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Register a new userAutomated Diagnosis of Intestinal Parasites: A new hybrid approach and its benefits
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Added by
Daniel Osaku
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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Intestinal parasites are responsible for several diseases in human beings. In order to eliminate the error-prone visual analysis of optical microscopy slides, we have investigated automated, fast, and low-cost systems for the diagnosis of human intestinal parasites. In this work, we present a hybrid approach that combines the opinion of two decision-making systems with complementary properties: ($DS_1$) a simpler system based on very fast handcrafted image feature extraction and support vector machine classification and ($DS_2$) a more complex system based on a deep neural network, Vgg-16, for image feature extraction and classification. $DS_1$ is much faster than $DS_2$, but it is less accurate than $DS_2$. Fortunately, the errors of $DS_1$ are not the same of $DS_2$. During training, we use a validation set to learn the probabilities of misclassification by $DS_1$ on each class based on its confidence values. When $DS_1$ quickly classifies all images from a microscopy slide, the method selects a number of images with higher chances of misclassification for characterization and reclassification by $DS_2$. Our hybrid system can improve the overall effectiveness without compromising efficiency, being suitable for the clinical routine -- a strategy that might be suitable for other real applications. As demonstrated on large datasets, the proposed system can achieve, on average, 94.9%, 87.8%, and 92.5% of Cohens Kappa on helminth eggs, helminth larvae, and protozoa cysts, respectively.
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Object detection remains as one of the most notorious open problems in computer vision. Despite large strides in accuracy in recent years, modern object detectors have started to saturate on popular benchmarks raising the question of how far we can reach with deep learning tools and tricks. Here, by employing 2 state-of-the-art object detection benchmarks, and analyzing more than 15 models over 4 large scale datasets, we I) carefully determine the upper bound in AP, which is 91.6% on VOC (test2007), 78.2% on COCO (val2017), and 58.9% on OpenImages V4 (validation), regardless of the IOU threshold. These numbers are much better than the mAP of the best model (47.9% on VOC, and 46.9% on COCO; IOUs=.5:.05:.95), II) characterize the sources of errors in object detectors, in a novel and intuitive way, and find that classification error (confusion with other classes and misses) explains the largest fraction of errors and weighs more than localization and duplicate errors, and III) analyze the invariance properties of models when surrounding context of an object is removed, when an object is placed in an incongruent background, and when images are blurred or flipped vertically. We find that models generate a lot of boxes on empty regions and that context is more important for detecting small objects than larger ones. Our work taps into the tight relationship between object detection and object recognition and offers insights for building better models. Our code is publicly available at https://github.com/aliborji/Deetctionupper bound.git.
Intraductal papillary mucinous neoplasm (IPMN) is a precursor to pancreatic ductal adenocarcinoma. While over half of patients are diagnosed with pancreatic cancer at a distant stage, patients who are diagnosed early enjoy a much higher 5-year survival rate of $34%$ compared to $3%$ in the former; hence, early diagnosis is key. Unique challenges in the medical imaging domain such as extremely limited annotated data sets and typically large 3D volumetric data have made it difficult for deep learning to secure a strong foothold. In this work, we construct two novel inflated deep network architectures, $textit{InceptINN}$ and $textit{DenseINN}$, for the task of diagnosing IPMN from multisequence (T1 and T2) MRI. These networks inflate their 2D layers to 3D and bootstrap weights from their 2D counterparts (Inceptionv3 and DenseNet121 respectively) trained on ImageNet to the new 3D kernels. We also extend the inflation process by further expanding the pre-trained kernels to handle any number of input modalities and different fusion strategies. This is one of the first studies to train an end-to-end deep network on multisequence MRI for IPMN diagnosis, and shows that our proposed novel inflated network architectures are able to handle the extremely limited training data (139 MRI scans), while providing an absolute improvement of $8.76%$ in accuracy for diagnosing IPMN over the current state-of-the-art. Code is publicly available at https://github.com/lalonderodney/INN-Inflated-Neural-Nets.
Research on image quality assessment (IQA) remains limited mainly due to our incomplete knowledge about human visual perception. Existing IQA algorithms have been designed or trained with insufficient subjective data with a small degree of stimulus variability. This has led to challenges for those algorithms to handle complexity and diversity of real-world digital content. Perceptual evidence from human subjects serves as a grounding for the development of advanced IQA algorithms. It is thus critical to acquire reliable subjective data with controlled perception experiments that faithfully reflect human behavioural responses to distortions in visual signals. In this paper, we present a new study of image quality perception where subjective ratings were collected in a controlled lab environment. We investigate how quality perception is affected by a combination of different categories of images and different types and levels of distortions. The database will be made publicly available to facilitate calibration and validation of IQA algorithms.
Action recognition is a crucial task for video understanding. In this paper, we present AutoVideo, a Python system for automated video action recognition. It currently supports seven action recognition algorithms and various pre-processing modules. Unlike the existing libraries that only provide model zoos, AutoVideo is built with the standard pipeline language. The basic building block is primitive, which wraps a pre-processing module or an algorithm with some hyperparameters. AutoVideo is highly modular and extendable. It can be easily combined with AutoML searchers. The pipeline language is quite general so that we can easily enrich AutoVideo with algorithms for various other video-related tasks in the future. AutoVideo is released under MIT license at https://github.com/datamllab/autovideo
Text detection in natural scene images for content analysis is an interesting task. The research community has seen some great developments for English/Mandarin text detection. However, Urdu text extraction in natural scene images is a task not well addressed. In this work, firstly, a new dataset is introduced for Urdu text in natural scene images. The dataset comprises of 500 standalone images acquired from real scenes. Secondly, the channel enhanced Maximally Stable Extremal Region (MSER) method is applied to extract Urdu text regions as candidates in an image. Two-stage filtering mechanism is applied to eliminate non-candidate regions. In the first stage, text and noise are classified based on their geometric properties. In the second stage, a support vector machine classifier is trained to discard non-text candidate regions. After this, text candidate regions are linked using centroid-based vertical and horizontal distances. Text lines are further analyzed by a different classifier based on HOG features to remove non-text regions. Extensive experimentation is performed on the locally developed dataset to evaluate the performance. The experimental results show good performance on test set images. The dataset will be made available for research use. To the best of our knowledge, the work is the first of its kind for the Urdu language and would provide a good dataset for free research use and serve as a baseline performance on the task of Urdu text extraction.
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