pwc-archive/papers-with-abstracts huggingface dataset:
Global Data Science Project for COVID-19
Authors: Toyotaro Suzumura, Dario Garcia-Gasulla, Sergio Alvarez Napagao, Irene Li, Hiroshi Maruyama, Hiroki Kanezashi, Raquel P'erez-Arnal, Kunihiko Miyoshi, Euma Ishii, Keita Suzuki, Sayaka Shiba, Mariko Kurokawa, Yuta Kanzawa, Naomi Nakagawa, Masatoshi Hanai, Yixin Li, Tianxiao Li
Date: 2020-06-10 00:00:00

This paper aims at providing the summary of the Global Data Science Project (GDSC) for COVID-19. as on May 31 2020. COVID-19 has largely impacted on our societies through both direct and indirect effects transmitted by the policy measures to counter the spread of viruses. We quantitatively analysed the multifaceted impacts of the COVID-19 pandemic on our societies including people's mobility, health, and social behaviour changes. People's mobility has changed significantly due to the implementation of travel restriction and quarantine measurements. Indeed, the physical distance has widened at international (cross-border), national and regional level. At international level, due to the travel restrictions, the number of international flights has plunged overall at around 88 percent during March. In particular, the number of flights connecting Europe dropped drastically in mid of March after the United States announced travel restrictions to Europe and the EU and participating countries agreed to close borders, at 84 percent decline compared to March 10th. Similarly, we examined the impacts of quarantine measures in the major city: Tokyo (Japan), New York City (the United States), and Barcelona (Spain). Within all three cities, we found the significant decline in traffic volume. We also identified the increased concern for mental health through the analysis of posts on social networking services such as Twitter and Instagram. Notably, in the beginning of April 2020, the number of post with #depression on Instagram doubled, which might reflect the rise in mental health awareness among Instagram users. Besides, we identified the changes in a wide range of people's social behaviors, as well as economic impacts through the analysis of Instagram data and primary survey data.
Time-Resolved fMRI Shared Response Model using Gaussian Process Factor Analysis
Authors: MohammadReza Ebrahimi, Navona Calarco, Kieran Campbell, Colin Hawco, Aristotle Voineskos, Ashish Khisti
Date: 2020-06-10 00:00:00
Tasks: Anatomy

Multi-subject fMRI studies are challenging due to the high variability of both brain anatomy and functional brain topographies across participants. An effective way of aggregating multi-subject fMRI data is to extract a shared representation that filters out unwanted variability among subjects. Some recent work has implemented probabilistic models to extract a shared representation in task fMRI. In the present work, we improve upon these models by incorporating temporal information in the common latent structures. We introduce a new model, Shared Gaussian Process Factor Analysis (S-GPFA), that discovers shared latent trajectories and subject-specific functional topographies, while modelling temporal correlation in fMRI data. We demonstrate the efficacy of our model in revealing ground truth latent structures using simulated data, and replicate experimental performance of time-segment matching and inter-subject similarity on the publicly available Raider and Sherlock datasets. We further test the utility of our model by analyzing its learned model parameters in the large multi-site SPINS dataset, on a social cognition task from participants with and without schizophrenia.
A gaze driven fast-forward method for first-person videos
Authors: Alan Carvalho Neves, Michel Melo Silva, Mario Fernando Montenegro Campos, Erickson Rangel Nascimento
Date: 2020-06-10 00:00:00

The growing data sharing and life-logging cultures are driving an unprecedented increase in the amount of unedited First-Person Videos. In this paper, we address the problem of accessing relevant information in First-Person Videos by creating an accelerated version of the input video and emphasizing the important moments to the recorder. Our method is based on an attention model driven by gaze and visual scene analysis that provides a semantic score of each frame of the input video. We performed several experimental evaluations on publicly available First-Person Videos datasets. The results show that our methodology can fast-forward videos emphasizing moments when the recorder visually interact with scene components while not including monotonous clips.
Using BibTeX to Automatically Generate Labeled Data for Citation Field Extraction
Authors: Dung Thai, Zhiyang Xu, Nicholas Monath, Boris Veytsman, Andrew McCallum
Date: 2020-06-09 00:00:00
Proceeding: AKBC 2020 6
Tasks: Management

Accurate parsing of citation reference strings is crucial to automatically construct scholarly databases such as Google Scholar or Semantic Scholar. Citation field extraction (CFE) is precisely this task---given a reference label which tokens refer to the authors, venue, title, editor, journal, pages, etc. Most methods for CFE are supervised and rely on training from labeled datasets that are quite small compared to the great variety of reference formats. BibTeX, the widely used reference management tool, provides a natural method to automatically generate and label training data for CFE. In this paper, we describe a technique for using BibTeX to generate, automatically, a large-scale 41M labeled strings), labeled dataset, that is four orders of magnitude larger than the current largest CFE dataset, namely the UMass Citation Field Extraction dataset [Anzaroot and McCallum, 2013]. We experimentally demonstrate how our dataset can be used to improve the performance of the UMass CFE using a RoBERTa-based [Liu et al., 2019] model. In comparison to previous SoTA, we achieve a 24.48% relative error reduction, achieving span level F1-scores of 96.3%.
Learning Functions to Study the Benefit of Multitask Learning
Authors: Gabriele Bettgenhäuser, Michael A. Hedderich, Dietrich Klakow
Date: 2020-06-09 00:00:00
Tasks: Mathematical Proofs, Symbolic Regression

We study and quantify the generalization patterns of multitask learning (MTL) models for sequence labeling tasks. MTL models are trained to optimize a set of related tasks jointly. Although multitask learning has achieved improved performance in some problems, there are also tasks that lose performance when trained together. These mixed results motivate us to study the factors that impact the performance of MTL models. We note that theoretical bounds and convergence rates for MTL models exist, but they rely on strong assumptions such as task relatedness and the use of balanced datasets. To remedy these limitations, we propose the creation of a task simulator and the use of Symbolic Regression to learn expressions relating model performance to possible factors of influence. For MTL, we study the model performance against the number of tasks (T), the number of samples per task (n) and the task relatedness measured by the adjusted mutual information (AMI). In our experiments, we could empirically find formulas relating model performance with factors of sqrt(n), sqrt(T), which are equivalent to sound mathematical proofs in Maurer[2016], and we went beyond by discovering that performance relates to a factor of sqrt(AMI).
Tree Annotations in LiDAR Data Using Point Densities and Convolutional Neural Networks
Authors: Ananya Gupta, Jonathan Byrne, David Moloney, Simon Watson, Hujun Yin
Date: 2020-06-09 00:00:00

LiDAR provides highly accurate 3D point clouds. However, data needs to be manually labelled in order to provide subsequent useful information. Manual annotation of such data is time consuming, tedious and error prone, and hence in this paper we present three automatic methods for annotating trees in LiDAR data. The first method requires high density point clouds and uses certain LiDAR data attributes for the purpose of tree identification, achieving almost 90% accuracy. The second method uses a voxel-based 3D Convolutional Neural Network on low density LiDAR datasets and is able to identify most large trees accurately but struggles with smaller ones due to the voxelisation process. The third method is a scaled version of the PointNet++ method and works directly on outdoor point clouds and achieves an F_score of 82.1% on the ISPRS benchmark dataset, comparable to the state-of-the-art methods but with increased efficiency.
ReCOVery: A Multimodal Repository for COVID-19 News Credibility Research
Authors: Xinyi Zhou, Apurva Mulay, Emilio Ferrara, Reza Zafarani
Date: 2020-06-09 00:00:00
Tasks: Articles

First identified in Wuhan, China, in December 2019, the outbreak of COVID-19 has been declared as a global emergency in January, and a pandemic in March 2020 by the World Health Organization (WHO). Along with this pandemic, we are also experiencing an "infodemic" of information with low credibility such as fake news and conspiracies. In this work, we present ReCOVery, a repository designed and constructed to facilitate research on combating such information regarding COVID-19. We first broadly search and investigate ~2,000 news publishers, from which 60 are identified with extreme [high or low] levels of credibility. By inheriting the credibility of the media on which they were published, a total of 2,029 news articles on coronavirus, published from January to May 2020, are collected in the repository, along with 140,820 tweets that reveal how these news articles have spread on the Twitter social network. The repository provides multimodal information of news articles on coronavirus, including textual, visual, temporal, and network information. The way that news credibility is obtained allows a trade-off between dataset scalability and label accuracy. Extensive experiments are conducted to present data statistics and distributions, as well as to provide baseline performances for predicting news credibility so that future methods can be compared. Our repository is available at http://coronavirus-fakenews.com.
Causal Discovery from Incomplete Data using An Encoder and Reinforcement Learning
Authors: Xiaoshui Huang, Fujin Zhu, Lois Holloway, Ali Haidar
Date: 2020-06-09 00:00:00
Tasks: Causal Discovery, Imputation, Missing Values, reinforcement-learning, Reinforcement Learning (RL)

Discovering causal structure among a set of variables is a fundamental problem in many domains. However, state-of-the-art methods seldom consider the possibility that the observational data has missing values (incomplete data), which is ubiquitous in many real-world situations. The missing value will significantly impair the performance and even make the causal discovery algorithms fail. In this paper, we propose an approach to discover causal structures from incomplete data by using a novel encoder and reinforcement learning (RL). The encoder is designed for missing data imputation as well as feature extraction. In particular, it learns to encode the currently available information (with missing values) into a robust feature representation which is then used to determine where to search the best graph. The encoder is integrated into a RL framework that can be optimized using the actor-critic algorithm. Our method takes the incomplete observational data as input and generates a causal structure graph. Experimental results on synthetic and real data demonstrate that our method can robustly generate causal structures from incomplete data. Compared with the direct combination of data imputation and causal discovery methods, our method performs generally better and can even obtain a performance gain as much as 43.2%.
Neural Methods for Point-wise Dependency Estimation
Authors: Yao-Hung Hubert Tsai, Han Zhao, Makoto Yamada, Louis-Philippe Morency, Ruslan Salakhutdinov
Date: 2020-06-09 00:00:00
Proceeding: NeurIPS 2020 12
Tasks: Cross-Modal Retrieval, Representation Learning, Retrieval

Since its inception, the neural estimation of mutual information (MI) has demonstrated the empirical success of modeling expected dependency between high-dimensional random variables. However, MI is an aggregate statistic and cannot be used to measure point-wise dependency between different events. In this work, instead of estimating the expected dependency, we focus on estimating point-wise dependency (PD), which quantitatively measures how likely two outcomes co-occur. We show that we can naturally obtain PD when we are optimizing MI neural variational bounds. However, optimizing these bounds is challenging due to its large variance in practice. To address this issue, we develop two methods (free of optimizing MI variational bounds): Probabilistic Classifier and Density-Ratio Fitting. We demonstrate the effectiveness of our approaches in 1) MI estimation, 2) self-supervised representation learning, and 3) cross-modal retrieval task.
3D Point Cloud Feature Explanations Using Gradient-Based Methods
Authors: Ananya Gupta, Simon Watson, Hujun Yin
Date: 2020-06-09 00:00:00

Explainability is an important factor to drive user trust in the use of neural networks for tasks with material impact. However, most of the work done in this area focuses on image analysis and does not take into account 3D data. We extend the saliency methods that have been shown to work on image data to deal with 3D data. We analyse the features in point clouds and voxel spaces and show that edges and corners in 3D data are deemed as important features while planar surfaces are deemed less important. The approach is model-agnostic and can provide useful information about learnt features. Driven by the insight that 3D data is inherently sparse, we visualise the features learnt by a voxel-based classification network and show that these features are also sparse and can be pruned relatively easily, leading to more efficient neural networks. Our results show that the Voxception-ResNet model can be pruned down to 5\% of its parameters with negligible loss in accuracy.
Deep Adversarial Koopman Model for Reaction-Diffusion systems
Authors: Kaushik Balakrishnan, Devesh Upadhyay
Date: 2020-06-09 00:00:00

Reaction-diffusion systems are ubiquitous in nature and in engineering applications, and are often modeled using a non-linear system of governing equations. While robust numerical methods exist to solve them, deep learning-based reduced ordermodels (ROMs) are gaining traction as they use linearized dynamical models to advance the solution in time. One such family of algorithms is based on Koopman theory, and this paper applies this numerical simulation strategy to reaction-diffusion systems. Adversarial and gradient losses are introduced, and are found to robustify the predictions. The proposed model is extended to handle missing training data as well as recasting the problem from a control perspective. The efficacy of these developments are demonstrated for two different reaction-diffusion problems: (1) the Kuramoto-Sivashinsky equation of chaos and (2) the Turing instability using the Gray-Scott model.
Resolution-Enhanced MRI-Guided Navigation of Spinal Cellular Injection Robot
Authors: Daniel Enrique Martinez, Waiman Meinhold, John Oshinski, Ai-Ping Hu, Jun Ueda
Date: 2020-06-09 00:00:00
Tasks: Navigate

This paper presents a method of navigating a surgical robot beyond the resolution of magnetic resonance imaging (MRI) by using a resolution enhancement technique enabled by high-precision piezoelectric actuation. The surgical robot was specifically designed for injecting stem cells into the spinal cord. This particular therapy can be performed in a shorter time by using a MRI-compatible robotic platform than by using a manual needle positioning platform. Imaging resolution of fiducial markers attached to the needle guide tubing was enhanced by reconstructing a high-resolution image from multiple images with sub-pixel movements of the robot. The parallel-plane direct-drive needle positioning mechanism positioned the needle guide with a high spatial precision that is two orders of magnitude higher than typical MRI resolution up to 1 mm. Reconstructed resolution enhanced images were used to navigate the robot precisely that would not have been possible by using standard MRI. Experiments were conducted to verify the effectiveness of the proposed enhanced-resolution image-guided intervention.
Machine Learning for Imaging Cherenkov Detectors
Authors: Cristiano Fanelli
Date: 2020-06-09 00:00:00
Tasks: BIG-bench Machine Learning

Imaging Cherenkov detectors are largely used in modern nuclear and particle physics experiments where cutting-edge solutions are needed to face always more growing computing demands. This is a fertile ground for AI-based approaches and at present we are witnessing the onset of new highly efficient and fast applications. This paper focuses on novel directions with applications to Cherenkov detectors. In particular, recent advances on detector design and calibration, as well as particle identification are presented.
Dual-stream Maximum Self-attention Multi-instance Learning
Authors: Bin Li, Kevin W. Eliceiri
Date: 2020-06-09 00:00:00
Tasks: Weakly-supervised Learning

Multi-instance learning (MIL) is a form of weakly supervised learning where a single class label is assigned to a bag of instances while the instance-level labels are not available. Training classifiers to accurately determine the bag label and instance labels is a challenging but critical task in many practical scenarios, such as computational histopathology. Recently, MIL models fully parameterized by neural networks have become popular due to the high flexibility and superior performance. Most of these models rely on attention mechanisms that assign attention scores across the instance embeddings in a bag and produce the bag embedding using an aggregation operator. In this paper, we proposed a dual-stream maximum self-attention MIL model (DSMIL) parameterized by neural networks. The first stream deploys a simple MIL max-pooling while the top-activated instance embedding is determined and used to obtain self-attention scores across instance embeddings in the second stream. Different from most of the previous methods, the proposed model jointly learns an instance classifier and a bag classifier based on the same instance embeddings. The experiments results show that our method achieves superior performance compared to the best MIL methods and demonstrates state-of-the-art performance on benchmark MIL datasets.
Locally Private Graph Neural Networks
Authors: Sina Sajadmanesh, Daniel Gatica-Perez
Date: 2020-06-09 00:00:00
Tasks: Federated Learning, Node Classification, Privacy Preserving, Privacy Preserving Deep Learning

Graph Neural Networks (GNNs) have demonstrated superior performance in learning node representations for various graph inference tasks. However, learning over graph data can raise privacy concerns when nodes represent people or human-related variables that involve sensitive or personal information. While numerous techniques have been proposed for privacy-preserving deep learning over non-relational data, there is less work addressing the privacy issues pertained to applying deep learning algorithms on graphs. In this paper, we study the problem of node data privacy, where graph nodes have potentially sensitive data that is kept private, but they could be beneficial for a central server for training a GNN over the graph. To address this problem, we develop a privacy-preserving, architecture-agnostic GNN learning algorithm with formal privacy guarantees based on Local Differential Privacy (LDP). Specifically, we propose an LDP encoder and an unbiased rectifier, by which the server can communicate with the graph nodes to privately collect their data and approximate the GNN's first layer. To further reduce the effect of the injected noise, we propose to prepend a simple graph convolution layer, called KProp, which is based on the multi-hop aggregation of the nodes' features acting as a denoising mechanism. Finally, we propose a robust training framework, in which we benefit from KProp's denoising capability to increase the accuracy of inference in the presence of noisy labels. Extensive experiments conducted over real-world datasets demonstrate that our method can maintain a satisfying level of accuracy with low privacy loss.
Novelty Detection via Robust Variational Autoencoding
Authors: Chieh-Hsin Lai, Dongmian Zou, Gilad Lerman
Date: 2020-06-09 00:00:00
Tasks: Dimensionality Reduction, Novelty Detection

We propose a new method for novelty detection that can tolerate high corruption of the training points, whereas previous works assumed either no or very low corruption. Our method trains a robust variational autoencoder (VAE), which aims to generate a model for the uncorrupted training points. To gain robustness to high corruption, we incorporate the following four changes to the common VAE: 1. Extracting crucial features of the latent code by a carefully designed dimension reduction component for distributions; 2. Modeling the latent distribution as a mixture of Gaussian low-rank inliers and full-rank outliers, where the testing only uses the inlier model; 3. Applying the Wasserstein-1 metric for regularization, instead of the Kullback-Leibler (KL) divergence; and 4. Using a robust error for reconstruction. We establish both robustness to outliers and suitability to low-rank modeling of the Wasserstein metric as opposed to the KL divergence. We illustrate state-of-the-art results on standard benchmarks.
GEOM: Energy-annotated molecular conformations for property prediction and molecular generation
Authors: Simon Axelrod, Rafael Gomez-Bombarelli
Date: 2020-06-09 00:00:00
Tasks: Property Prediction, Transfer Learning

Machine learning (ML) outperforms traditional approaches in many molecular design tasks. ML models usually predict molecular properties from a 2D chemical graph or a single 3D structure, but neither of these representations accounts for the ensemble of 3D conformers that are accessible to a molecule. Property prediction could be improved by using conformer ensembles as input, but there is no large-scale dataset that contains graphs annotated with accurate conformers and experimental data. Here we use advanced sampling and semi-empirical density functional theory (DFT) to generate 37 million molecular conformations for over 450,000 molecules. The Geometric Ensemble Of Molecules (GEOM) dataset contains conformers for 133,000 species from QM9, and 317,000 species with experimental data related to biophysics, physiology, and physical chemistry. Ensembles of 1,511 species with BACE-1 inhibition data are also labeled with high-quality DFT free energies in an implicit water solvent, and 534 ensembles are further optimized with DFT. GEOM will assist in the development of models that predict properties from conformer ensembles, and generative models that sample 3D conformations.
Knowledge Distillation: A Survey
Authors: Jianping Gou, Baosheng Yu, Stephen John Maybank, DaCheng Tao
Date: 2020-06-09 00:00:00
Tasks: Knowledge Distillation, Model Compression, Neural Architecture Search, Quantization, Survey

In recent years, deep neural networks have been successful in both industry and academia, especially for computer vision tasks. The great success of deep learning is mainly due to its scalability to encode large-scale data and to maneuver billions of model parameters. However, it is a challenge to deploy these cumbersome deep models on devices with limited resources, e.g., mobile phones and embedded devices, not only because of the high computational complexity but also the large storage requirements. To this end, a variety of model compression and acceleration techniques have been developed. As a representative type of model compression and acceleration, knowledge distillation effectively learns a small student model from a large teacher model. It has received rapid increasing attention from the community. This paper provides a comprehensive survey of knowledge distillation from the perspectives of knowledge categories, training schemes, teacher-student architecture, distillation algorithms, performance comparison and applications. Furthermore, challenges in knowledge distillation are briefly reviewed and comments on future research are discussed and forwarded.