pwc-archive/papers-with-abstracts huggingface dataset:
Pose Estimation of Specular and Symmetrical Objects
Authors: Jiaming Hu, Hongyi Ling, Priyam Parashar, Aayush Naik, Henrik Christensen
Date: 2020-10-31 00:00:00
Tasks: 6D Pose Estimation, Pose Estimation, Template Matching

In the robotic industry, specular and textureless metallic components are ubiquitous. The 6D pose estimation of such objects with only a monocular RGB camera is difficult because of the absence of rich texture features. Furthermore, the appearance of specularity heavily depends on the camera viewpoint and environmental light conditions making traditional methods, like template matching, fail. In the last 30 years, pose estimation of the specular object has been a consistent challenge, and most related works require massive knowledge modeling effort for light setups, environment, or the object surface. On the other hand, recent works exhibit the feasibility of 6D pose estimation on a monocular camera with convolutional neural networks(CNNs) however they mostly use opaque objects for evaluation. This paper provides a data-driven solution to estimate the 6D pose of specular objects for grasping them, proposes a cost function for handling symmetry, and demonstrates experimental results showing the system's feasibility.
Segmentation of Infrared Breast Images Using MultiResUnet Neural Network
Authors: Ange Lou, Shuyue Guan, Nada Kamona, Murray Loew
Date: 2020-10-31 00:00:00
Tasks: Segmentation

Breast cancer is the second leading cause of death for women in the U.S. Early detection of breast cancer is key to higher survival rates of breast cancer patients. We are investigating infrared (IR) thermography as a noninvasive adjunct to mammography for breast cancer screening. IR imaging is radiation-free, pain-free, and non-contact. Automatic segmentation of the breast area from the acquired full-size breast IR images will help limit the area for tumor search, as well as reduce the time and effort costs of manual segmentation. Autoencoder-like convolutional and deconvolutional neural networks (C-DCNN) had been applied to automatically segment the breast area in IR images in previous studies. In this study, we applied a state-of-the-art deep-learning segmentation model, MultiResUnet, which consists of an encoder part to capture features and a decoder part for precise localization. It was used to segment the breast area by using a set of breast IR images, collected in our pilot study by imaging breast cancer patients and normal volunteers with a thermal infrared camera (N2 Imager). The database we used has 450 images, acquired from 14 patients and 16 volunteers. We used a thresholding method to remove interference in the raw images and remapped them from the original 16-bit to 8-bit, and then cropped and segmented the 8-bit images manually. Experiments using leave-one-out cross-validation (LOOCV) and comparison with the ground-truth images by using Tanimoto similarity show that the average accuracy of MultiResUnet is 91.47%, which is about 2% higher than that of the autoencoder. MultiResUnet offers a better approach to segment breast IR images than our previous model.
A comparison of Monte Carlo dropout and bootstrap aggregation on the performance and uncertainty estimation in radiation therapy dose prediction with deep learning neural networks
Authors: Dan Nguyen, Azar Sadeghnejad Barkousaraie, Gyanendra Bohara, Anjali Balagopal, Rafe McBeth, Mu-Han Lin, Steve Jiang
Date: 2020-11-01 00:00:00

Recently, artificial intelligence technologies and algorithms have become a major focus for advancements in treatment planning for radiation therapy. As these are starting to become incorporated into the clinical workflow, a major concern from clinicians is not whether the model is accurate, but whether the model can express to a human operator when it does not know if its answer is correct. We propose to use Monte Carlo dropout (MCDO) and the bootstrap aggregation (bagging) technique on deep learning models to produce uncertainty estimations for radiation therapy dose prediction. We show that both models are capable of generating a reasonable uncertainty map, and, with our proposed scaling technique, creating interpretable uncertainties and bounds on the prediction and any relevant metrics. Performance-wise, bagging provides statistically significant reduced loss value and errors in most of the metrics investigated in this study. The addition of bagging was able to further reduce errors by another 0.34% for Dmean and 0.19% for Dmax, on average, when compared to the baseline framework. Overall, the bagging framework provided significantly lower MAE of 2.62, as opposed to the baseline framework's MAE of 2.87. The usefulness of bagging, from solely a performance standpoint, does highly depend on the problem and the acceptable predictive error, and its high upfront computational cost during training should be factored in to deciding whether it is advantageous to use it. In terms of deployment with uncertainty estimations turned on, both frameworks offer the same performance time of about 12 seconds. As an ensemble-based metaheuristic, bagging can be used with existing machine learning architectures to improve stability and performance, and MCDO can be applied to any deep learning models that have dropout as part of their architecture.
Two-layer clustering-based sparsifying transform learning for low-dose CT reconstruction
Authors: Xikai Yang, Yong Long, Saiprasad Ravishankar
Date: 2020-11-01 00:00:00
Tasks: Clustering, CT Reconstruction, Image Reconstruction

Achieving high-quality reconstructions from low-dose computed tomography (LDCT) measurements is of much importance in clinical settings. Model-based image reconstruction methods have been proven to be effective in removing artifacts in LDCT. In this work, we propose an approach to learn a rich two-layer clustering-based sparsifying transform model (MCST2), where image patches and their subsequent feature maps (filter residuals) are clustered into groups with different learned sparsifying filters per group. We investigate a penalized weighted least squares (PWLS) approach for LDCT reconstruction incorporating learned MCST2 priors. Experimental results show the superior performance of the proposed PWLS-MCST2 approach compared to other related recent schemes.
Dynamic radiomics: a new methodology to extract quantitative time-related features from tomographic images
Authors: Fengying Che, Ruichuan Shi, Jian Wu, Haoran Li, Shuqin Li, Weixing Chen, Hao Zhang, Zhi Li, Xiaoyu Cui
Date: 2020-11-01 00:00:00
Tasks: Diagnostic

The feature extraction methods of radiomics are mainly based on static tomographic images at a certain moment, while the occurrence and development of disease is a dynamic process that cannot be fully reflected by only static characteristics. This study proposes a new dynamic radiomics feature extraction workflow that uses time-dependent tomographic images of the same patient, focuses on the changes in image features over time, and then quantifies them as new dynamic features for diagnostic or prognostic evaluation. We first define the mathematical paradigm of dynamic radiomics and introduce three specific methods that can describe the transformation process of features over time. Three different clinical problems are used to validate the performance of the proposed dynamic feature with conventional 2D and 3D static features.
Generating Correct Answers for Progressive Matrices Intelligence Tests
Authors: Niv Pekar, Yaniv Benny, Lior Wolf
Date: 2020-11-01 00:00:00
Proceeding: NeurIPS 2020 12
Tasks: Multiple-choice

Raven's Progressive Matrices are multiple-choice intelligence tests, where one tries to complete the missing location in a $3\times 3$ grid of abstract images. Previous attempts to address this test have focused solely on selecting the right answer out of the multiple choices. In this work, we focus, instead, on generating a correct answer given the grid, without seeing the choices, which is a harder task, by definition. The proposed neural model combines multiple advances in generative models, including employing multiple pathways through the same network, using the reparameterization trick along two pathways to make their encoding compatible, a dynamic application of variational losses, and a complex perceptual loss that is coupled with a selective backpropagation procedure. Our algorithm is able not only to generate a set of plausible answers, but also to be competitive to the state of the art methods in multiple-choice tests.
Learning Euler's Elastica Model for Medical Image Segmentation
Authors: Xu Chen, Xiangde Luo, Yitian Zhao, Shaoting Zhang, Guotai Wang, Yalin Zheng
Date: 2020-11-01 00:00:00
Tasks: Image Segmentation, Medical Image Segmentation, model, Segmentation, Semantic Segmentation

Image segmentation is a fundamental topic in image processing and has been studied for many decades. Deep learning-based supervised segmentation models have achieved state-of-the-art performance but most of them are limited by using pixel-wise loss functions for training without geometrical constraints. Inspired by Euler's Elastica model and recent active contour models introduced into the field of deep learning, we propose a novel active contour with elastica (ACE) loss function incorporating Elastica (curvature and length) and region information as geometrically-natural constraints for the image segmentation tasks. We introduce the mean curvature i.e. the average of all principal curvatures, as a more effective image prior to representing curvature in our ACE loss function. Furthermore, based on the definition of the mean curvature, we propose a fast solution to approximate the ACE loss in three-dimensional (3D) by using Laplace operators for 3D image segmentation. We evaluate our ACE loss function on four 2D and 3D natural and biomedical image datasets. Our results show that the proposed loss function outperforms other mainstream loss functions on different segmentation networks. Our source code is available at https://github.com/HiLab-git/ACELoss.
Triage of Potential COVID-19 Patients from Chest X-ray Images using Hierarchical Convolutional Networks
Authors: Kapal Dev, Sunder Ali Khowaja, Ankur Singh Bist, Vaibhav Saini, Surbhi Bhatia
Date: 2020-11-01 00:00:00
Tasks: Binary Classification

The current COVID-19 pandemic has motivated the researchers to use artificial intelligence techniques for a potential alternative to reverse transcription-polymerase chain reaction (RT-PCR) due to the limited scale of testing. The chest X-ray (CXR) is one of the alternatives to achieve fast diagnosis but the unavailability of large-scale annotated data makes the clinical implementation of machine learning-based COVID detection difficult. Another issue is the usage of ImageNet pre-trained networks which does not extract reliable feature representations from medical images. In this paper, we propose the use of hierarchical convolutional network (HCN) architecture to naturally augment the data along with diversified features. The HCN uses the first convolution layer from COVIDNet followed by the convolutional layers from well-known pre-trained networks to extract the features. The use of the convolution layer from COVIDNet ensures the extraction of representations relevant to the CXR modality. We also propose the use of ECOC for encoding multiclass problems to binary classification for improving the recognition performance. Experimental results show that HCN architecture is capable of achieving better results in comparison to the existing studies. The proposed method can accurately triage potential COVID-19 patients through CXR images for sharing the testing load and increasing the testing capacity.
Tracking Partially-Occluded Deformable Objects while Enforcing Geometric Constraints
Authors: YiXuan Wang, Dale McConachie, Dmitry Berenson
Date: 2020-11-01 00:00:00
Tasks: Object

In order to manipulate a deformable object, such as rope or cloth, in unstructured environments, robots need a way to estimate its current shape. However, tracking the shape of a deformable object can be challenging because of the object's high flexibility, (self-)occlusion, and interaction with obstacles. Building a high-fidelity physics simulation to aid in tracking is difficult for novel environments. Instead we focus on tracking the object based on RGBD images and geometric motion estimates and obstacles. Our key contributions over previous work in this vein are: 1) A better way to handle severe occlusion by using a motion model to regularize the tracking estimate; and 2) The formulation of \textit{convex} geometric constraints, which allow us to prevent self-intersection and penetration into known obstacles via a post-processing step. These contributions allow us to outperform previous methods by a large margin in terms of accuracy in scenarios with severe occlusion and obstacles.
Brain Tumor Classification Using Medial Residual Encoder Layers
Authors: Zahra Sobhaninia, Nader Karimi, Pejman Khadivi, Roshank Roshandel, Shadrokh Samavi
Date: 2020-11-01 00:00:00
Tasks: Brain Tumor Classification, Classification, General Classification, image-classification, Image Classification

According to the World Health Organization (WHO), cancer is the second leading cause of death worldwide, responsible for over 9.5 million deaths in 2018 alone. Brain tumors count for one out of every four cancer deaths. Therefore, accurate and timely diagnosis of brain tumors will lead to more effective treatments. Physicians classify brain tumors only with biopsy operation by brain surgery, and after diagnosing the type of tumor, a treatment plan is considered for the patient. Automatic systems based on machine learning algorithms can allow physicians to diagnose brain tumors with noninvasive measures. To date, several image classification approaches have been proposed to aid diagnosis and treatment. For brain tumor classification in this work, we offer a system based on deep learning, containing encoder blocks. These blocks are fed with post-max-pooling features as residual learning. Our approach shows promising results by improving the tumor classification accuracy in Magnetic resonance imaging (MRI) images using a limited medical image dataset. Experimental evaluations of this model on a dataset consisting of 3064 MR images show 95.98% accuracy, which is better than previous studies on this database.
Bifurcated Autoencoder for Segmentation of COVID-19 Infected Regions in CT Images
Authors: Parham Yazdekhasty, Ali Zindar, Zahra Nabizadeh-ShahreBabak, Roshank Roshandel, Pejman Khadivi, Nader Karimi, Shadrokh Samavi
Date: 2020-11-01 00:00:00
Tasks: Decoder, Segmentation

The new coronavirus infection has shocked the world since early 2020 with its aggressive outbreak. Rapid detection of the disease saves lives, and relying on medical imaging (Computed Tomography and X-ray) to detect infected lungs has shown to be effective. Deep learning and convolutional neural networks have been used for image analysis in this context. However, accurate identification of infected regions has proven challenging for two main reasons. Firstly, the characteristics of infected areas differ in different images. Secondly, insufficient training data makes it challenging to train various machine learning algorithms, including deep-learning models. This paper proposes an approach to segment lung regions infected by COVID-19 to help cardiologists diagnose the disease more accurately, faster, and more manageable. We propose a bifurcated 2-D model for two types of segmentation. This model uses a shared encoder and a bifurcated connection to two separate decoders. One decoder is for segmentation of the healthy region of the lungs, while the other is for the segmentation of the infected regions. Experiments on publically available images show that the bifurcated structure segments infected regions of the lungs better than state of the art.
nnU-Net for Brain Tumor Segmentation
Authors: Fabian Isensee, Paul F. Jaeger, Peter M. Full, Philipp Vollmuth, Klaus H. Maier-Hein
Date: 2020-11-02 00:00:00
Tasks: Brain Tumor Segmentation, Data Augmentation, Segmentation, Tumor Segmentation

We apply nnU-Net to the segmentation task of the BraTS 2020 challenge. The unmodified nnU-Net baseline configuration already achieves a respectable result. By incorporating BraTS-specific modifications regarding postprocessing, region-based training, a more aggressive data augmentation as well as several minor modifications to the nnUNet pipeline we are able to improve its segmentation performance substantially. We furthermore re-implement the BraTS ranking scheme to determine which of our nnU-Net variants best fits the requirements imposed by it. Our final ensemble took the first place in the BraTS 2020 competition with Dice scores of 88.95, 85.06 and 82.03 and HD95 values of 8.498,17.337 and 17.805 for whole tumor, tumor core and enhancing tumor, respectively.
Deep Learning in Computer-Aided Diagnosis and Treatment of Tumors: A Survey
Authors: Dan Zhao, Guizhi Xu, Zhenghua Xu, Thomas Lukasiewicz, Minmin Xue, Zhigang Fu
Date: 2020-11-02 00:00:00
Tasks: Deep Learning

Computer-Aided Diagnosis and Treatment of Tumors is a hot topic of deep learning in recent years, which constitutes a series of medical tasks, such as detection of tumor markers, the outline of tumor leisures, subtypes and stages of tumors, prediction of therapeutic effect, and drug development. Meanwhile, there are some deep learning models with precise positioning and excellent performance produced in mainstream task scenarios. Thus follow to introduce deep learning methods from task-orient, mainly focus on the improvements for medical tasks. Then to summarize the recent progress in four stages of tumor diagnosis and treatment, which named In-Vitro Diagnosis (IVD), Imaging Diagnosis (ID), Pathological Diagnosis (PD), and Treatment Planning (TP). According to the specific data types and medical tasks of each stage, we present the applications of deep learning in the Computer-Aided Diagnosis and Treatment of Tumors and analyzing the excellent works therein. This survey concludes by discussing research issues and suggesting challenges for future improvement.
ASIST: Annotation-free synthetic instance segmentation and tracking for microscope video analysis
Authors: Quan Liu, Isabella M. Gaeta, Mengyang Zhao, Ruining Deng, Aadarsh Jha, Bryan A. Millis, Anita Mahadevan-Jansen, Matthew J. Tyska, Yuankai Huo
Date: 2020-11-02 00:00:00
Tasks: Generative Adversarial Network, Image Segmentation, Instance Segmentation, Segmentation, Semantic Segmentation

Instance object segmentation and tracking provide comprehensive quantification of objects across microscope videos. The recent single-stage pixel-embedding based deep learning approach has shown its superior performance compared with "segment-then-associate" two-stage solutions. However, one major limitation of applying a supervised pixel-embedding based method to microscope videos is the resource-intensive manual labeling, which involves tracing hundreds of overlapped objects with their temporal associations across video frames. Inspired by the recent generative adversarial network (GAN) based annotation-free image segmentation, we propose a novel annotation-free synthetic instance segmentation and tracking (ASIST) algorithm for analyzing microscope videos of sub-cellular microvilli. The contributions of this paper are three-fold: (1) proposing a new annotation-free video analysis paradigm is proposed. (2) aggregating the embedding based instance segmentation and tracking with annotation-free synthetic learning as a holistic framework; and (3) to the best of our knowledge, this is first study to investigate microvilli instance segmentation and tracking using embedding based deep learning. From the experimental results, the proposed annotation-free method achieved superior performance compared with supervised learning.
AVECL-UMONS database for audio-visual event classification and localization
Authors: Mathilde Brousmiche, Stéphane Dupont, Jean Rouat
Date: 2020-10-02 00:00:00
Tasks: General Classification

We introduce the AVECL-UMons dataset for audio-visual event classification and localization in the context of office environments. The audio-visual dataset is composed of 11 event classes recorded at several realistic positions in two different rooms. Two types of sequences are recorded according to the number of events in the sequence. The dataset comprises 2662 unilabel sequences and 2724 multilabel sequences corresponding to a total of 5.24 hours. The dataset is publicly accessible online : https://zenodo.org/record/3965492#.X09wsobgrCI.
Depth Ranging Performance Evaluation and Improvement for RGB-D Cameras on Field-Based High-Throughput Phenotyping Robots
Authors: Zhengqiang Fan, Na Sun, Quan Qiu, Chunjiang Zhao
Date: 2020-11-02 00:00:00

RGB-D cameras have been successfully used for indoor High-ThroughpuT Phenotyping (HTTP). However, their capability and feasibility for in-field HTTP still need to be evaluated, due to the noise and disturbances generated by unstable illumination, specular reflection, and diffuse reflection, etc. To solve these problems, we evaluated the depth-ranging performances of two consumer-level RGB-D cameras (RealSense D435i and Kinect V2) under in-field HTTP scenarios, and proposed a strategy to compensate the depth measurement error. For performance evaluation, we focused on determining their optimal ranging areas for different crop organs. Based on the evaluation results, we proposed a brightness-and-distance-based Support Vector Regression Strategy, to compensate the ranging error. Furthermore, we analyzed the depth filling rate of two RGB-D cameras under different lighting intensities. Experimental results showed that: 1) For RealSense D435i, its effective ranging area is [0.160, 1.400] m, and in-field filling rate is approximately 90%. 2) For Kinect V2, it has a high ranging accuracy in the [0.497, 1.200] m, but its in-field filling rate is less than 24.9%. 3) Our error compensation model can effectively reduce the influences of lighting intensity and target distance. The maximum MSE and minimum R2 of this model are 0.029 and 0.867, respectively. To sum up, RealSense D435i has better ranging performances than Kinect V2 on in-field HTTP.
Brain tumor segmentation with self-ensembled, deeply-supervised 3D U-net neural networks: a BraTS 2020 challenge solution
Authors: Theophraste Henry, Alexandre Carre, Marvin Lerousseau, Theo Estienne, Charlotte Robert, Nikos Paragios, Eric Deutsch
Date: 2020-10-30 00:00:00
Tasks: Brain Tumor Segmentation, Management, Segmentation, Tumor Segmentation

Brain tumor segmentation is a critical task for patient's disease management. In order to automate and standardize this task, we trained multiple U-net like neural networks, mainly with deep supervision and stochastic weight averaging, on the Multimodal Brain Tumor Segmentation Challenge (BraTS) 2020 training dataset. Two independent ensembles of models from two different training pipelines were trained, and each produced a brain tumor segmentation map. These two labelmaps per patient were then merged, taking into account the performance of each ensemble for specific tumor subregions. Our performance on the online validation dataset with test time augmentation were as follows: Dice of 0.81, 0.91 and 0.85; Hausdorff (95%) of 20.6, 4,3, 5.7 mm for the enhancing tumor, whole tumor and tumor core, respectively. Similarly, our solution achieved a Dice of 0.79, 0.89 and 0.84, as well as Hausdorff (95%) of 20.4, 6.7 and 19.5mm on the final test dataset, ranking us among the top ten teams. More complicated training schemes and neural network architectures were investigated without significant performance gain at the cost of greatly increased training time. Overall, our approach yielded good and balanced performance for each tumor subregion. Our solution is open sourced at https://github.com/lescientifik/open_brats2020.