A regularized ensemble framework of deep learning for cancer detection from multi-class, imbalanced training data

2018 ◽  
Vol 77 ◽  
pp. 160-172 ◽  
Author(s):  
Xiaohui Yuan ◽  
Lijun Xie ◽  
Mohamed Abouelenien
2019 ◽  
Vol 9 (22) ◽  
pp. 4749
Author(s):  
Lingyun Jiang ◽  
Kai Qiao ◽  
Linyuan Wang ◽  
Chi Zhang ◽  
Jian Chen ◽  
...  

Decoding human brain activities, especially reconstructing human visual stimuli via functional magnetic resonance imaging (fMRI), has gained increasing attention in recent years. However, the high dimensionality and small quantity of fMRI data impose restrictions on satisfactory reconstruction, especially for the reconstruction method with deep learning requiring huge amounts of labelled samples. When compared with the deep learning method, humans can recognize a new image because our human visual system is naturally capable of extracting features from any object and comparing them. Inspired by this visual mechanism, we introduced the mechanism of comparison into deep learning method to realize better visual reconstruction by making full use of each sample and the relationship of the sample pair by learning to compare. In this way, we proposed a Siamese reconstruction network (SRN) method. By using the SRN, we improved upon the satisfying results on two fMRI recording datasets, providing 72.5% accuracy on the digit dataset and 44.6% accuracy on the character dataset. Essentially, this manner can increase the training data about from n samples to 2n sample pairs, which takes full advantage of the limited quantity of training samples. The SRN learns to converge sample pairs of the same class or disperse sample pairs of different class in feature space.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Xin Mao ◽  
Jun Kang Chow ◽  
Pin Siang Tan ◽  
Kuan-fu Liu ◽  
Jimmy Wu ◽  
...  

AbstractAutomatic bird detection in ornithological analyses is limited by the accuracy of existing models, due to the lack of training data and the difficulties in extracting the fine-grained features required to distinguish bird species. Here we apply the domain randomization strategy to enhance the accuracy of the deep learning models in bird detection. Trained with virtual birds of sufficient variations in different environments, the model tends to focus on the fine-grained features of birds and achieves higher accuracies. Based on the 100 terabytes of 2-month continuous monitoring data of egrets, our results cover the findings using conventional manual observations, e.g., vertical stratification of egrets according to body size, and also open up opportunities of long-term bird surveys requiring intensive monitoring that is impractical using conventional methods, e.g., the weather influences on egrets, and the relationship of the migration schedules between the great egrets and little egrets.


Sensors ◽  
2021 ◽  
Vol 21 (8) ◽  
pp. 2611
Author(s):  
Andrew Shepley ◽  
Greg Falzon ◽  
Christopher Lawson ◽  
Paul Meek ◽  
Paul Kwan

Image data is one of the primary sources of ecological data used in biodiversity conservation and management worldwide. However, classifying and interpreting large numbers of images is time and resource expensive, particularly in the context of camera trapping. Deep learning models have been used to achieve this task but are often not suited to specific applications due to their inability to generalise to new environments and inconsistent performance. Models need to be developed for specific species cohorts and environments, but the technical skills required to achieve this are a key barrier to the accessibility of this technology to ecologists. Thus, there is a strong need to democratize access to deep learning technologies by providing an easy-to-use software application allowing non-technical users to train custom object detectors. U-Infuse addresses this issue by providing ecologists with the ability to train customised models using publicly available images and/or their own images without specific technical expertise. Auto-annotation and annotation editing functionalities minimize the constraints of manually annotating and pre-processing large numbers of images. U-Infuse is a free and open-source software solution that supports both multiclass and single class training and object detection, allowing ecologists to access deep learning technologies usually only available to computer scientists, on their own device, customised for their application, without sharing intellectual property or sensitive data. It provides ecological practitioners with the ability to (i) easily achieve object detection within a user-friendly GUI, generating a species distribution report, and other useful statistics, (ii) custom train deep learning models using publicly available and custom training data, (iii) achieve supervised auto-annotation of images for further training, with the benefit of editing annotations to ensure quality datasets. Broad adoption of U-Infuse by ecological practitioners will improve ecological image analysis and processing by allowing significantly more image data to be processed with minimal expenditure of time and resources, particularly for camera trap images. Ease of training and use of transfer learning means domain-specific models can be trained rapidly, and frequently updated without the need for computer science expertise, or data sharing, protecting intellectual property and privacy.


2021 ◽  
Author(s):  
Birgid Schömig-Markiefka ◽  
Alexey Pryalukhin ◽  
Wolfgang Hulla ◽  
Andrey Bychkov ◽  
Junya Fukuoka ◽  
...  

AbstractDigital pathology provides a possibility for computational analysis of histological slides and automatization of routine pathological tasks. Histological slides are very heterogeneous concerning staining, sections’ thickness, and artifacts arising during tissue processing, cutting, staining, and digitization. In this study, we digitally reproduce major types of artifacts. Using six datasets from four different institutions digitized by different scanner systems, we systematically explore artifacts’ influence on the accuracy of the pre-trained, validated, deep learning-based model for prostate cancer detection in histological slides. We provide evidence that any histological artifact dependent on severity can lead to a substantial loss in model performance. Strategies for the prevention of diagnostic model accuracy losses in the context of artifacts are warranted. Stress-testing of diagnostic models using synthetically generated artifacts might be an essential step during clinical validation of deep learning-based algorithms.


Diagnostics ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1052
Author(s):  
Leang Sim Nguon ◽  
Kangwon Seo ◽  
Jung-Hyun Lim ◽  
Tae-Jun Song ◽  
Sung-Hyun Cho ◽  
...  

Mucinous cystic neoplasms (MCN) and serous cystic neoplasms (SCN) account for a large portion of solitary pancreatic cystic neoplasms (PCN). In this study we implemented a convolutional neural network (CNN) model using ResNet50 to differentiate between MCN and SCN. The training data were collected retrospectively from 59 MCN and 49 SCN patients from two different hospitals. Data augmentation was used to enhance the size and quality of training datasets. Fine-tuning training approaches were utilized by adopting the pre-trained model from transfer learning while training selected layers. Testing of the network was conducted by varying the endoscopic ultrasonography (EUS) image sizes and positions to evaluate the network performance for differentiation. The proposed network model achieved up to 82.75% accuracy and a 0.88 (95% CI: 0.817–0.930) area under curve (AUC) score. The performance of the implemented deep learning networks in decision-making using only EUS images is comparable to that of traditional manual decision-making using EUS images along with supporting clinical information. Gradient-weighted class activation mapping (Grad-CAM) confirmed that the network model learned the features from the cyst region accurately. This study proves the feasibility of diagnosing MCN and SCN using a deep learning network model. Further improvement using more datasets is needed.


2021 ◽  
Vol 11 (6) ◽  
pp. 2866
Author(s):  
Damheo Lee ◽  
Donghyun Kim ◽  
Seung Yun ◽  
Sanghun Kim

In this paper, we propose a new method for code-switching (CS) automatic speech recognition (ASR) in Korean. First, the phonetic variations in English pronunciation spoken by Korean speakers should be considered. Thus, we tried to find a unified pronunciation model based on phonetic knowledge and deep learning. Second, we extracted the CS sentences semantically similar to the target domain and then applied the language model (LM) adaptation to solve the biased modeling toward Korean due to the imbalanced training data. In this experiment, training data were AI Hub (1033 h) in Korean and Librispeech (960 h) in English. As a result, when compared to the baseline, the proposed method improved the error reduction rate (ERR) by up to 11.6% with phonetic variant modeling and by 17.3% when semantically similar sentences were applied to the LM adaptation. If we considered only English words, the word correction rate improved up to 24.2% compared to that of the baseline. The proposed method seems to be very effective in CS speech recognition.


2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Xinyang Li ◽  
Guoxun Zhang ◽  
Hui Qiao ◽  
Feng Bao ◽  
Yue Deng ◽  
...  

AbstractThe development of deep learning and open access to a substantial collection of imaging data together provide a potential solution for computational image transformation, which is gradually changing the landscape of optical imaging and biomedical research. However, current implementations of deep learning usually operate in a supervised manner, and their reliance on laborious and error-prone data annotation procedures remains a barrier to more general applicability. Here, we propose an unsupervised image transformation to facilitate the utilization of deep learning for optical microscopy, even in some cases in which supervised models cannot be applied. Through the introduction of a saliency constraint, the unsupervised model, named Unsupervised content-preserving Transformation for Optical Microscopy (UTOM), can learn the mapping between two image domains without requiring paired training data while avoiding distortions of the image content. UTOM shows promising performance in a wide range of biomedical image transformation tasks, including in silico histological staining, fluorescence image restoration, and virtual fluorescence labeling. Quantitative evaluations reveal that UTOM achieves stable and high-fidelity image transformations across different imaging conditions and modalities. We anticipate that our framework will encourage a paradigm shift in training neural networks and enable more applications of artificial intelligence in biomedical imaging.


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