OpenRaiser/Intern-Atlas huggingface dataset:
Prediction of the onset of cardiovascular diseases from electronic health records using multi-task gated recurrent units
Venue: arXiv cs.LG 2020
Year: 2020

In this work, we propose a multi-task recurrent neural network with attention mechanism for predicting cardiovascular events from electronic health records (EHRs) at different time horizons. The proposed approach is compared to a standard clinical risk predictor (QRISK) and machine learning alternatives using 5-year data from a NHS Foundation Trust. The proposed model outperforms standard clinical risk scores in predicting stroke (AUC=0.85) and myocardial infarction (AUC=0.89), considering the largest time horizon. Benefit of using an \gls{mt} setting becomes visible for very short time horizons, which results in an AUC increase between 2-6%. Further, we explored the importance of individual features and attention weights in predicting cardiovascular events. Our results indicate that the recurrent neural network approach benefits from the hospital longitudinal information and demonstrates how machine learning techniques can be applied to secondary care.
Vehicle Detection of Multi-source Remote Sensing Data Using Active Fine-tuning Network
Venue: arXiv cs.CV 2020
Year: 2020

Vehicle detection in remote sensing images has attracted increasing interest in recent years. However, its detection ability is limited due to lack of well-annotated samples, especially in densely crowded scenes. Furthermore, since a list of remotely sensed data sources is available, efficient exploitation of useful information from multi-source data for better vehicle detection is challenging. To solve the above issues, a multi-source active fine-tuning vehicle detection (Ms-AFt) framework is proposed, which integrates transfer learning, segmentation, and active classification into a unified framework for auto-labeling and detection. The proposed Ms-AFt employs a fine-tuning network to firstly generate a vehicle training set from an unlabeled dataset. To cope with the diversity of vehicle categories, a multi-source based segmentation branch is then designed to construct additional candidate object sets. The separation of high quality vehicles is realized by a designed attentive classifications network. Finally, all three branches are combined to achieve vehicle detection. Extensive experimental results conducted on two open ISPRS benchmark datasets, namely the Vaihingen village and Potsdam city datasets, demonstrate the superiority and effectiveness of the proposed Ms-AFt for vehicle detection. In addition, the generalization ability of Ms-AFt in dense remote sensing scenes is further verified on stereo aerial imagery of a large camping site.
Detecting Deepfake Videos: An Analysis of Three Techniques
Venue: arXiv cs.CV 2020
Year: 2020

Recent advances in deepfake generating algorithms that produce manipulated media have had dangerous implications in privacy, security and mass communication. Efforts to combat this issue have risen in the form of competitions and funding for research to detect deepfakes. This paper presents three techniques and algorithms: convolutional LSTM, eye blink detection and grayscale histograms-pursued while participating in the Deepfake Detection Challenge. We assessed the current knowledge about deepfake videos, a more severe version of manipulated media, and previous methods used, and found relevance in the grayscale histogram technique over others. We discussed the implications of each method developed and provided further steps to improve the given findings.
Smooth Deformation Field-based Mismatch Removal in Real-time
Venue: arXiv cs.CV 2020
Year: 2020

This paper studies the mismatch removal problem, which may serve as the subsequent step of feature matching. Non-rigid deformation makes it difficult to remove mismatches because no parametric transformation can be found. To solve this problem, we first propose an algorithm based on the re-weighting and 1-point RANSAC strategy (R1P-RNSC), which is a parametric method under a reasonable assumption that the non-rigid deformation can be approximately represented by multiple locally rigid transformations. R1P-RNSC is fast but suffers from a drawback that the local smoothing information cannot be taken into account. Then, we propose a non-parametric algorithm based on the expectation maximization algorithm and dual quaternion (EMDQ) representation to generate the smooth deformation field. The two algorithms compensate for the drawbacks of each other. Specifically, EMDQ needs good initial values provided by R1P-RNSC, and R1P-RNSC needs EMDQ for refinement. Experimental results with real-world data demonstrate that the combination of the two algorithms has the best accuracy compared to other state-of-the-art methods, which can handle up to 85% of outliers in real-time. The ability to generate dense deformation field from sparse matches with outliers in real-time makes the proposed algorithms have many potential applications, such as non-rigid registration and SLAM.
CoNES: Convex Natural Evolutionary Strategies
Venue: arXiv cs.LG 2020
Year: 2020

We present a novel algorithm -- convex natural evolutionary strategies (CoNES) -- for optimizing high-dimensional blackbox functions by leveraging tools from convex optimization and information geometry. CoNES is formulated as an efficiently-solvable convex program that adapts the evolutionary strategies (ES) gradient estimate to promote rapid convergence. The resulting algorithm is invariant to the parameterization of the belief distribution. Our numerical results demonstrate that CoNES vastly outperforms conventional blackbox optimization methods on a suite of functions used for benchmarking blackbox optimizers. Furthermore, CoNES demonstrates the ability to converge faster than conventional blackbox methods on a selection of OpenAI's MuJoCo reinforcement learning tasks for locomotion.
Investigation of the Effect of Incidental Fear Privacy Behavioral Intention (Technical Report)
Venue: arXiv cs.HC 2020
Year: 2020

Background. Incidental emotions users feel during their online activities may alter their privacy behavioral intentions. Aim. We investigate the effect of incidental affect (fear and happiness) on privacy behavioral intention. Method. We recruited $330$ participants for a within-subjects experiment in three random-controlled user studies. The participants were exposed to three conditions \textsf{neutral}, \textsf{fear}, \textsf{happiness} with standardised stimuli videos for incidental affect induction. Fear and happiness were assigned in random order. The participants' privacy behavioural intentions (PBI) were measured followed by a Positive and Negative Affect Schedule (PANAS-X) manipulation check on self-reported affect. The PBI and PANAS-X were compared across treatment conditions. Results. We observed a statistically significant difference in PBI and Protection Intention in neutral-fear and neutral-happy comparisons. However across fear and happy conditions, we did not observe any statistically significant change in PBI scores. Conclusions. We offer the first systematic analysis of the impact of incidental affects on Privacy Behavioral Intention (PBI) and its sub-constructs. We are the first to offer a fine-grained analysis of neutral-affect comparisons and interactions offering insights in hitherto unexplained phenomena reported in the field.
Privacy Engineering Meets Software Engineering. On the Challenges of Engineering Privacy ByDesign
Venue: arXiv cs.SE 2020
Year: 2020

Current day software development relies heavily on the use of service architectures and on agile iterative development methods to design, implement, and deploy systems. These practices result in systems made up of multiple services that introduce new data flows and evolving designs that escape the control of a single designer. Academic privacy engineering literature typically abstracts away such conditions of software production in order to achieve generalizable results. Yet, through a systematic study of the literature, we show that proposed solutions inevitably make assumptions about software architectures, development methods and scope of designer control that are misaligned with current practices. These misalignments are likely to pose an obstacle to operationalizing privacy engineering solutions in the wild. Specifically, we identify important limitations in the approaches that researchers take to design and evaluate privacy enhancing technologies which ripple to proposals for privacy engineering methodologies. Based on our analysis, we delineate research and actions needed to re-align research with practice, changes that serve a precondition for the operationalization of academic privacy results in common software engineering practices.
Diversity-By-Design for Dependable and Secure Cyber-Physical Systems: A Survey
Venue: arXiv cs.CR 2020
Year: 2020

Diversity-based security approaches have been studied for several decades since the 1970's. The concept of diversity-by-design emerged in the 1980's and, since then, diversity-based system design research has been explored to build more secure and dependable systems. In this work, we are particularly interested in providing an in-depth, comprehensive survey of existing diversity-based approaches, insights, and future work directions for those who want to conduct research on developing secure and dependable cyber-physical systems (CPSs) using diversity as a system design feature. To be specific, this survey paper provides: (i) The common concept of diversity based on a multidisciplinary study of diversity from nine different fields along with the historical evolution of diversity-by-design for security; (ii) The design principles of diversity-based approaches; (iii) The key benefits and caveats of using diversity-by-design; (iv) The key concerns of CPS environments in introducing diversity-by-design; (v) A variety of existing diversity-based approaches based on five different classifications; (vi) The types of attacks mitigated by existing diversity-based approaches; (vii) The overall trends of evaluation methodologies used in diversity-based approaches, in terms of metrics, datasets, and testbeds; and (viii) The insights, lessons, and gaps identified from this extensive survey.
Principles for data analysis workflows
Venue: arXiv cs.CY 2020
Year: 2020

Traditional data science education often omits training on research workflows: the process that moves a scientific investigation from raw data to coherent research question to insightful contribution. In this paper, we elaborate basic principles of a reproducible data analysis workflow by defining three phases: the Exploratory, Refinement, and Polishing Phases. Each workflow phase is roughly centered around the audience to whom research decisions, methodologies, and results are being immediately communicated. Importantly, each phase can also give rise to a number of research products beyond traditional academic publications. Where relevant, we draw analogies between principles for data-intensive research workflows and established practice in software development. The guidance provided here is not intended to be a strict rulebook; rather, the suggestions for practices and tools to advance reproducible, sound data-intensive analysis may furnish support for both students and current professionals.
Market Pricing for Matroid Rank Valuations
Venue: arXiv cs.GT 2020
Year: 2020

In this paper, we study the problem of maximizing social welfare in combinatorial markets through pricing schemes. We consider the existence of prices that are capable to achieve optimal social welfare without a central tie-breaking coordinator. In the case of two buyers with rank valuations, we give polynomial-time algorithms that always find such prices when one of the matroids is a simple partition matroid or both matroids are strongly base orderable. This result partially answers a question raised by Düetting and Végh in 2017. We further formalize a weighted variant of the conjecture of Düetting and Végh, and show that the weighted variant can be reduced to the unweighted one based on the weight-splitting theorem for weighted matroid intersection by Frank. We also show that a similar reduction technique works for M${}^\natural$-concave functions, or equivalently, gross substitutes functions.
Tackling scalability issues in mining path patterns from knowledge graphs: a preliminary study
Venue: arXiv cs.DB 2020
Year: 2020

Features mined from knowledge graphs are widely used within multiple knowledge discovery tasks such as classification or fact-checking. Here, we consider a given set of vertices, called seed vertices, and focus on mining their associated neighboring vertices, paths, and, more generally, path patterns that involve classes of ontologies linked with knowledge graphs. Due to the combinatorial nature and the increasing size of real-world knowledge graphs, the task of mining these patterns immediately entails scalability issues. In this paper, we address these issues by proposing a pattern mining approach that relies on a set of constraints (e.g., support or degree thresholds) and the monotonicity property. As our motivation comes from the mining of real-world knowledge graphs, we illustrate our approach with PGxLOD, a biomedical knowledge graph.
Prioritized Multi-Criteria Federated Learning
Venue: arXiv cs.LG 2020
Year: 2020

In Machine Learning scenarios, privacy is a crucial concern when models have to be trained with private data coming from users of a service, such as a recommender system, a location-based mobile service, a mobile phone text messaging service providing next word prediction, or a face image classification system. The main issue is that, often, data are collected, transferred, and processed by third parties. These transactions violate new regulations, such as GDPR. Furthermore, users usually are not willing to share private data such as their visited locations, the text messages they wrote, or the photo they took with a third party. On the other hand, users appreciate services that work based on their behaviors and preferences. In order to address these issues, Federated Learning (FL) has been recently proposed as a means to build ML models based on private datasets distributed over a large number of clients, while preventing data leakage. A federation of users is asked to train a same global model on their private data, while a central coordinating server receives locally computed updates by clients and aggregate them to obtain a better global model, without the need to use clients' actual data. In this work, we extend the FL approach by pushing forward the state-of-the-art approaches in the aggregation step of FL, which we deem crucial for building a high-quality global model. Specifically, we propose an approach that takes into account a suite of client-specific criteria that constitute the basis for assigning a score to each client based on a priority of criteria defined by the service provider. Extensive experiments on two publicly available datasets indicate the merits of the proposed approach compared to standard FL baseline.
A fast approximate skeleton with guarantees for any cloud of points in a Euclidean space
Venue: arXiv cs.CG 2020
Year: 2020

The tree reconstruction problem is to find an embedded straight-line tree that approximates a given cloud of unorganized points in $\mathbb{R}^m$ up to a certain error. A practical solution to this problem will accelerate a discovery of new colloidal products with desired physical properties such as viscosity. We define the Approximate Skeleton of any finite point cloud $C$ in a Euclidean space with theoretical guarantees. The Approximate Skeleton ASk$(C)$ always belongs to a given offset of $C$, i.e. the maximum distance from $C$ to ASk$(C)$ can be a given maximum error. The number of vertices in the Approximate Skeleton is close to the minimum number in an optimal tree by factor 2. The new Approximate Skeleton of any unorganized point cloud $C$ is computed in a near linear time in the number of points in $C$. Finally, the Approximate Skeleton outperforms past skeletonization algorithms on the size and accuracy of reconstruction for a large dataset of real micelles and random clouds.
Multi-dimensional Long-Run Average Problems for Vector Addition Systems with States
Venue: arXiv cs.FL 2020
Year: 2020

A vector addition system with states (VASS) consists of a finite set of states and counters. A transition changes the current state to the next state, and every counter is either incremented, or decremented, or left unchanged. A state and value for each counter is a configuration; and a computation is an infinite sequence of configurations with transitions between successive configurations. A probabilistic VASS consists of a VASS along with a probability distribution over the transitions for each state. Qualitative properties such as state and configuration reachability have been widely studied for VASS. In this work we consider multi-dimensional long-run average objectives for VASS and probabilistic VASS. For a counter, the cost of a configuration is the value of the counter; and the long-run average value of a computation for the counter is the long-run average of the costs of the configurations in the computation. The multi-dimensional long-run average problem given a VASS and a threshold value for each counter, asks whether there is a computation such that for each counter the long-run average value for the counter does not exceed the respective threshold. For probabilistic VASS, instead of the existence of a computation, we consider whether the expected long-run average value for each counter does not exceed the respective threshold. Our main results are as follows: we show that the multi-dimensional long-run average problem (a) is NP-complete for integer-valued VASS; (b) is undecidable for natural-valued VASS (i.e., nonnegative counters); and (c) can be solved in polynomial time for probabilistic integer-valued VASS, and probabilistic natural-valued VASS when all computations are non-terminating.
Edge-Preserving Guided Semantic Segmentation for VIPriors Challenge
Venue: arXiv cs.CV 2020
Year: 2020

Semantic segmentation is one of the most attractive research fields in computer vision. In the VIPriors challenge, only very limited numbers of training samples are allowed, leading to that the current state-of-the-art and deep learning-based semantic segmentation techniques are hard to train well. To overcome this shortcoming, therefore, we propose edge-preserving guidance to obtain the extra prior information, to avoid the overfitting under small-scale training dataset. First, a two-channeled convolutional layer is concatenated to the last layer of the conventional semantic segmentation network. Then, an edge map is calculated from the ground truth by Sobel operation and followed by concatenating a hard-thresholding operation to indicate whether the pixel is the edge or not. Then, the two-dimensional cross-entropy loss is adopted to calculate the loss between the predicted edge map and its ground truth, termed as an edge-preserving loss. In this way, the continuity of boundaries between different instances can be forced by the proposed edge-preserving loss. Experiments demonstrate that the proposed method can achieve excellent performance under small-scale training set, compared to state-of-the-art semantic segmentation techniques.
Vision-based Estimation of MDS-UPDRS Gait Scores for Assessing Parkinson's Disease Motor Severity
Venue: arXiv cs.CV 2020
Year: 2020

Parkinson's disease (PD) is a progressive neurological disorder primarily affecting motor function resulting in tremor at rest, rigidity, bradykinesia, and postural instability. The physical severity of PD impairments can be quantified through the Movement Disorder Society Unified Parkinson's Disease Rating Scale (MDS-UPDRS), a widely used clinical rating scale. Accurate and quantitative assessment of disease progression is critical to developing a treatment that slows or stops further advancement of the disease. Prior work has mainly focused on dopamine transport neuroimaging for diagnosis or costly and intrusive wearables evaluating motor impairments. For the first time, we propose a computer vision-based model that observes non-intrusive video recordings of individuals, extracts their 3D body skeletons, tracks them through time, and classifies the movements according to the MDS-UPDRS gait scores. Experimental results show that our proposed method performs significantly better than chance and competing methods with an F1-score of 0.83 and a balanced accuracy of 81%. This is the first benchmark for classifying PD patients based on MDS-UPDRS gait severity and could be an objective biomarker for disease severity. Our work demonstrates how computer-assisted technologies can be used to non-intrusively monitor patients and their motor impairments. The code is available at https://github.com/mlu355/PD-Motor-Severity-Estimation.
SummPip: Unsupervised Multi-Document Summarization with Sentence Graph Compression
Venue: arXiv cs.CL 2020
Year: 2020

Obtaining training data for multi-document summarization (MDS) is time consuming and resource-intensive, so recent neural models can only be trained for limited domains. In this paper, we propose SummPip: an unsupervised method for multi-document summarization, in which we convert the original documents to a sentence graph, taking both linguistic and deep representation into account, then apply spectral clustering to obtain multiple clusters of sentences, and finally compress each cluster to generate the final summary. Experiments on Multi-News and DUC-2004 datasets show that our method is competitive to previous unsupervised methods and is even comparable to the neural supervised approaches. In addition, human evaluation shows our system produces consistent and complete summaries compared to human written ones.
A large-scale comparative analysis of Coding Standard conformance in Open-Source Data Science projects
Venue: arXiv cs.SE 2020
Year: 2020

Background: Meeting the growing industry demand for Data Science requires cross-disciplinary teams that can translate machine learning research into production-ready code. Software engineering teams value adherence to coding standards as an indication of code readability, maintainability, and developer expertise. However, there are no large-scale empirical studies of coding standards focused specifically on Data Science projects. Aims: This study investigates the extent to which Data Science projects follow code standards. In particular, which standards are followed, which are ignored, and how does this differ to traditional software projects? Method: We compare a corpus of 1048 Open-Source Data Science projects to a reference group of 1099 non-Data Science projects with a similar level of quality and maturity. Results: Data Science projects suffer from a significantly higher rate of functions that use an excessive numbers of parameters and local variables. Data Science projects also follow different variable naming conventions to non-Data Science projects. Conclusions: The differences indicate that Data Science codebases are distinct from traditional software codebases and do not follow traditional software engineering conventions. Our conjecture is that this may be because traditional software engineering conventions are inappropriate in the context of Data Science projects.
A dichotomy theorem for nonuniform CSPs simplified
Venue: arXiv cs.CC 2020
Year: 2020

In a non-uniform Constraint Satisfaction problem CSP(G), where G is a set of relations on a finite set A, the goal is to find an assignment of values to variables subject to constraints imposed on specified sets of variables using the relations from G. The Dichotomy Conjecture for the non-uniform CSP states that for every constraint language G the problem CSP(G) is either solvable in polynomial time or is NP-complete. It was proposed by Feder and Vardi in their seminal 1993 paper. In this paper we confirm the Dichotomy Conjecture.