatology

Clinical-Grade Detection of Microsatellite Instability in Colorectal Tumors by Deep Learning

Amelie Echle et al.

GASTROENTEROLOGY (2020)

Article Multidisciplinary Sciences

Explainable artificial intelligence model to predict acute critical illness from electronic health records

Simon Meyer Lauritsen et al.

NATURE COMMUNICATIONS (2020)

Letter Multidisciplinary Sciences

Transparency and reproducibility in artificial intelligence

Benjamin Haibe-Kains et al.

NATURE (2020)

Article Biochemistry & Molecular Biology

Guidelines for clinical trial protocols for interventions involving artificial intelligence: the SPIRIT-AI extension

Samantha Cruz Rivera et al.

NATURE MEDICINE (2020)

Article Multidisciplinary Sciences

A robust and interpretable end-to-end deep learning model for cytometry data

Zicheng Hu et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Article Computer Science, Information Systems

Delta Lake: High-Performance ACID Table Storage over Cloud Object Stores

Michael Armbrust et al.

PROCEEDINGS OF THE VLDB ENDOWMENT (2020)

Article Biochemical Research Methods

Isabl Platform, a digital biobank for processing multimodal patient data

Juan S. Medina-Martinez et al.

BMC BIOINFORMATICS (2020)

Article Biochemistry & Molecular Biology

High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue

Yang Liu et al.

Review Oncology

Discovery through clinical sequencing in oncology

Mark T. A. Donoghue et al.

NATURE CANCER (2020)

Article Health Care Sciences & Services

The future of digital health with federated learning

Nicola Rieke et al.

NPJ DIGITAL MEDICINE (2020)

Article Computer Science, Information Systems

Reducing Annotation Burden Through Multimodal Learning

Kevin Lopez et al.

FRONTIERS IN BIG DATA (2020)

Article Oncology

Pan-cancer image-based detection of clinically actionable genetic alterations

Jakob Nikolas Kather et al.

NATURE CANCER (2020)

Review Genetics & Heredity

Integrative single-cell analysis

Tim Stuart et al.

NATURE REVIEWS GENETICS (2019)

Article Biochemical Research Methods

Integrated structural variation and point mutation signatures in cancer genomes using correlated topic models

Tyler Funnell et al.

PLOS COMPUTATIONAL BIOLOGY (2019)

Article Genetics & Heredity

SALMON: Survival Analysis Learning With Multi-Omics Neural Networks on Breast Cancer

Zhi Huang et al.

FRONTIERS IN GENETICS (2019)

Article Multidisciplinary Sciences

Genome-wide cell-free DNA fragmentation in patients with cancer

Stephen Cristiano et al.

NATURE (2019)

Article Biochemistry & Molecular Biology

End-to-end lung cancer screening with three-dimensional deep learning on low-dose chest computed tomography

Diego Ardila et al.

NATURE MEDICINE (2019)

Article Medicine, General & Internal

Alpelisib for PIK3CA-Mutated, Hormone Receptor-Positive Advanced Breast Cancer

Fabrice Andre et al.

NEW ENGLAND JOURNAL OF MEDICINE (2019)

Article Multidisciplinary Sciences

Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis

Silas Maniatis et al.

SCIENCE (2019)

Article Biochemical Research Methods

Deep learning with multimodal representation for pancancer prognosis prediction

Anika Cheerla et al.

BIOINFORMATICS (2019)

Article Multidisciplinary Sciences

A clinically applicable approach to continuous prediction of future acute kidney injury

Nenad Tomasev et al.

NATURE (2019)

Article Biochemistry & Molecular Biology

Deep learning can predict microsatellite instability directly from histology in gastrointestinal cancer

Jakob Nikolas Kather et al.

NATURE MEDICINE (2019)

Article Biochemistry & Molecular Biology

Clinical-grade computational pathology using weakly supervised deep learning on whole slide images

Gabriele Campanella et al.

NATURE MEDICINE (2019)

Article Genetics & Heredity

MildInt: Deep Learning-Based Multimodal Longitudinal Data Integration Framework

Garam Lee et al.

FRONTIERS IN GENETICS (2019)

Article Oncology

Artificial intelligence in digital pathology - new tools for diagnosis and precision oncology

Kaustav Bera et al.

NATURE REVIEWS CLINICAL ONCOLOGY (2019)

Article Multidisciplinary Sciences

Pan-cancer whole-genome analyses of metastatic solid tumours

Peter Priestley et al.

NATURE (2019)

Article Multidisciplinary Sciences

The clinical KRAS(G12C) inhibitor AMG 510 drives anti-tumour immunity

Jude Canon et al.

NATURE (2019)

Article Biochemistry & Molecular Biology

Deep learning-based classification of mesothelioma improves prediction of patient outcome

Pierre Courtiol et al.

NATURE MEDICINE (2019)

Article Genetics & Heredity

Tumor mutational load predicts survival after immunotherapy across multiple cancer types

Robert M. Samstein et al.

NATURE GENETICS (2019)

Article Computer Science, Artificial Intelligence

Stop explaining black box machine learning models for high stakes decisions and use interpretable models instead

Cynthia Rudin

NATURE MACHINE INTELLIGENCE (2019)

Review Multidisciplinary Sciences

A brief introduction to weakly supervised learning

Zhi-Hua Zhou

NATIONAL SCIENCE REVIEW (2018)

Article Biochemical Research Methods

Predicting Cancer Drug Response using a Recommender System

Chayaporn Suphavilai et al.

BIOINFORMATICS (2018)

Article Oncology

Machine Learning-Based Radiomics for Molecular Subtyping of Gliomas

Chia-Feng Lu et al.

CLINICAL CANCER RESEARCH (2018)

Article Medicine, General & Internal

Durable Remissions with Ivosidenib in IDH1-Mutated Relapsed or Refractory AML

C. D. DiNardo et al.

NEW ENGLAND JOURNAL OF MEDICINE (2018)

Article Medicine, General & Internal

Efficacy of Larotrectinib in TRK Fusion-Positive Cancers in Adults and Children

A. Drilon et al.

NEW ENGLAND JOURNAL OF MEDICINE (2018)

Article Multidisciplinary Sciences

Predicting cancer outcomes from histology and genomics using convolutional networks

Pooya Mobadersany et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)

Article Multidisciplinary Sciences

An anatomic transcriptional atlas of human glioblastoma

Ralph B. Puchalski et al.

SCIENCE (2018)

Article Medicine, General & Internal

Deep Convolutional Neural Networks Enable Discrimination of Heterogeneous Digital Pathology Images

Pegah Khosravi et al.

EBIOMEDICINE (2018)

Article Oncology

The Genomic Landscape of Endocrine-Resistant Advanced Breast Cancers

Pedram Razavi et al.

CANCER CELL (2018)

Article Genetics & Heredity

Copy number signatures and mutational processes in ovarian carcinoma

Geoff Macintyre et al.

NATURE GENETICS (2018)

Article Biochemistry & Molecular Biology

Classification and mutation prediction from non-small cell lung cancer histopathology images using deep learning

Nicolas Coudray et al.

NATURE MEDICINE (2018)

Article Multidisciplinary Sciences

Sensitive tumour detection and classification using plasma cell-free DNA methylomes

Shu Yi Shen et al.

NATURE (2018)

Article Multidisciplinary Sciences

Multi-omic tumor data reveal diversity of molecular mechanisms that correlate with survival

Daniele Ramazzotti et al.

NATURE COMMUNICATIONS (2018)

Article Medicine, General & Internal

Deep learning for lung cancer prognostication: A retrospective multi-cohort radiomics study

Ahmed Hosny et al.

PLOS MEDICINE (2018)

Article Oncology

Deep Learning-Based Multi-Omics Integration Robustly Predicts Survival in Liver Cancer

Kumardeep Chaudharyl et al.

CLINICAL CANCER RESEARCH (2018)

Proceedings Paper Computer Science, Cybernetics

Multimodal Local-Global Ranking Fusion for Emotion Recognition

Paul Pu Liang et al.

ICMI'18: PROCEEDINGS OF THE 20TH ACM INTERNATIONAL CONFERENCE ON MULTIMODAL INTERACTION (2018)

Review Oncology

Artificial intelligence in radiology

Ahmed Hosny et al.

NATURE REVIEWS CANCER (2018)

Article Oncology

Clinical Utility of Prospective Molecular Characterization in Advanced Endometrial Cancer

Tara E. Soumerai et al.

CLINICAL CANCER RESEARCH (2018)

Article Oncology

Study of early stage non-small-cell lung cancer using Orbitrap-based global serum metabolomics

Agnieszka Klupczynska et al.

JOURNAL OF CANCER RESEARCH AND CLINICAL ONCOLOGY (2017)

Article Multidisciplinary Sciences

Mismatch repair deficiency predicts response of solid tumors to PD-1 blockade

Dung T. Le et al.

SCIENCE (2017)

Review Biotechnology & Applied Microbiology

Multi-omics approaches to disease

Yehudit Hasin et al.

GENOME BIOLOGY (2017)

Article Engineering, Biomedical

Stain Normalization using Sparse AutoEncoders (StalloSA): Application to digital pathology

Andrew Janowczyk et al.

COMPUTERIZED MEDICAL IMAGING AND GRAPHICS (2017)

Proceedings Paper Computer Science, Artificial Intelligence

Densely Connected Convolutional Networks

Gao Huang et al.

30TH IEEE CONFERENCE ON COMPUTER VISION AND PATTERN RECOGNITION (CVPR 2017) (2017)

Article Biochemical Research Methods

Joint analysis of histopathology image features and gene expression in breast cancer

Vlad Popovici et al.

BMC BIOINFORMATICS (2016)

Article Medicine, General & Internal

Niraparib Maintenance Therapy in Platinum-Sensitive, Recurrent Ovarian Cancer

M. R. Mirza et al.

NEW ENGLAND JOURNAL OF MEDICINE (2016)

Article Radiology, Nuclear Medicine & Medical Imaging

Radiomics: Images Are More than Pictures, They Are Data

Robert J. Gillies et al.

RADIOLOGY (2016)

Review Multidisciplinary Sciences

Deep learning

Yann LeCun et al.

NATURE (2015)

Article Medicine, General & Internal

Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas

Daniel J. Brat et al.

NEW ENGLAND JOURNAL OF MEDICINE (2015)

Article Radiology, Nuclear Medicine & Medical Imaging

The Cancer Imaging Archive (TCIA): Maintaining and Operating a Public Information Repository

Kenneth Clark et al.

JOURNAL OF DIGITAL IMAGING (2013)

Article Health Care Sciences & Services

Caveats for the Use of Operational Electronic Health Record Data in Comparative Effectiveness Research

William R. Hersh et al.

MEDICAL CARE (2013)

Article Radiology, Nuclear Medicine & Medical Imaging

MR Imaging Predictors of Molecular Profile and Survival: Multi-institutional Study of the TCGA Glioblastoma Data Set

David A. Gutman et al.

RADIOLOGY (2013)

Article Medicine, General & Internal

Improved Survival with MEK Inhibition in BRAF-Mutated Melanoma

Keith T. Flaherty et al.

NEW ENGLAND JOURNAL OF MEDICINE (2012)

Article Radiology, Nuclear Medicine & Medical Imaging

Multimodality Computer-Aided Breast Cancer Diagnosis with FFDM and DCE-MRI

Yading Yuan et al.

ACADEMIC RADIOLOGY (2010)

Article Medicine, General & Internal

Gefitinib or Chemotherapy for Non-Small-Cell Lung Cancer with Mutated EGFR.

Makoto Maemondo et al.

NEW ENGLAND JOURNAL OF MEDICINE (2010)

Article Medicine, General & Internal

CONSORT 2010 Explanation and Elaboration: updated guidelines for reporting parallel group randomised trials

David Moher et al.

BMJ-BRITISH MEDICAL JOURNAL (2010)

Article Computer Science, Interdisciplinary Applications

Exploiting missing clinical data in Bayesian network modeling for predicting medical problems

Jau-Huei Lin et al.

JOURNAL OF BIOMEDICAL INFORMATICS (2008)

Article Biochemistry & Molecular Biology

The Stanford Tissue Microarray Database

Robert J. Marinelli et al.

NUCLEIC ACIDS RESEARCH (2008)

Article Pathology

Factors to keep in mind when introducing virtual microscopy

K Glatz-Krieger et al.

VIRCHOWS ARCHIV (2006)

Article Medicine, General & Internal

Use of chemotherapy plus a monoclonal antibody against HER2 for metastatic breast cancer that overexpresses HER2.

DJ Slamon et al.

NEW ENGLAND JOURNAL OF MEDICINE (2001)