OpenRaiser/Intern-Atlas huggingface dataset:
Author-Based Analysis of Conference versus Journal Publication in Computer Science
Venue: arXiv cs.DL 2018
Year: 2018

Conference publications in computer science (CS) have attracted scholarly attention due to their unique status as a main research outlet unlike other science fields where journals are dominantly used for communicating research findings. One frequent research question has been how different conference and journal publications are, considering a paper as a unit of analysis. This study takes an author-based approach to analyze publishing patterns of 517,763 scholars who have ever published both in CS conferences and journals for the last 57 years, as recorded in DBLP. The analysis shows that the majority of CS scholars tend to make their scholarly debut, publish more papers, and collaborate with more coauthors in conferences than in journals. Importantly, conference papers seem to serve as a distinct channel of scholarly communication, not a mere preceding step to journal publications: coauthors and title words of authors across conferences and journals tend not to overlap much. This study corroborates findings of previous studies on this topic from a distinctive perspective and suggests that conference authorship in CS calls for more special attention from scholars and administrators outside CS who have focused on journal publications to mine authorship data and evaluate scholarly performance.
A new Integer Linear Program for the Steiner Tree Problem with Revenues, Budget and Hop Constraints
Venue: arXiv cs.DM 2018
Year: 2018

The Steiner tree problem with revenues, budgets and hop constraints (STPRBH) is a variant of the classical Steiner tree problem. This problem asks for a subtree in a given graph with maximum revenues corresponding to its nodes, where its total edge costs respect the given budget, and the number of edges between each node and its root does not exceed the hop limit. We introduce a new binary linear program with polynomial size based on partial-ordering, which (up to our knowledge) for the first time solves all STPRBH instances from the DIMACS benchmark set to optimality. The set contains graphs with up to 500 nodes and 12500 edges.
Gradient Similarity: An Explainable Approach to Detect Adversarial Attacks against Deep Learning
Venue: arXiv cs.CV 2018
Year: 2018

Deep neural networks are susceptible to small-but-specific adversarial perturbations capable of deceiving the network. This vulnerability can lead to potentially harmful consequences in security-critical applications. To address this vulnerability, we propose a novel metric called \emph{Gradient Similarity} that allows us to capture the influence of training data on test inputs. We show that \emph{Gradient Similarity} behaves differently for normal and adversarial inputs, and enables us to detect a variety of adversarial attacks with a near perfect ROC-AUC of 95-100\%. Even white-box adversaries equipped with perfect knowledge of the system cannot bypass our detector easily. On the MNIST dataset, white-box attacks are either detected with a high ROC-AUC of 87-96\%, or require very high distortion to bypass our detector.
Intention to Use SMS Vaccination Reminder and Management System among Health Centers in Malaysia: The Mediating Effect of Attitude
Venue: arXiv cs.CY 2018
Year: 2018

The purpose of this study is to find out influential factors of intention to use the proposed system among health centers by considering the technology acceptance model as the underlying theory. The proposed model of this study is tested using data collected from self-directed questionnaires filled up by 70 nurses in government hospitals and government clinics in Malaysia. A research method, which is based on the multi-analytical approach of Multiple Regression Analysis and Artificial Neural Networks, helps to refine the results of this study. The compatibility of the proposed system only has a significant and positive effect on attitude to use the system among other factors. Moreover, health centers' intention to use the system is further influenced by their perceived usefulness than their attitude to use. The mediating effect of Attitude is also proved. However, there is not any statistically significant difference in Intention scores accounting for the participants' demographic characteristics. The implication of this study is that by developing the system, which fits to the current procedures of health centers, we give them positive feelings. IT educational programs also should be provided for nurses to identify the benefits of the proposed system. It is also important to consider the indirect effects from independent variables on intention to use the system. However, the system does not require to consider the demographic characteristics of its end users.
Towards automatic initialization of registration algorithms using simulated endoscopy images
Venue: arXiv cs.CV 2018
Year: 2018

Registering images from different modalities is an active area of research in computer aided medical interventions. Several registration algorithms have been developed, many of which achieve high accuracy. However, these results are dependent on many factors, including the quality of the extracted features or segmentations being registered as well as the initial alignment. Although several methods have been developed towards improving segmentation algorithms and automating the segmentation process, few automatic initialization algorithms have been explored. In many cases, the initial alignment from which a registration is initiated is performed manually, which interferes with the clinical workflow. Our aim is to use scene classification in endoscopic procedures to achieve coarse alignment of the endoscope and a preoperative image of the anatomy. In this paper, we show using simulated scenes that a neural network can predict the region of anatomy (with respect to a preoperative image) that the endoscope is located in by observing a single endoscopic video frame. With limited training and without any hyperparameter tuning, our method achieves an accuracy of 76.53 (+/-1.19)%. There are several avenues for improvement, making this a promising direction of research. Code is available at https://github.com/AyushiSinha/AutoInitialization.
State-aware Anti-drift Robust Correlation Tracking
Venue: arXiv cs.CV 2018
Year: 2018

Correlation filter (CF) based trackers have aroused increasing attentions in visual tracking field due to the superior performance on several datasets while maintaining high running speed. For each frame, an ideal filter is trained in order to discriminate the target from its surrounding background. Considering that the target always undergoes external and internal interference during tracking procedure, the trained filter should take consideration of not only the external distractions but also the target appearance variation synchronously. To this end, we present a State-aware Anti-drift Tracker (SAT) in this paper, which jointly model the discrimination and reliability information in filter learning. Specifically, global context patches are incorporated into filter training stage to better distinguish the target from backgrounds. Meanwhile, a color-based reliable mask is learned to encourage the filter to focus on more reliable regions suitable for tracking. We show that the proposed optimization problem could be efficiently solved using Alternative Direction Method of Multipliers and fully carried out in Fourier domain. Extensive experiments are conducted on OTB-100 datasets to compare the SAT tracker (both hand-crafted feature and CNN feature) with other relevant state-of-the-art methods. Both quantitative and qualitative evaluations further demonstrate the effectiveness and robustness of the proposed work.
Successive Convex Approximation Algorithms for Sparse Signal Estimation with Nonconvex Regularizations
Venue: arXiv cs.LG 2018
Year: 2018

In this paper, we propose a successive convex approximation framework for sparse optimization where the nonsmooth regularization function in the objective function is nonconvex and it can be written as the difference of two convex functions. The proposed framework is based on a nontrivial combination of the majorization-minimization framework and the successive convex approximation framework proposed in literature for a convex regularization function. The proposed framework has several attractive features, namely, i) flexibility, as different choices of the approximate function lead to different type of algorithms; ii) fast convergence, as the problem structure can be better exploited by a proper choice of the approximate function and the stepsize is calculated by the line search; iii) low complexity, as the approximate function is convex and the line search scheme is carried out over a differentiable function; iv) guaranteed convergence to a stationary point. We demonstrate these features by two example applications in subspace learning, namely, the network anomaly detection problem and the sparse subspace clustering problem. Customizing the proposed framework by adopting the best-response type approximation, we obtain soft-thresholding with exact line search algorithms for which all elements of the unknown parameter are updated in parallel according to closed-form expressions. The attractive features of the proposed algorithms are illustrated numerically.
Beyond One-hot Encoding: lower dimensional target embedding
Venue: arXiv cs.CV 2018
Year: 2018

Target encoding plays a central role when learning Convolutional Neural Networks. In this realm, One-hot encoding is the most prevalent strategy due to its simplicity. However, this so widespread encoding schema assumes a flat label space, thus ignoring rich relationships existing among labels that can be exploited during training. In large-scale datasets, data does not span the full label space, but instead lies in a low-dimensional output manifold. Following this observation, we embed the targets into a low-dimensional space, drastically improving convergence speed while preserving accuracy. Our contribution is two fold: (i) We show that random projections of the label space are a valid tool to find such lower dimensional embeddings, boosting dramatically convergence rates at zero computational cost; and (ii) we propose a normalized eigenrepresentation of the class manifold that encodes the targets with minimal information loss, improving the accuracy of random projections encoding while enjoying the same convergence rates. Experiments on CIFAR-100, CUB200-2011, Imagenet, and MIT Places demonstrate that the proposed approach drastically improves convergence speed while reaching very competitive accuracy rates.
DeepSDCS: Dissecting cancer proliferation heterogeneity in Ki67 digital whole slide images
Venue: arXiv cs.CV 2018
Year: 2018

Ki67 is an important biomarker for breast cancer. Classification of positive and negative Ki67 cells in histology slides is a common approach to determine cancer proliferation status. However, there is a lack of generalizable and accurate methods to automate Ki67 scoring in large-scale patient cohorts. In this work, we have employed a novel deep learning technique based on hypercolumn descriptors for cell classification in Ki67 images. Specifically, we developed the Simultaneous Detection and Cell Segmentation (DeepSDCS) network to perform cell segmentation and detection. VGG16 network was used for the training and fine tuning to training data. We extracted the hypercolumn descriptors of each cell to form the vector of activation from specific layers to capture features at different granularity. Features from these layers that correspond to the same pixel were propagated using a stochastic gradient descent optimizer to yield the detection of the nuclei and the final cell segmentations. Subsequently, seeds generated from cell segmentation were propagated to a spatially constrained convolutional neural network for the classification of the cells into stromal, lymphocyte, Ki67-positive cancer cell, and Ki67-negative cancer cell. We validated its accuracy in the context of a large-scale clinical trial of oestrogen-receptor-positive breast cancer. We achieved 99.06% and 89.59% accuracy on two separate test sets of Ki67 stained breast cancer dataset comprising biopsy and whole-slide images.
Feature Selection for Unsupervised Domain Adaptation using Optimal Transport
Venue: arXiv cs.LG 2018
Year: 2018

In this paper, we propose a new feature selection method for unsupervised domain adaptation based on the emerging optimal transportation theory. We build upon a recent theoretical analysis of optimal transport in domain adaptation and show that it can directly suggest a feature selection procedure leveraging the shift between the domains. Based on this, we propose a novel algorithm that aims to sort features by their similarity across the source and target domains, where the order is obtained by analyzing the coupling matrix representing the solution of the proposed optimal transportation problem. We evaluate our method on a well-known benchmark data set and illustrate its capability of selecting correlated features leading to better classification performances. Furthermore, we show that the proposed algorithm can be used as a pre-processing step for existing domain adaptation techniques ensuring an important speed-up in terms of the computational time while maintaining comparable results. Finally, we validate our algorithm on clinical imaging databases for computer-aided diagnosis task with promising results.
Securing the Storage Data Path with SGX Enclaves
Venue: arXiv cs.CR 2018
Year: 2018

We explore the use of SGX enclaves as a means to improve the security of handling keys and data in storage systems. We study two main configurations for SGX computations, as they apply to performing data-at-rest encryption in a storage system. The first configuration aims to protect the encryption keys used in the encryption process. The second configuration aims to protect both the encryption keys and the data, thus providing end-to-end security of the entire data path. Our main contribution is an evaluation of the viability of SGX for data-at-rest encryption from a performance perspective and an understanding of the details that go into using enclaves in a performance sensitive environment. Our tests paint a complex picture: On the one hand SGX can indeed achieve high encryption and decryption throughput, comparable to running without SGX. On the other hand, there are many subtleties to achieving such performance and careful design choices and testing are required.
Introduction to OXPath
Venue: arXiv cs.PL 2018
Year: 2018

Contemporary web pages with increasingly sophisticated interfaces rival traditional desktop applications for interface complexity and are often called web applications or RIA (Rich Internet Applications). They often require the execution of JavaScript in a web browser and can call AJAX requests to dynamically generate the content, reacting to user interaction. From the automatic data acquisition point of view, thus, it is essential to be able to correctly render web pages and mimic user actions to obtain relevant data from the web page content. Briefly, to obtain data through existing Web interfaces and transform it into structured form, contemporary wrappers should be able to: 1) interact with sophisticated interfaces of web applications; 2) precisely acquire relevant data; 3) scale with the number of crawled web pages or states of web application; 4) have an embeddable programming API for integration with existing web technologies. OXPath is a state-of-the-art technology, which is compliant with these requirements and demonstrated its efficiency in comprehensive experiments. OXPath integrates Firefox for correct rendering of web pages and extends XPath 1.0 for the DOM node selection, interaction, and extraction. It provides means for converting extracted data into different formats, such as XML, JSON, CSV, and saving data into relational databases. This tutorial explains main features of the OXPath language and the setup of a suitable working environment. The guidelines for using OXPath are provided in the form of prototypical examples.
From clusters to queries: exploiting uncertainty in the modularity landscape of complex networks
Venue: arXiv cs.SI 2018
Year: 2018

Uncovering latent community structure in complex networks is a field that has received an enormous amount of attention. Unfortunately, whilst potentially very powerful, unsupervised methods for uncovering labels based on topology alone has been shown to suffer from several difficulties. For example, the search space for many module extraction approaches, such as the modularity maximisation algorithm, appears to be extremely glassy, with many high valued solutions that lack any real similarity to one another. However, in this paper we argue that this is not a flaw with the modularity maximisation algorithm but, rather, information that can be used to aid the context specific classification of functional relationships between vertices. Formally, we present an approach for generating a high value modularity consensus space for a network, based on the ensemble space of locally optimal modular partitions. We then use this approach to uncover latent relationships, given small query sets. The methods developed in this paper are applied to biological and social datasets with ground-truth label data, using a small number of examples used as seed sets to uncover relationships. When tested on both real and synthetic datasets our method is shown to achieve high levels of classification accuracy in a context specific manner, with results comparable to random walk with restart methods.
Effective Wireless Scheduling via Hypergraph Sketches
Venue: arXiv cs.NI 2018
Year: 2018

An overarching issue in resource management of wireless networks is assessing their capacity: How much communication can be achieved in a network, utilizing all the tools available: power control, scheduling, routing, channel assignment and rate adjustment? We propose the first framework for approximation algorithms in the physical model of wireless interference that addresses these questions in full. The approximations obtained are at most doubly logarithmic in the link length and rate diversity. Where previous bounds are known, this gives an exponential improvement (or better). A key contribution is showing that the complex interference relationship of the physical model can be simplified, at a small cost, into a novel type of amenable conflict graphs. We also show that the approximation obtained is provably the best possible for any conflict graph formulation.
Robust pose tracking with a joint model of appearance and shape
Venue: arXiv cs.CV 2018
Year: 2018

We present a novel approach for estimating the 2D pose of an articulated object with an application to automated video analysis of small laboratory animals. We have found that deformable part models developed for humans, exemplified by the flexible mixture of parts (FMP) model, typically fail on challenging animal poses. We argue that beyond encoding appearance and spatial relations, shape is needed to overcome the lack of distinctive landmarks on laboratory animal bodies. In our approach, a shape consistent FMP (scFMP) model computes promising pose candidates after a standard FMP model is used to rapidly discard false part detections. This "cascaded" approach combines the relative strengths of spatial-relations, appearance and shape representations and is shown to yield significant improvements over the original FMP model as well as a representative deep neural network baseline.
Deep Semi Supervised Generative Learning for Automated PD-L1 Tumor Cell Scoring on NSCLC Tissue Needle Biopsies
Venue: arXiv cs.CV 2018
Year: 2018

The level of PD-L1 expression in immunohistochemistry (IHC) assays is a key biomarker for the identification of Non-Small-Cell-Lung-Cancer (NSCLC) patients that may respond to anti PD-1/PD-L1 treatments. The quantification of PD-L1 expression currently includes the visual estimation of a Tumor Cell (TC) score by a pathologist and consists of evaluating the ratio of PD-L1 positive and PD-L1 negative tumor cells. Known challenges like differences in positivity estimation around clinically relevant cut-offs and sub-optimal quality of samples makes visual scoring tedious and subjective, yielding a scoring variability between pathologists. In this work, we propose a novel deep learning solution that enables the first automated and objective scoring of PD-L1 expression in late stage NSCLC needle biopsies. To account for the low amount of tissue available in biopsy images and to restrict the amount of manual annotations necessary for training, we explore the use of semi-supervised approaches against standard fully supervised methods. We consolidate the manual annotations used for training as well the visual TC scores used for quantitative evaluation with multiple pathologists. Concordance measures computed on a set of slides unseen during training provide evidence that our automatic scoring method matches visual scoring on the considered dataset while ensuring repeatability and objectivity.
Mutual-Excitation of Cryptocurrency Market Returns and Social Media Topics
Venue: arXiv cs.SI 2018
Year: 2018

Cryptocurrencies have recently experienced a new wave of price volatility and interest; activity within social media communities relating to cryptocurrencies has increased significantly. There is currently limited documented knowledge of factors which could indicate future price movements. This paper aims to decipher relationships between cryptocurrency price changes and topic discussion on social media to provide, among other things, an understanding of which topics are indicative of future price movements. To achieve this a well-known dynamic topic modelling approach is applied to social media communication to retrieve information about the temporal occurrence of various topics. A Hawkes model is then applied to find interactions between topics and cryptocurrency prices. The results show particular topics tend to precede certain types of price movements, for example the discussion of 'risk and investment vs trading' being indicative of price falls, the discussion of 'substantial price movements' being indicative of volatility, and the discussion of 'fundamental cryptocurrency value' by technical communities being indicative of price rises. The knowledge of topic relationships gained here could be built into a real-time system, providing trading or alerting signals.
Deep Learning Based Instance Segmentation in 3D Biomedical Images Using Weak Annotation
Venue: arXiv cs.CV 2018
Year: 2018

Instance segmentation in 3D images is a fundamental task in biomedical image analysis. While deep learning models often work well for 2D instance segmentation, 3D instance segmentation still faces critical challenges, such as insufficient training data due to various annotation difficulties in 3D biomedical images. Common 3D annotation methods (e.g., full voxel annotation) incur high workloads and costs for labeling enough instances for training deep learning 3D instance segmentation models. In this paper, we propose a new weak annotation approach for training a fast deep learning 3D instance segmentation model without using full voxel mask annotation. Our approach needs only 3D bounding boxes for all instances and full voxel annotation for a small fraction of the instances, and uses a novel two-stage 3D instance segmentation model utilizing these two kinds of annotation, respectively. We evaluate our approach on several biomedical image datasets, and the experimental results show that (1) with full annotated boxes and a small amount of masks, our approach can achieve similar performance as the best known methods using full annotation, and (2) with similar annotation time, our approach outperforms the best known methods that use full annotation.