pwc-archive/papers-with-abstracts huggingface dataset:
Construction and Usage of a Human Body Common Coordinate Framework Comprising Clinical, Semantic, and Spatial Ontologies
Authors: Katy Börner, Ellen M. Quardokus, Bruce W. Herr II, Leonard E. Cross, Elizabeth G. Record, Yingnan Ju, Andreas D. Bueckle, James P. Sluka, Jonathan C. Silverstein, Kristen M. Browne, Sanjay Jain, Clive H. Wasserfall, Marda L. Jorgensen, Jeffrey M. Spraggins, Nathan H. Patterson, Mark A. Musen, Griffin M. Weber
Date: 2020-07-28 00:00:00

The National Institutes of Health's (NIH) Human Biomolecular Atlas Program (HuBMAP) aims to create a comprehensive high-resolution atlas of all the cells in the healthy human body. Multiple laboratories across the United States are collecting tissue specimens from different organs of donors who vary in sex, age, and body size. Integrating and harmonizing the data derived from these samples and 'mapping' them into a common three-dimensional (3D) space is a major challenge. The key to making this possible is a 'Common Coordinate Framework' (CCF), which provides a semantically annotated, 3D reference system for the entire body. The CCF enables contributors to HuBMAP to 'register' specimens and datasets within a common spatial reference system, and it supports a standardized way to query and 'explore' data in a spatially and semantically explicit manner. [...] This paper describes the construction and usage of a CCF for the human body and its reference implementation in HuBMAP. The CCF consists of (1) a CCF Clinical Ontology, which provides metadata about the specimen and donor (the 'who'); (2) a CCF Semantic Ontology, which describes 'what' part of the body a sample came from and details anatomical structures, cell types, and biomarkers (ASCT+B); and (3) a CCF Spatial Ontology, which indicates 'where' a tissue sample is located in a 3D coordinate system. An initial version of all three CCF ontologies has been implemented for the first HuBMAP Portal release. It was successfully used by Tissue Mapping Centers to semantically annotate and spatially register 48 kidney and spleen tissue blocks. The blocks can be queried and explored in their clinical, semantic, and spatial context via the CCF user interface in the HuBMAP Portal.
Modeling Behaviour to Predict User State: Self-Reports as Ground Truth
Authors: Julian Frommel, Regan L. Mandryk
Date: 2020-07-28 00:00:00
Tasks: Position

Methods that detect user states such as emotions are useful for interactive systems. In this position paper, we argue for model-based approaches that are trained on user behaviour and self-reported user state as ground truths. In an application context, they record behaviour, extract relevant features, and use the models to predict user states. We describe how this approach can be implemented and discuss its benefits in comparison to solely self-reports in an application and to models of behaviour without the selfreport ground truths. Finally, we discuss shortcomings of this approach by considering its drawbacks and limitations.
Enhancement of Retinal Fundus Images via Pixel Color Amplification
Authors: Alex Gaudio, Asim Smailagic, Aurélio Campilho
Date: 2020-07-28 00:00:00
Tasks: Segmentation

We propose a pixel color amplification theory and family of enhancement methods to facilitate segmentation tasks on retinal images. Our novel re-interpretation of the image distortion model underlying dehazing theory shows how three existing priors commonly used by the dehazing community and a novel fourth prior are related. We utilize the theory to develop a family of enhancement methods for retinal images, including novel methods for whole image brightening and darkening. We show a novel derivation of the Unsharp Masking algorithm. We evaluate the enhancement methods as a pre-processing step to a challenging multi-task segmentation problem and show large increases in performance on all tasks, with Dice score increases over a no-enhancement baseline by as much as 0.491. We provide evidence that our enhancement preprocessing is useful for unbalanced and difficult data. We show that the enhancements can perform class balancing by composing them together.
Measuring prominence of scientific work in online news as a proxy for impact
Authors: James Ravenscroft, Amanda Clare, Maria Liakata
Date: 2020-07-28 00:00:00
Tasks: Articles, Semantic Similarity, Semantic Textual Similarity

The impact made by a scientific paper on the work of other academics has many established metrics, including metrics based on citation counts and social media commenting. However, determination of the impact of a scientific paper on the wider society is less well established. For example, is it important for scientific work to be newsworthy? Here we present a new corpus of newspaper articles linked to the scientific papers that they describe. We find that Impact Case studies submitted to the UK Research Excellence Framework (REF) 2014 that refer to scientific papers mentioned in newspaper articles were awarded a higher score in the REF assessment. The papers associated with these case studies also feature prominently in the newspaper articles. We hypothesise that such prominence can be a useful proxy for societal impact. We therefore provide a novel baseline approach for measuring the prominence of scientific papers mentioned within news articles. Our measurement of prominence is based on semantic similarity through a graph-based ranking algorithm. We find that scientific papers with an associated REF case study are more likely to have a stronger prominence score. This supports our hypothesis that linguistic prominence in news can be used to suggest the wider non-academic impact of scientific work.
On the Quantum versus Classical Learnability of Discrete Distributions
Authors: Ryan Sweke, Jean-Pierre Seifert, Dominik Hangleiter, Jens Eisert
Date: 2020-07-28 00:00:00

Here we study the comparative power of classical and quantum learners for generative modelling within the Probably Approximately Correct (PAC) framework. More specifically we consider the following task: Given samples from some unknown discrete probability distribution, output with high probability an efficient algorithm for generating new samples from a good approximation of the original distribution. Our primary result is the explicit construction of a class of discrete probability distributions which, under the decisional Diffie-Hellman assumption, is provably not efficiently PAC learnable by a classical generative modelling algorithm, but for which we construct an efficient quantum learner. This class of distributions therefore provides a concrete example of a generative modelling problem for which quantum learners exhibit a provable advantage over classical learning algorithms. In addition, we discuss techniques for proving classical generative modelling hardness results, as well as the relationship between the PAC learnability of Boolean functions and the PAC learnability of discrete probability distributions.
Extending LOUPE for K-space Under-sampling Pattern Optimization in Multi-coil MRI
Authors: Jinwei Zhang, Hang Zhang, Alan Wang, Qihao Zhang, Mert Sabuncu, Pascal Spincemaille, Thanh D. Nguyen, Yi Wang
Date: 2020-07-28 00:00:00

The previously established LOUPE (Learning-based Optimization of the Under-sampling Pattern) framework for optimizing the k-space sampling pattern in MRI was extended in three folds: firstly, fully sampled multi-coil k-space data from the scanner, rather than simulated k-space data from magnitude MR images in LOUPE, was retrospectively under-sampled to optimize the under-sampling pattern of in-vivo k-space data; secondly, binary stochastic k-space sampling, rather than approximate stochastic k-space sampling of LOUPE during training, was applied together with a straight-through (ST) estimator to estimate the gradient of the threshold operation in a neural network; thirdly, modified unrolled optimization network, rather than modified U-Net in LOUPE, was used as the reconstruction network in order to reconstruct multi-coil data properly and reduce the dependency on training data. Experimental results show that when dealing with the in-vivo k-space data, unrolled optimization network with binary under-sampling block and ST estimator had better reconstruction performance compared to the ones with either U-Net reconstruction network or approximate sampling pattern optimization network, and once trained, the learned optimal sampling pattern worked better than the hand-crafted variable density sampling pattern when deployed with other conventional reconstruction methods.
Learning from Scale-Invariant Examples for Domain Adaptation in Semantic Segmentation
Authors: M. Naseer Subhani, Mohsen Ali
Date: 2020-07-28 00:00:00
Proceeding: ECCV 2020 8
Tasks: Domain Adaptation, Image-to-Image Translation, Segmentation, Self-Supervised Learning, Semantic Segmentation, Synthetic-to-Real Translation, Unsupervised Domain Adaptation

Self-supervised learning approaches for unsupervised domain adaptation (UDA) of semantic segmentation models suffer from challenges of predicting and selecting reasonable good quality pseudo labels. In this paper, we propose a novel approach of exploiting scale-invariance property of the semantic segmentation model for self-supervised domain adaptation. Our algorithm is based on a reasonable assumption that, in general, regardless of the size of the object and stuff (given context) the semantic labeling should be unchanged. We show that this constraint is violated over the images of the target domain, and hence could be used to transfer labels in-between differently scaled patches. Specifically, we show that semantic segmentation model produces output with high entropy when presented with scaled-up patches of target domain, in comparison to when presented original size images. These scale-invariant examples are extracted from the most confident images of the target domain. Dynamic class specific entropy thresholding mechanism is presented to filter out unreliable pseudo-labels. Furthermore, we also incorporate the focal loss to tackle the problem of class imbalance in self-supervised learning. Extensive experiments have been performed, and results indicate that exploiting the scale-invariant labeling, we outperform existing self-supervised based state-of-the-art domain adaptation methods. Specifically, we achieve 1.3% and 3.8% of lead for GTA5 to Cityscapes and SYNTHIA to Cityscapes with VGG16-FCN8 baseline network.
Towards Ecologically Valid Research on Language User Interfaces
Authors: Harm de Vries, Dzmitry Bahdanau, Christopher Manning
Date: 2020-07-28 00:00:00
Tasks: BIG-bench Machine Learning, valid

Language User Interfaces (LUIs) could improve human-machine interaction for a wide variety of tasks, such as playing music, getting insights from databases, or instructing domestic robots. In contrast to traditional hand-crafted approaches, recent work attempts to build LUIs in a data-driven way using modern deep learning methods. To satisfy the data needs of such learning algorithms, researchers have constructed benchmarks that emphasize the quantity of collected data at the cost of its naturalness and relevance to real-world LUI use cases. As a consequence, research findings on such benchmarks might not be relevant for developing practical LUIs. The goal of this paper is to bootstrap the discussion around this issue, which we refer to as the benchmarks' low ecological validity. To this end, we describe what we deem an ideal methodology for machine learning research on LUIs and categorize five common ways in which recent benchmarks deviate from it. We give concrete examples of the five kinds of deviations and their consequences. Lastly, we offer a number of recommendations as to how to increase the ecological validity of machine learning research on LUIs.
Cassandra: Detecting Trojaned Networks from Adversarial Perturbations
Authors: Xiao-Yu Zhang, Ajmal Mian, Rohit Gupta, Nazanin Rahnavard, Mubarak Shah
Date: 2020-07-28 00:00:00
Tasks: Adversarial Defense, Anomaly Detection

Deep neural networks are being widely deployed for many critical tasks due to their high classification accuracy. In many cases, pre-trained models are sourced from vendors who may have disrupted the training pipeline to insert Trojan behaviors into the models. These malicious behaviors can be triggered at the adversary's will and hence, cause a serious threat to the widespread deployment of deep models. We propose a method to verify if a pre-trained model is Trojaned or benign. Our method captures fingerprints of neural networks in the form of adversarial perturbations learned from the network gradients. Inserting backdoors into a network alters its decision boundaries which are effectively encoded in their adversarial perturbations. We train a two stream network for Trojan detection from its global ($L_\infty$ and $L_2$ bounded) perturbations and the localized region of high energy within each perturbation. The former encodes decision boundaries of the network and latter encodes the unknown trigger shape. We also propose an anomaly detection method to identify the target class in a Trojaned network. Our methods are invariant to the trigger type, trigger size, training data and network architecture. We evaluate our methods on MNIST, NIST-Round0 and NIST-Round1 datasets, with up to 1,000 pre-trained models making this the largest study to date on Trojaned network detection, and achieve over 92\% detection accuracy to set the new state-of-the-art.
A Convolutional Neural Network for gaze preference detection: A potential tool for diagnostics of autism spectrum disorder in children
Authors: Dennis Núñez Fernández, Franklin Barrientos Porras, Robert H. Gilman, Macarena Vittet Mondonedo, Patricia Sheen, Mirko Zimic
Date: 2020-07-28 00:00:00
Tasks: Diagnostic, Gaze Prediction

Early diagnosis of autism spectrum disorder (ASD) is known to improve the quality of life of affected individuals. However, diagnosis is often delayed even in wealthier countries including the US, largely due to the fact that gold standard diagnostic tools such as the Autism Diagnostic Observation Schedule (ADOS) and the Autism Diagnostic Interview-Revised (ADI-R) are time consuming and require expertise to administer. This trend is even more pronounced lower resources settings due to a lack of trained experts. As a result, alternative, less technical methods that leverage the unique ways in which children with ASD react to visual stimulation in a controlled environment have been developed to help facilitate early diagnosis. Previous studies have shown that, when exposed to a video that presents both social and abstract scenes side by side, a child with ASD will focus their attention towards the abstract images on the screen to a greater extent than a child without ASD. Such differential responses make it possible to implement an algorithm for the rapid diagnosis of ASD based on eye tracking against different visual stimuli. Here we propose a convolutional neural network (CNN) algorithm for gaze prediction using images extracted from a one-minute stimulus video. Our model achieved a high accuracy rate and robustness for prediction of gaze direction with independent persons and employing a different camera than the one used during testing. In addition to this, the proposed algorithm achieves a fast response time, providing a near real-time evaluation of ASD. Thereby, by applying the proposed method, we could significantly reduce the diagnosis time and facilitate the diagnosis of ASD in low resource regions.
Munchausen Reinforcement Learning
Authors: Nino Vieillard, Olivier Pietquin, Matthieu Geist
Date: 2020-07-28 00:00:00
Proceeding: NeurIPS 2020 12
Tasks: Atari Games, reinforcement-learning, Reinforcement Learning, Reinforcement Learning (RL)

Bootstrapping is a core mechanism in Reinforcement Learning (RL). Most algorithms, based on temporal differences, replace the true value of a transiting state by their current estimate of this value. Yet, another estimate could be leveraged to bootstrap RL: the current policy. Our core contribution stands in a very simple idea: adding the scaled log-policy to the immediate reward. We show that slightly modifying Deep Q-Network (DQN) in that way provides an agent that is competitive with distributional methods on Atari games, without making use of distributional RL, n-step returns or prioritized replay. To demonstrate the versatility of this idea, we also use it together with an Implicit Quantile Network (IQN). The resulting agent outperforms Rainbow on Atari, installing a new State of the Art with very little modifications to the original algorithm. To add to this empirical study, we provide strong theoretical insights on what happens under the hood -- implicit Kullback-Leibler regularization and increase of the action-gap.
AiR: Attention with Reasoning Capability
Authors: Shi Chen, Ming Jiang, Jinhui Yang, Qi Zhao
Date: 2020-07-28 00:00:00
Proceeding: ECCV 2020 8

While attention has been an increasingly popular component in deep neural networks to both interpret and boost performance of models, little work has examined how attention progresses to accomplish a task and whether it is reasonable. In this work, we propose an Attention with Reasoning capability (AiR) framework that uses attention to understand and improve the process leading to task outcomes. We first define an evaluation metric based on a sequence of atomic reasoning operations, enabling quantitative measurement of attention that considers the reasoning process. We then collect human eye-tracking and answer correctness data, and analyze various machine and human attentions on their reasoning capability and how they impact task performance. Furthermore, we propose a supervision method to jointly and progressively optimize attention, reasoning, and task performance so that models learn to look at regions of interests by following a reasoning process. We demonstrate the effectiveness of the proposed framework in analyzing and modeling attention with better reasoning capability and task performance. The code and data are available at https://github.com/szzexpoi/AiR
DeepMP for Non-Negative Sparse Decomposition
Authors: Konstantinos A. Voulgaris, Mike E. Davies, Mehrdad Yaghoobi
Date: 2020-07-28 00:00:00

Non-negative signals form an important class of sparse signals. Many algorithms have already beenproposed to recover such non-negative representations, where greedy and convex relaxed algorithms are among the most popular methods. The greedy techniques are low computational cost algorithms, which have also been modified to incorporate the non-negativity of the representations. One such modification has been proposed for Matching Pursuit (MP) based algorithms, which first chooses positive coefficients and uses a non-negative optimisation technique that guarantees the non-negativity of the coefficients. The performance of greedy algorithms, like all non-exhaustive search methods, suffer from high coherence with the linear generative model, called the dictionary. We here first reformulate the non-negative matching pursuit algorithm in the form of a deep neural network. We then show that the proposed model after training yields a significant improvement in terms of exact recovery performance, compared to other non-trained greedy algorithms, while keeping the complexity low.
A framework for optimizing COVID-19 testing policy using a Multi Armed Bandit approach
Authors: Hagit Grushka-Cohen, Raphael Cohen, Bracha Shapira, Jacob Moran-Gilad, Lior Rokach
Date: 2020-07-28 00:00:00
Tasks: Decision Making, Multi-Armed Bandits

Testing is an important part of tackling the COVID-19 pandemic. Availability of testing is a bottleneck due to constrained resources and effective prioritization of individuals is necessary. Here, we discuss the impact of different prioritization policies on COVID-19 patient discovery and the ability of governments and health organizations to use the results for effective decision making. We suggest a framework for testing that balances the maximal discovery of positive individuals with the need for population-based surveillance aimed at understanding disease spread and characteristics. This framework draws from similar approaches to prioritization in the domain of cyber-security based on ranking individuals using a risk score and then reserving a portion of the capacity for random sampling. This approach is an application of Multi-Armed-Bandits maximizing exploration/exploitation of the underlying distribution. We find that individuals can be ranked for effective testing using a few simple features, and that ranking them using such models we can capture 65% (CI: 64.7%-68.3%) of the positive individuals using less than 20% of the testing capacity or 92.1% (CI: 91.1%-93.2%) of positives individuals using 70% of the capacity, allowing reserving a significant portion of the tests for population studies. Our approach allows experts and decision-makers to tailor the resulting policies as needed allowing transparency into the ranking policy and the ability to understand the disease spread in the population and react quickly and in an informed manner.
Efficient OCT Image Segmentation Using Neural Architecture Search
Authors: Saba Heidari Gheshlaghi, Omid Dehzangi, Ali Dabouei, Annahita Amireskandari, Ali Rezai, Nasser M. Nasrabadi
Date: 2020-07-28 00:00:00
Tasks: Image Segmentation, Neural Architecture Search, Segmentation, Semantic Segmentation, Super-Resolution

In this work, we propose a Neural Architecture Search (NAS) for retinal layer segmentation in Optical Coherence Tomography (OCT) scans. We incorporate the Unet architecture in the NAS framework as its backbone for the segmentation of the retinal layers in our collected and pre-processed OCT image dataset. At the pre-processing stage, we conduct super resolution and image processing techniques on the raw OCT scans to improve the quality of the raw images. For our search strategy, different primitive operations are suggested to find the down- & up-sampling cell blocks, and the binary gate method is applied to make the search strategy practical for the task in hand. We empirically evaluated our method on our in-house OCT dataset. The experimental results demonstrate that the self-adapting NAS-Unet architecture substantially outperformed the competitive human-designed architecture by achieving 95.4% in mean Intersection over Union metric and 78.7% in Dice similarity coefficient.
An Uncertainty-aware Transfer Learning-based Framework for Covid-19 Diagnosis
Authors: Afshar Shamsi Jokandan, Hamzeh Asgharnezhad, Shirin Shamsi Jokandan, Abbas Khosravi, Parham M. Kebria, Darius Nahavandi, Saeid Nahavandi, Dipti Srinivasan
Date: 2020-07-26 00:00:00
Tasks: Computed Tomography (CT), COVID-19 Diagnosis, Specificity, Transfer Learning

The early and reliable detection of COVID-19 infected patients is essential to prevent and limit its outbreak. The PCR tests for COVID-19 detection are not available in many countries and also there are genuine concerns about their reliability and performance. Motivated by these shortcomings, this paper proposes a deep uncertainty-aware transfer learning framework for COVID-19 detection using medical images. Four popular convolutional neural networks (CNNs) including VGG16, ResNet50, DenseNet121, and InceptionResNetV2 are first applied to extract deep features from chest X-ray and computed tomography (CT) images. Extracted features are then processed by different machine learning and statistical modelling techniques to identify COVID-19 cases. We also calculate and report the epistemic uncertainty of classification results to identify regions where the trained models are not confident about their decisions (out of distribution problem). Comprehensive simulation results for X-ray and CT image datasets indicate that linear support vector machine and neural network models achieve the best results as measured by accuracy, sensitivity, specificity, and AUC. Also it is found that predictive uncertainty estimates are much higher for CT images compared to X-ray images.