OpenRaiser/Intern-Atlas huggingface dataset:
A Survey on Nonconvex Regularization Based Sparse and Low-Rank Recovery in Signal Processing, Statistics, and Machine Learning
Venue: arXiv cs.IT 2019
Year: 2019

In the past decade, sparse and low-rank recovery have drawn much attention in many areas such as signal/image processing, statistics, bioinformatics and machine learning. To achieve sparsity and/or low-rankness inducing, the $\ell_1$ norm and nuclear norm are of the most popular regularization penalties due to their convexity. While the $\ell_1$ and nuclear norm are convenient as the related convex optimization problems are usually tractable, it has been shown in many applications that a nonconvex penalty can yield significantly better performance. In recent, nonconvex regularization based sparse and low-rank recovery is of considerable interest and it in fact is a main driver of the recent progress in nonconvex and nonsmooth optimization. This paper gives an overview of this topic in various fields in signal processing, statistics and machine learning, including compressive sensing (CS), sparse regression and variable selection, sparse signals separation, sparse principal component analysis (PCA), large covariance and inverse covariance matrices estimation, matrix completion, and robust PCA. We present recent developments of nonconvex regularization based sparse and low-rank recovery in these fields, addressing the issues of penalty selection, applications and the convergence of nonconvex algorithms. Code is available at https://github.com/FWen/ncreg.git.
Decentralized Tube-based Model Predictive Control of Uncertain Nonlinear Multi-Agent Systems
Venue: arXiv cs.SY 2019
Year: 2019

This paper addresses the problem of decentralized tube-based nonlinear Model Predictive Control (NMPC) for a class of uncertain nonlinear continuous-time multi-agent systems with additive and bounded disturbance. In particular, the problem of robust navigation of a multi-agent system to predefined states of the workspace while using only local information is addressed, under certain distance and control input constraints. We propose a decentralized feedback control protocol that consists of two terms: a nominal control input, which is computed online and is the outcome of a Decentralized Finite Horizon Optimal Control Problem (DFHOCP) that each agent solves at every sampling time, for its nominal system dynamics; and an additive state feedback law which is computed offline and guarantees that the real trajectories of each agent will belong to a hyper-tube centered along the nominal trajectory, for all times. The volume of the hyper-tube depends on the upper bound of the disturbances as well as the bounds of the derivatives of the dynamics. In addition, by introducing certain distance constraints, the proposed scheme guarantees that the initially connected agents remain connected for all times. Under standard assumptions that arise in nominal NMPC schemes, controllability assumptions as well as communication capabilities between the agents, we guarantee that the multi-agent system is ISS (Input to State Stable) with respect to the disturbances, for all initial conditions satisfying the state constraints. Simulation results verify the correctness of the proposed framework.
Linguistic data mining with complex networks: a stylometric-oriented approach
Venue: arXiv cs.CL 2019
Year: 2019

By representing a text by a set of words and their co-occurrences, one obtains a word-adjacency network being a reduced representation of a given language sample. In this paper, the possibility of using network representation to extract information about individual language styles of literary texts is studied. By determining selected quantitative characteristics of the networks and applying machine learning algorithms, it is possible to distinguish between texts of different authors. Within the studied set of texts, English and Polish, a properly rescaled weighted clustering coefficients and weighted degrees of only a few nodes in the word-adjacency networks are sufficient to obtain the authorship attribution accuracy over 90%. A correspondence between the text authorship and the word-adjacency network structure can therefore be found. The network representation allows to distinguish individual language styles by comparing the way the authors use particular words and punctuation marks. The presented approach can be viewed as a generalization of the authorship attribution methods based on simple lexical features. Additionally, other network parameters are studied, both local and global ones, for both the unweighted and weighted networks. Their potential to capture the writing style diversity is discussed; some differences between languages are observed.
Code generation for generally mapped finite elements
Venue: arXiv cs.MS 2019
Year: 2019

Many classical finite elements such as the Argyris and Bell elements have long been absent from high-level PDE software. Building on recent theoretical work, we describe how to implement very general finite element transformations in FInAT and hence into the Firedrake finite element system. Numerical results evaluate the new elements, comparing them to existing methods for classical problems. For a second order model problem, we find that new elements give smooth solutions at a mild increase in cost over standard Lagrange elements. For fourth-order problems, however, the newly-enabled methods significantly outperform interior penalty formulations. We also give some advanced use cases, solving the nonlinear Cahn-Hilliard equation and some biharmonic eigenvalue problems (including Chladni plates) using $C^1$ discretizations.
Improving Conditional Sequence Generative Adversarial Networks by Stepwise Evaluation
Venue: arXiv cs.CL 2019
Year: 2019

Sequence generative adversarial networks (SeqGAN) have been used to improve conditional sequence generation tasks, for example, chit-chat dialogue generation. To stabilize the training of SeqGAN, Monte Carlo tree search (MCTS) or reward at every generation step (REGS) is used to evaluate the goodness of a generated subsequence. MCTS is computationally intensive, but the performance of REGS is worse than MCTS. In this paper, we propose stepwise GAN (StepGAN), in which the discriminator is modified to automatically assign scores quantifying the goodness of each subsequence at every generation step. StepGAN has significantly less computational costs than MCTS. We demonstrate that StepGAN outperforms previous GAN-based methods on both synthetic experiment and chit-chat dialogue generation.
Optimization of MIMO Device-to-Device Networks via Matrix Fractional Programming: A Minorization-Maximization Approach
Venue: arXiv cs.IT 2019
Year: 2019

Interference management is a fundamental issue in device-to-device (D2D) communications whenever the transmitter-and-receiver pairs are located in close proximity and frequencies are fully reused, so active links may severely interfere with each other. This paper devises an optimization strategy named FPLinQ to coordinate the link scheduling decisions among the interfering links, along with power control and beamforming. The key enabler is a novel optimization method called matrix fractional programming (FP) that generalizes previous scalar and vector forms of FP in allowing multiple data streams per link. From a theoretical perspective, this paper provides a deeper understanding of FP by showing a connection to the minorization-maximization (MM) algorithm. From an application perspective, this paper shows that as compared to the existing methods for coordinating scheduling in the D2D network, such as FlashLinQ, ITLinQ, and ITLinQ+, the proposed FPLinQ approach is more general in allowing multiple antennas at both the transmitters and the receivers, and further in allowing arbitrary and multiple possible associations between the devices via matching. Numerical results show that FPLinQ significantly outperforms the previous state-of-the-art in a typical D2D communication environment.
Progressive Operational Perceptron with Memory
Venue: arXiv cs.NE 2019
Year: 2019

Generalized Operational Perceptron (GOP) was proposed to generalize the linear neuron model in the traditional Multilayer Perceptron (MLP) and this model can mimic the synaptic connections of the biological neurons that have nonlinear neurochemical behaviours. Progressive Operational Perceptron (POP) is a multilayer network composing of GOPs which is formed layer-wise progressively. In this work, we propose major modifications that can accelerate as well as augment the progressive learning procedure of POP by incorporating an information-preserving, linear projection path from the input to the output layer at each progressive step. The proposed extensions can be interpreted as a mechanism that provides direct information extracted from the previously learned layers to the network, hence the term "memory". This allows the network to learn deeper architectures with better data representations. An extensive set of experiments show that the proposed modifications can surpass the learning capability of the original POPs and other related algorithms.
Adversarial training for multi-context joint entity and relation extraction
Venue: arXiv cs.CL 2019
Year: 2019

Adversarial training (AT) is a regularization method that can be used to improve the robustness of neural network methods by adding small perturbations in the training data. We show how to use AT for the tasks of entity recognition and relation extraction. In particular, we demonstrate that applying AT to a general purpose baseline model for jointly extracting entities and relations, allows improving the state-of-the-art effectiveness on several datasets in different contexts (i.e., news, biomedical, and real estate data) and for different languages (English and Dutch).
The variable quality of metadata about biological samples used in biomedical experiments
Venue: arXiv cs.DB 2019
Year: 2019

We present an analytical study of the quality of metadata about samples used in biomedical experiments. The metadata under analysis are stored in two well-known databases: BioSample---a repository managed by the National Center for Biotechnology Information (NCBI), and BioSamples---a repository managed by the European Bioinformatics Institute (EBI). We tested whether 11.4M sample metadata records in the two repositories are populated with values that fulfill the stated requirements for such values. Our study revealed multiple anomalies in the metadata. Most metadata field names and their values are not standardized or controlled. Even simple binary or numeric fields are often populated with inadequate values of different data types. By clustering metadata field names, we discovered there are often many distinct ways to represent the same aspect of a sample. Overall, the metadata we analyzed reveal that there is a lack of principled mechanisms to enforce and validate metadata requirements. The significant aberrancies that we found in the metadata are likely to impede search and secondary use of the associated datasets.
A Survey on Food Computing
Venue: arXiv cs.CY 2019
Year: 2019

Food is very essential for human life and it is fundamental to the human experience. Food-related study may support multifarious applications and services, such as guiding the human behavior, improving the human health and understanding the culinary culture. With the rapid development of social networks, mobile networks, and Internet of Things (IoT), people commonly upload, share, and record food images, recipes, cooking videos, and food diaries, leading to large-scale food data. Large-scale food data offers rich knowledge about food and can help tackle many central issues of human society. Therefore, it is time to group several disparate issues related to food computing. Food computing acquires and analyzes heterogenous food data from disparate sources for perception, recognition, retrieval, recommendation, and monitoring of food. In food computing, computational approaches are applied to address food related issues in medicine, biology, gastronomy and agronomy. Both large-scale food data and recent breakthroughs in computer science are transforming the way we analyze food data. Therefore, vast amounts of work has been conducted in the food area, targeting different food-oriented tasks and applications. However, there are very few systematic reviews, which shape this area well and provide a comprehensive and in-depth summary of current efforts or detail open problems in this area. In this paper, we formalize food computing and present such a comprehensive overview of various emerging concepts, methods, and tasks. We summarize key challenges and future directions ahead for food computing. This is the first comprehensive survey that targets the study of computing technology for the food area and also offers a collection of research studies and technologies to benefit researchers and practitioners working in different food-related fields.
Cross Subspace Alignment and the Asymptotic Capacity of $X$-Secure $T$-Private Information Retrieval
Venue: arXiv cs.IT 2019
Year: 2019

$X$-secure and $T$-private information retrieval (XSTPIR) is a form of private information retrieval where data security is guaranteed against collusion among up to $X$ servers and the user's privacy is guaranteed against collusion among up to $T$ servers. The capacity of XSTPIR is characterized for arbitrary number of servers $N$, and arbitrary security and privacy thresholds $X$ and $T$, in the limit as the number of messages $K\rightarrow\infty$. Capacity is also characterized for any number of messages if either $N=3, X=T=1$ or if $N\leq X+T$. Insights are drawn from these results, about aligning versus decoding noise, dependence of PIR rate on field size, and robustness to symmetric security constraints. In particular, the idea of cross subspace alignment, i.e., introducing a subspace dependence between Reed-Solomon code parameters, emerges as the optimal way to align undesired terms while keeping desired terms resolvable.
Capacity-Achieving Private Information Retrieval Codes with Optimal Message Size and Upload Cost
Venue: arXiv cs.IT 2019
Year: 2019

We propose a new capacity-achieving code for the private information retrieval (PIR) problem, and show that it has the minimum message size (being one less than the number of servers) and the minimum upload cost (being roughly linear in the number of messages) among a general class of capacity-achieving codes, and in particular, among all capacity-achieving linear codes. Different from existing code constructions, the proposed code is asymmetric, and this asymmetry appears to be the key factor leading to the optimal message size and the optimal upload cost. The converse results on the message size and the upload cost are obtained by a strategic analysis of the information theoretic proof of the PIR capacity, from which a set of critical properties of any capacity-achieving code in the code class of interest is extracted. The symmetry structure of the PIR problem is then analyzed, which allows us to construct symmetric codes from asymmetric ones, yielding a meaningful bridge between the proposed code and existing ones in the literature.
Role of Intonation in Scoring Spoken English
Venue: arXiv cs.CL 2019
Year: 2019

In this paper, we have introduced and evaluated intonation based feature for scoring the English speech of nonnative English speakers in Indian context. For this, we created an automated spoken English scoring engine to learn from the manual evaluation of spoken English. This involved using an existing Automatic Speech Recognition (ASR) engine to convert the speech to text. Thereafter, macro features like accuracy, fluency and prosodic features were used to build a scoring model. In the process, we introduced SimIntonation, short for similarity between spoken intonation pattern and "ideal" i.e. training intonation pattern. Our results show that it is a highly predictive feature under controlled environment. We also categorized interword pauses into 4 distinct types for a granular evaluation of pauses and their impact on speech evaluation. Moreover, we took steps to moderate test difficulty through its evaluation across parameters like difficult word count, average sentence readability and lexical density. Our results show that macro features like accuracy and intonation, and micro features like pause-topography are strongly predictive. The scoring of spoken English is not within the purview of this paper.
Attention Gated Networks: Learning to Leverage Salient Regions in Medical Images
Venue: arXiv cs.CV 2019
Year: 2019

We propose a novel attention gate (AG) model for medical image analysis that automatically learns to focus on target structures of varying shapes and sizes. Models trained with AGs implicitly learn to suppress irrelevant regions in an input image while highlighting salient features useful for a specific task. This enables us to eliminate the necessity of using explicit external tissue/organ localisation modules when using convolutional neural networks (CNNs). AGs can be easily integrated into standard CNN models such as VGG or U-Net architectures with minimal computational overhead while increasing the model sensitivity and prediction accuracy. The proposed AG models are evaluated on a variety of tasks, including medical image classification and segmentation. For classification, we demonstrate the use case of AGs in scan plane detection for fetal ultrasound screening. We show that the proposed attention mechanism can provide efficient object localisation while improving the overall prediction performance by reducing false positives. For segmentation, the proposed architecture is evaluated on two large 3D CT abdominal datasets with manual annotations for multiple organs. Experimental results show that AG models consistently improve the prediction performance of the base architectures across different datasets and training sizes while preserving computational efficiency. Moreover, AGs guide the model activations to be focused around salient regions, which provides better insights into how model predictions are made. The source code for the proposed AG models is publicly available.
"Should I Worry?" A Cross-Cultural Examination of Account Security Incident Response
Venue: arXiv cs.CR 2019
Year: 2019

Digital security technology is able to identify and prevent many threats to users accounts. However, some threats remain that, to provide reliable security, require human intervention: e.g., through users paying attention to warning messages or completing secondary authentication procedures. While prior work has broadly explored people's mental models of digital security threats, we know little about users' precise, in-the-moment response process to in-the-wild threats. In this work, we conduct a series of qualitative interviews (n=67) with users who had recently experienced suspicious login incidents on their real Facebook accounts in order to explore this process of account security incident response. We find a common process across participants from five countries -- with differing online and offline cultures -- allowing us to identify areas for future technical development to best support user security. We provide additional insights on the unique nature of incident-response information seeking, known attacker threat models, and lessons learned from a large, cross-cultural qualitative study of digital security.
Detection and Mitigation of Attacks on Transportation Networks as a Multi-Stage Security Game
Venue: arXiv cs.CR 2019
Year: 2019

In recent years, state-of-the-art traffic-control devices have evolved from standalone hardware to networked smart devices. Smart traffic control enables operators to decrease traffic congestion and environmental impact by acquiring real-time traffic data and changing traffic signals from fixed to adaptive schedules. However, these capabilities have inadvertently exposed traffic control to a wide range of cyber-attacks, which adversaries can easily mount through wireless networks or even through the Internet. Indeed, recent studies have found that a large number of traffic signals that are deployed in practice suffer from exploitable vulnerabilities, which adversaries may use to take control of the devices. Thanks to the hardware-based failsafes that most devices employ, adversaries cannot cause traffic accidents directly by setting compromised signals to dangerous configurations. Nonetheless, an adversary could cause disastrous traffic congestion by changing the schedule of compromised traffic signals, thereby effectively crippling the transportation network. To provide theoretical foundations for the protection of transportation networks from these attacks, we introduce a game-theoretic model of launching, detecting, and mitigating attacks that tamper with traffic-signal schedules. We show that finding optimal strategies is a computationally challenging problem, and we propose efficient heuristic algorithms for finding near optimal strategies. We also introduce a Gaussian-process based anomaly detector, which can alert operators to ongoing attacks. Finally, we evaluate our algorithms and the proposed detector using numerical experiments based on the SUMO traffic simulator.
Ranked Schröder Trees
Venue: arXiv cs.DS 2019
Year: 2019

In biology, a phylogenetic tree is a tool to represent the evolutionary relationship between species. Unfortunately, the classical Schröder tree model is not adapted to take into account the chronology between the branching nodes. In particular, it does not answer the question: how many different phylogenetic stories lead to the creation of n species and what is the average time to get there? In this paper, we enrich this model in two distinct ways in order to obtain two ranked tree models for phylogenetics, i.e. models coding chronology. For that purpose, we first develop a model of (strongly) increasing Schröder trees, symbolically described in the classical context of increasing labeling. Then we introduce a generalization for the labeling with some unusual order constraint in Analytic Combinatorics (namely the weakly increasing trees). Although these models are direct extensions of the Schröder tree model, it appears that they are also in one-to-one correspondence with several classical combinatorial objects. Through the paper, we present these links, exhibit some parameters in typical large trees and conclude the studies with efficient uniform samplers.