scholarly journals Automated and Manual Quantification of Tumour Cellularity in Digital Slides for Tumour Burden Assessment

2019 ◽  
Author(s):  
Shazia Akbar ◽  
Mohammad Peikari ◽  
Sherine Salama ◽  
Azadeh Y. Panah ◽  
Sharon Nofech-Mozes ◽  
...  
Keyword(s):  
Artificial Intelligence ◽  
Neural Networks ◽  
Deep Neural Networks ◽  
Traditional Approach ◽  
Quantitative Measure ◽  
Image Data ◽  
Qualitative Assessment ◽  
Residual Cancer Burden ◽  
Manual Analysis ◽  
Tumour Cellularity

AbstractAimsThe residual cancer burden index is an important quantitative measure used for assessing treatment response following neoadjuvant therapy for breast cancer. It has shown to be predictive of overall survival and is composed of two key metrics: qualitative assessment of lymph nodes and the percentage of invasive or in-situ tumour cellularity (TC) in the tumour bed (TB). Currently, TC is assessed through eye-balling of routine histopathology slides estimating the proportion of tumour cells within the TB. With the advances in production of digitized slides and increasing availability of slide scanners in pathology laboratories, there is potential to measure TC using automated algorithms with greater precision and accuracy.MethodsWe describe two methods for automated TC scoring: 1) a traditional approach to image analysis development whereby we mimic the pathologists’ workflow, and 2) a recent development in artificial intelligence in which features are learned automatically in deep neural networks using image data alone.ResultsWe show strong agreements between automated and manual analysis of digital slides. Agreements between our trained deep neural networks and experts in this study (0.82) approach the inter-rater agreements between pathologists (0.89). We also reveal properties that are captured when we apply deep neural network to whole slide images, and discuss the potential of using such visualisations to improve upon TC assessment in the future.ConclusionsTC scoring can be successfully automated by leveraging recent advancements in artificial intelligence, thereby alleviating the burden of manual analysis.

scholarly journals Automated and Manual Quantification of Tumour Cellularity in Digital Slides for Tumour Burden Assessment

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Shazia Akbar ◽  
Mohammad Peikari ◽  
Sherine Salama ◽  
Azadeh Yazdan Panah ◽  
Sharon Nofech-Mozes ◽  
...  
Keyword(s):  
Neural Networks ◽  
Deep Neural Networks ◽  
Traditional Approach ◽  
Quantitative Measure ◽  
Image Data ◽  
Qualitative Assessment ◽  
Residual Cancer Burden ◽  
Automated Algorithms ◽  
Tumour Cellularity

Abstract The residual cancer burden index is an important quantitative measure used for assessing treatment response following neoadjuvant therapy for breast cancer. It has shown to be predictive of overall survival and is composed of two key metrics: qualitative assessment of lymph nodes and the percentage of invasive or in situ tumour cellularity (TC) in the tumour bed (TB). Currently, TC is assessed through eye-balling of routine histopathology slides estimating the proportion of tumour cells within the TB. With the advances in production of digitized slides and increasing availability of slide scanners in pathology laboratories, there is potential to measure TC using automated algorithms with greater precision and accuracy. We describe two methods for automated TC scoring: 1) a traditional approach to image analysis development whereby we mimic the pathologists’ workflow, and 2) a recent development in artificial intelligence in which features are learned automatically in deep neural networks using image data alone. We show strong agreements between automated and manual analysis of digital slides. Agreements between our trained deep neural networks and experts in this study (0.82) approach the inter-rater agreements between pathologists (0.89). We also reveal properties that are captured when we apply deep neural network to whole slide images, and discuss the potential of using such visualisations to improve upon TC assessment in the future.

scholarly journals Towards pixel-to-pixel deep nucleus detection in microscopy images

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Fuyong Xing ◽  
Yuanpu Xie ◽  
Xiaoshuang Shi ◽  
Pingjun Chen ◽  
Zizhao Zhang ◽  
...  
Keyword(s):  
Neural Networks ◽  
Large Scale ◽  
Deep Neural Networks ◽  
Image Data ◽  
Fine Tuning ◽  
Cell Detection ◽  
Imaging Protocol ◽  
Microscopy Image ◽  
Microscopy Images ◽  
Target Data

Abstract Background Nucleus or cell detection is a fundamental task in microscopy image analysis and supports many other quantitative studies such as object counting, segmentation, tracking, etc. Deep neural networks are emerging as a powerful tool for biomedical image computing; in particular, convolutional neural networks have been widely applied to nucleus/cell detection in microscopy images. However, almost all models are tailored for specific datasets and their applicability to other microscopy image data remains unknown. Some existing studies casually learn and evaluate deep neural networks on multiple microscopy datasets, but there are still several critical, open questions to be addressed. Results We analyze the applicability of deep models specifically for nucleus detection across a wide variety of microscopy image data. More specifically, we present a fully convolutional network-based regression model and extensively evaluate it on large-scale digital pathology and microscopy image datasets, which consist of 23 organs (or cancer diseases) and come from multiple institutions. We demonstrate that for a specific target dataset, training with images from the same types of organs might be usually necessary for nucleus detection. Although the images can be visually similar due to the same staining technique and imaging protocol, deep models learned with images from different organs might not deliver desirable results and would require model fine-tuning to be on a par with those trained with target data. We also observe that training with a mixture of target and other/non-target data does not always mean a higher accuracy of nucleus detection, and it might require proper data manipulation during model training to achieve good performance. Conclusions We conduct a systematic case study on deep models for nucleus detection in a wide variety of microscopy images, aiming to address several important but previously understudied questions. We present and extensively evaluate an end-to-end, pixel-to-pixel fully convolutional regression network and report a few significant findings, some of which might have not been reported in previous studies. The model performance analysis and observations would be helpful to nucleus detection in microscopy images.

scholarly journals Critical Assessment of Artificial Intelligence Methods for Prediction of hERG Channel Inhibition in the ‘Big Data’ Era

2020 ◽  
Author(s):  
Vishal Babu Siramshetty ◽  
Dac-Trung Nguyen ◽  
Natalia J. Martinez ◽  
Anton Simeonov ◽  
Noel T. Southall ◽  
...  
Keyword(s):  
Artificial Intelligence ◽  
Neural Networks ◽  
Big Data ◽  
Recurrent Neural Networks ◽  
Deep Neural Networks ◽  
Prediction Models ◽  
Chemical Space ◽  
Superior Performance ◽  
Gradient Boosting ◽  
Artificial Intelligence Methods

The rise of novel artificial intelligence methods necessitates a comparison of this wave of new approaches with classical machine learning for a typical drug discovery project. Inhibition of the potassium ion channel, whose alpha subunit is encoded by human Ether-à-go-go-Related Gene (hERG), leads to prolonged QT interval of the cardiac action potential and is a significant safety pharmacology target for the development of new medicines. Several computational approaches have been employed to develop prediction models for assessment of hERG liabilities of small molecules including recent work using deep learning methods. Here we perform a comprehensive comparison of prediction models based on classical (random forests and gradient boosting) and modern (deep neural networks and recurrent neural networks) artificial intelligence methods. The training set (~9000 compounds) was compiled by integrating hERG bioactivity data from ChEMBL database with experimental data generated from an in-house, high-throughput thallium flux assay. We utilized different molecular descriptors including the latent descriptors, which are real-valued continuous vectors derived from chemical autoencoders trained on a large chemical space (> 1.5 million compounds). The models were prospectively validated on ~840 in-house compounds screened in the same thallium flux assay. The deep neural networks performed significantly better than the classical methods with the latent descriptors. The recurrent neural networks that operate on SMILES provided highest model sensitivity. The best models were merged into a consensus model that offered superior performance compared to reference models from academic and commercial domains. Further, we shed light on the potential of artificial intelligence methods to exploit the chemistry big data and generate novel chemical representations useful in predictive modeling and tailoring new chemical space.<br>

A Review of Recent Deep Learning Models in COVID-19 Diagnosis

2021 ◽  
Vol 6 (5) ◽  
pp. 10-15
Author(s):  
Ela Bhattacharya ◽  
D. Bhattacharya
Keyword(s):  
Artificial Intelligence ◽  
Neural Networks ◽  
Deep Learning ◽  
Deep Neural Networks ◽  
Test Results ◽  
Learning Models ◽  
Future Directions ◽  
Human Contact ◽  
The World ◽  
Short Span

COVID-19 has emerged as the latest worrisome pandemic, which is reported to have its outbreak in Wuhan, China. The infection spreads by means of human contact, as a result, it has caused massive infections across 200 countries around the world. Artificial intelligence has likewise contributed to managing the COVID-19 pandemic in various aspects within a short span of time. Deep Neural Networks that are explored in this paper have contributed to the detection of COVID-19 from imaging sources. The datasets, pre-processing, segmentation, feature extraction, classification and test results which can be useful for discovering future directions in the domain of automatic diagnosis of the disease, utilizing artificial intelligence-based frameworks, have been investigated in this paper.

Enhanced Fusion of Deep Neural Networks for Classification of Benchmark High-Resolution Image Data Sets

2018 ◽  
Vol 15 (9) ◽  
pp. 1451-1455 ◽  
Author(s):  
Grant J. Scott ◽  
Kyle C. Hagan ◽  
Richard A. Marcum ◽  
James Alex Hurt ◽  
Derek T. Anderson ◽  
...  
Keyword(s):  
Neural Networks ◽  
High Resolution ◽  
Deep Neural Networks ◽  
Image Data ◽  
Data Sets ◽  
Resolution Image ◽  
High Resolution Image

scholarly journals Technical note: AI-Track-tive: automated fission track recognition using computer vision (Artificial Intelligence)

2020 ◽  
Author(s):  
Simon Nachtergaele ◽  
Johan De Grave
Keyword(s):  
Artificial Intelligence ◽  
Neural Networks ◽  
Computer Vision ◽  
Deep Neural Networks ◽  
Fission Track ◽  
Detection Algorithm ◽  
Technical Note ◽  
Success Rates ◽  
Automatic Counting ◽  
First Time

Abstract. Artificial intelligence techniques such as deep neural networks and computer vision are developed for fission track recognition and included in a computer program for the first time. These deep neural networks use the Yolov3 object detection algorithm, which is currently one of the most powerful and fastest object recognition algorithms. These deep neural networks can be used in new software called AI-Track-tive. The developed program successfully finds most of the fission tracks in the microscope images, however, the user still needs to supervise the automatic counting. The success rates of the automatic recognition range from 70 % to 100 % depending on the areal track densities in apatite and (muscovite) external detector. The success rate generally decreases for images with high areal track densities, because overlapping tracks are less easily recognizable for computer vision techniques.

scholarly journals Deep neural network: Recognize Data Management of Artificial Intelligence in Retail

2019 ◽  
Vol 8 (10) ◽  
pp. 3594-3596
Keyword(s):  
Artificial Intelligence ◽  
Neural Networks ◽  
Data Management ◽  
Deep Neural Networks ◽  
Data Management System ◽  
Research Approach ◽  
Vast Amount ◽  
Retail Business ◽  
Combining Data ◽  
Hidden Layer

Deep neural networks with the artificial intelligence on Machine Learning (ML) algorithms constitute the best design specifically to deal with vast amount of data for retail business. The limited research approach is referred towards reducing memory consumption on integrating ML algorithms on data management system. This paper proposed combining data management and deep neural networks, ideas to build systems, which vast amount data can share in the database system. Therefore, ML algorithm has a pattern with multi-hidden layer that can use to synthesis different decision within a minimum processing. Finally, system precede and follow a NoSQL layers of a model employs in-memory database compression techniques and executes data management challenges with large datasets successfully.

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