Integrative Deep Learning for PanCancer Molecular Subtype Classification Using Histopathological Images and RNAseq Data

2020 ◽  
Author(s):  
Fatima Zare ◽  
Javad Noorbakhsh ◽  
Tianyu Wang ◽  
Jeffrey H. Chuang ◽  
Sheida Nabavi
Keyword(s):  
Deep Learning ◽  
Molecular Subtype ◽  
Subtype Classification ◽  
Rnaseq Data ◽  
Histopathological Images

scholarly journals DeepCC: a novel deep learning-based framework for cancer molecular subtype classification

Oncogenesis ◽  
2019 ◽  
Vol 8 (9) ◽  
Author(s):  
Feng Gao ◽  
Wei Wang ◽  
Miaomiao Tan ◽  
Lina Zhu ◽  
Yuchen Zhang ◽  
...  
Keyword(s):  
Deep Learning ◽  
Molecular Subtype ◽  
Subtype Classification

scholarly journals NIMG-08. PREDICTION OF LOWER-GRADE GLIOMA MOLECULAR SUBTYPES USING DEEP LEARNING

2020 ◽  
Vol 22 (Supplement_2) ◽  
pp. ii148-ii148
Author(s):  
Yoshihiro Muragaki ◽  
Yutaka Matsui ◽  
Takashi Maruyama ◽  
Masayuki Nitta ◽  
Taiichi Saito ◽  
...  
Keyword(s):  
Deep Learning ◽  
Cross Validation ◽  
Molecular Subtype ◽  
Learning Model ◽  
Group Classification ◽  
Training Dataset ◽  
Lower Grade ◽  
Test Dataset ◽  
Ct Data ◽  
Deep Learning Model

Abstract INTRODUCTION It is useful to know the molecular subtype of lower-grade gliomas (LGG) when deciding on a treatment strategy. This study aims to diagnose this preoperatively. METHODS A deep learning model was developed to predict the 3-group molecular subtype using multimodal data including magnetic resonance imaging (MRI), positron emission tomography (PET), and computed tomography (CT). The performance was evaluated using leave-one-out cross validation with a dataset containing information from 217 LGG patients. RESULTS The model performed best when the dataset contained MRI, PET, and CT data. The model could predict the molecular subtype with an accuracy of 96.6% for the training dataset and 68.7% for the test dataset. The model achieved test accuracies of 58.5%, 60.4%, and 59.4% when the dataset contained only MRI, MRI and PET, and MRI and CT data, respectively. The conventional method used to predict mutations in the isocitrate dehydrogenase (IDH) gene and the codeletion of chromosome arms 1p and 19q (1p/19q) sequentially had an overall accuracy of 65.9%. This is 2.8 percent point lower than the proposed method, which predicts the 3-group molecular subtype directly. CONCLUSIONS AND FUTURE PERSPECTIVE A deep learning model was developed to diagnose the molecular subtype preoperatively based on multi-modality data in order to predict the 3-group classification directly. Cross-validation showed that the proposed model had an overall accuracy of 68.7% for the test dataset. This is the first model to double the expected value for a 3-group classification problem, when predicting the LGG molecular subtype. We plan to apply the techniques of heat map and/or segmentation for an increase in prediction accuracy.

scholarly journals Deep Learning for the Classification of Non-Hodgkin Lymphoma on Histopathological Images

Cancers ◽  
2021 ◽  
Vol 13 (10) ◽  
pp. 2419
Author(s):  
Georg Steinbuss ◽  
Mark Kriegsmann ◽  
Christiane Zgorzelski ◽  
Alexander Brobeil ◽  
Benjamin Goeppert ◽  
...  
Keyword(s):  
Deep Learning ◽  
Hodgkin Lymphoma ◽  
Expert Knowledge ◽  
B Cell Lymphoma ◽  
High Accuracy ◽  
Lymphocytic Leukemia ◽  
Non Hodgkin Lymphoma ◽  
Image Patches ◽  
Histopathological Images

The diagnosis and the subtyping of non-Hodgkin lymphoma (NHL) are challenging and require expert knowledge, great experience, thorough morphological analysis, and often additional expensive immunohistological and molecular methods. As these requirements are not always available, supplemental methods supporting morphological-based decision making and potentially entity subtyping are required. Deep learning methods have been shown to classify histopathological images with high accuracy, but data on NHL subtyping are limited. After annotation of histopathological whole-slide images and image patch extraction, we trained and optimized an EfficientNet convolutional neuronal network algorithm on 84,139 image patches from 629 patients and evaluated its potential to classify tumor-free reference lymph nodes, nodal small lymphocytic lymphoma/chronic lymphocytic leukemia, and nodal diffuse large B-cell lymphoma. The optimized algorithm achieved an accuracy of 95.56% on an independent test set including 16,960 image patches from 125 patients after the application of quality controls. Automatic classification of NHL is possible with high accuracy using deep learning on histopathological images and routine diagnostic applications should be pursued.

NIMG-46. SYSTEMATIC LITERATURE REVIEW OF ARTIFICIAL INTELLIGENCE ALGORITHMS USING PRE-THERAPY MR IMAGING FOR GLIOMA MOLECULAR SUBTYPE CLASSIFICATION

2021 ◽  
Vol 23 (Supplement_6) ◽  
pp. vi139-vi139
Author(s):  
Jan Lost ◽  
Tej Verma ◽  
Niklas Tillmanns ◽  
W R Brim ◽  
Harry Subramanian ◽  
...  
Keyword(s):  
Artificial Intelligence ◽  
Machine Learning ◽  
Deep Learning ◽  
Literature Review ◽  
Prediction Accuracy ◽  
Molecular Subtypes ◽  
Molecular Subtype ◽  
Tumor Resection ◽  
Support Vector ◽  
Hospital Data

Abstract PURPOSE Identifying molecular subtypes in gliomas has prognostic and therapeutic value, traditionally after invasive neurosurgical tumor resection or biopsy. Recent advances using artificial intelligence (AI) show promise in using pre-therapy imaging for predicting molecular subtype. We performed a systematic review of recent literature on AI methods used to predict molecular subtypes of gliomas. METHODS Literature review conforming to PRSIMA guidelines was performed for publications prior to February 2021 using 4 databases: Ovid Embase, Ovid MEDLINE, Cochrane trials (CENTRAL), and Web of Science core-collection. Keywords included: artificial intelligence, machine learning, deep learning, radiomics, magnetic resonance imaging, glioma, and glioblastoma. Non-machine learning and non-human studies were excluded. Screening was performed using Covidence software. Bias analysis was done using TRIPOD guidelines. RESULTS 11,727 abstracts were retrieved. After applying initial screening exclusion criteria, 1,135 full text reviews were performed, with 82 papers remaining for data extraction. 57% used retrospective single center hospital data, 31.6% used TCIA and BRATS, and 11.4% analyzed multicenter hospital data. An average of 146 patients (range 34-462 patients) were included. Algorithms predicting IDH status comprised 51.8% of studies, MGMT 18.1%, and 1p19q 6.0%. Machine learning methods were used in 71.4%, deep learning in 27.4%, and 1.2% directly compared both methods. The most common algorithm for machine learning were support vector machine (43.3%), and for deep learning convolutional neural network (68.4%). Mean prediction accuracy was 76.6%. CONCLUSION Machine learning is the predominant method for image-based prediction of glioma molecular subtypes. Major limitations include limited datasets (60.2% with under 150 patients) and thus limited generalizability of findings. We recommend using larger annotated datasets for AI network training and testing in order to create more robust AI algorithms, which will provide better prediction accuracy to real world clinical datasets and provide tools that can be translated to clinical practice.

scholarly journals A Deep Learning Model for Molecular Label Transfer that Enables Cancer Cell Identification from Histopathology Images

2021 ◽  
Author(s):  
Andrew Su ◽  
HoJoon Lee ◽  
Xiao Tan ◽  
Carlos J Suarez ◽  
Noemi Andor ◽  
...  
Keyword(s):  
Deep Learning ◽  
Initial Step ◽  
Classification Systems ◽  
Interactive Tools ◽  
Histopathologic Evaluation ◽  
Histopathological Images ◽  
Novel Method ◽  
Histopathology Images ◽  
Transfer Method ◽  
Learning Software

Deep learning cancer classification systems have the potential to improve cancer diagnosis. However, development of these computational approaches depends on prior annotation through a pathologist. This initial step relying on a manual, low-resolution, time-consuming process is highly variable and subject to observer variance. To address this issue, we developed a novel method, H&E Molecular neural network (HEMnet). This two-step process utilises immunohistochemistry as an initial molecular label for cancer cells on a H&E image and then we train a cancer classifier on the overlapping clinical histopathological images. Using this molecular transfer method, we show that HEMnet accurately distinguishes colorectal cancer from normal tissue at high resolution without the need for an initial manual histopathologic evaluation. Our validation study using histopathology images from TCGA samples accurately estimates tumour purity. Overall, our method provides a path towards a fully automated delineation of any type of tumor so long as there is a cancer-oriented molecular stain available for subsequent learning. Software, tutorials and interactive tools are available at: https://github.com/BiomedicalMachineLearning/HEMnet

scholarly journals Breast Cancer Multi-classification from Histopathological Images with Structured Deep Learning Model

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Zhongyi Han ◽  
Benzheng Wei ◽  
Yuanjie Zheng ◽  
Yilong Yin ◽  
Kejian Li ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Deep Learning ◽  
Learning Model ◽  
Histopathological Images ◽  
Multi Classification ◽  
Deep Learning Model
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