pwc-archive/papers-with-abstracts huggingface dataset:
Integrating Data and Image Domain Deep Learning for Limited Angle Tomography using Consensus Equilibrium
Authors: Muhammad Usman Ghani, W. Clem Karl
Date: 2019-08-31 00:00:00
Tasks: Computed Tomography (CT)

Computed Tomography (CT) is a non-invasive imaging modality with applications ranging from healthcare to security. It reconstructs cross-sectional images of an object using a collection of projection data collected at different angles. Conventional methods, such as FBP, require that the projection data be uniformly acquired over the complete angular range. In some applications, it is not possible to acquire such data. Security is one such domain where non-rotational scanning configurations are being developed which violate the complete data assumption. Conventional methods produce images from such data that are filled with artifacts. The recent success of deep learning (DL) methods has inspired researchers to post-process these artifact laden images using deep neural networks (DNNs). This approach has seen limited success on real CT problems. Another approach has been to pre-process the incomplete data using DNNs aiming to avoid the creation of artifacts altogether. Due to imperfections in the learning process, this approach can still leave perceptible residual artifacts. In this work, we aim to combine the power of deep learning in both the data and image domains through a two-step process based on the consensus equilibrium (CE) framework. Specifically, we use conditional generative adversarial networks (cGANs) in both the data and the image domain for enhanced performance and efficient computation and combine them through a consensus process. We demonstrate the effectiveness of our approach on a real security CT dataset for a challenging 90 degree limited-angle problem. The same framework can be applied to other limited data problems arising in applications such as electron microscopy, non-destructive evaluation, and medical imaging.
Gland Segmentation in Histopathology Images Using Deep Networks and Handcrafted Features
Authors: Safiyeh Rezaei, Ali Emami, Hamidreza Zarrabi, Shima Rafiei, Kayvan Najarian, Nader Karimi, Shadrokh Samavi, S. M. Reza Soroushmehr
Date: 2019-08-31 00:00:00
Tasks: Medical Diagnosis, Prognosis, Segmentation

Histopathology images contain essential information for medical diagnosis and prognosis of cancerous disease. Segmentation of glands in histopathology images is a primary step for analysis and diagnosis of an unhealthy patient. Due to the widespread application and the great success of deep neural networks in intelligent medical diagnosis and histopathology, we propose a modified version of LinkNet for gland segmentation and recognition of malignant cases. We show that using specific handcrafted features such as invariant local binary pattern drastically improves the system performance. The experimental results demonstrate the competency of the proposed system against state-of-the-art methods. We achieved the best results in testing on section B images of the Warwick-QU dataset and obtained comparable results on section A images.
Fetal Ultrasound Image Segmentation for Measuring Biometric Parameters Using Multi-Task Deep Learning
Authors: Zahra Sobhaninia, Shima Rafiei, Ali Emami, Nader Karimi, Kayvan Najarian, Shadrokh Samavi, S. M. Reza Soroushmehr
Date: 2019-08-31 00:00:00
Tasks: Image Segmentation, Segmentation, Semantic Segmentation

Ultrasound imaging is a standard examination during pregnancy that can be used for measuring specific biometric parameters towards prenatal diagnosis and estimating gestational age. Fetal head circumference (HC) is one of the significant factors to determine the fetus growth and health. In this paper, a multi-task deep convolutional neural network is proposed for automatic segmentation and estimation of HC ellipse by minimizing a compound cost function composed of segmentation dice score and MSE of ellipse parameters. Experimental results on fetus ultrasound dataset in different trimesters of pregnancy show that the segmentation results and the extracted HC match well with the radiologist annotations. The obtained dice scores of the fetal head segmentation and the accuracy of HC evaluations are comparable to the state-of-the-art.
VisualPhishNet: Zero-Day Phishing Website Detection by Visual Similarity
Authors: Sahar Abdelnabi, Katharina Krombholz, Mario Fritz
Date: 2019-09-01 00:00:00
Tasks: Phishing Website Detection, Triplet, valid

Phishing websites are still a major threat in today's Internet ecosystem. Despite numerous previous efforts, similarity-based detection methods do not offer sufficient protection for the trusted websites - in particular against unseen phishing pages. This paper contributes VisualPhishNet, a new similarity-based phishing detection framework, based on a triplet Convolutional Neural Network (CNN). VisualPhishNet learns profiles for websites in order to detect phishing websites by a similarity metric that can generalize to pages with new visual appearances. We furthermore present VisualPhish, the largest dataset to date that facilitates visual phishing detection in an ecologically valid manner. We show that our method outperforms previous visual similarity phishing detection approaches by a large margin while being robust against a range of evasion attacks.
Deep Learning Algorithms to Isolate and Quantify the Structures of the Anterior Segment in Optical Coherence Tomography Images
Authors: Tan Hung Pham, Sripad Krishna Devalla, Aloysius Ang, Soh Zhi Da, Alexandre H. Thiery, Craig Boote, Ching-Yu Cheng, Victor Koh, Michael J. A. Girard
Date: 2019-09-01 00:00:00
Tasks: Management

Accurate isolation and quantification of intraocular dimensions in the anterior segment (AS) of the eye using optical coherence tomography (OCT) images is important in the diagnosis and treatment of many eye diseases, especially angle closure glaucoma. In this study, we developed a deep convolutional neural network (DCNN) for the localization of the scleral spur, and the segmentation of anterior segment structures (iris, corneo-sclera shell, anterior chamber). With limited training data, the DCNN was able to detect the scleral spur on unseen ASOCT images as accurately as an experienced ophthalmologist; and simultaneously isolated the anterior segment structures with a Dice coefficient of 95.7%. We then automatically extracted eight clinically relevant ASOCT parameters and proposed an automated quality check process that asserts the reliability of these parameters. When combined with an OCT machine capable of imaging multiple radial sections, the algorithms can provide a more complete objective assessment. This is an essential step toward providing a robust automated framework for reliable quantification of ASOCT scans, for applications in the diagnosis and management of angle closure glaucoma.
A Semi-Automated Usability Evaluation Framework for Interactive Image Segmentation Systems
Authors: Mario Amrehn, Stefan Steidl, Reinier Kortekaas, Maddalena Strumia, Markus Weingarten, Markus Kowarschik, Andreas Maier
Date: 2019-09-01 00:00:00
Tasks: Image Segmentation, Interactive Segmentation, Segmentation, Semantic Segmentation

For complex segmentation tasks, the achievable accuracy of fully automated systems is inherently limited. Specifically, when a precise segmentation result is desired for a small amount of given data sets, semi-automatic methods exhibit a clear benefit for the user. The optimization of human computer interaction (HCI) is an essential part of interactive image segmentation. Nevertheless, publications introducing novel interactive segmentation systems (ISS) often lack an objective comparison of HCI aspects. It is demonstrated, that even when the underlying segmentation algorithm is the same throughout interactive prototypes, their user experience may vary substantially. As a result, users prefer simple interfaces as well as a considerable degree of freedom to control each iterative step of the segmentation. In this article, an objective method for the comparison of ISS is proposed, based on extensive user studies. A summative qualitative content analysis is conducted via abstraction of visual and verbal feedback given by the participants. A direct assessment of the segmentation system is executed by the users via the system usability scale (SUS) and AttrakDiff-2 questionnaires. Furthermore, an approximation of the findings regarding usability aspects in those studies is introduced, conducted solely from the system-measurable user actions during their usage of interactive segmentation prototypes. The prediction of all questionnaire results has an average relative error of 8.9%, which is close to the expected precision of the questionnaire results themselves. This automated evaluation scheme may significantly reduce the resources necessary to investigate each variation of a prototype's user interface (UI) features and segmentation methodologies.
Resource Optimized Neural Architecture Search for 3D Medical Image Segmentation
Authors: Woong Bae, Seungho Lee, Yeha Lee, Beomhee Park, Minki Chung, Kyu-Hwan Jung
Date: 2019-09-02 00:00:00
Tasks: GPU, Image Segmentation, Medical Image Segmentation, Neural Architecture Search, Reinforcement Learning, Segmentation, Semantic Segmentation

Neural Architecture Search (NAS), a framework which automates the task of designing neural networks, has recently been actively studied in the field of deep learning. However, there are only a few NAS methods suitable for 3D medical image segmentation. Medical 3D images are generally very large; thus it is difficult to apply previous NAS methods due to their GPU computational burden and long training time. We propose the resource-optimized neural architecture search method which can be applied to 3D medical segmentation tasks in a short training time (1.39 days for 1GB dataset) using a small amount of computation power (one RTX 2080Ti, 10.8GB GPU memory). Excellent performance can also be achieved without retraining(fine-tuning) which is essential in most NAS methods. These advantages can be achieved by using a reinforcement learning-based controller with parameter sharing and focusing on the optimal search space configuration of macro search rather than micro search. Our experiments demonstrate that the proposed NAS method outperforms manually designed networks with state-of-the-art performance in 3D medical image segmentation.
Reinforcement Learning-based Automatic Diagnosis of Acute Appendicitis in Abdominal CT
Authors: Walid Abdullah Al, Il Dong Yun, Kyong Joon Lee
Date: 2019-09-02 00:00:00
Tasks: Anatomy, reinforcement-learning, Reinforcement Learning, Reinforcement Learning (RL)

Acute appendicitis characterized by a painful inflammation of the vermiform appendix is one of the most common surgical emergencies. Localizing the appendix is challenging due to its unclear anatomy amidst the complex colon-structure as observed in the conventional CT views, resulting in a time-consuming diagnosis. End-to-end learning of a convolutional neural network (CNN) is also not likely to be useful because of the negligible size of the appendix compared with the abdominal CT volume. With no prior computational approaches to the best of our knowledge, we propose the first computerized automation for acute appendicitis diagnosis. In our approach, we utilize a reinforcement learning agent deployed in the lower abdominal region to obtain the appendix location first to reduce the search space for diagnosis. Then, we obtain the classification scores (i.e., the likelihood of acute appendicitis) for the local neighborhood around the localized position, using a CNN trained only on a small appendix patch per volume. From the spatial representation of the resultant scores, we finally define a region of low-entropy (RLE) to choose the optimal diagnosis score, which helps improve the classification accuracy showing robustness even under high appendix localization error cases. In our experiment with 319 abdominal CT volumes, the proposed RLE-based decision with prior localization showed significant improvement over the standard CNN-based diagnosis approaches.
Kidney tumor segmentation using an ensembling multi-stage deep learning approach. A contribution to the KiTS19 challenge
Authors: Gianmarco Santini, Noémi Moreau, Mathieu Rubeaux
Date: 2019-09-02 00:00:00
Tasks: Prognosis, Segmentation, Tumor Segmentation

Precise characterization of the kidney and kidney tumor characteristics is of outmost importance in the context of kidney cancer treatment, especially for nephron sparing surgery which requires a precise localization of the tissues to be removed. The need for accurate and automatic delineation tools is at the origin of the KiTS19 challenge. It aims at accelerating the research and development in this field to aid prognosis and treatment planning by providing a characterized dataset of 300 CT scans to be segmented. To address the challenge, we proposed an automatic, multi-stage, 2.5D deep learning-based segmentation approach based on Residual UNet framework. An ensembling operation is added at the end to combine prediction results from previous stages reducing the variance between single models. Our neural network segmentation algorithm reaches a mean Dice score of 0.96 and 0.74 for kidney and kidney tumors, respectively on 90 unseen test cases. The results obtained are promising and could be improved by incorporating prior knowledge about the benign cysts that regularly lower the tumor segmentation results.
miniSAM: A Flexible Factor Graph Non-linear Least Squares Optimization Framework
Authors: Jing Dong, Zhaoyang Lv
Date: 2019-09-03 00:00:00
Tasks: Benchmarking, Motion Planning, Simultaneous Localization and Mapping

Many problems in computer vision and robotics can be phrased as non-linear least squares optimization problems represented by factor graphs, for example, simultaneous localization and mapping (SLAM), structure from motion (SfM), motion planning, and control. We have developed an open-source C++/Python framework miniSAM, for solving such factor graph based least squares problems. Compared to most existing frameworks for least squares solvers, miniSAM has (1) full Python/NumPy API, which enables more agile development and easy binding with existing Python projects, and (2) a wide list of sparse linear solvers, including CUDA enabled sparse linear solvers. Our benchmarking results shows miniSAM offers comparable performances on various types of problems, with more flexible and smoother development experience.
Hyper-Pairing Network for Multi-Phase Pancreatic Ductal Adenocarcinoma Segmentation
Authors: Yuyin Zhou, Yingwei Li, Zhishuai Zhang, Yan Wang, Angtian Wang, Elliot Fishman, Alan Yuille, Seyoun Park
Date: 2019-09-03 00:00:00

Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal cancers with an overall five-year survival rate of 8%. Due to subtle texture changes of PDAC, pancreatic dual-phase imaging is recommended for better diagnosis of pancreatic disease. In this study, we aim at enhancing PDAC automatic segmentation by integrating multi-phase information (i.e., arterial phase and venous phase). To this end, we present Hyper-Pairing Network (HPN), a 3D fully convolution neural network which effectively integrates information from different phases. The proposed approach consists of a dual path network where the two parallel streams are interconnected with hyper-connections for intensive information exchange. Additionally, a pairing loss is added to encourage the commonality between high-level feature representations of different phases. Compared to prior arts which use single phase data, HPN reports a significant improvement up to 7.73% (from 56.21% to 63.94%) in terms of DSC.
CGC-Net: Cell Graph Convolutional Network for Grading of Colorectal Cancer Histology Images
Authors: Yanning Zhou, Simon Graham, Navid Alemi Koohbanani, Muhammad Shaban, Pheng-Ann Heng, Nasir Rajpoot
Date: 2019-09-03 00:00:00

Colorectal cancer (CRC) grading is typically carried out by assessing the degree of gland formation within histology images. To do this, it is important to consider the overall tissue micro-environment by assessing the cell-level information along with the morphology of the gland. However, current automated methods for CRC grading typically utilise small image patches and therefore fail to incorporate the entire tissue micro-architecture for grading purposes. To overcome the challenges of CRC grading, we present a novel cell-graph convolutional neural network (CGC-Net) that converts each large histology image into a graph, where each node is represented by a nucleus within the original image and cellular interactions are denoted as edges between these nodes according to node similarity. The CGC-Net utilises nuclear appearance features in addition to the spatial location of nodes to further boost the performance of the algorithm. To enable nodes to fuse multi-scale information, we introduce Adaptive GraphSage, which is a graph convolution technique that combines multi-level features in a data-driven way. Furthermore, to deal with redundancy in the graph, we propose a sampling technique that removes nodes in areas of dense nuclear activity. We show that modeling the image as a graph enables us to effectively consider a much larger image (around 16$\times$ larger) than traditional patch-based approaches and model the complex structure of the tissue micro-environment. We construct cell graphs with an average of over 3,000 nodes on a large CRC histology image dataset and report state-of-the-art results as compared to recent patch-based as well as contextual patch-based techniques, demonstrating the effectiveness of our method.
3DSiameseNet to Analyze Brain MRI
Authors: Cecilia Ostertag, Marie Beurton-Aimar, Thierry Urruty
Date: 2019-09-03 00:00:00

Prediction of the cognitive evolution of a person susceptible to develop a neurodegenerative disorder is crucial to provide an appropriate treatment as soon as possible. In this paper we propose a 3D siamese network designed to extract features from whole-brain 3D MRI images. We show that it is possible to extract meaningful features using convolution layers, reducing the need of classical image processing operations such as segmentation or pre-computing features such as cortical thickness. To lead this study we used the Alzheimer's Disease Neuroimaging Initiative (ADNI), a public data base of 3D MRI brain images. A set of 247 subjects has been extracted, all of the subjects having 2 images in a range of 12 months. In order to measure the evolution of the patients states we have compared these 2 images. Our work has been inspired at the beginning by an article of Bhagwat et al. in 2018, who have proposed a siamese network to predict the status of patients but without any convolutional layers and reducing the MRI images to a vector of features extracted from predefined ROIs. We show that our network achieves an accuracy of 90\% in the classification of cognitively declining VS stable patients. This result has been obtained without the help of a cognitive score and with a small number of patients comparing to the current datasets size claimed in deep learning domain.
A Tool for Super-Resolving Multimodal Clinical MRI
Authors: Mikael Brudfors, Yael Balbastre, Parashkev Nachev, John Ashburner
Date: 2019-09-03 00:00:00
Tasks: Diversity

We present a tool for resolution recovery in multimodal clinical magnetic resonance imaging (MRI). Such images exhibit great variability, both biological and instrumental. This variability makes automated processing with neuroimaging analysis software very challenging. This leaves intelligence extractable only from large-scale analyses of clinical data untapped, and impedes the introduction of automated predictive systems in clinical care. The tool presented in this paper enables such processing, via inference in a generative model of thick-sliced, multi-contrast MR scans. All model parameters are estimated from the observed data, without the need for manual tuning. The model-driven nature of the approach means that no type of training is needed for applicability to the diversity of MR contrasts present in a clinical context. We show on simulated data that the proposed approach outperforms conventional model-based techniques, and on a large hospital dataset of multimodal MRIs that the tool can successfully super-resolve very thick-sliced images. The implementation is available from https://github.com/brudfors/spm_superres.
Combining Multi-Sequence and Synthetic Images for Improved Segmentation of Late Gadolinium Enhancement Cardiac MRI
Authors: Víctor M. Campello, Carlos Martín-Isla, Cristian Izquierdo, Steffen E. Petersen, Miguel A. González Ballester, Karim Lekadir
Date: 2019-09-03 00:00:00
Tasks: Cardiac Segmentation, Data Augmentation, Generative Adversarial Network, MRI segmentation, Segmentation, Translation

Accurate segmentation of the cardiac boundaries in late gadolinium enhancement magnetic resonance images (LGE-MRI) is a fundamental step for accurate quantification of scar tissue. However, while there are many solutions for automatic cardiac segmentation of cine images, the presence of scar tissue can make the correct delineation of the myocardium in LGE-MRI challenging even for human experts. As part of the Multi-Sequence Cardiac MR Segmentation Challenge, we propose a solution for LGE-MRI segmentation based on two components. First, a generative adversarial network is trained for the task of modality-to-modality translation between cine and LGE-MRI sequences to obtain extra synthetic images for both modalities. Second, a deep learning model is trained for segmentation with different combinations of original, augmented and synthetic sequences. Our results based on three magnetic resonance sequences (LGE, bSSFP and T2) from 45 different patients show that the multi-sequence model training integrating synthetic images and data augmentation improves in the segmentation over conventional training with real datasets. In conclusion, the accuracy of the segmentation of LGE-MRI images can be improved by using complementary information provided by non-contrast MRI sequences.
Cloudy with high chance of DBMS: A 10-year prediction for Enterprise-Grade ML
Authors: Ashvin Agrawal, Rony Chatterjee, Carlo Curino, Avrilia Floratou, Neha Gowdal, Matteo Interlandi, Alekh Jindal, Kostantinos Karanasos, Subru Krishnan, Brian Kroth, Jyoti Leeka, Kwanghyun Park, Hiren Patel, Olga Poppe, Fotis Psallidas, Raghu Ramakrishnan, Abhishek Roy, Karla Saur, Rathijit Sen, Markus Weimer, Travis Wright, Yiwen Zhu
Date: 2019-08-30 00:00:00
Tasks: Management

Machine learning (ML) has proven itself in high-value web applications such as search ranking and is emerging as a powerful tool in a much broader range of enterprise scenarios including voice recognition and conversational understanding for customer support, autotuning for videoconferencing, intelligent feedback loops in large-scale sysops, manufacturing and autonomous vehicle management, complex financial predictions, just to name a few. Meanwhile, as the value of data is increasingly recognized and monetized, concerns about securing valuable data and risks to individual privacy have been growing. Consequently, rigorous data management has emerged as a key requirement in enterprise settings. How will these trends (ML growing popularity, and stricter data governance) intersect? What are the unmet requirements for applying ML in enterprise settings? What are the technical challenges for the DB community to solve? In this paper, we present our vision of how ML and database systems are likely to come together, and early steps we take towards making this vision a reality.