OpenRaiser/Intern-Atlas huggingface dataset:
Cross-lingual Semantic Parsing
Venue: arXiv cs.CL 2018
Year: 2018

We introduce the task of cross-lingual semantic parsing: mapping content provided in a source language into a meaning representation based on a target language. We present: (1) a meaning representation designed to allow systems to target varying levels of structural complexity (shallow to deep analysis), (2) an evaluation metric to measure the similarity between system output and reference meaning representations, (3) an end-to-end model with a novel copy mechanism that supports intrasentential coreference, and (4) an evaluation dataset where experiments show our model outperforms strong baselines by at least 1.18 F1 score.
Learning Myelin Content in Multiple Sclerosis from Multimodal MRI through Adversarial Training
Venue: arXiv cs.CV 2018
Year: 2018

Multiple sclerosis (MS) is a demyelinating disease of the central nervous system (CNS). A reliable measure of the tissue myelin content is therefore essential for the understanding of the physiopathology of MS, tracking progression and assessing treatment efficacy. Positron emission tomography (PET) with $[^{11} \mbox{C}] \mbox{PIB}$ has been proposed as a promising biomarker for measuring myelin content changes in-vivo in MS. However, PET imaging is expensive and invasive due to the injection of a radioactive tracer. On the contrary, magnetic resonance imaging (MRI) is a non-invasive, widely available technique, but existing MRI sequences do not provide, to date, a reliable, specific, or direct marker of either demyelination or remyelination. In this work, we therefore propose Sketcher-Refiner Generative Adversarial Networks (GANs) with specifically designed adversarial loss functions to predict the PET-derived myelin content map from a combination of MRI modalities. The prediction problem is solved by a sketch-refinement process in which the sketcher generates the preliminary anatomical and physiological information and the refiner refines and generates images reflecting the tissue myelin content in the human brain. We evaluated the ability of our method to predict myelin content at both global and voxel-wise levels. The evaluation results show that the demyelination in lesion regions and myelin content in normal-appearing white matter (NAWM) can be well predicted by our method. The method has the potential to become a useful tool for clinical management of patients with MS.
Bridgeout: stochastic bridge regularization for deep neural networks
Venue: arXiv cs.NE 2018
Year: 2018

A major challenge in training deep neural networks is overfitting, i.e. inferior performance on unseen test examples compared to performance on training examples. To reduce overfitting, stochastic regularization methods have shown superior performance compared to deterministic weight penalties on a number of image recognition tasks. Stochastic methods such as Dropout and Shakeout, in expectation, are equivalent to imposing a ridge and elastic-net penalty on the model parameters, respectively. However, the choice of the norm of weight penalty is problem dependent and is not restricted to $\{L_1,L_2\}$. Therefore, in this paper we propose the Bridgeout stochastic regularization technique and prove that it is equivalent to an $L_q$ penalty on the weights, where the norm $q$ can be learned as a hyperparameter from data. Experimental results show that Bridgeout results in sparse model weights, improved gradients and superior classification performance compared to Dropout and Shakeout on synthetic and real datasets.
HeteroMed: Heterogeneous Information Network for Medical Diagnosis
Venue: arXiv cs.AI 2018
Year: 2018

With the recent availability of Electronic Health Records (EHR) and great opportunities they offer for advancing medical informatics, there has been growing interest in mining EHR for improving quality of care. Disease diagnosis due to its sensitive nature, huge costs of error, and complexity has become an increasingly important focus of research in past years. Existing studies model EHR by capturing co-occurrence of clinical events to learn their latent embeddings. However, relations among clinical events carry various semantics and contribute differently to disease diagnosis which gives precedence to a more advanced modeling of heterogeneous data types and relations in EHR data than existing solutions. To address these issues, we represent how high-dimensional EHR data and its rich relationships can be suitably translated into HeteroMed, a heterogeneous information network for robust medical diagnosis. Our modeling approach allows for straightforward handling of missing values and heterogeneity of data. HeteroMed exploits metapaths to capture higher level and semantically important relations contributing to disease diagnosis. Furthermore, it employs a joint embedding framework to tailor clinical event representations to the disease diagnosis goal. To the best of our knowledge, this is the first study to use Heterogeneous Information Network for modeling clinical data and disease diagnosis. Experimental results of our study show superior performance of HeteroMed compared to prior methods in prediction of exact diagnosis codes and general disease cohorts. Moreover, HeteroMed outperforms baseline models in capturing similarities of clinical events which are examined qualitatively through case studies.
Adversarial Training for Community Question Answer Selection Based on Multi-scale Matching
Venue: arXiv cs.CL 2018
Year: 2018

Community-based question answering (CQA) websites represent an important source of information. As a result, the problem of matching the most valuable answers to their corresponding questions has become an increasingly popular research topic. We frame this task as a binary (relevant/irrelevant) classification problem, and present an adversarial training framework to alleviate label imbalance issue. We employ a generative model to iteratively sample a subset of challenging negative samples to fool our classification model. Both models are alternatively optimized using REINFORCE algorithm. The proposed method is completely different from previous ones, where negative samples in training set are directly used or uniformly down-sampled. Further, we propose using Multi-scale Matching which explicitly inspects the correlation between words and ngrams of different levels of granularity. We evaluate the proposed method on SemEval 2016 and SemEval 2017 datasets and achieves state-of-the-art or similar performance.
Decoupled Networks
Venue: arXiv cs.CV 2018
Year: 2018

Inner product-based convolution has been a central component of convolutional neural networks (CNNs) and the key to learning visual representations. Inspired by the observation that CNN-learned features are naturally decoupled with the norm of features corresponding to the intra-class variation and the angle corresponding to the semantic difference, we propose a generic decoupled learning framework which models the intra-class variation and semantic difference independently. Specifically, we first reparametrize the inner product to a decoupled form and then generalize it to the decoupled convolution operator which serves as the building block of our decoupled networks. We present several effective instances of the decoupled convolution operator. Each decoupled operator is well motivated and has an intuitive geometric interpretation. Based on these decoupled operators, we further propose to directly learn the operator from data. Extensive experiments show that such decoupled reparameterization renders significant performance gain with easier convergence and stronger robustness.
Large Receptive Field Networks for High-Scale Image Super-Resolution
Venue: arXiv cs.CV 2018
Year: 2018

Convolutional Neural Networks have been the backbone of recent rapid progress in Single-Image Super-Resolution. However, existing networks are very deep with many network parameters, thus having a large memory footprint and being challenging to train. We propose Large Receptive Field Networks which strive to directly expand the receptive field of Super-Resolution networks without increasing depth or parameter count. In particular, we use two different methods to expand the network receptive field: 1-D separable kernels and atrous convolutions. We conduct considerable experiments to study the performance of various arrangement schemes of the 1-D separable kernels and atrous convolution in terms of accuracy (PSNR / SSIM), parameter count, and speed, while focusing on the more challenging high upscaling factors. Extensive benchmark evaluations demonstrate the effectiveness of our approach.
Exchange of Renewable Energy among Prosumers using Blockchain with Dynamic Pricing
Venue: arXiv cs.GT 2018
Year: 2018

We consider users which may have renewable energy harvesting devices, or distributed generators. Such users can behave as consumer or producer (hence, we denote them as prosumers) at different time instances. A prosumer may sell the energy to other prosumers in exchange of money. We consider a demand response model, where the price of conventional energy depends on the total demand of all the prosumers at a certain time. A prosumer depending on its own utility has to select the amount of energy it wants to buy either from the grid or from other prosumers, or the amount of excess energy it wants to sell to other prosumers. However, the strategy, and the payoff of a prosumer inherently depends on the strategy of other prosumers as a prosumer can only buy if the other prosumers are willing to sell. We formulate the problem as a coupled constrained game, and seek to obtain the generalized Nash equilibrium. We show that the game is a concave potential game and show that there exists a unique generalized Nash equilibrium. We consider that a platform will set the price for distributed interchange of energy among the prosumers in order to minimize the consumption of the conventional energy. We propose a distributed algorithm where the platform sets a price to each prosumer, and then each prosumer at a certain time only optimizes its own payoff. The prosumer then updates the price depending on the supply and demand for each prosumer. We show that the algorithm converges to an optimal generalized Nash equilibrium. The distributed algorithm also provides an optimal price for the exchange market.
syGlass: Interactive Exploration of Multidimensional Images Using Virtual Reality Head-mounted Displays
Venue: arXiv cs.GR 2018
Year: 2018

The quest for deeper understanding of biological systems has driven the acquisition of increasingly larger multidimensional image datasets. Inspecting and manipulating data of this complexity is very challenging in traditional visualization systems. We developed syGlass, a software package capable of visualizing large scale volumetric data with inexpensive virtual reality head-mounted display technology. This allows leveraging stereoscopic vision to significantly improve perception of complex 3D structures, and provides immersive interaction with data directly in 3D. We accomplished this by developing highly optimized data flow and volume rendering pipelines, tested on datasets up to 16TB in size, as well as tools available in a virtual reality GUI to support advanced data exploration, annotation, and cataloguing.
Constructing Locally Dense Point Clouds Using OpenSfM and ORB-SLAM2
Venue: arXiv cs.CV 2018
Year: 2018

This paper aims at finding a method to register two different point clouds constructed by ORB-SLAM2 and OpenSfM. To do this, we post some tags with unique textures in the scene and take videos and photos of that area. Then we take short videos of only the tags to extract their features. By matching the ORB feature of the tags with their corresponding features in the scene, it is then possible to localize the position of these tags both in point clouds constructed by ORB-SLAM2 and OpenSfM. Thus, the best transformation matrix between two point clouds can be calculated, and the two point clouds can be aligned.
Clinical Assistant Diagnosis for Electronic Medical Record Based on Convolutional Neural Network
Venue: arXiv cs.CL 2018
Year: 2018

Automatically extracting useful information from electronic medical records along with conducting disease diagnoses is a promising task for both clinical decision support(CDS) and neural language processing(NLP). Most of the existing systems are based on artificially constructed knowledge bases, and then auxiliary diagnosis is done by rule matching. In this study, we present a clinical intelligent decision approach based on Convolutional Neural Networks(CNN), which can automatically extract high-level semantic information of electronic medical records and then perform automatic diagnosis without artificial construction of rules or knowledge bases. We use collected 18,590 copies of the real-world clinical electronic medical records to train and test the proposed model. Experimental results show that the proposed model can achieve 98.67\% accuracy and 96.02\% recall, which strongly supports that using convolutional neural network to automatically learn high-level semantic features of electronic medical records and then conduct assist diagnosis is feasible and effective.
Representational Issues in the Debate on the Standard Model of the Mind
Venue: arXiv cs.AI 2018
Year: 2018

In this paper we discuss some of the issues concerning the Memory and Content aspects in the recent debate on the identification of a Standard Model of the Mind (Laird, Lebiere, and Rosenbloom in press). In particular, we focus on the representational models concerning the Declarative Memories of current Cognitive Architectures (CAs). In doing so we outline some of the main problems affecting the current CAs and suggest that the Conceptual Spaces, a representational framework developed by Gardenfors, is worth-considering to address such problems. Finally, we briefly analyze the alternative representational assumptions employed in the three CAs constituting the current baseline for the Standard Model (i.e. SOAR, ACT-R and Sigma). In doing so, we point out the respective differences and discuss their implications in the light of the analyzed problems.
A Coinductive Approach to Proving Reachability Properties in Logically Constrained Term Rewriting Systems
Venue: arXiv cs.LO 2018
Year: 2018

We introduce a sound and complete coinductive proof system for reachability properties in transition systems generated by logically constrained term rewriting rules over an order-sorted signature modulo builtins. A key feature of the calculus is a circularity proof rule, which allows to obtain finite representations of the infinite coinductive proofs.
ARCHANGEL: Trusted Archives of Digital Public Documents
Venue: arXiv cs.DL 2018
Year: 2018

We present ARCHANGEL; a de-centralised platform for ensuring the long-term integrity of digital documents stored within public archives. Document integrity is fundamental to public trust in archives. Yet currently that trust is built upon institutional reputation --- trust at face value in a centralised authority, like a national government archive or University. ARCHANGEL proposes a shift to a technological underscoring of that trust, using distributed ledger technology (DLT) to cryptographically guarantee the provenance, immutability and so the integrity of archived documents. We describe the ARCHANGEL architecture, and report on a prototype of that architecture build over the Ethereum infrastructure. We report early evaluation and feedback of ARCHANGEL from stakeholders in the research data archives space.
Phase-field modeling of brittle fracture with multi-level hp-FEM and the finite cell method
Venue: arXiv cs.CE 2018
Year: 2018

The difficulties in dealing with discontinuities related to a sharp crack are overcome in the phase-field approach for fracture by modeling the crack as a diffusive object being described by a continuous field having high gradients. The discrete crack limit case is approached for a small length-scale parameter that controls the width of the transition region between the fully broken and the undamaged phases. From a computational standpoint, this necessitates fine meshes, at least locally, in order to accurately resolve the phase-field profile. In the classical approach, phase-field models are computed on a fixed mesh that is a priori refined in the areas where the crack is expected to propagate. This on the other hand curbs the convenience of using phase-field models for unknown crack paths and its ability to handle complex crack propagation patterns. In this work, we overcome this issue by employing the multi-level hp-refinement technique that enables a dynamically changing mesh which in turn allows the refinement to remain local at singularities and high gradients without problems of hanging nodes. Yet, in case of complex geometries, mesh generation and in particular local refinement becomes non-trivial. We address this issue by integrating a two-dimensional phase-field framework for brittle fracture with the finite cell method (FCM). The FCM based on high-order finite elements is a non-geometry-conforming discretization technique wherein the physical domain is embedded into a larger fictitious domain of simple geometry that can be easily discretized. This facilitates mesh generation for complex geometries and supports local refinement. Numerical examples including a comparison to a validation experiment illustrate the applicability of the multi-level hp-refinement and the FCM in the context of phase-field simulations.
Nonlinear state-space modelling of the kinematics of an oscillating circular cylinder in a fluid flow
Venue: arXiv cs.SY 2018
Year: 2018

The flow-induced vibration of bluff bodies is an important problem of many marine, civil, or mechanical engineers. In the design phase of such structures, it is vital to obtain good predictions of the fluid forces acting on the structure. Current methods rely on computational fluid dynamic simulations (CFD), with a too high computational cost to be effectively used in the design phase or for control applications. Alternative methods use heuristic mathematical models of the fluid forces, but these lack the accuracy (they often assume the system to be linear) or flexibility to be useful over a wide operating range. In this work we show that it is possible to build an accurate, flexible and low-computational-cost mathematical model using nonlinear system identification techniques. This model is data driven: it is trained over a user-defined region of interest using data obtained from experiments or simulations, or both. Here we use a Van der Pol oscillator as well as CFD simulations of an oscillating circular cylinder to generate the training data. Then a discrete-time polynomial nonlinear state-space model is fit to the data. This model relates the oscillation of the cylinder to the force that the fluid exerts on the cylinder. The model is finally validated over a wide range of oscillation frequencies and amplitudes, both inside and outside the so-called lock-in region. We show that forces simulated by the model are in good agreement with the data obtained from CFD.
Abdominal multi-organ segmentation with organ-attention networks and statistical fusion
Venue: arXiv cs.CV 2018
Year: 2018

Accurate and robust segmentation of abdominal organs on CT is essential for many clinical applications such as computer-aided diagnosis and computer-aided surgery. But this task is challenging due to the weak boundaries of organs, the complexity of the background, and the variable sizes of different organs. To address these challenges, we introduce a novel framework for multi-organ segmentation by using organ-attention networks with reverse connections (OAN-RCs) which are applied to 2D views, of the 3D CT volume, and output estimates which are combined by statistical fusion exploiting structural similarity. OAN is a two-stage deep convolutional network, where deep network features from the first stage are combined with the original image, in a second stage, to reduce the complex background and enhance the discriminative information for the target organs. RCs are added to the first stage to give the lower layers semantic information thereby enabling them to adapt to the sizes of different organs. Our networks are trained on 2D views enabling us to use holistic information and allowing efficient computation. To compensate for the limited cross-sectional information of the original 3D volumetric CT, multi-sectional images are reconstructed from the three different 2D view directions. Then we combine the segmentation results from the different views using statistical fusion, with a novel term relating the structural similarity of the 2D views to the original 3D structure. To train the network and evaluate results, 13 structures were manually annotated by four human raters and confirmed by a senior expert on 236 normal cases. We tested our algorithm and computed Dice-Sorensen similarity coefficients and surface distances for evaluating our estimates of the 13 structures. Our experiments show that the proposed approach outperforms 2D- and 3D-patch based state-of-the-art methods.
Joint Enhancement and Denoising Method via Sequential Decomposition
Venue: arXiv cs.CV 2018
Year: 2018

Many low-light enhancement methods ignore intensive noise in original images. As a result, they often simultaneously enhance the noise as well. Furthermore, extra denoising procedures adopted by most methods ruin the details. In this paper, we introduce a joint low-light enhancement and denoising strategy, aimed at obtaining well-enhanced low-light images while getting rid of the inherent noise issue simultaneously. The proposed method performs Retinex model based decomposition in a successive sequence, which sequentially estimates a piece-wise smoothed illumination and a noise-suppressed reflectance. After getting the illumination and reflectance map, we adjust the illumination layer and generate our enhancement result. In this noise-suppressed sequential decomposition process we enforce the spatial smoothness on each component and skillfully make use of weight matrices to suppress the noise and improve the contrast. Results of extensive experiments demonstrate the effectiveness and practicability of our method. It performs well for a wide variety of images, and achieves better or comparable quality compared with the state-of-the-art methods.
Parallel and I/O-efficient Randomisation of Massive Networks using Global Curveball Trades
Venue: arXiv cs.DS 2018
Year: 2018

Graph randomisation is a crucial task in the analysis and synthesis of networks. It is typically implemented as an edge switching process (ESMC) repeatedly swapping the nodes of random edge pairs while maintaining the degrees involved. Curveball is a novel approach that instead considers the whole neighbourhoods of randomly drawn node pairs. Its Markov chain converges to a uniform distribution, and experiments suggest that it requires less steps than the established ESMC. Since trades however are more expensive, we study Curveball's practical runtime by introducing the first efficient Curveball algorithms: the I/O-efficient EM-CB for simple undirected graphs and its internal memory pendant IM-CB. Further, we investigate global trades processing every node in a graph during a single super step, and show that undirected global trades converge to a uniform distribution and perform superior in practice. We then discuss EM-GCB and EM-PGCB for global trades and give experimental evidence that EM-PGCB achieves the quality of the state-of-the-art ESMC algorithm EM-ES nearly one order of magnitude faster.