scholarly journals A deep learning system can accurately classify primary and metastatic cancers based on patterns of passenger mutations

2017 ◽  
Author(s):  
Wei Jiao ◽  
Gurnit Atwal ◽  
Paz Polak ◽  
Rosa Karlic ◽  
Edwin Cuppen ◽  
...  
Keyword(s):  
Deep Learning ◽  
Learning System ◽  
Driver Mutations ◽  
Metastatic Tumour ◽  
Cancer Type ◽  
Cell Of Origin ◽  
Metastatic Recurrence ◽  
Learning Classifier ◽  
Previously Treated ◽  
Passenger Mutations

In cancer, the primary tumour's organ of origin and histopathology are the strongest determinants of its clinical behaviour, but in 3% of the time a cancer patient presents with metastatic tumour and no obvious primary. Challenges also arise when distinguishing a metastatic recurrence of a previously treated cancer from the emergence of a new one. Here we train a deep learning classifier to predict cancer type based on patterns of somatic passenger mutations detected in whole genome sequencing (WGS) of 2606 tumours representing 24 common cancer types. Our classifier achieves an accuracy of 91% on held-out tumor samples and 82% and 85% respectively on independent primary and metastatic samples, roughly double the accuracy of trained pathologists when presented with a metastatic tumour without knowledge of the primary. Surprisingly, adding information on driver mutations reduced classifier accuracy. Our results have immediate clinical applicability, underscoring how patterns of somatic passenger mutations encode the state of the cell of origin, and can inform future strategies to detect the source of cell-free circulating tumour DNA.

scholarly journals A deep learning system can classify primary and metastatic cancers using passenger mutation patterns, but how does it really compare to current pathological diagnosis in a well-designed diagnostic accuracy study?

2021 ◽  
Author(s):  
Wendy A Cooper ◽  
Laveniya Satgunaseelan ◽  
Ruta Gupta
Keyword(s):  
Deep Learning ◽  
External Validation ◽  
Vital Role ◽  
International Standards ◽  
Learning System ◽  
Cancer Type ◽  
Cell Of Origin ◽  
Diagnostic Standards ◽  
Accuracy Study ◽  
Passenger Mutations

In a recent study published in Nature Communications by Jiao W et al, a deep learning classifier was trained to predict cancer type based on somatic passenger mutations identified using whole genome sequencing (WGS) as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. The data show patterns of somatic passenger mutations differ between tumours with different cell of origin. Overall, the system had an accuracy of 91% in a cross-validation setting using the training set, and 88% and 83% using external validation sets of primary and metastatic tumours respectively. Surprisingly, this is claimed to be twice as accurate as trained pathologists, based on a 27 year old reference from 1993 prior to availability and routine utilisation of immunohistochemistry (IHC) in diagnostic pathology and is not a reflection of current diagnostic standards. We discuss the vital role of pathology in patient care and the importance of using international standards if deep learning methods are to be used in the clinical setting.

scholarly journals Development and validation of a deep learning system to screen vision-threatening conditions in high myopia using optical coherence tomography images

2020 ◽  
pp. bjophthalmol-2020-317825
Author(s):  
Yonghao Li ◽  
Weibo Feng ◽  
Xiujuan Zhao ◽  
Bingqian Liu ◽  
Yan Zhang ◽  
...  
Keyword(s):  
Optical Coherence Tomography ◽  
Deep Learning ◽  
High Myopia ◽  
Large Scale ◽  
Learning System ◽  
Youden Index ◽  
Optical Coherence ◽  
Test Dataset ◽  
Independent Test ◽  
Independent Test Dataset

Background/aimsTo apply deep learning technology to develop an artificial intelligence (AI) system that can identify vision-threatening conditions in high myopia patients based on optical coherence tomography (OCT) macular images.MethodsIn this cross-sectional, prospective study, a total of 5505 qualified OCT macular images obtained from 1048 high myopia patients admitted to Zhongshan Ophthalmic Centre (ZOC) from 2012 to 2017 were selected for the development of the AI system. The independent test dataset included 412 images obtained from 91 high myopia patients recruited at ZOC from January 2019 to May 2019. We adopted the InceptionResnetV2 architecture to train four independent convolutional neural network (CNN) models to identify the following four vision-threatening conditions in high myopia: retinoschisis, macular hole, retinal detachment and pathological myopic choroidal neovascularisation. Focal Loss was used to address class imbalance, and optimal operating thresholds were determined according to the Youden Index.ResultsIn the independent test dataset, the areas under the receiver operating characteristic curves were high for all conditions (0.961 to 0.999). Our AI system achieved sensitivities equal to or even better than those of retina specialists as well as high specificities (greater than 90%). Moreover, our AI system provided a transparent and interpretable diagnosis with heatmaps.ConclusionsWe used OCT macular images for the development of CNN models to identify vision-threatening conditions in high myopia patients. Our models achieved reliable sensitivities and high specificities, comparable to those of retina specialists and may be applied for large-scale high myopia screening and patient follow-up.

scholarly journals A deep-learning system to classify lung X-ray images into normal/pneumonia class

2020 ◽  
Vol 101 ◽  
pp. 209
Author(s):  
R. Baskaran ◽  
B. Ajay Rajasekaran ◽  
V. Rajinikanth
Keyword(s):  
Deep Learning ◽  
Learning System ◽  
X Ray

scholarly journals Deep-learning-based high-resolution recognition of fractional-spatial-mode-encoded data for free-space optical communications

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Youngbin Na ◽  
Do-Kyeong Ko
Keyword(s):  
Deep Learning ◽  
Communication Systems ◽  
Degrees Of Freedom ◽  
Image Transmission ◽  
Data Traffic ◽  
Free Space Optical ◽  
Learning Classifier ◽  
Communication Capacity ◽  
Data Rates ◽  
Mode Space

AbstractStructured light with spatial degrees of freedom (DoF) is considered a potential solution to address the unprecedented demand for data traffic, but there is a limit to effectively improving the communication capacity by its integer quantization. We propose a data transmission system using fractional mode encoding and deep-learning decoding. Spatial modes of Bessel-Gaussian beams separated by fractional intervals are employed to represent 8-bit symbols. Data encoded by switching phase holograms is efficiently decoded by a deep-learning classifier that only requires the intensity profile of transmitted modes. Our results show that the trained model can simultaneously recognize two independent DoF without any mode sorter and precisely detect small differences between fractional modes. Moreover, the proposed scheme successfully achieves image transmission despite its densely packed mode space. This research will present a new approach to realizing higher data rates for advanced optical communication systems.

Endoscopic prediction of submucosal invasion in Barrett’s cancer with the use of Artificial Intelligence: A pilot Study

Endoscopy ◽  
2020 ◽  
Author(s):  
Alanna Ebigbo ◽  
Robert Mendel ◽  
Tobias Rückert ◽  
Laurin Schuster ◽  
Andreas Probst ◽  
...  
Keyword(s):  
Artificial Intelligence ◽  
Deep Learning ◽  
Pilot Study ◽  
White Light ◽  
Submucosal Invasion ◽  
Learning System ◽  
Endoscopic Images ◽  
Barrett’S Cancer ◽  
Significant Difference ◽  
Sensitivity Specificity

Background and aims: The accurate differentiation between T1a and T1b Barrett’s cancer has both therapeutic and prognostic implications but is challenging even for experienced physicians. We trained an Artificial Intelligence (AI) system on the basis of deep artificial neural networks (deep learning) to differentiate between T1a and T1b Barrett’s cancer white-light images. Methods: Endoscopic images from three tertiary care centres in Germany were collected retrospectively. A deep learning system was trained and tested using the principles of cross-validation. A total of 230 white-light endoscopic images (108 T1a and 122 T1b) was evaluated with the AI-system. For comparison, the images were also classified by experts specialized in endoscopic diagnosis and treatment of Barrett’s cancer. Results: The sensitivity, specificity, F1 and accuracy of the AI-system in the differentiation between T1a and T1b cancer lesions was 0.77, 0.64, 0.73 and 0.71, respectively. There was no statistically significant difference between the performance of the AI-system and that of human experts with sensitivity, specificity, F1 and accuracy of 0.63, 0.78, 0.67 and 0.70 respectively. Conclusion: This pilot study demonstrates the first multicenter application of an AI-based system in the prediction of submucosal invasion in endoscopic images of Barrett’s cancer. AI scored equal to international experts in the field, but more work is necessary to improve the system and apply it to video sequences and in a real-life setting. Nevertheless, the correct prediction of submucosal invasion in Barret´s cancer remains challenging for both experts and AI.

scholarly journals Performance Comparison of Deep Learning Autoencoders for Cancer Subtype Detection Using Multi-Omics Data

Cancers ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 2013
Author(s):  
Edian F. Franco ◽  
Pratip Rana ◽  
Aline Cruz ◽  
Víctor V. Calderón ◽  
Vasco Azevedo ◽  
...  
Keyword(s):  
Deep Learning ◽  
Data Fusion ◽  
Similarity Measures ◽  
Research Problem ◽  
Optimal Number ◽  
Performance Comparison ◽  
The Cancer Genome Atlas ◽  
Cancer Type ◽  
Omics Data ◽  
Cancer Subtype

A heterogeneous disease such as cancer is activated through multiple pathways and different perturbations. Depending upon the activated pathway(s), the survival of the patients varies significantly and shows different efficacy to various drugs. Therefore, cancer subtype detection using genomics level data is a significant research problem. Subtype detection is often a complex problem, and in most cases, needs multi-omics data fusion to achieve accurate subtyping. Different data fusion and subtyping approaches have been proposed over the years, such as kernel-based fusion, matrix factorization, and deep learning autoencoders. In this paper, we compared the performance of different deep learning autoencoders for cancer subtype detection. We performed cancer subtype detection on four different cancer types from The Cancer Genome Atlas (TCGA) datasets using four autoencoder implementations. We also predicted the optimal number of subtypes in a cancer type using the silhouette score and found that the detected subtypes exhibit significant differences in survival profiles. Furthermore, we compared the effect of feature selection and similarity measures for subtype detection. For further evaluation, we used the Glioblastoma multiforme (GBM) dataset and identified the differentially expressed genes in each of the subtypes. The results obtained are consistent with other genomic studies and can be corroborated with the involved pathways and biological functions. Thus, it shows that the results from the autoencoders, obtained through the interaction of different datatypes of cancer, can be used for the prediction and characterization of patient subgroups and survival profiles.

A deep learning system for automated, multi-modality 2D segmentation of vertebral bodies and intervertebral discs

Bone ◽  
2021 ◽  
pp. 115972
Author(s):  
Abhinav Suri ◽  
Brandon C. Jones ◽  
Grace Ng ◽  
Nancy Anabaraonye ◽  
Patrick Beyrer ◽  
...  
Keyword(s):  
Deep Learning ◽  
Intervertebral Discs ◽  
Learning System ◽  
Vertebral Bodies

Towards Underwater Sustainability using ROV Equipped with Deep Learning System

2020 ◽  
Author(s):  
Yi-Chia Wu ◽  
Po-Yen Shih ◽  
Li-Perng Chen ◽  
Chia-Chin Wang ◽  
Hooman Samani
Keyword(s):  
Deep Learning ◽  
Learning System

scholarly journals A deep learning classifier for digital breast tomosynthesis

2021 ◽  
Vol 83 ◽  
pp. 184-193
Author(s):  
R. Ricciardi ◽  
G. Mettivier ◽  
M. Staffa ◽  
A. Sarno ◽  
G. Acampora ◽  
...  
Keyword(s):  
Deep Learning ◽  
Digital Breast Tomosynthesis ◽  
Breast Tomosynthesis ◽  
Learning Classifier

scholarly journals Machine learning applied on chest x-ray can aid in the diagnosis of COVID-19: a first experience from Lombardy, Italy

2021 ◽  
Vol 5 (1) ◽  
Author(s):  
Isabella Castiglioni ◽  
Davide Ippolito ◽  
Matteo Interlenghi ◽  
Caterina Beatrice Monti ◽  
Christian Salvatore ◽  
...  
Keyword(s):  
Deep Learning ◽  
Area Under The Curve ◽  
Clinical Information ◽  
Training Dataset ◽  
Independent Dataset ◽  
X Ray ◽  
Learning Classifier ◽  
Chest X Ray ◽  
Polymerase Chain ◽  
Deep Learning Model

Abstract Background We aimed to train and test a deep learning classifier to support the diagnosis of coronavirus disease 2019 (COVID-19) using chest x-ray (CXR) on a cohort of subjects from two hospitals in Lombardy, Italy. Methods We used for training and validation an ensemble of ten convolutional neural networks (CNNs) with mainly bedside CXRs of 250 COVID-19 and 250 non-COVID-19 subjects from two hospitals (Centres 1 and 2). We then tested such system on bedside CXRs of an independent group of 110 patients (74 COVID-19, 36 non-COVID-19) from one of the two hospitals. A retrospective reading was performed by two radiologists in the absence of any clinical information, with the aim to differentiate COVID-19 from non-COVID-19 patients. Real-time polymerase chain reaction served as the reference standard. Results At 10-fold cross-validation, our deep learning model classified COVID-19 and non-COVID-19 patients with 0.78 sensitivity (95% confidence interval [CI] 0.74–0.81), 0.82 specificity (95% CI 0.78–0.85), and 0.89 area under the curve (AUC) (95% CI 0.86–0.91). For the independent dataset, deep learning showed 0.80 sensitivity (95% CI 0.72–0.86) (59/74), 0.81 specificity (29/36) (95% CI 0.73–0.87), and 0.81 AUC (95% CI 0.73–0.87). Radiologists’ reading obtained 0.63 sensitivity (95% CI 0.52–0.74) and 0.78 specificity (95% CI 0.61–0.90) in Centre 1 and 0.64 sensitivity (95% CI 0.52–0.74) and 0.86 specificity (95% CI 0.71–0.95) in Centre 2. Conclusions This preliminary experience based on ten CNNs trained on a limited training dataset shows an interesting potential of deep learning for COVID-19 diagnosis. Such tool is in training with new CXRs to further increase its performance.

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