pwc-archive/papers-with-abstracts huggingface dataset:
Weakly-supervised 3D Shape Completion in the Wild
Authors: Jiayuan Gu, Wei-Chiu Ma, Sivabalan Manivasagam, Wenyuan Zeng, ZiHao Wang, Yuwen Xiong, Hao Su, Raquel Urtasun
Date: 2020-08-20 00:00:00
Proceeding: ECCV 2020 8
Tasks: Point Cloud Registration, Pose Estimation

3D shape completion for real data is important but challenging, since partial point clouds acquired by real-world sensors are usually sparse, noisy and unaligned. Different from previous methods, we address the problem of learning 3D complete shape from unaligned and real-world partial point clouds. To this end, we propose a weakly-supervised method to estimate both 3D canonical shape and 6-DoF pose for alignment, given multiple partial observations associated with the same instance. The network jointly optimizes canonical shapes and poses with multi-view geometry constraints during training, and can infer the complete shape given a single partial point cloud. Moreover, learned pose estimation can facilitate partial point cloud registration. Experiments on both synthetic and real data show that it is feasible and promising to learn 3D shape completion through large-scale data without shape and pose supervision.
Inner Cell Mass and Trophectoderm Segmentation in Human Blastocyst Images using Deep Neural Network
Authors: Md Yousuf Harun, Thomas Huang, Aaron T. Ohta
Date: 2020-08-19 00:00:00
Tasks: Segmentation

Embryo quality assessment based on morphological attributes is important for achieving higher pregnancy rates from in vitro fertilization (IVF). The accurate segmentation of the embryo's inner cell mass (ICM) and trophectoderm epithelium (TE) is important, as these parameters can help to predict the embryo viability and live birth potential. However, segmentation of the ICM and TE is difficult due to variations in their shape and similarities in their textures, both with each other and with their surroundings. To tackle this problem, a deep neural network (DNN) based segmentation approach was implemented. The DNN can identify the ICM region with 99.1% accuracy, 94.9% precision, 93.8% recall, a 94.3% Dice Coefficient, and a 89.3% Jaccard Index. It can extract the TE region with 98.3% accuracy, 91.8% precision, 93.2% recall, a 92.5% Dice Coefficient, and a 85.3% Jaccard Index.
Self-Supervised Ultrasound to MRI Fetal Brain Image Synthesis
Authors: Jianbo Jiao, Ana I. L. Namburete, Aris T. Papageorghiou, J. Alison Noble
Date: 2020-08-19 00:00:00
Tasks: Image Generation, Medical Image Analysis

Fetal brain magnetic resonance imaging (MRI) offers exquisite images of the developing brain but is not suitable for second-trimester anomaly screening, for which ultrasound (US) is employed. Although expert sonographers are adept at reading US images, MR images which closely resemble anatomical images are much easier for non-experts to interpret. Thus in this paper we propose to generate MR-like images directly from clinical US images. In medical image analysis such a capability is potentially useful as well, for instance for automatic US-MRI registration and fusion. The proposed model is end-to-end trainable and self-supervised without any external annotations. Specifically, based on an assumption that the US and MRI data share a similar anatomical latent space, we first utilise a network to extract the shared latent features, which are then used for MRI synthesis. Since paired data is unavailable for our study (and rare in practice), pixel-level constraints are infeasible to apply. We instead propose to enforce the distributions to be statistically indistinguishable, by adversarial learning in both the image domain and feature space. To regularise the anatomical structures between US and MRI during synthesis, we further propose an adversarial structural constraint. A new cross-modal attention technique is proposed to utilise non-local spatial information, by encouraging multi-modal knowledge fusion and propagation. We extend the approach to consider the case where 3D auxiliary information (e.g., 3D neighbours and a 3D location index) from volumetric data is also available, and show that this improves image synthesis. The proposed approach is evaluated quantitatively and qualitatively with comparison to real fetal MR images and other approaches to synthesis, demonstrating its feasibility of synthesising realistic MR images.
iPhantom: a framework for automated creation of individualized computational phantoms and its application to CT organ dosimetry
Authors: Wanyi Fu, Shobhit Sharma, Ehsan Abadi, Alexandros-Stavros Iliopoulos, Qi. Wang, Joseph Y. Lo, Xiaobai Sun, William P. Segars, Ehsan Samei
Date: 2020-08-20 00:00:00

Objective: This study aims to develop and validate a novel framework, iPhantom, for automated creation of patient-specific phantoms or digital-twins (DT) using patient medical images. The framework is applied to assess radiation dose to radiosensitive organs in CT imaging of individual patients. Method: From patient CT images, iPhantom segments selected anchor organs (e.g. liver, bones, pancreas) using a learning-based model developed for multi-organ CT segmentation. Organs challenging to segment (e.g. intestines) are incorporated from a matched phantom template, using a diffeomorphic registration model developed for multi-organ phantom-voxels. The resulting full-patient phantoms are used to assess organ doses during routine CT exams. Result: iPhantom was validated on both the XCAT (n=50) and an independent clinical (n=10) dataset with similar accuracy. iPhantom precisely predicted all organ locations with good accuracy of Dice Similarity Coefficients (DSC) >0.6 for anchor organs and DSC of 0.3-0.9 for all other organs. iPhantom showed less than 10% dose errors for the majority of organs, which was notably superior to the state-of-the-art baseline method (20-35% dose errors). Conclusion: iPhantom enables automated and accurate creation of patient-specific phantoms and, for the first time, provides sufficient and automated patient-specific dose estimates for CT dosimetry. Significance: The new framework brings the creation and application of CHPs to the level of individual CHPs through automation, achieving a wider and precise organ localization, paving the way for clinical monitoring, and personalized optimization, and large-scale research.
Single Image Super-Resolution via a Holistic Attention Network
Authors: Ben Niu, Weilei Wen, Wenqi Ren, Xiangde Zhang, Lianping Yang, Shuzhen Wang, Kaihao Zhang, Xiaochun Cao, Haifeng Shen
Date: 2020-08-20 00:00:00
Proceeding: ECCV 2020 8
Tasks: Image Super-Resolution, Super-Resolution

Informative features play a crucial role in the single image super-resolution task. Channel attention has been demonstrated to be effective for preserving information-rich features in each layer. However, channel attention treats each convolution layer as a separate process that misses the correlation among different layers. To address this problem, we propose a new holistic attention network (HAN), which consists of a layer attention module (LAM) and a channel-spatial attention module (CSAM), to model the holistic interdependencies among layers, channels, and positions. Specifically, the proposed LAM adaptively emphasizes hierarchical features by considering correlations among layers. Meanwhile, CSAM learns the confidence at all the positions of each channel to selectively capture more informative features. Extensive experiments demonstrate that the proposed HAN performs favorably against the state-of-the-art single image super-resolution approaches.
Facial movement synergies and Action Unit detection from distal wearable Electromyography and Computer Vision
Authors: Monica Perusquia-Hernandez, Felix Dollack, Chun Kwang Tan, Shushi Namba, Saho Ayabe-Kanamura, Kenji Suzuki
Date: 2020-08-20 00:00:00
Tasks: Action Unit Detection, Electromyography (EMG)

Distal facial Electromyography (EMG) can be used to detect smiles and frowns with reasonable accuracy. It capitalizes on volume conduction to detect relevant muscle activity, even when the electrodes are not placed directly on the source muscle. The main advantage of this method is to prevent occlusion and obstruction of the facial expression production, whilst allowing EMG measurements. However, measuring EMG distally entails that the exact source of the facial movement is unknown. We propose a novel method to estimate specific Facial Action Units (AUs) from distal facial EMG and Computer Vision (CV). This method is based on Independent Component Analysis (ICA), Non-Negative Matrix Factorization (NNMF), and sorting of the resulting components to determine which is the most likely to correspond to each CV-labeled action unit (AU). Performance on the detection of AU06 (Orbicularis Oculi) and AU12 (Zygomaticus Major) was estimated by calculating the agreement with Human Coders. The results of our proposed algorithm showed an accuracy of 81% and a Cohen's Kappa of 0.49 for AU6; and accuracy of 82% and a Cohen's Kappa of 0.53 for AU12. This demonstrates the potential of distal EMG to detect individual facial movements. Using this multimodal method, several AU synergies were identified. We quantified the co-occurrence and timing of AU6 and AU12 in posed and spontaneous smiles using the human-coded labels, and for comparison, using the continuous CV-labels. The co-occurrence analysis was also performed on the EMG-based labels to uncover the relationship between muscle synergies and the kinematics of visible facial movement.
Uncertainty Estimation in Medical Image Denoising with Bayesian Deep Image Prior
Authors: Max-Heinrich Laves, Malte Tölle, Tobias Ortmaier
Date: 2020-08-20 00:00:00
Tasks: Denoising, Image Denoising, Medical Image Denoising, Uncertainty Quantification

Uncertainty quantification in inverse medical imaging tasks with deep learning has received little attention. However, deep models trained on large data sets tend to hallucinate and create artifacts in the reconstructed output that are not anatomically present. We use a randomly initialized convolutional network as parameterization of the reconstructed image and perform gradient descent to match the observation, which is known as deep image prior. In this case, the reconstruction does not suffer from hallucinations as no prior training is performed. We extend this to a Bayesian approach with Monte Carlo dropout to quantify both aleatoric and epistemic uncertainty. The presented method is evaluated on the task of denoising different medical imaging modalities. The experimental results show that our approach yields well-calibrated uncertainty. That is, the predictive uncertainty correlates with the predictive error. This allows for reliable uncertainty estimates and can tackle the problem of hallucinations and artifacts in inverse medical imaging tasks.
Deep learning-based transformation of the H&E stain into special stains
Authors: Kevin de Haan, Yijie Zhang, Jonathan E. Zuckerman, Tairan Liu, Anthony E. Sisk, Miguel F. P. Diaz, Kuang-Yu Jen, Alexander Nobori, Sofia Liou, Sarah Zhang, Rana Riahi, Yair Rivenson, W. Dean Wallace, Aydogan Ozcan
Date: 2020-08-20 00:00:00
Tasks: Diagnostic

Pathology is practiced by visual inspection of histochemically stained slides. Most commonly, the hematoxylin and eosin (H&E) stain is used in the diagnostic workflow and it is the gold standard for cancer diagnosis. However, in many cases, especially for non-neoplastic diseases, additional "special stains" are used to provide different levels of contrast and color to tissue components and allow pathologists to get a clearer diagnostic picture. In this study, we demonstrate the utility of supervised learning-based computational stain transformation from H&E to different special stains (Masson's Trichrome, periodic acid-Schiff and Jones silver stain) using tissue sections from kidney needle core biopsies. Based on evaluation by three renal pathologists, followed by adjudication by a fourth renal pathologist, we show that the generation of virtual special stains from existing H&E images improves the diagnosis in several non-neoplastic kidney diseases sampled from 58 unique subjects. A second study performed by three pathologists found that the quality of the special stains generated by the stain transformation network was statistically equivalent to those generated through standard histochemical staining. As the transformation of H&E images into special stains can be achieved within 1 min or less per patient core specimen slide, this stain-to-stain transformation framework can improve the quality of the preliminary diagnosis when additional special stains are needed, along with significant savings in time and cost, reducing the burden on healthcare system and patients.
BOIL: Towards Representation Change for Few-shot Learning
Authors: Jaehoon Oh, Hyungjun Yoo, ChangHwan Kim, Se-Young Yun
Date: 2020-08-20 00:00:00
Proceeding: ICLR 2021 1
Tasks: Few-Shot Learning, Meta-Learning

Model Agnostic Meta-Learning (MAML) is one of the most representative of gradient-based meta-learning algorithms. MAML learns new tasks with a few data samples using inner updates from a meta-initialization point and learns the meta-initialization parameters with outer updates. It has recently been hypothesized that representation reuse, which makes little change in efficient representations, is the dominant factor in the performance of the meta-initialized model through MAML in contrast to representation change, which causes a significant change in representations. In this study, we investigate the necessity of representation change for the ultimate goal of few-shot learning, which is solving domain-agnostic tasks. To this aim, we propose a novel meta-learning algorithm, called BOIL (Body Only update in Inner Loop), which updates only the body (extractor) of the model and freezes the head (classifier) during inner loop updates. BOIL leverages representation change rather than representation reuse. This is because feature vectors (representations) have to move quickly to their corresponding frozen head vectors. We visualize this property using cosine similarity, CKA, and empirical results without the head. BOIL empirically shows significant performance improvement over MAML, particularly on cross-domain tasks. The results imply that representation change in gradient-based meta-learning approaches is a critical component.
A Systematic Survey of Regularization and Normalization in GANs
Authors: Ziqiang Li, Muhammad Usman, Rentuo Tao, Pengfei Xia, Chaoyue Wang, Huanhuan Chen, Bin Li
Date: 2020-08-19 00:00:00
Tasks: Data Augmentation, Survey

Generative Adversarial Networks (GANs) have been widely applied in different scenarios thanks to the development of deep neural networks. The original GAN was proposed based on the non-parametric assumption of the infinite capacity of networks. However, it is still unknown whether GANs can fit the target distribution without any prior information. Due to the overconfident assumption, many issues remain unaddressed in GANs' training, such as non-convergence, mode collapses, gradient vanishing. Regularization and normalization are common methods of introducing prior information to stabilize training and improve discrimination. Although a handful number of regularization and normalization methods have been proposed for GANs, to the best of our knowledge, there exists no comprehensive survey that primarily focuses on objectives and development of these methods, apart from some in-comprehensive and limited scope studies. In this work, we conduct a comprehensive survey on the regularization and normalization techniques from different perspectives of GANs training. First, we systematically describe different perspectives of GANs training and thus obtain the different objectives of regularization and normalization. Based on these objectives, we propose a new taxonomy. Furthermore, we compare the performance of the mainstream methods on different datasets and investigate the applications of regularization and normalization techniques that have been frequently employed in state-of-the-art GANs. Finally, we highlight potential future directions of research in this domain. Code and studies related to the regularization and normalization of GANs in this work is summarized on https://github.com/iceli1007/GANs-Regularization-Review.
$β$-Variational Classifiers Under Attack
Authors: Marco Maggipinto, Matteo Terzi, Gian Antonio Susto
Date: 2020-08-20 00:00:00

Deep Neural networks have gained lots of attention in recent years thanks to the breakthroughs obtained in the field of Computer Vision. However, despite their popularity, it has been shown that they provide limited robustness in their predictions. In particular, it is possible to synthesise small adversarial perturbations that imperceptibly modify a correctly classified input data, making the network confidently misclassify it. This has led to a plethora of different methods to try to improve robustness or detect the presence of these perturbations. In this paper, we perform an analysis of $\beta$-Variational Classifiers, a particular class of methods that not only solve a specific classification task, but also provide a generative component that is able to generate new samples from the input distribution. More in details, we study their robustness and detection capabilities, together with some novel insights on the generative part of the model.
A New Perspective on Stabilizing GANs training: Direct Adversarial Training
Authors: Ziqiang Li, Pengfei Xia, Rentuo Tao, Hongjing Niu, Bin Li
Date: 2020-08-19 00:00:00
Tasks: Adversarial Attack, Image Generation

Generative Adversarial Networks (GANs) are the most popular image generation models that have achieved remarkable progress on various computer vision tasks. However, training instability is still one of the open problems for all GAN-based algorithms. Quite a number of methods have been proposed to stabilize the training of GANs, the focuses of which were respectively put on the loss functions, regularization and normalization technologies, training algorithms, and model architectures. Different from the above methods, in this paper, a new perspective on stabilizing GANs training is presented. It is found that sometimes the images produced by the generator act like adversarial examples of the discriminator during the training process, which may be part of the reason causing the unstable training of GANs. With this finding, we propose the Direct Adversarial Training (DAT) method to stabilize the training process of GANs. Furthermore, we prove that the DAT method is able to minimize the Lipschitz constant of the discriminator adaptively. The advanced performance of DAT is verified on multiple loss functions, network architectures, hyper-parameters, and datasets. Specifically, DAT achieves significant improvements of 11.5% FID on CIFAR-100 unconditional generation based on SSGAN, 10.5% FID on STL-10 unconditional generation based on SSGAN, and 13.2% FID on LSUN-Bedroom unconditional generation based on SSGAN. Code will be available at https://github.com/iceli1007/DAT-GAN
A Survey on Text Simplification
Authors: Punardeep Sikka, Vijay Mago
Date: 2020-08-19 00:00:00
Tasks: Semantic Similarity, Semantic Textual Similarity, Survey, Text Simplification

Text Simplification (TS) aims to reduce the linguistic complexity of content to make it easier to understand. Research in TS has been of keen interest, especially as approaches to TS have shifted from manual, hand-crafted rules to automated simplification. This survey seeks to provide a comprehensive overview of TS, including a brief description of earlier approaches used, discussion of various aspects of simplification (lexical, semantic and syntactic), and latest techniques being utilized in the field. We note that the research in the field has clearly shifted towards utilizing deep learning techniques to perform TS, with a specific focus on developing solutions to combat the lack of data available for simplification. We also include a discussion of datasets and evaluations metrics commonly used, along with discussion of related fields within Natural Language Processing (NLP), like semantic similarity.
Assigning function to protein-protein interactions: a weakly supervised BioBERT based approach using PubMed abstracts
Authors: Aparna Elangovan, Melissa Davis, Karin Verspoor
Date: 2020-08-20 00:00:00

Motivation: Protein-protein interactions (PPI) are critical to the function of proteins in both normal and diseased cells, and many critical protein functions are mediated by interactions.Knowledge of the nature of these interactions is important for the construction of networks to analyse biological data. However, only a small percentage of PPIs captured in protein interaction databases have annotations of function available, e.g. only 4% of PPI are functionally annotated in the IntAct database. Here, we aim to label the function type of PPIs by extracting relationships described in PubMed abstracts. Method: We create a weakly supervised dataset from the IntAct PPI database containing interacting protein pairs with annotated function and associated abstracts from the PubMed database. We apply a state-of-the-art deep learning technique for biomedical natural language processing tasks, BioBERT, to build a model - dubbed PPI-BioBERT - for identifying the function of PPIs. In order to extract high quality PPI functions at large scale, we use an ensemble of PPI-BioBERT models to improve uncertainty estimation and apply an interaction type-specific threshold to counteract the effects of variations in the number of training samples per interaction type. Results: We scan 18 million PubMed abstracts to automatically identify 3253 new typed PPIs, including phosphorylation and acetylation interactions, with an overall precision of 46% (87% for acetylation) based on a human-reviewed sample. This work demonstrates that analysis of biomedical abstracts for PPI function extraction is a feasible approach to substantially increasing the number of interactions annotated with function captured in online databases.
Lite Training Strategies for Portuguese-English and English-Portuguese Translation
Authors: Alexandre Lopes, Rodrigo Nogueira, Roberto Lotufo, Helio Pedrini
Date: 2020-08-20 00:00:00
Proceeding: WMT (EMNLP) 2020 11
Tasks: GPU, Machine Translation, Translation

Despite the widespread adoption of deep learning for machine translation, it is still expensive to develop high-quality translation models. In this work, we investigate the use of pre-trained models, such as T5 for Portuguese-English and English-Portuguese translation tasks using low-cost hardware. We explore the use of Portuguese and English pre-trained language models and propose an adaptation of the English tokenizer to represent Portuguese characters, such as diaeresis, acute and grave accents. We compare our models to the Google Translate API and MarianMT on a subset of the ParaCrawl dataset, as well as to the winning submission to the WMT19 Biomedical Translation Shared Task. We also describe our submission to the WMT20 Biomedical Translation Shared Task. Our results show that our models have a competitive performance to state-of-the-art models while being trained on modest hardware (a single 8GB gaming GPU for nine days). Our data, models and code are available at https://github.com/unicamp-dl/Lite-T5-Translation.