OpenRaiser/Intern-Atlas huggingface dataset:
Efficient and Explicit Balanced Primer Codes
Venue: arXiv cs.IT 2019
Year: 2019

To equip DNA-based data storage with random-access capabilities, Yazdi et al. (2018) prepended DNA strands with specially chosen address sequences called primers and provided certain design criteria for these primers. We provide explicit constructions of error-correcting codes that are suitable as primer addresses and equip these constructions with efficient encoding algorithms. Specifically, our constructions take cyclic or linear codes as inputs and produce sets of primers with similar error-correcting capabilities. Using certain classes of BCH codes, we obtain infinite families of primer sets of length $n$, minimum distance $d$ with $(d + 1) \log_4 n + O(1)$ redundant symbols. Our techniques involve reversible cyclic codes (1964), an encoding method of Tavares et al. (1971) and Knuth's balancing technique (1986). In our investigation, we also construct efficient and explicit binary balanced error-correcting codes and codes for DNA computing.
Detecting and Diagnosing Energy Issues for Mobile Applications
Venue: arXiv cs.SE 2019
Year: 2019

Energy efficiency is an important criterion to judge the quality of mobile apps, but one third of our randomly sampled apps suffer from energy issues that can quickly drain battery power. To understand these issues, we conducted an empirical study on 27 well-maintained apps such as Chrome and Firefox, whose issue tracking systems are publicly accessible. Our study revealed that the main root causes of energy issues include unnecessary workload and excessively frequent operations. Surprisingly, these issues are beyond the application of present technology on energy issue detection. We also found that 20.6% of energy issues can only manifest themselves under specific contexts such as poor network performance, but such contexts are again neglected by present technology. Therefore, we proposed a novel testing framework for detecting energy issues in real-world apps. Our framework examines apps with well-designed input sequences and runtime contexts. To identify the root causes mentioned above, we employed a machine learning algorithm to cluster the workloads and further evaluate their necessity. For the issues concealed by the specific contexts, we carefully set up several execution contexts to pinpoint them. More importantly, we developed leading edge technology, e.g. pre-designing input sequences with potential energy overuse and tuning tests on-the-fly, to achieve high efficacy in detecting energy issues. A large-scale evaluation shows that 91.6% issues detected in our test were previously unknown to developers. On average, these issues double the energy costs of the apps. Furthermore, our test achieves a low number of false positives. Finally, we show how our test reports can help developers fix the issues.
Breaching the privacy of connected vehicles network
Venue: arXiv cs.CR 2019
Year: 2019

Connected Vehicles network is designed to provide a secure and private method for drivers to use the most efficiently the roads in certain area. When dealing with the scenario of car to access points connectivity (Wi-Fi, 3G, LTE), the vehicles are connected by central authority like cloud. Thus, they can be monitored and analyzed by the cloud which can provide certain services to the driver, i.e. usage based insurance (UBI), entertainment services, navigation etc. The main objective of this work is to show that by analyzing the information about a driver which is provided to the usage based insurance companies, it is possible to get additional private data, even if the basic data in first look, seems not so harmful. In this work, we present an analysis of a novel approach for reconstructing the path of driver from other driving attributes, such as cornering events, average speed and total driving time. We show that, in some cases, it is possible to reconstruct the path of driver, while not knowing the target point of the trip.
A Distance Map Regularized CNN for Cardiac Cine MR Image Segmentation
Venue: arXiv cs.CV 2019
Year: 2019

Cardiac image segmentation is a critical process for generating personalized models of the heart and for quantifying cardiac performance parameters. Several convolutional neural network (CNN) architectures have been proposed to segment the heart chambers from cardiac cine MR images. Here we propose a multi-task learning (MTL)-based regularization framework for cardiac MR image segmentation. The network is trained to perform the main task of semantic segmentation, along with a simultaneous, auxiliary task of pixel-wise distance map regression. The proposed distance map regularizer is a decoder network added to the bottleneck layer of an existing CNN architecture, facilitating the network to learn robust global features. The regularizer block is removed after training, so that the original number of network parameters does not change. We show that the proposed regularization method improves both binary and multi-class segmentation performance over the corresponding state-of-the-art CNN architectures on two publicly available cardiac cine MRI datasets, obtaining average dice coefficient of 0.84$\pm$0.03 and 0.91$\pm$0.04, respectively. Furthermore, we also demonstrate improved generalization performance of the distance map regularized network on cross-dataset segmentation, showing as much as 42% improvement in myocardium Dice coefficient from 0.56$\pm$0.28 to 0.80$\pm$0.14.
Speaker Adaptation for End-to-End CTC Models
Venue: arXiv cs.CL 2019
Year: 2019

We propose two approaches for speaker adaptation in end-to-end (E2E) automatic speech recognition systems. One is Kullback-Leibler divergence (KLD) regularization and the other is multi-task learning (MTL). Both approaches aim to address the data sparsity especially output target sparsity issue of speaker adaptation in E2E systems. The KLD regularization adapts a model by forcing the output distribution from the adapted model to be close to the unadapted one. The MTL utilizes a jointly trained auxiliary task to improve the performance of the main task. We investigated our approaches on E2E connectionist temporal classification (CTC) models with three different types of output units. Experiments on the Microsoft short message dictation task demonstrated that MTL outperforms KLD regularization. In particular, the MTL adaptation obtained 8.8\% and 4.0\% relative word error rate reductions (WERRs) for supervised and unsupervised adaptations for the word CTC model, and 9.6% and 3.8% relative WERRs for the mix-unit CTC model, respectively.
UTPO: User's Trust Profile Ontology - Modeling trust towards Online Health Information Sources
Venue: arXiv cs.CY 2019
Year: 2019

Despite the overwhelming quantity of health information that is available online today, finding reliable and trustworthy information is still challenging, even when advanced recommender systems are used. To tackle this challenge and improve our recommended sources, we need to first understand and capture the user behavior of what is considered to be trustworthy. This paper presents a taxonomy of relevant factors that influence user' trust towards online health information sources. We design a survey experiment to validate the taxonomical factors, and propose an ontology using the taxonomy of factors, such that each user's trust could be modeled as an instance of our ontology and this could later be used programmatically to recommend trustworthy information sources. Our work will inform the design of personalized recommendation systems and websites to improve online delivery of health information.
How Reliable is the Crowdsourced Knowledge of Security Implementation?
Venue: arXiv cs.SE 2019
Year: 2019

Stack Overflow (SO) is the most popular online Q&A site for developers to share their expertise in solving programming issues. Given multiple answers to certain questions, developers may take the accepted answer, the answer from a person with high reputation, or the one frequently suggested. However, researchers recently observed exploitable security vulnerabilities in popular SO answers. This observation inspires us to explore the following questions: How much can we trust the security implementation suggestions on SO? If suggested answers are vulnerable, can developers rely on the community's dynamics to infer the vulnerability and identify a secure counterpart? To answer these highly important questions, we conducted a study on SO posts by contrasting secure and insecure advices with the community-given content evaluation. We investigated whether SO incentive mechanism is effective in improving security properties of distributed code examples. Moreover, we also traced duplicated answers to assess whether the community behavior facilitates propagation of secure and insecure code suggestions. We compiled 953 different groups of similar security-related code examples and labeled their security, identifying 785 secure answer posts and 644 insecure ones. Compared with secure suggestions, insecure ones had higher view counts (36,508 vs. 18,713), received a higher score (14 vs. 5), and had significantly more duplicates (3.8 vs. 3.0) on average. 34% of the posts provided by highly reputable so-called trusted users were insecure. Our findings show that there are lots of insecure snippets on SO, while the community-given feedback does not allow differentiating secure from insecure choices. Moreover, the reputation mechanism fails in indicating trustworthy users with respect to security questions, ultimately leaving other users wandering around alone in a software security minefield.
The ISTI Rapid Response on Exploring Cloud Computing 2018
Venue: arXiv cs.DC 2019
Year: 2019

This report describes eighteen projects that explored how commercial cloud computing services can be utilized for scientific computation at national laboratories. These demonstrations ranged from deploying proprietary software in a cloud environment to leveraging established cloud-based analytics workflows for processing scientific datasets. By and large, the projects were successful and collectively they suggest that cloud computing can be a valuable computational resource for scientific computation at national laboratories.
Deep Reinforcement Learning for Imbalanced Classification
Venue: arXiv cs.LG 2019
Year: 2019

Data in real-world application often exhibit skewed class distribution which poses an intense challenge for machine learning. Conventional classification algorithms are not effective in the case of imbalanced data distribution, and may fail when the data distribution is highly imbalanced. To address this issue, we propose a general imbalanced classification model based on deep reinforcement learning. We formulate the classification problem as a sequential decision-making process and solve it by deep Q-learning network. The agent performs a classification action on one sample at each time step, and the environment evaluates the classification action and returns a reward to the agent. The reward from minority class sample is larger so the agent is more sensitive to the minority class. The agent finally finds an optimal classification policy in imbalanced data under the guidance of specific reward function and beneficial learning environment. Experiments show that our proposed model outperforms the other imbalanced classification algorithms, and it can identify more minority samples and has great classification performance.
Control of a 2-DoF robotic arm using a P300-based brain-computer interface
Venue: arXiv cs.HC 2019
Year: 2019

In this study, a novel control algorithm for a P-300 based brain-computer interface is fully developed to control a 2-DoF robotic arm. Eight subjects including 5 men and 3 women, perform a 2-dimensional target tracking task in a simulated environment. Their EEG signals from visual cortex are recorded and P-300 components are extracted and evaluated to perform a real-time BCI based controller. The volunteer's intention is recognized and will be decoded as an appropriate command to control the cursor. The final goal of the system is to control a simulated robotic arm in a 2-dimensional space for writing some English letters. The results show that the system allows the robot end-effector to move between arbitrary positions in a point-to-point session with the desired accuracy. This model is tested on and compared with Dataset II of the BCI Competition. The best result is obtained with a multi-class SVM solution as the classifier, with a recognition rate of 97 percent, without pre-channel selection.
Deep Convolutional Neural Networks for Imaging Data Based Survival Analysis of Rectal Cancer
Venue: arXiv cs.CV 2019
Year: 2019

Recent radiomic studies have witnessed promising performance of deep learning techniques in learning radiomic features and fusing multimodal imaging data. Most existing deep learning based radiomic studies build predictive models in a setting of pattern classification, not appropriate for survival analysis studies where some data samples have incomplete observations. To improve existing survival analysis techniques whose performance is hinged on imaging features, we propose a deep learning method to build survival regression models by optimizing imaging features with deep convolutional neural networks (CNNs) in a proportional hazards model. To make the CNNs applicable to tumors with varied sizes, a spatial pyramid pooling strategy is adopted. Our method has been validated based on a simulated imaging dataset and a FDG-PET/CT dataset of rectal cancer patients treated for locally advanced rectal cancer. Compared with survival prediction models built upon hand-crafted radiomic features using Cox proportional hazards model and random survival forests, our method achieved competitive prediction performance.
Bilinear Supervised Hashing Based on 2D Image Features
Venue: arXiv cs.CV 2019
Year: 2019

Hashing has been recognized as an efficient representation learning method to effectively handle big data due to its low computational complexity and memory cost. Most of the existing hashing methods focus on learning the low-dimensional vectorized binary features based on the high-dimensional raw vectorized features. However, studies on how to obtain preferable binary codes from the original 2D image features for retrieval is very limited. This paper proposes a bilinear supervised discrete hashing (BSDH) method based on 2D image features which utilizes bilinear projections to binarize the image matrix features such that the intrinsic characteristics in the 2D image space are preserved in the learned binary codes. Meanwhile, the bilinear projection approximation and vectorization binary codes regression are seamlessly integrated together to formulate the final robust learning framework. Furthermore, a discrete optimization strategy is developed to alternatively update each variable for obtaining the high-quality binary codes. In addition, two 2D image features, traditional SURF-based FVLAD feature and CNN-based AlexConv5 feature are designed for further improving the performance of the proposed BSDH method. Results of extensive experiments conducted on four benchmark datasets show that the proposed BSDH method almost outperforms all competing hashing methods with different input features by different evaluation protocols.
Center of Gravity-based Approach for Modeling Dynamics of Multisection Continuum Arms
Venue: arXiv cs.RO 2019
Year: 2019

Multisection continuum arms offer complementary characteristics to those of traditional rigid-bodied robots. Inspired by biological appendages, such as elephant trunks and octopus arms, these robots trade rigidity for compliance, accuracy for safety, and therefore exhibit strong potential for applications in human-occupied spaces. Prior work has demonstrated their superiority in operation in congested spaces and manipulation of irregularly-shaped objects. However, they are yet to be widely applied outside laboratory spaces. One key reason is that, due to compliance, they are difficult to control. Sophisticated and numerically efficient dynamic models are a necessity to implement dynamic control. In this paper, we propose a novel, numerically stable, center of gravity-based dynamic model for variable-length multisection continuum arms. The model can accommodate continuum robots having any number of sections with varying physical dimensions. The dynamic algorithm is of O(n2) complexity, runs at 9.5 kHz, simulates 6-8 times faster than real-time for a three-section continuum robot, and therefore is ideally suited for real-time control implementations. The model accuracy is validated numerically against an integral-dynamic model proposed by the authors and experimentally for a three-section, pneumatically actuated variable-length multisection continuum arm. This is the first sub real-time dynamic model based on a smooth continuous deformation model for variable-length multisection continuum arms.
Channel Locality Block: A Variant of Squeeze-and-Excitation
Venue: arXiv cs.LG 2019
Year: 2019

Attention mechanism is a hot spot in deep learning field. Using channel attention model is an effective method for improving the performance of the convolutional neural network. Squeeze-and-Excitation block takes advantage of the channel dependence, selectively emphasizing the important channels and compressing the relatively useless channel. In this paper, we proposed a variant of SE block based on channel locality. Instead of using full connection layers to explore the global channel dependence, we adopt convolutional layers to learn the correlation between the nearby channels. We term this new algorithm Channel Locality(C-Local) block. We evaluate SE block and C-Local block by applying them to different CNNs architectures on cifar-10 dataset. We observed that our C-Local block got higher accuracy than SE block did.
Walking the Dog Fast in Practice: Algorithm Engineering of the Fréchet Distance
Venue: arXiv cs.CG 2019
Year: 2019

The Fréchet distance provides a natural and intuitive measure for the popular task of computing the similarity of two (polygonal) curves. While a simple algorithm computes it in near-quadratic time, a strongly subquadratic algorithm cannot exist unless the Strong Exponential Time Hypothesis fails. Still, fast practical implementations of the Fréchet distance, in particular for realistic input curves, are highly desirable. This has even lead to a designated competition, the ACM SIGSPATIAL GIS Cup 2017: Here, the challenge was to implement a near-neighbor data structure under the Fréchet distance. The bottleneck of the top three implementations turned out to be precisely the decision procedure for the Fréchet distance. In this work, we present a fast, certifying implementation for deciding the Fréchet distance, in order to (1) complement its pessimistic worst-case hardness by an empirical analysis on realistic input data and to (2) improve the state of the art for the GIS Cup challenge. We experimentally evaluate our implementation on a large benchmark consisting of several data sets (including handwritten characters and GPS trajectories). Compared to the winning implementation of the GIS Cup, we obtain running time improvements of up to more than two orders of magnitude for the decision procedure and of up to a factor of 30 for queries to the near-neighbor data structure.
Optimal Network Control in Partially-Controllable Networks
Venue: arXiv cs.NI 2019
Year: 2019

The effectiveness of many optimal network control algorithms (e.g., BackPressure) relies on the premise that all of the nodes are fully controllable. However, these algorithms may yield poor performance in a partially-controllable network where a subset of nodes are uncontrollable and use some unknown policy. Such a partially-controllable model is of increasing importance in real-world networked systems such as overlay-underlay networks. In this paper, we design optimal network control algorithms that can stabilize a partially-controllable network. We first study the scenario where uncontrollable nodes use a queue-agnostic policy, and propose a low-complexity throughput-optimal algorithm, called Tracking-MaxWeight (TMW), which enhances the original MaxWeight algorithm with an explicit learning of the policy used by uncontrollable nodes. Next, we investigate the scenario where uncontrollable nodes use a queue-dependent policy and the problem is formulated as an MDP with unknown queueing dynamics. We propose a new reinforcement learning algorithm, called Truncated Upper Confidence Reinforcement Learning (TUCRL), and prove that TUCRL achieves tunable three-way tradeoffs between throughput, delay and convergence rate.
RayNet: Learning Volumetric 3D Reconstruction with Ray Potentials
Venue: arXiv cs.CV 2019
Year: 2019

In this paper, we consider the problem of reconstructing a dense 3D model using images captured from different views. Recent methods based on convolutional neural networks (CNN) allow learning the entire task from data. However, they do not incorporate the physics of image formation such as perspective geometry and occlusion. Instead, classical approaches based on Markov Random Fields (MRF) with ray-potentials explicitly model these physical processes, but they cannot cope with large surface appearance variations across different viewpoints. In this paper, we propose RayNet, which combines the strengths of both frameworks. RayNet integrates a CNN that learns view-invariant feature representations with an MRF that explicitly encodes the physics of perspective projection and occlusion. We train RayNet end-to-end using empirical risk minimization. We thoroughly evaluate our approach on challenging real-world datasets and demonstrate its benefits over a piece-wise trained baseline, hand-crafted models as well as other learning-based approaches.
Many Independent Objective (MIO) Algorithm for Test Suite Generation
Venue: arXiv cs.SE 2019
Year: 2019

Automatically generating test suites is intrinsically a multi-objective problem, as any of the testing targets (e.g, statements to execute or mutants to kill) is an objective on its own. Test suite generation has peculiarities that are quite different from other more regular optimisation problems. For example, given an existing test suite, one can add more tests to cover the remaining objectives. One would like the smallest number of small tests to cover as many objectives as possible, but that is a secondary goal compared to covering those targets in the first place. Furthermore, the amount of objectives in software testing can quickly become unmanageable, in the order of (tens/hundreds of) thousands, especially for system testing of industrial size systems. Traditional multi-objective optimisation algorithms can already start to struggle with just four or five objectives to optimize. To overcome these issues, different techniques have been proposed, like for example the Whole Test Suite (WTS) approach and the Many-Objective Sorting Algorithm (MOSA). However, those techniques might not scale well to very large numbers of objectives and limited search budgets (a typical case in system testing). In this paper, we propose a novel algorithm, called Many Independent Objective (MIO) algorithm. This algorithm is designed and tailored based on the specific properties of test suite generation. An empirical study, on a set of artificial and actual software, shows that the MIO algorithm can achieve higher coverage compared to WTS and MOSA, as it can better exploit the peculiarities of test suite generation.