pwc-archive/papers-with-abstracts huggingface dataset:
snpQT: flexible, reproducible, and comprehensive quality control and imputation of genomic data
Authors: Christina Vasilopoulou, Benjamin Wingfield, Andrew P. Morris, William Duddy
Date: 2021-05-05 00:00:00
Tasks: Imputation

Motivation: Quality control of genomic data is an essential but complicated multi-step procedure, often requiring separate installation and expert familiarity with a combination of disparate bioinformatics tools. Results: To provide an automated solution that retains comprehensive quality checks and flexible workflow architecture, we have developed snpQT, a scalable, stand-alone software pipeline, offering some 36 discrete quality filters or correction steps, with plots before-and-after user-modifiable thresholding. This includes build conversion, population stratification against 1,000 Genomes data, population outlier removal, and built-in imputation with its own pre- and post- quality controls. Common input formats are used and users need not be superusers nor have any prior coding experience. A comprehensive online tutorial and installation guide is provided through to GWAS (https://snpqt.readthedocs.io/en/latest/), introducing snpQT using a synthetic demonstration dataset and a real-world Amyotrophic Lateral Sclerosis SNP-array dataset. Availability: snpQT is open source and freely available at https://github.com/nebfield/snpQT Contact: Vasilopoulou-C@ulster.ac.uk, w.duddy@ulster.ac.uk
A Digital Twin of a Compartmental Epidemiological Model based on a Stieltjes Differential Equation
Authors: Iván Area, F. J. Fernández, Juan J. Nieto, F. Adrián F. Tojo
Date: 2021-04-29 00:00:00

We introduce a digital twin of the classical compartmental SIR (Susceptible, Infected, Recovered) epidemic model and study the interrelation between the digital twin and the system. In doing so, we use Stieltjes derivatives to feed the data from the real system to the virtual model which, in return, improves it in real time. As a byproduct of the model, we present a precise mathematical definition of solution to the problem. We also analyze the existence and uniqueness of solutions, introduce the concept of Main Digital Twin and present some numerical simulations with real data of the COVID-19 epidemic, showing the accuracy of the proposed ideas.
Modelling the Second Covid-19 Wave in Mumbai
Authors: Sandeep Juneja, Daksh Mittal
Date: 2021-05-05 00:00:00

India has been hit by a huge second wave of Covid-19 that started in mid-February 2021. Mumbai was amongst the first cities to see the increase. In this report, we use our agent based simulator to computationally study the second wave in Mumbai. We build upon our earlier analysis, where projections were made from November 2020 onwards. We use our simulator to conduct an extensive scenario analysis - we play out many plausible scenarios through varying economic activity, reinfection levels, population compliance, infectiveness, prevalence and lethality of the possible variant strains, and infection spread via local trains to arrive at those that may better explain the second wave fatality numbers. We observe and highlight that timings of peak and valley of the fatalities in the second wave are robust to many plausible scenarios, suggesting that they are likely to be accurate projections for Mumbai. During the second wave, the observed fatalities were low in February and mid-March and saw a phase change or a steep increase in the growth rate after around late March. We conduct extensive experiments to replicate this observed sharp convexity. This is not an easy phenomena to replicate, and we find that explanations such as increased laxity in the population, increased reinfections, increased intensity of infections in Mumbai transportation, increased lethality in the virus, or a combination amongst them, generally do a poor job of matching this pattern. We find that the most likely explanation is presence of small amount of extremely infective variant on February 1 that grows rapidly thereafter and becomes a dominant strain by Mid-March. From a prescriptive view, this points to an urgent need for extensive and continuous genome sequencing to establish existence and prevalence of different virus strains in Mumbai and in India, as they evolve over time.
Herd immunity for Covid-19 in homogeneous populations
Authors: Janaina P. Zingano, Paulo R. Zingano, Alessandra M. Silva, Carolina P. Zingano
Date: 2021-05-05 00:00:00

In this note we estimate herd immunity levels for the Covid-19 epidemic using a standard SEIR system that models the disease dynamics in homogeneous populations. The results obtained are indicative of values between 80% and 90% for unprotected, fully susceptible populations. Basic protective measures such as hand hygiene and mask wearing may be effective to lower herd immunity levels down to values between 50% and 60% of the total population.
Simulation and estimation of a point-process market-model with a matching engine
Authors: Ivan Jericevich, Patrick Chang, Tim Gebbie
Date: 2021-05-05 00:00:00
Tasks: Management

The extent to which a matching engine can cloud the modelling of underlying order submission and management processes in a financial market remains an unanswered concern with regards to market models. Here we consider a 10-variate Hawkes process with simple rules to simulate common order types which are submitted to a matching engine. Hawkes processes can be used to model the time and order of events, and how these events relate to each other. However, they provide a freedom with regards to implementation mechanics relating to the prices and volumes of injected orders. This allows us to consider a reference Hawkes model and two additional models which have rules that change the behaviour of limit orders. The resulting trade and quote data from the simulations are then calibrated and compared with the original order generating process to determine the extent with which implementation rules can distort model parameters. Evidence from validation and hypothesis tests suggest that the true model specification can be significantly distorted by market mechanics, and that practical considerations not directly due to model specification can be important with regards to model identification within an inherently asynchronous trading environment.
A Geometric Analysis of Neural Collapse with Unconstrained Features
Authors: Zhihui Zhu, Tianyu Ding, Jinxin Zhou, Xiao Li, Chong You, Jeremias Sulam, Qing Qu
Date: 2021-05-06 00:00:00
Proceeding: NeurIPS 2021 12
Tasks: global-optimization

We provide the first global optimization landscape analysis of $Neural\;Collapse$ -- an intriguing empirical phenomenon that arises in the last-layer classifiers and features of neural networks during the terminal phase of training. As recently reported by Papyan et al., this phenomenon implies that ($i$) the class means and the last-layer classifiers all collapse to the vertices of a Simplex Equiangular Tight Frame (ETF) up to scaling, and ($ii$) cross-example within-class variability of last-layer activations collapses to zero. We study the problem based on a simplified $unconstrained\;feature\;model$, which isolates the topmost layers from the classifier of the neural network. In this context, we show that the classical cross-entropy loss with weight decay has a benign global landscape, in the sense that the only global minimizers are the Simplex ETFs while all other critical points are strict saddles whose Hessian exhibit negative curvature directions. In contrast to existing landscape analysis for deep neural networks which is often disconnected from practice, our analysis of the simplified model not only does it explain what kind of features are learned in the last layer, but it also shows why they can be efficiently optimized in the simplified settings, matching the empirical observations in practical deep network architectures. These findings could have profound implications for optimization, generalization, and robustness of broad interests. For example, our experiments demonstrate that one may set the feature dimension equal to the number of classes and fix the last-layer classifier to be a Simplex ETF for network training, which reduces memory cost by over $20\%$ on ResNet18 without sacrificing the generalization performance.
LGGNet: Learning from Local-Global-Graph Representations for Brain-Computer Interface
Authors: Yi Ding, Neethu Robinson, Chengxuan Tong, Qiuhao Zeng, Cuntai Guan
Date: 2021-05-05 00:00:00
Tasks: Brain Computer Interface, EEG, EEG Emotion Recognition, Electroencephalogram (EEG), Graph Neural Network

Neuropsychological studies suggest that co-operative activities among different brain functional areas drive high-level cognitive processes. To learn the brain activities within and among different functional areas of the brain, we propose LGGNet, a novel neurologically inspired graph neural network, to learn local-global-graph representations of electroencephalography (EEG) for Brain-Computer Interface (BCI). The input layer of LGGNet comprises a series of temporal convolutions with multi-scale 1D convolutional kernels and kernel-level attentive fusion. It captures temporal dynamics of EEG which then serves as input to the proposed local and global graph-filtering layers. Using a defined neurophysiologically meaningful set of local and global graphs, LGGNet models the complex relations within and among functional areas of the brain. Under the robust nested cross-validation settings, the proposed method is evaluated on three publicly available datasets for four types of cognitive classification tasks, namely, the attention, fatigue, emotion, and preference classification tasks. LGGNet is compared with state-of-the-art methods, such as DeepConvNet, EEGNet, R2G-STNN, TSception, RGNN, AMCNN-DGCN, HRNN and GraphNet. The results show that LGGNet outperforms these methods, and the improvements are statistically significant (p<0.05) in most cases. The results show that bringing neuroscience prior knowledge into neural network design yields an improvement of classification performance. The source code can be found at https://github.com/yi-ding-cs/LGG
WTR: A Test Collection for Web Table Retrieval
Authors: Zhiyu Chen, Shuo Zhang, Brian D. Davison
Date: 2021-05-05 00:00:00
Tasks: Retrieval, Table Retrieval

We describe the development, characteristics and availability of a test collection for the task of Web table retrieval, which uses a large-scale Web Table Corpora extracted from the Common Crawl. Since a Web table usually has rich context information such as the page title and surrounding paragraphs, we not only provide relevance judgments of query-table pairs, but also the relevance judgments of query-table context pairs with respect to a query, which are ignored by previous test collections. To facilitate future research with this benchmark, we provide details about how the dataset is pre-processed and also baseline results from both traditional and recently proposed table retrieval methods. Our experimental results show that proper usage of context labels can benefit previous table retrieval methods.
Weakly Supervised Action Selection Learning in Video
Authors: Junwei Ma, Satya Krishna Gorti, Maksims Volkovs, Guangwei Yu
Date: 2021-05-06 00:00:00
Proceeding: CVPR 2021 1
Tasks: Temporal Localization, Weakly Supervised Action Localization

Localizing actions in video is a core task in computer vision. The weakly supervised temporal localization problem investigates whether this task can be adequately solved with only video-level labels, significantly reducing the amount of expensive and error-prone annotation that is required. A common approach is to train a frame-level classifier where frames with the highest class probability are selected to make a video-level prediction. Frame level activations are then used for localization. However, the absence of frame-level annotations cause the classifier to impart class bias on every frame. To address this, we propose the Action Selection Learning (ASL) approach to capture the general concept of action, a property we refer to as "actionness". Under ASL, the model is trained with a novel class-agnostic task to predict which frames will be selected by the classifier. Empirically, we show that ASL outperforms leading baselines on two popular benchmarks THUMOS-14 and ActivityNet-1.2, with 10.3% and 5.7% relative improvement respectively. We further analyze the properties of ASL and demonstrate the importance of actionness. Full code for this work is available here: https://github.com/layer6ai-labs/ASL.
Do You Even Need Attention? A Stack of Feed-Forward Layers Does Surprisingly Well on ImageNet
Authors: Luke Melas-Kyriazi
Date: 2021-05-06 00:00:00
Tasks: image-classification, Image Classification

The strong performance of vision transformers on image classification and other vision tasks is often attributed to the design of their multi-head attention layers. However, the extent to which attention is responsible for this strong performance remains unclear. In this short report, we ask: is the attention layer even necessary? Specifically, we replace the attention layer in a vision transformer with a feed-forward layer applied over the patch dimension. The resulting architecture is simply a series of feed-forward layers applied over the patch and feature dimensions in an alternating fashion. In experiments on ImageNet, this architecture performs surprisingly well: a ViT/DeiT-base-sized model obtains 74.9\% top-1 accuracy, compared to 77.9\% and 79.9\% for ViT and DeiT respectively. These results indicate that aspects of vision transformers other than attention, such as the patch embedding, may be more responsible for their strong performance than previously thought. We hope these results prompt the community to spend more time trying to understand why our current models are as effective as they are.
Contextual Bandits with Sparse Data in Web setting
Authors: Björn H Eriksson
Date: 2021-05-06 00:00:00
Tasks: Articles, Dimensionality Reduction, Multi-Armed Bandits

This paper is a scoping study to identify current methods used in handling sparse data with contextual bandits in web settings. The area is highly current and state of the art methods are identified. The years 2017-2020 are investigated, and 19 method articles are identified, and two review articles. Five categories of methods are described, making it easy to choose how to address sparse data using contextual bandits with a method available for modification in the specific setting of concern. In addition, each method has multiple techniques to choose from for future evaluation. The problem areas are also mentioned that each article covers. An overall updated understanding of sparse data problems using contextual bandits in web settings is given. The identified methods are policy evaluation (off-line and on-line) , hybrid-method, model representation (clusters and deep neural networks), dimensionality reduction, and simulation.
Algorithmic Ethics: Formalization and Verification of Autonomous Vehicle Obligations
Authors: Colin Shea-Blymyer, Houssam Abbas
Date: 2021-05-06 00:00:00
Tasks: Ethics, Self-Driving Cars

We develop a formal framework for automatic reasoning about the obligations of autonomous cyber-physical systems, including their social and ethical obligations. Obligations, permissions and prohibitions are distinct from a system's mission, and are a necessary part of specifying advanced, adaptive AI-equipped systems. They need a dedicated deontic logic of obligations to formalize them. Most existing deontic logics lack corresponding algorithms and system models that permit automatic verification. We demonstrate how a particular deontic logic, Dominance Act Utilitarianism (DAU), is a suitable starting point for formalizing the obligations of autonomous systems like self-driving cars. We demonstrate its usefulness by formalizing a subset of Responsibility-Sensitive Safety (RSS) in DAU; RSS is an industrial proposal for how self-driving cars should and should not behave in traffic. We show that certain logical consequences of RSS are undesirable, indicating a need to further refine the proposal. We also demonstrate how obligations can change over time, which is necessary for long-term autonomy. We then demonstrate a model-checking algorithm for DAU formulas on weighted transition systems, and illustrate it by model-checking obligations of a self-driving car controller from the literature.
Two4Two: Evaluating Interpretable Machine Learning - A Synthetic Dataset For Controlled Experiments
Authors: Martin Schuessler, Philipp Weiß, Leon Sixt
Date: 2021-05-06 00:00:00
Tasks: BIG-bench Machine Learning, image-classification, Image Classification, Interpretable Machine Learning

A growing number of approaches exist to generate explanations for image classification. However, few of these approaches are subjected to human-subject evaluations, partly because it is challenging to design controlled experiments with natural image datasets, as they leave essential factors out of the researcher's control. With our approach, researchers can describe their desired dataset with only a few parameters. Based on these, our library generates synthetic image data of two 3D abstract animals. The resulting data is suitable for algorithmic as well as human-subject evaluations. Our user study results demonstrate that our method can create biases predictive enough for a classifier and subtle enough to be noticeable only to every second participant inspecting the data visually. Our approach significantly lowers the barrier for conducting human subject evaluations, thereby facilitating more rigorous investigations into interpretable machine learning. For our library and datasets see, https://github.com/mschuessler/two4two/
Neural Algorithmic Reasoning
Authors: Petar Veličković, Charles Blundell
Date: 2021-05-06 00:00:00
Tasks: Deep Learning

Algorithms have been fundamental to recent global technological advances and, in particular, they have been the cornerstone of technical advances in one field rapidly being applied to another. We argue that algorithms possess fundamentally different qualities to deep learning methods, and this strongly suggests that, were deep learning methods better able to mimic algorithms, generalisation of the sort seen with algorithms would become possible with deep learning -- something far out of the reach of current machine learning methods. Furthermore, by representing elements in a continuous space of learnt algorithms, neural networks are able to adapt known algorithms more closely to real-world problems, potentially finding more efficient and pragmatic solutions than those proposed by human computer scientists. Here we present neural algorithmic reasoning -- the art of building neural networks that are able to execute algorithmic computation -- and provide our opinion on its transformative potential for running classical algorithms on inputs previously considered inaccessible to them.
On the Ethical Limits of Natural Language Processing on Legal Text
Authors: Dimitrios Tsarapatsanis, Nikolaos Aletras
Date: 2021-05-06 00:00:00
Proceeding: Findings (ACL) 2021 8
Tasks: Diversity

Natural language processing (NLP) methods for analyzing legal text offer legal scholars and practitioners a range of tools allowing to empirically analyze law on a large scale. However, researchers seem to struggle when it comes to identifying ethical limits to using NLP systems for acquiring genuine insights both about the law and the systems' predictive capacity. In this paper we set out a number of ways in which to think systematically about such issues. We place emphasis on three crucial normative parameters which have, to the best of our knowledge, been underestimated by current debates: (a) the importance of academic freedom, (b) the existence of a wide diversity of legal and ethical norms domestically but even more so internationally and (c) the threat of moralism in research related to computational law. For each of these three parameters we provide specific recommendations for the legal NLP community. Our discussion is structured around the study of a real-life scenario that has prompted recent debate in the legal NLP research community.
Meta-Learning-Based Deep Reinforcement Learning for Multiobjective Optimization Problems
Authors: Zizhen Zhang, Zhiyuan Wu, Hang Zhang, Jiahai Wang
Date: 2021-05-06 00:00:00
Tasks: Combinatorial Optimization, Deep Reinforcement Learning, Diversity, Meta-Learning, Multiobjective Optimization, reinforcement-learning, Reinforcement Learning, Reinforcement Learning (RL)

Deep reinforcement learning (DRL) has recently shown its success in tackling complex combinatorial optimization problems. When these problems are extended to multiobjective ones, it becomes difficult for the existing DRL approaches to flexibly and efficiently deal with multiple subproblems determined by weight decomposition of objectives. This paper proposes a concise meta-learning-based DRL approach. It first trains a meta-model by meta-learning. The meta-model is fine-tuned with a few update steps to derive submodels for the corresponding subproblems. The Pareto front is then built accordingly. Compared with other learning-based methods, our method can greatly shorten the training time of multiple submodels. Due to the rapid and excellent adaptability of the meta-model, more submodels can be derived so as to increase the quality and diversity of the found solutions. The computational experiments on multiobjective traveling salesman problems and multiobjective vehicle routing problem with time windows demonstrate the superiority of our method over most of learning-based and iteration-based approaches.
Digital Voodoo Dolls
Authors: Marija Slavkovik, Clemens Stachl, Caroline Pitman, Jonathan Askonas
Date: 2021-05-06 00:00:00

An institution, be it a body of government, commercial enterprise, or a service, cannot interact directly with a person. Instead, a model is created to represent us. We argue the existence of a new high-fidelity type of person model which we call a digital voodoo doll. We conceptualize it and compare its features with existing models of persons. Digital voodoo dolls are distinguished by existing completely beyond the influence and control of the person they represent. We discuss the ethical issues that such a lack of accountability creates and argue how these concerns can be mitigated.
Deep Weighted Consensus: Dense correspondence confidence maps for 3D shape registration
Authors: Dvir Ginzburg, Dan Raviv
Date: 2021-05-06 00:00:00

We present a new paradigm for rigid alignment between point clouds based on learnable weighted consensus which is robust to noise as well as the full spectrum of the rotation group. Current models, learnable or axiomatic, work well for constrained orientations and limited noise levels, usually by an end-to-end learner or an iterative scheme. However, real-world tasks require us to deal with large rotations as well as outliers and all known models fail to deliver. Here we present a different direction. We claim that we can align point clouds out of sampled matched points according to confidence level derived from a dense, soft alignment map. The pipeline is differentiable, and converges under large rotations in the full spectrum of SO(3), even with high noise levels. We compared the network to recently presented methods such as DCP, PointNetLK, RPM-Net, PRnet, and axiomatic methods such as ICP and Go-ICP. We report here a fundamental boost in performance.