pwc-archive/papers-with-abstracts huggingface dataset:
COVID-FACT: A Fully-Automated Capsule Network-based Framework for Identification of COVID-19 Cases from Chest CT scans
Authors: Shahin Heidarian, Parnian Afshar, Nastaran Enshaei, Farnoosh Naderkhani, Anastasia Oikonomou, S. Farokh Atashzar, Faranak Babaki Fard, Kaveh Samimi, Konstantinos N. Plataniotis, Arash Mohammadi, Moezedin Javad Rafiee
Date: 2020-10-30 00:00:00
Tasks: Computed Tomography (CT), Data Augmentation, Diagnostic, Sensitivity, Specificity

The newly discovered Corona virus Disease 2019 (COVID-19) has been globally spreading and causing hundreds of thousands of deaths around the world as of its first emergence in late 2019. Computed tomography (CT) scans have shown distinctive features and higher sensitivity compared to other diagnostic tests, in particular the current gold standard, i.e., the Reverse Transcription Polymerase Chain Reaction (RT-PCR) test. Current deep learning-based algorithms are mainly developed based on Convolutional Neural Networks (CNNs) to identify COVID-19 pneumonia cases. CNNs, however, require extensive data augmentation and large datasets to identify detailed spatial relations between image instances. Furthermore, existing algorithms utilizing CT scans, either extend slice-level predictions to patient-level ones using a simple thresholding mechanism or rely on a sophisticated infection segmentation to identify the disease. In this paper, we propose a two-stage fully-automated CT-based framework for identification of COVID-19 positive cases referred to as the "COVID-FACT". COVID-FACT utilizes Capsule Networks, as its main building blocks and is, therefore, capable of capturing spatial information. In particular, to make the proposed COVID-FACT independent from sophisticated segmentation of the area of infection, slices demonstrating infection are detected at the first stage and the second stage is responsible for classifying patients into COVID and non-COVID cases. COVID-FACT detects slices with infection, and identifies positive COVID-19 cases using an in-house CT scan dataset, containing COVID-19, community acquired pneumonia, and normal cases. Based on our experiments, COVID-FACT achieves an accuracy of 90.82%, a sensitivity of 94.55%, a specificity of 86.04%, and an Area Under the Curve (AUC) of 0.98, while depending on far less supervision and annotation, in comparison to its counterparts.
Deep Hurdle Networks for Zero-Inflated Multi-Target Regression: Application to Multiple Species Abundance Estimation
Authors: Shufeng Kong, Junwen Bai, Jae Hee Lee, Di Chen, Andrew Allyn, Michelle Stuart, Malin Pinsky, Katherine Mills, Carla P. Gomes
Date: 2020-10-30 00:00:00
Tasks: Multi-target regression, regression

A key problem in computational sustainability is to understand the distribution of species across landscapes over time. This question gives rise to challenging large-scale prediction problems since (i) hundreds of species have to be simultaneously modeled and (ii) the survey data are usually inflated with zeros due to the absence of species for a large number of sites. The problem of tackling both issues simultaneously, which we refer to as the zero-inflated multi-target regression problem, has not been addressed by previous methods in statistics and machine learning. In this paper, we propose a novel deep model for the zero-inflated multi-target regression problem. To this end, we first model the joint distribution of multiple response variables as a multivariate probit model and then couple the positive outcomes with a multivariate log-normal distribution. By penalizing the difference between the two distributions' covariance matrices, a link between both distributions is established. The whole model is cast as an end-to-end learning framework and we provide an efficient learning algorithm for our model that can be fully implemented on GPUs. We show that our model outperforms the existing state-of-the-art baselines on two challenging real-world species distribution datasets concerning bird and fish populations.
FLANNEL: Focal Loss Based Neural Network Ensemble for COVID-19 Detection
Authors: Zhi Qiao, Austin Bae, Lucas M. Glass, Cao Xiao, Jimeng Sun
Date: 2020-10-30 00:00:00

To test the possibility of differentiating chest x-ray images of COVID-19 against other pneumonia and healthy patients using deep neural networks. We construct the X-ray imaging data from two publicly available sources, which include 5508 chest x-ray images across 2874 patients with four classes: normal, bacterial pneumonia, non-COVID-19 viral pneumonia, and COVID-19. To identify COVID-19, we propose a Focal Loss Based Neural Ensemble Network (FLANNEL), a flexible module to ensemble several convolutional neural network (CNN) models and fuse with a focal loss for accurate COVID-19 detection on class imbalance data. FLANNEL consistently outperforms baseline models on COVID-19 identification task in all metrics. Compared with the best baseline, FLANNEL shows a higher macro-F1 score with 6% relative increase on Covid-19 identification task where it achieves 0.7833(0.07) in Precision, 0.8609(0.03) in Recall, and 0.8168(0.03) F1 score.
Semantic Labeling Using a Deep Contextualized Language Model
Authors: Mohamed Trabelsi, Jin Cao, Jeff Heflin
Date: 2020-10-30 00:00:00
Tasks: Language Modeling, Language Modelling

Generating schema labels automatically for column values of data tables has many data science applications such as schema matching, and data discovery and linking. For example, automatically extracted tables with missing headers can be filled by the predicted schema labels which significantly minimizes human effort. Furthermore, the predicted labels can reduce the impact of inconsistent names across multiple data tables. Understanding the connection between column values and contextual information is an important yet neglected aspect as previously proposed methods treat each column independently. In this paper, we propose a context-aware semantic labeling method using both the column values and context. Our new method is based on a new setting for semantic labeling, where we sequentially predict labels for an input table with missing headers. We incorporate both the values and context of each data column using the pre-trained contextualized language model, BERT, that has achieved significant improvements in multiple natural language processing tasks. To our knowledge, we are the first to successfully apply BERT to solve the semantic labeling task. We evaluate our approach using two real-world datasets from different domains, and we demonstrate substantial improvements in terms of evaluation metrics over state-of-the-art feature-based methods.
SMOT: Single-Shot Multi Object Tracking
Authors: Wei Li, Yuanjun Xiong, Shuo Yang, Siqi Deng, Wei Xia
Date: 2020-10-30 00:00:00
Tasks: Multi-Object Tracking, Object, Object Tracking

We present single-shot multi-object tracker (SMOT), a new tracking framework that converts any single-shot detector (SSD) model into an online multiple object tracker, which emphasizes simultaneously detecting and tracking of the object paths. Contrary to the existing tracking by detection approaches which suffer from errors made by the object detectors, SMOT adopts the recently proposed scheme of tracking by re-detection. We combine this scheme with SSD detectors by proposing a novel tracking anchor assignment module. With this design SMOT is able to generate tracklets with a constant per-frame runtime. A light-weighted linkage algorithm is then used for online tracklet linking. On three benchmarks of object tracking: Hannah, Music Videos, and MOT17, the proposed SMOT achieves state-of-the-art performance.
Multimodal Metric Learning for Tag-based Music Retrieval
Authors: Minz Won, Sergio Oramas, Oriol Nieto, Fabien Gouyon, Xavier Serra
Date: 2020-10-30 00:00:00
Tasks: Cross-Modal Retrieval, Metric Learning, Music Tagging, Retrieval, TAG, Triplet, Word Embeddings

Tag-based music retrieval is crucial to browse large-scale music libraries efficiently. Hence, automatic music tagging has been actively explored, mostly as a classification task, which has an inherent limitation: a fixed vocabulary. On the other hand, metric learning enables flexible vocabularies by using pretrained word embeddings as side information. Also, metric learning has already proven its suitability for cross-modal retrieval tasks in other domains (e.g., text-to-image) by jointly learning a multimodal embedding space. In this paper, we investigate three ideas to successfully introduce multimodal metric learning for tag-based music retrieval: elaborate triplet sampling, acoustic and cultural music information, and domain-specific word embeddings. Our experimental results show that the proposed ideas enhance the retrieval system quantitatively, and qualitatively. Furthermore, we release the MSD500, a subset of the Million Song Dataset (MSD) containing 500 cleaned tags, 7 manually annotated tag categories, and user taste profiles.
PersGNN: Applying Topological Data Analysis and Geometric Deep Learning to Structure-Based Protein Function Prediction
Authors: Nicolas Swenson, Aditi S. Krishnapriyan, Aydin Buluc, Dmitriy Morozov, Katherine Yelick
Date: 2020-10-30 00:00:00
Tasks: Graph Representation Learning, Protein Function Prediction, Representation Learning, Topological Data Analysis

Understanding protein structure-function relationships is a key challenge in computational biology, with applications across the biotechnology and pharmaceutical industries. While it is known that protein structure directly impacts protein function, many functional prediction tasks use only protein sequence. In this work, we isolate protein structure to make functional annotations for proteins in the Protein Data Bank in order to study the expressiveness of different structure-based prediction schemes. We present PersGNN - an end-to-end trainable deep learning model that combines graph representation learning with topological data analysis to capture a complex set of both local and global structural features. While variations of these techniques have been successfully applied to proteins before, we demonstrate that our hybridized approach, PersGNN, outperforms either method on its own as well as a baseline neural network that learns from the same information. PersGNN achieves a 9.3% boost in area under the precision recall curve (AUPR) compared to the best individual model, as well as high F1 scores across different gene ontology categories, indicating the transferability of this approach.
CliniQG4QA: Generating Diverse Questions for Domain Adaptation of Clinical Question Answering
Authors: Xiang Yue, Xinliang Frederick Zhang, Ziyu Yao, Simon Lin, Huan Sun
Date: 2020-10-30 00:00:00
Tasks: Domain Adaptation, Question Answering, Question Generation, Question-Generation

Clinical question answering (QA) aims to automatically answer questions from medical professionals based on clinical texts. Studies show that neural QA models trained on one corpus may not generalize well to new clinical texts from a different institute or a different patient group, where large-scale QA pairs are not readily available for model retraining. To address this challenge, we propose a simple yet effective framework, CliniQG4QA, which leverages question generation (QG) to synthesize QA pairs on new clinical contexts and boosts QA models without requiring manual annotations. In order to generate diverse types of questions that are essential for training QA models, we further introduce a seq2seq-based question phrase prediction (QPP) module that can be used together with most existing QG models to diversify the generation. Our comprehensive experiment results show that the QA corpus generated by our framework can improve QA models on the new contexts (up to 8% absolute gain in terms of Exact Match), and that the QPP module plays a crucial role in achieving the gain.
POMO: Policy Optimization with Multiple Optima for Reinforcement Learning
Authors: Yeong-Dae Kwon, Jinho Choo, Byoungjip Kim, Iljoo Yoon, Youngjune Gwon, Seungjai Min
Date: 2020-10-30 00:00:00
Proceeding: NeurIPS 2020 12
Tasks: Combinatorial Optimization, reinforcement-learning, Reinforcement Learning, Reinforcement Learning (RL)

In neural combinatorial optimization (CO), reinforcement learning (RL) can turn a deep neural net into a fast, powerful heuristic solver of NP-hard problems. This approach has a great potential in practical applications because it allows near-optimal solutions to be found without expert guides armed with substantial domain knowledge. We introduce Policy Optimization with Multiple Optima (POMO), an end-to-end approach for building such a heuristic solver. POMO is applicable to a wide range of CO problems. It is designed to exploit the symmetries in the representation of a CO solution. POMO uses a modified REINFORCE algorithm that forces diverse rollouts towards all optimal solutions. Empirically, the low-variance baseline of POMO makes RL training fast and stable, and it is more resistant to local minima compared to previous approaches. We also introduce a new augmentation-based inference method, which accompanies POMO nicely. We demonstrate the effectiveness of POMO by solving three popular NP-hard problems, namely, traveling salesman (TSP), capacitated vehicle routing (CVRP), and 0-1 knapsack (KP). For all three, our solver based on POMO shows a significant improvement in performance over all recent learned heuristics. In particular, we achieve the optimality gap of 0.14% with TSP100 while reducing inference time by more than an order of magnitude.
Loss re-scaling VQA: Revisiting the LanguagePrior Problem from a Class-imbalance View
Authors: Yangyang Guo, Liqiang Nie, Zhiyong Cheng, Qi Tian, Min Zhang
Date: 2020-10-30 00:00:00
Tasks: Face Recognition, image-classification, Image Classification, Question Answering, Visual Question Answering, Visual Question Answering (VQA)

Recent studies have pointed out that many well-developed Visual Question Answering (VQA) models are heavily affected by the language prior problem, which refers to making predictions based on the co-occurrence pattern between textual questions and answers instead of reasoning visual contents. To tackle it, most existing methods focus on enhancing visual feature learning to reduce this superficial textual shortcut influence on VQA model decisions. However, limited effort has been devoted to providing an explicit interpretation for its inherent cause. It thus lacks a good guidance for the research community to move forward in a purposeful way, resulting in model construction perplexity in overcoming this non-trivial problem. In this paper, we propose to interpret the language prior problem in VQA from a class-imbalance view. Concretely, we design a novel interpretation scheme whereby the loss of mis-predicted frequent and sparse answers of the same question type is distinctly exhibited during the late training phase. It explicitly reveals why the VQA model tends to produce a frequent yet obviously wrong answer, to a given question whose right answer is sparse in the training set. Based upon this observation, we further develop a novel loss re-scaling approach to assign different weights to each answer based on the training data statistics for computing the final loss. We apply our approach into three baselines and the experimental results on two VQA-CP benchmark datasets evidently demonstrate its effectiveness. In addition, we also justify the validity of the class imbalance interpretation scheme on other computer vision tasks, such as face recognition and image classification.
COVI-AgentSim: an Agent-based Model for Evaluating Methods of Digital Contact Tracing
Authors: Prateek Gupta, Tegan Maharaj, Martin Weiss, Nasim Rahaman, Hannah Alsdurf, Abhinav Sharma, Nanor Minoyan, Soren Harnois-Leblanc, Victor Schmidt, Pierre-Luc St. Charles, Tristan Deleu, Andrew Williams, Akshay Patel, Meng Qu, Olexa Bilaniuk, Gaétan Marceau Caron, Pierre Luc Carrier, Satya Ortiz-Gagné, Marc-Andre Rousseau, David Buckeridge, Joumana Ghosn, Yang Zhang, Bernhard Schölkopf, Jian Tang, Irina Rish, Christopher Pal, Joanna Merckx, Eilif B. Muller, Yoshua Bengio
Date: 2020-10-30 00:00:00
Tasks: Virology

The rapid global spread of COVID-19 has led to an unprecedented demand for effective methods to mitigate the spread of the disease, and various digital contact tracing (DCT) methods have emerged as a component of the solution. In order to make informed public health choices, there is a need for tools which allow evaluation and comparison of DCT methods. We introduce an agent-based compartmental simulator we call COVI-AgentSim, integrating detailed consideration of virology, disease progression, social contact networks, and mobility patterns, based on parameters derived from empirical research. We verify by comparing to real data that COVI-AgentSim is able to reproduce realistic COVID-19 spread dynamics, and perform a sensitivity analysis to verify that the relative performance of contact tracing methods are consistent across a range of settings. We use COVI-AgentSim to perform cost-benefit analyses comparing no DCT to: 1) standard binary contact tracing (BCT) that assigns binary recommendations based on binary test results; and 2) a rule-based method for feature-based contact tracing (FCT) that assigns a graded level of recommendation based on diverse individual features. We find all DCT methods consistently reduce the spread of the disease, and that the advantage of FCT over BCT is maintained over a wide range of adoption rates. Feature-based methods of contact tracing avert more disability-adjusted life years (DALYs) per socioeconomic cost (measured by productive hours lost). Our results suggest any DCT method can help save lives, support re-opening of economies, and prevent second-wave outbreaks, and that FCT methods are a promising direction for enriching BCT using self-reported symptoms, yielding earlier warning signals and a significantly reduced spread of the virus per socioeconomic cost.
PIINET: A 360-degree Panoramic Image Inpainting Network Using a Cube Map
Authors: Seo Woo Han, Doug Young Suh
Date: 2020-10-30 00:00:00
Tasks: Deep Learning, Image Inpainting

Inpainting has been continuously studied in the field of computer vision. As artificial intelligence technology developed, deep learning technology was introduced in inpainting research, helping to improve performance. Currently, the input target of an inpainting algorithm using deep learning has been studied from a single image to a video. However, deep learning-based inpainting technology for panoramic images has not been actively studied. We propose a 360-degree panoramic image inpainting method using generative adversarial networks (GANs). The proposed network inputs a 360-degree equirectangular format panoramic image converts it into a cube map format, which has relatively little distortion and uses it as a training network. Since the cube map format is used, the correlation of the six sides of the cube map should be considered. Therefore, all faces of the cube map are used as input for the whole discriminative network, and each face of the cube map is used as input for the slice discriminative network to determine the authenticity of the generated image. The proposed network performed qualitatively better than existing single-image inpainting algorithms and baseline algorithms.
Guaranteeing Safety of Learned Perception Modules via Measurement-Robust Control Barrier Functions
Authors: Sarah Dean, Andrew J. Taylor, Ryan K. Cosner, Benjamin Recht, Aaron D. Ames
Date: 2020-10-30 00:00:00

Modern nonlinear control theory seeks to develop feedback controllers that endow systems with properties such as safety and stability. The guarantees ensured by these controllers often rely on accurate estimates of the system state for determining control actions. In practice, measurement model uncertainty can lead to error in state estimates that degrades these guarantees. In this paper, we seek to unify techniques from control theory and machine learning to synthesize controllers that achieve safety in the presence of measurement model uncertainty. We define the notion of a Measurement-Robust Control Barrier Function (MR-CBF) as a tool for determining safe control inputs when facing measurement model uncertainty. Furthermore, MR-CBFs are used to inform sampling methodologies for learning-based perception systems and quantify tolerable error in the resulting learned models. We demonstrate the efficacy of MR-CBFs in achieving safety with measurement model uncertainty on a simulated Segway system.
Unsupervised One-shot Learning of Both Specific Instances and Generalised Classes with a Hippocampal Architecture
Authors: Gideon Kowadlo, Abdelrahman Ahmed, David Rawlinson
Date: 2020-10-30 00:00:00
Tasks: One-Shot Learning

Established experimental procedures for one-shot machine learning do not test the ability to learn or remember specific instances of classes, a key feature of animal intelligence. Distinguishing specific instances is necessary for many real-world tasks, such as remembering which cup belongs to you. Generalisation within classes conflicts with the ability to separate instances of classes, making it difficult to achieve both capabilities within a single architecture. We propose an extension to the standard Omniglot classification-generalisation framework that additionally tests the ability to distinguish specific instances after one exposure and introduces noise and occlusion corruption. Learning is defined as an ability to classify as well as recall training samples. Complementary Learning Systems (CLS) is a popular model of mammalian brain regions believed to play a crucial role in learning from a single exposure to a stimulus. We created an artificial neural network implementation of CLS and applied it to the extended Omniglot benchmark. Our unsupervised model demonstrates comparable performance to existing supervised ANNs on the Omniglot classification task (requiring generalisation), without the need for domain-specific inductive biases. On the extended Omniglot instance-recognition task, the same model also demonstrates significantly better performance than a baseline nearest-neighbour approach, given partial occlusion and noise.
Modern strategies for time series regression
Authors: Stephanie Clark, Rob J Hyndman, Dan Pagendam, Louise M Ryan
Date: 2020-10-29 00:00:00
Tasks: BIG-bench Machine Learning, regression, Time Series, Time Series Analysis, Time Series Regression

This paper discusses several modern approaches to regression analysis involving time series data where some of the predictor variables are also indexed by time. We discuss classical statistical approaches as well as methods that have been proposed recently in the machine learning literature. The approaches are compared and contrasted, and it will be seen that there are advantages and disadvantages to most currently available approaches. There is ample room for methodological developments in this area. The work is motivated by an application involving the prediction of water levels as a function of rainfall and other climate variables in an aquifer in eastern Australia.