pwc-archive/papers-with-abstracts huggingface dataset:
Exploring Large Context for Cerebral Aneurysm Segmentation
Authors: Jun Ma, Ziwei Nie
Date: 2020-12-30 00:00:00
Tasks: Segmentation

Automated segmentation of aneurysms from 3D CT is important for the diagnosis, monitoring, and treatment planning of the cerebral aneurysm disease. This short paper briefly presents the main technique details of the aneurysm segmentation method in the MICCAI 2020 CADA challenge. The main contribution is that we configure the 3D U-Net with a large patch size, which can obtain the large context. Our method ranked second on the MICCAI 2020 CADA testing dataset with an average Jaccard of 0.7593. Our code and trained models are publicly available at \url{https://github.com/JunMa11/CADA2020}.
Medico Multimedia Task at MediaEval 2020: Automatic Polyp Segmentation
Authors: Debesh Jha, Steven A. Hicks, Krister Emanuelsen, Håvard Johansen, Dag Johansen, Thomas de Lange, Michael A. Riegler, Pål Halvorsen
Date: 2020-12-30 00:00:00

Colorectal cancer is the third most common cause of cancer worldwide. According to Global cancer statistics 2018, the incidence of colorectal cancer is increasing in both developing and developed countries. Early detection of colon anomalies such as polyps is important for cancer prevention, and automatic polyp segmentation can play a crucial role for this. Regardless of the recent advancement in early detection and treatment options, the estimated polyp miss rate is still around 20\%. Support via an automated computer-aided diagnosis system could be one of the potential solutions for the overlooked polyps. Such detection systems can help low-cost design solutions and save doctors time, which they could for example use to perform more patient examinations. In this paper, we introduce the 2020 Medico challenge, provide some information on related work and the dataset, describe the task and evaluation metrics, and discuss the necessity of organizing the Medico challenge.
DDANet: Dual Decoder Attention Network for Automatic Polyp Segmentation
Authors: Nikhil Kumar Tomar, Debesh Jha, Sharib Ali, Håvard D. Johansen, Dag Johansen, Michael A. Riegler, Pål Halvorsen
Date: 2020-12-30 00:00:00
Tasks: Colorectal Polyps Characterization, Decision Making, Decoder, Medical Image Segmentation, Real-Time Semantic Segmentation, Semantic Segmentation

Colonoscopy is the gold standard for examination and detection of colorectal polyps. Localization and delineation of polyps can play a vital role in treatment (e.g., surgical planning) and prognostic decision making. Polyp segmentation can provide detailed boundary information for clinical analysis. Convolutional neural networks have improved the performance in colonoscopy. However, polyps usually possess various challenges, such as intra-and inter-class variation and noise. While manual labeling for polyp assessment requires time from experts and is prone to human error (e.g., missed lesions), an automated, accurate, and fast segmentation can improve the quality of delineated lesion boundaries and reduce missed rate. The Endotect challenge provides an opportunity to benchmark computer vision methods by training on the publicly available Hyperkvasir and testing on a separate unseen dataset. In this paper, we propose a novel architecture called ``DDANet'' based on a dual decoder attention network. Our experiments demonstrate that the model trained on the Kvasir-SEG dataset and tested on an unseen dataset achieves a dice coefficient of 0.7874, mIoU of 0.7010, recall of 0.7987, and a precision of 0.8577, demonstrating the generalization ability of our model.
Automatic Polyp Segmentation using U-Net-ResNet50
Authors: Saruar Alam, Nikhil Kumar Tomar, Aarati Thakur, Debesh Jha, Ashish Rauniyar
Date: 2020-12-30 00:00:00
Tasks: Medical Image Segmentation, Segmentation

Polyps are the predecessors to colorectal cancer which is considered as one of the leading causes of cancer-related deaths worldwide. Colonoscopy is the standard procedure for the identification, localization, and removal of colorectal polyps. Due to variability in shape, size, and surrounding tissue similarity, colorectal polyps are often missed by the clinicians during colonoscopy. With the use of an automatic, accurate, and fast polyp segmentation method during the colonoscopy, many colorectal polyps can be easily detected and removed. The ``Medico automatic polyp segmentation challenge'' provides an opportunity to study polyp segmentation and build an efficient and accurate segmentation algorithm. We use the U-Net with pre-trained ResNet50 as the encoder for the polyp segmentation. The model is trained on Kvasir-SEG dataset provided for the challenge and tested on the organizer's dataset and achieves a dice coefficient of 0.8154, Jaccard of 0.7396, recall of 0.8533, precision of 0.8532, accuracy of 0.9506, and F2 score of 0.8272, demonstrating the generalization ability of our model.
Some Algorithms on Exact, Approximate and Error-Tolerant Graph Matching
Authors: Shri Prakash Dwivedi
Date: 2020-12-30 00:00:00
Tasks: Graph Matching, Graph Similarity, Position

The graph is one of the most widely used mathematical structures in engineering and science because of its representational power and inherent ability to demonstrate the relationship between objects. The objective of this work is to introduce the novel graph matching techniques using the representational power of the graph and apply it to structural pattern recognition applications. We present an extensive survey of various exact and inexact graph matching techniques. Graph matching using the concept of homeomorphism is presented. A category of graph matching algorithms is presented, which reduces the graph size by removing the less important nodes using some measure of relevance. We present an approach to error-tolerant graph matching using node contraction where the given graph is transformed into another graph by contracting smaller degree nodes. We use this scheme to extend the notion of graph edit distance, which can be used as a trade-off between execution time and accuracy. We describe an approach to graph matching by utilizing the various node centrality information, which reduces the graph size by removing a fraction of nodes from both graphs based on a given centrality measure. The graph matching problem is inherently linked to the geometry and topology of graphs. We introduce a novel approach to measure graph similarity using geometric graphs. We define the vertex distance between two geometric graphs using the position of their vertices and show it to be a metric over the set of all graphs with vertices only. We define edge distance between two graphs based on the angular orientation, length and position of the edges. Then we combine the notion of vertex distance and edge distance to define the graph distance between two geometric graphs and show it to be a metric. Finally, we use the proposed graph similarity framework to perform exact and error-tolerant graph matching.
MRI brain tumor segmentation and uncertainty estimation using 3D-UNet architectures
Authors: Laura Mora Ballestar, Veronica Vilaplana
Date: 2020-12-30 00:00:00
Tasks: Brain Tumor Segmentation, Data Augmentation, Decoder, Diagnostic, Medical Diagnosis, Segmentation, Tumor Segmentation

Automation of brain tumor segmentation in 3D magnetic resonance images (MRIs) is key to assess the diagnostic and treatment of the disease. In recent years, convolutional neural networks (CNNs) have shown improved results in the task. However, high memory consumption is still a problem in 3D-CNNs. Moreover, most methods do not include uncertainty information, which is especially critical in medical diagnosis. This work studies 3D encoder-decoder architectures trained with patch-based techniques to reduce memory consumption and decrease the effect of unbalanced data. The different trained models are then used to create an ensemble that leverages the properties of each model, thus increasing the performance. We also introduce voxel-wise uncertainty information, both epistemic and aleatoric using test-time dropout (TTD) and data-augmentation (TTA) respectively. In addition, a hybrid approach is proposed that helps increase the accuracy of the segmentation. The model and uncertainty estimation measurements proposed in this work have been used in the BraTS'20 Challenge for task 1 and 3 regarding tumor segmentation and uncertainty estimation.
H2NF-Net for Brain Tumor Segmentation using Multimodal MR Imaging: 2nd Place Solution to BraTS Challenge 2020 Segmentation Task
Authors: Haozhe Jia, Weidong Cai, Heng Huang, Yong Xia
Date: 2020-12-30 00:00:00
Tasks: Brain Tumor Segmentation, Segmentation, Tumor Segmentation

In this paper, we propose a Hybrid High-resolution and Non-local Feature Network (H2NF-Net) to segment brain tumor in multimodal MR images. Our H2NF-Net uses the single and cascaded HNF-Nets to segment different brain tumor sub-regions and combines the predictions together as the final segmentation. We trained and evaluated our model on the Multimodal Brain Tumor Segmentation Challenge (BraTS) 2020 dataset. The results on the test set show that the combination of the single and cascaded models achieved average Dice scores of 0.78751, 0.91290, and 0.85461, as well as Hausdorff distances ($95\%$) of 26.57525, 4.18426, and 4.97162 for the enhancing tumor, whole tumor, and tumor core, respectively. Our method won the second place in the BraTS 2020 challenge segmentation task out of nearly 80 participants.
FREA-Unet: Frequency-aware U-net for Modality Transfer
Authors: Hajar Emami, Qiong Liu, Ming Dong
Date: 2020-12-31 00:00:00
Tasks: Image Generation

While Positron emission tomography (PET) imaging has been widely used in diagnosis of number of diseases, it has costly acquisition process which involves radiation exposure to patients. However, magnetic resonance imaging (MRI) is a safer imaging modality that does not involve patient's exposure to radiation. Therefore, a need exists for an efficient and automated PET image generation from MRI data. In this paper, we propose a new frequency-aware attention U-net for generating synthetic PET images. Specifically, we incorporate attention mechanism into different U-net layers responsible for estimating low/high frequency scales of the image. Our frequency-aware attention Unet computes the attention scores for feature maps in low/high frequency layers and use it to help the model focus more on the most important regions, leading to more realistic output images. Experimental results on 30 subjects from Alzheimers Disease Neuroimaging Initiative (ADNI) dataset demonstrate good performance of the proposed model in PET image synthesis that achieved superior performance, both qualitative and quantitative, over current state-of-the-arts.
New Bag of Deep Visual Words based features to classify chest x-ray images for COVID-19 diagnosis
Authors: Chiranjibi Sitaula, Sunil Aryal
Date: 2020-12-31 00:00:00
Tasks: COVID-19 Diagnosis

Because the infection by Severe Acute Respiratory Syndrome Coronavirus 2 (COVID-19) causes the pneumonia-like effect in the lungs, the examination of chest x-rays can help to diagnose the diseases. For automatic analysis of images, they are represented in machines by a set of semantic features. Deep Learning (DL) models are widely used to extract features from images. General deep features may not be appropriate to represent chest x-rays as they have a few semantic regions. Though the Bag of Visual Words (BoVW) based features are shown to be more appropriate for x-ray type of images, existing BoVW features may not capture enough information to differentiate COVID-19 infection from other pneumonia-related infections. In this paper, we propose a new BoVW method over deep features, called Bag of Deep Visual Words (BoDVW), by removing the feature map normalization step and adding deep features normalization step on the raw feature maps. This helps to preserve the semantics of each feature map that may have important clues to differentiate COVID-19 from pneumonia. We evaluate the effectiveness of our proposed BoDVW features in chest x-rays classification using Support Vector Machine (SVM) to diagnose COVID-19. Our results on a publicly available COVID-19 x-ray dataset reveal that our features produce stable and prominent classification accuracy, particularly differentiating COVID-19 infection from other pneumonia, in shorter computation time compared to the state-of-the-art methods. Thus, our method could be a very useful tool for quick diagnosis of COVID-19 patients on a large scale.
Survey of the Detection and Classification of Pulmonary Lesions via CT and X-Ray
Authors: Yixuan Sun, Chengyao Li, Qian Zhang, Aimin Zhou, Guixu Zhang
Date: 2020-12-31 00:00:00
Tasks: General Classification

In recent years, the prevalence of several pulmonary diseases, especially the coronavirus disease 2019 (COVID-19) pandemic, has attracted worldwide attention. These diseases can be effectively diagnosed and treated with the help of lung imaging. With the development of deep learning technology and the emergence of many public medical image datasets, the diagnosis of lung diseases via medical imaging has been further improved. This article reviews pulmonary CT and X-ray image detection and classification in the last decade. It also provides an overview of the detection of lung nodules, pneumonia, and other common lung lesions based on the imaging characteristics of various lesions. Furthermore, this review introduces 26 commonly used public medical image datasets, summarizes the latest technology, and discusses current challenges and future research directions.
Colonoscopy Polyp Detection: Domain Adaptation From Medical Report Images to Real-time Videos
Authors: Zhi-Qin Zhan, Huazhu Fu, Yan-Yao Yang, Jingjing Chen, Jie Liu, Yu-Gang Jiang
Date: 2020-12-31 00:00:00
Tasks: Domain Adaptation

Automatic colorectal polyp detection in colonoscopy video is a fundamental task, which has received a lot of attention. Manually annotating polyp region in a large scale video dataset is time-consuming and expensive, which limits the development of deep learning techniques. A compromise is to train the target model by using labeled images and infer on colonoscopy videos. However, there are several issues between the image-based training and video-based inference, including domain differences, lack of positive samples, and temporal smoothness. To address these issues, we propose an Image-video-joint polyp detection network (Ivy-Net) to address the domain gap between colonoscopy images from historical medical reports and real-time videos. In our Ivy-Net, a modified mixup is utilized to generate training data by combining the positive images and negative video frames at the pixel level, which could learn the domain adaptive representations and augment the positive samples. Simultaneously, a temporal coherence regularization (TCR) is proposed to introduce the smooth constraint on feature-level in adjacent frames and improve polyp detection by unlabeled colonoscopy videos. For evaluation, a new large colonoscopy polyp dataset is collected, which contains 3056 images from historical medical reports of 889 positive patients and 7.5-hour videos of 69 patients (28 positive). The experiments on the collected dataset demonstrate that our Ivy-Net achieves the state-of-the-art result on colonoscopy video.
Exploiting Shared Knowledge from Non-COVID Lesions for Annotation-Efficient COVID-19 CT Lung Infection Segmentation
Authors: Yichi Zhang, Qingcheng Liao, Lin Yuan, He Zhu, Jiezhen Xing, Jicong Zhang
Date: 2020-12-31 00:00:00
Tasks: Computed Tomography (CT), Lesion Segmentation, Segmentation

The novel Coronavirus disease (COVID-19) is a highly contagious virus and has spread all over the world, posing an extremely serious threat to all countries. Automatic lung infection segmentation from computed tomography (CT) plays an important role in the quantitative analysis of COVID-19. However, the major challenge lies in the inadequacy of annotated COVID-19 datasets. Currently, there are several public non-COVID lung lesion segmentation datasets, providing the potential for generalizing useful information to the related COVID-19 segmentation task. In this paper, we propose a novel relation-driven collaborative learning model to exploit shared knowledge from non-COVID lesions for annotation-efficient COVID-19 CT lung infection segmentation. The model consists of a general encoder to capture general lung lesion features based on multiple non-COVID lesions, and a target encoder to focus on task-specific features based on COVID-19 infections. Features extracted from the two parallel encoders are concatenated for the subsequent decoder part. We develop a collaborative learning scheme to regularize feature-level relation consistency of given input and encourage the model to learn more general and discriminative representation of COVID-19 infections. Extensive experiments demonstrate that trained with limited COVID-19 data, exploiting shared knowledge from non-COVID lesions can further improve state-of-the-art performance with up to 3.0% in dice similarity coefficient and 4.2% in normalized surface dice. Our proposed method promotes new insights into annotation-efficient deep learning for COVID-19 infection segmentation and illustrates strong potential for real-world applications in the global fight against COVID-19 in the absence of sufficient high-quality annotations.
Searching a Raw Video Database using Natural Language Queries
Authors: Sriram Krishna, Siddarth Vinay, Srinivas K S
Date: 2020-12-31 00:00:00
Tasks: Natural Language Queries

The number of videos being produced and consequently stored in databases for video streaming platforms has been increasing exponentially over time. This vast database should be easily index-able to find the requisite clip or video to match the given search specification, preferably in the form of a textual query. This work aims to provide an end-to-end pipeline to search a video database with a voice query from the end user. The pipeline makes use of Recurrent Neural Networks in combination with Convolutional Neural Networks to generate captions of the video clips present in the database.
Estimating Uncertainty in Neural Networks for Cardiac MRI Segmentation: A Benchmark Study
Authors: Matthew Ng, Fumin Guo, Labonny Biswas, Steffen E. Petersen, Stefan K. Piechnik, Stefan Neubauer, Graham Wright
Date: 2020-12-31 00:00:00
Tasks: Image Segmentation, MRI segmentation, Segmentation, Semantic Segmentation

Objective: Convolutional neural networks (CNNs) have demonstrated promise in automated cardiac magnetic resonance image segmentation. However, when using CNNs in a large real-world dataset, it is important to quantify segmentation uncertainty and identify segmentations which could be problematic. In this work, we performed a systematic study of Bayesian and non-Bayesian methods for estimating uncertainty in segmentation neural networks. Methods: We evaluated Bayes by Backprop, Monte Carlo Dropout, Deep Ensembles, and Stochastic Segmentation Networks in terms of segmentation accuracy, probability calibration, uncertainty on out-of-distribution images, and segmentation quality control. Results: We observed that Deep Ensembles outperformed the other methods except for images with heavy noise and blurring distortions. We showed that Bayes by Backprop is more robust to noise distortions while Stochastic Segmentation Networks are more resistant to blurring distortions. For segmentation quality control, we showed that segmentation uncertainty is correlated with segmentation accuracy for all the methods. With the incorporation of uncertainty estimates, we were able to reduce the percentage of poor segmentation to 5% by flagging 31--48% of the most uncertain segmentations for manual review, substantially lower than random review without using neural network uncertainty (reviewing 75--78% of all images). Conclusion: This work provides a comprehensive evaluation of uncertainty estimation methods and showed that Deep Ensembles outperformed other methods in most cases. Significance: Neural network uncertainty measures can help identify potentially inaccurate segmentations and alert users for manual review.
Hybrid Interest Modeling for Long-tailed Users
Authors: Lifang Deng, Jin Niu, Angulia Yang, Qidi Xu, Xiang Fu, Jiandong Zhang, AnXiang Zeng
Date: 2020-12-29 00:00:00
Tasks: Clustering, Recommendation Systems, Self-Supervised Learning

User behavior modeling is a key technique for recommender systems. However, most methods focus on head users with large-scale interactions and hence suffer from data sparsity issues. Several solutions integrate side information such as demographic features and product reviews, another is to transfer knowledge from other rich data sources. We argue that current methods are limited by the strict privacy policy and have low scalability in real-world applications and few works consider the behavioral characteristics behind long-tailed users. In this work, we propose the Hybrid Interest Modeling (HIM) network to hybrid both personalized interest and semi-personalized interest in learning long-tailed users' preferences in the recommendation. To achieve this, we first design the User Behavior Pyramid (UBP) module to capture the fine-grained personalized interest of high confidence from sparse even noisy positive feedbacks. Moreover, the individual interaction is too sparse and not enough for modeling user interest adequately, we design the User Behavior Clustering (UBC) module to learn latent user interest groups with self-supervised learning mechanism novelly, which capture coarse-grained semi-personalized interest from group-item interaction data. Extensive experiments on both public and industrial datasets verify the superiority of HIM compared with the state-of-the-art baselines.
Supporting Human Memory by Reconstructing Personal Episodic Narratives from Digital Traces
Authors: Varvara Kalokyri, Alexander Borgida, Amélie Marian
Date: 2020-12-29 00:00:00

Numerous applications capture in digital form aspects of people's lives. The resulting data, which we call Personal Digital Traces - PDTs, can be used to help reconstruct people's episodic memories and connect to their past personal events. This reconstruction has several applications, from helping patients with neurodegenerative diseases recall past events to gathering clues from multiple sources to identify recent contacts and places visited - a critical new application for the current health crisis. This paper takes steps towards integrating, connecting and summarizing the heterogeneous collection of data into episodic narratives using scripts - prototypical plans for everyday activities. Specifically, we propose a matching algorithm that groups several digital traces from many different sources into script instances (episodes), and we provide a technique for ranking the likelihood of candidate episodes. We report on the results of a study based on the personal data of real users, which gives evidence that our episode reconstruction technique 1) successfully integrates and combines traces from different sources into coherent episodes, and 2) augments users' memory of their past actions.