OpenRaiser/Intern-Atlas huggingface dataset:
OpenBioLink: A benchmarking framework for large-scale biomedical link prediction
Venue: arXiv cs.AI 2020
Year: 2020

SUMMARY: Recently, novel machine-learning algorithms have shown potential for predicting undiscovered links in biomedical knowledge networks. However, dedicated benchmarks for measuring algorithmic progress have not yet emerged. With OpenBioLink, we introduce a large-scale, high-quality and highly challenging biomedical link prediction benchmark to transparently and reproducibly evaluate such algorithms. Furthermore, we present preliminary baseline evaluation results. AVAILABILITY AND IMPLEMENTATION: Source code, data and supplementary files are openly available at https://github.com/OpenBioLink/OpenBioLink CONTACT: matthias.samwald ((at)) meduniwien.ac.at
PLIERS: A Process that Integrates User-Centered Methods into Programming Language Design
Venue: arXiv cs.HC 2020
Year: 2020

Programming language design requires making many usability-related design decisions. However, existing HCI methods can be impractical to apply to programming languages: they have high iteration costs, programmers require significant learning time, and user performance has high variance. To address these problems, we adapted both formative and summative HCI methods to make them more suitable for programming language design. We integrated these methods into a new process, PLIERS, for designing programming languages in a user-centered way. We evaluated PLIERS by using it to design two new programming languages. Glacier extends Java to enable programmers to express immutability properties effectively and easily. Obsidian is a language for blockchains that includes verification of critical safety properties. Summative usability studies showed that programmers were able to program effectively in both languages after short training periods.
Context-Aware Dynamic Feature Extraction for 3D Object Detection in Point Clouds
Venue: arXiv cs.CV 2020
Year: 2020

Varying density of point clouds increases the difficulty of 3D detection. In this paper, we present a context-aware dynamic network (CADNet) to capture the variance of density by considering both point context and semantic context. Point-level contexts are generated from original point clouds to enlarge the effective receptive filed. They are extracted around the voxelized pillars based on our extended voxelization method and processed with the context encoder in parallel with the pillar features. With a large perception range, we are able to capture the variance of features for potential objects and generate attentive spatial guidance to help adjust the strengths for different regions. In the region proposal network, considering the limited representation ability of traditional convolution where same kernels are shared among different samples and positions, we propose a decomposable dynamic convolutional layer to adapt to the variance of input features by learning from local semantic context. It adaptively generates the position-dependent coefficients for multiple fixed kernels and combines them to convolve with local feature windows. Based on our dynamic convolution, we design a dual-path convolution block to further improve the representation ability. We conduct experiments with our Network on KITTI dataset and achieve good performance on 3D detection task for both precision and speed. Our one-stage detector outperforms SECOND and PointPillars by a large margin and achieves the speed of 30 FPS.
3D Beamforming based Dynamic TDD Interference Mitigation Scheme
Venue: arXiv cs.NI 2020
Year: 2020

Dynamic Time Division Duplexing (D-TDD) allows cells to accommodate asymmetric traffic variations with high resource assignment flexibility. However, this feature is limited by two additional types of interference between cells in opposite transmission direction: downlink (DL) to uplink (UL) and UL to DL interference. Therefore, using this mode with macro-cell deployments requires interference mitigation techniques to reduce the strong DL to UL interference. 3D beamforming is an efficient technique that minimizes interference and enhances performance by exploiting a large 2D array of antennas intelligently. Combining D-TDD and 3D beamforming can make D-TDD feasible for macro-cells. The aim of this work is to provide a 3D beamforming analytical model in a D-TDD based macro-cells' deployment where beamforming horizontal and vertical radiation patterns depend on the spatial distribution of random users' locations. We evaluate interference in terms of Interference to Signal Ratio (ISR). We show that the cumulative ISR can be written in terms of convergent series and its expectation is an almost sure convergent series. Different numerical results are presented to justify the applicability of this scheme.
A Collaborative Ecosystem for Digital Coptic Studies
Venue: arXiv cs.CL 2020
Year: 2020

Scholarship on underresourced languages bring with them a variety of challenges which make access to the full spectrum of source materials and their evaluation difficult. For Coptic in particular, large scale analyses and any kind of quantitative work become difficult due to the fragmentation of manuscripts, the highly fusional nature of an incorporational morphology, and the complications of dealing with influences from Hellenistic era Greek, among other concerns. Many of these challenges, however, can be addressed using Digital Humanities tools and standards. In this paper, we outline some of the latest developments in Coptic Scriptorium, a DH project dedicated to bringing Coptic resources online in uniform, machine readable, and openly available formats. Collaborative web-based tools create online 'virtual departments' in which scholars dispersed sparsely across the globe can collaborate, and natural language processing tools counterbalance the scarcity of trained editors by enabling machine processing of Coptic text to produce searchable, annotated corpora.
REFINED (REpresentation of Features as Images with NEighborhood Dependencies): A novel feature representation for Convolutional Neural Networks
Venue: arXiv cs.LG 2020
Year: 2020

Deep learning with Convolutional Neural Networks has shown great promise in various areas of image-based classification and enhancement but is often unsuitable for predictive modeling involving non-image based features or features without spatial correlations. We present a novel approach for representation of high dimensional feature vector in a compact image form, termed REFINED (REpresentation of Features as Images with NEighborhood Dependencies), that is conducible for convolutional neural network based deep learning. We consider the correlations between features to generate a compact representation of the features in the form of a two-dimensional image using minimization of pairwise distances similar to multi-dimensional scaling. We hypothesize that this approach enables embedded feature selection and integrated with Convolutional Neural Network based Deep Learning can produce more accurate predictions as compared to Artificial Neural Networks, Random Forests and Support Vector Regression. We illustrate the superior predictive performance of the proposed representation, as compared to existing approaches, using synthetic datasets, cell line efficacy prediction based on drug chemical descriptors for NCI60 dataset and drug sensitivity prediction based on transcriptomic data and chemical descriptors using GDSC dataset. Results illustrated on both synthetic and biological datasets shows the higher prediction accuracy of the proposed framework as compared to existing methodologies while maintaining desirable properties in terms of bias and feature extraction.
Learning Improvement Heuristics for Solving Routing Problems
Venue: arXiv cs.AI 2020
Year: 2020

Recent studies in using deep learning to solve routing problems focus on construction heuristics, the solutions of which are still far from optimality. Improvement heuristics have great potential to narrow this gap by iteratively refining a solution. However, classic improvement heuristics are all guided by hand-crafted rules which may limit their performance. In this paper, we propose a deep reinforcement learning framework to learn the improvement heuristics for routing problems. We design a self-attention based deep architecture as the policy network to guide the selection of next solution. We apply our method to two important routing problems, i.e. travelling salesman problem (TSP) and capacitated vehicle routing problem (CVRP). Experiments show that our method outperforms state-of-the-art deep learning based approaches. The learned policies are more effective than the traditional hand-crafted ones, and can be further enhanced by simple diversifying strategies. Moreover, the policies generalize well to different problem sizes, initial solutions and even real-world dataset.
An Integral Representation of the Logarithmic Function with Applications in Information Theory
Venue: arXiv cs.IT 2020
Year: 2020

We explore a well-known integral representation of the logarithmic function, and demonstrate its usefulness in obtaining compact, easily-computable exact formulas for quantities that involve expectations and higher moments of the logarithm of a positive random variable (or the logarithm of a sum of positive random variables). The integral representation of the logarithm is proved useful in a variety of information-theoretic applications, including universal lossless data compression, entropy and differential entropy evaluations, and the calculation of the ergodic capacity of the single-input, multiple-output (SIMO) Gaussian channel with random parameters (known to both transmitter and receiver). This integral representation and its variants are anticipated to serve as a useful tool in additional applications, as a rigorous alternative to the popular (but non-rigorous) replica method (at least in some situations).
Smart Contract Repair
Venue: arXiv cs.SE 2020
Year: 2020

Smart contracts are automated or self-enforcing contracts that can be used to exchange assets without having to place trust in third parties. Many commercial transactions use smart contracts due to their potential benefits in terms of secure peer-to-peer transactions independent of external parties. Experience shows that many commonly used smart contracts are vulnerable to serious malicious attacks which may enable attackers to steal valuable assets of involving parties. There is therefore a need to apply analysis and automated repair techniques to detect and repair bugs in smart contracts before being deployed. In this work, we present the first general-purpose automated smart contract repair approach that is also gas-aware. Our repair method is search-based and searches among mutations of the buggy contract. Our method also considers the gas usage of the candidate patches by leveraging our novel notion of gas dominance relationship. We have made our smart contract repair tool SCRepair available open-source, for investigation by the wider community.
Automatic Financial Feature Construction
Venue: arXiv cs.LG 2020
Year: 2020

In automatic financial feature construction task, the state-of-the-art technic leverages reverse polish expression to represent the features, then use genetic programming (GP) to conduct its evolution process. In this paper, we propose a new framework based on neural network, alpha discovery neural network (ADNN). In this work, we made several contributions. Firstly, in this task, we make full use of neural network overwhelming advantage in feature extraction to construct highly informative features. Secondly, we use domain knowledge to design the object function, batch size, and sampling rules. Thirdly, we use pre-training to replace the GP evolution process. According to neural network universal approximation theorem, pre-training can conduct a more effective and explainable evolution process. Experiment shows that ADNN can remarkably produce more diversified and higher informative features than GP. Besides, ADNN can serve as a data augmentation algorithm. It further improves the the performance of financial features constructed by GP.
An Interval-Valued Utility Theory for Decision Making with Dempster-Shafer Belief Functions
Venue: arXiv cs.AI 2020
Year: 2020

The main goal of this paper is to describe an axiomatic utility theory for Dempster-Shafer belief function lotteries. The axiomatic framework used is analogous to von Neumann-Morgenstern's utility theory for probabilistic lotteries as described by Luce and Raiffa. Unlike the probabilistic case, our axiomatic framework leads to interval-valued utilities, and therefore, to a partial (incomplete) preference order on the set of all belief function lotteries. If the belief function reference lotteries we use are Bayesian belief functions, then our representation theorem coincides with Jaffray's representation theorem for his linear utility theory for belief functions. We illustrate our representation theorem using some examples discussed in the literature, and we propose a simple model for assessing utilities based on an interval-valued pessimism index representing a decision-maker's attitude to ambiguity and indeterminacy. Finally, we compare our decision theory with those proposed by Jaffray, Smets, Dubois et al., Giang and Shenoy, and Shafer.
Document Sub-structure in Neural Machine Translation
Venue: arXiv cs.CL 2020
Year: 2020

Current approaches to machine translation (MT) either translate sentences in isolation, disregarding the context they appear in, or model context at the level of the full document, without a notion of any internal structure the document may have. In this work we consider the fact that documents are rarely homogeneous blocks of text, but rather consist of parts covering different topics. Some documents, such as biographies and encyclopedia entries, have highly predictable, regular structures in which sections are characterised by different topics. We draw inspiration from Louis and Webber (2014) who use this information to improve statistical MT and transfer their proposal into the framework of neural MT. We compare two different methods of including information about the topic of the section within which each sentence is found: one using side constraints and the other using a cache-based model. We create and release the data on which we run our experiments - parallel corpora for three language pairs (Chinese-English, French-English, Bulgarian-English) from Wikipedia biographies, which we extract automatically, preserving the boundaries of sections within the articles.
Deep Poisoning: Towards Robust Image Data Sharing against Visual Disclosure
Venue: arXiv cs.CV 2020
Year: 2020

Due to respectively limited training data, different entities addressing the same vision task based on certain sensitive images may not train a robust deep network. This paper introduces a new vision task where various entities share task-specific image data to enlarge each other's training data volume without visually disclosing sensitive contents (e.g. illegal images). Then, we present a new structure-based training regime to enable different entities learn task-specific and reconstruction-proof image representations for image data sharing. Specifically, each entity learns a private Deep Poisoning Module (DPM) and insert it to a pre-trained deep network, which is designed to perform the specific vision task. The DPM deliberately poisons convolutional image features to prevent image reconstructions, while ensuring that the altered image data is functionally equivalent to the non-poisoned data for the specific vision task. Given this equivalence, the poisoned features shared from one entity could be used by another entity for further model refinement. Experimental results on image classification prove the efficacy of the proposed method.
#MeTooMA: Multi-Aspect Annotations of Tweets Related to the MeToo Movement
Venue: arXiv cs.CL 2020
Year: 2020

In this paper, we present a dataset containing 9,973 tweets related to the MeToo movement that were manually annotated for five different linguistic aspects: relevance, stance, hate speech, sarcasm, and dialogue acts. We present a detailed account of the data collection and annotation processes. The annotations have a very high inter-annotator agreement (0.79 to 0.93 k-alpha) due to the domain expertise of the annotators and clear annotation instructions. We analyze the data in terms of geographical distribution, label correlations, and keywords. Lastly, we present some potential use cases of this dataset. We expect this dataset would be of great interest to psycholinguists, socio-linguists, and computational linguists to study the discursive space of digitally mobilized social movements on sensitive issues like sexual harassment.
Local Parametric Surface Approximation With Automatic Order Selection From Position Data
Venue: arXiv cs.RO 2020
Year: 2020

Acquiring an anatomical map from position data is important for medical applications where catheters interact with soft tissues. To improve autonomous navigation in these settings, we require information beyond nonparametric maps typically available. We present an algorithm for local surface approximation from position data with automatic surface order selection. The traditional surface fitting objective function is derived from a Bayesian perspective. Posterior probabilities from the occupancy map are incorporated as weights on points selected for surface fitting. Our novel iterative algorithm incorporates surface order selection using the Bayesian information criterion. Simulations demonstrate the ability to automatically select surface order consistent with the latent surface in the presence of noise. Results on human procedure data are also presented.
Joint Learning of Generative Translator and Classifier for Visually Similar Classes
Venue: arXiv cs.CV 2020
Year: 2020

In this paper, we propose a Generative Translation Classification Network (GTCN) for improving visual classification accuracy in settings where classes are visually similar and data is scarce. For this purpose, we propose joint learning from a scratch to train a classifier and a generative stochastic translation network end-to-end. The translation network is used to perform on-line data augmentation across classes, whereas previous works have mostly involved domain adaptation. To help the model further benefit from this data-augmentation, we introduce an adaptive fade-in loss and a quadruplet loss. We perform experiments on multiple datasets to demonstrate the proposed method's performance in varied settings. Of particular interest, training on 40% of the dataset is enough for our model to surpass the performance of baselines trained on the full dataset. When our architecture is trained on the full dataset, we achieve comparable performance with state-of-the-art methods despite using a light-weight architecture.
On Wyner's Common Information in the Gaussian Case
Venue: arXiv cs.IT 2020
Year: 2020

Wyner's Common Information and a natural relaxation are studied in the special case of Gaussian random variables. The relaxation replaces conditional independence by a bound on the conditional mutual information. The main contribution is the proof that Gaussian auxiliaries are optimal, leading to a closed-form formula. As a corollary, the proof technique also establishes the optimality of Gaussian auxiliaries for the Gaussian Gray-Wyner network, a long-standing open problem.
Domain Agnostic Feature Learning for Image and Video Based Face Anti-spoofing
Venue: arXiv cs.CV 2020
Year: 2020

Nowadays, the increasingly growing number of mobile and computing devices has led to a demand for safer user authentication systems. Face anti-spoofing is a measure towards this direction for bio-metric user authentication, and in particular face recognition, that tries to prevent spoof attacks. The state-of-the-art anti-spoofing techniques leverage the ability of deep neural networks to learn discriminative features, based on cues from the training set images or video samples, in an effort to detect spoof attacks. However, due to the particular nature of the problem, i.e. large variability due to factors like different backgrounds, lighting conditions, camera resolutions, spoof materials, etc., these techniques typically fail to generalize to new samples. In this paper, we explicitly tackle this problem and propose a class-conditional domain discriminator module, that, coupled with a gradient reversal layer, tries to generate live and spoof features that are discriminative, but at the same time robust against the aforementioned variability factors. Extensive experimental analysis shows the effectiveness of the proposed method over existing image- and video-based anti-spoofing techniques, both in terms of numerical improvement as well as when visualizing the learned features.
ITENE: Intrinsic Transfer Entropy Neural Estimator
Venue: arXiv cs.IT 2020
Year: 2020

Quantifying the directionality of information flow is instrumental in understanding, and possibly controlling, the operation of many complex systems, such as transportation, social, neural, or gene-regulatory networks. The standard Transfer Entropy (TE) metric follows Granger's causality principle by measuring the Mutual Information (MI) between the past states of a source signal $X$ and the future state of a target signal $Y$ while conditioning on past states of $Y$. Hence, the TE quantifies the improvement, as measured by the log-loss, in the prediction of the target sequence $Y$ that can be accrued when, in addition to the past of $Y$, one also has available past samples from $X$. However, by conditioning on the past of $Y$, the TE also measures information that can be synergistically extracted by observing both the past of $X$ and $Y$, and not solely the past of $X$. Building on a private key agreement formulation, the Intrinsic TE (ITE) aims to discount such synergistic information to quantify the degree to which $X$ is \emph{individually} predictive of $Y$, independent of $Y$'s past. In this paper, an estimator of the ITE is proposed that is inspired by the recently proposed Mutual Information Neural Estimation (MINE). The estimator is based on variational bound on the KL divergence, two-sample neural network classifiers, and the pathwise estimator of Monte Carlo gradients.
Improved Explanatory Efficacy on Human Affect and Workload through Interactive Process in Artificial Intelligence
Venue: arXiv cs.HC 2020
Year: 2020

Despite recent advances in the field of explainable artificial intelligence systems, a concrete quantitative measure for evaluating the usability of such systems is nonexistent. Ensuring the success of an explanatory interface in interacting with users requires a cyclic, symbiotic relationship between human and artificial intelligence. We, therefore, propose explanatory efficacy, a novel metric for evaluating the strength of the cyclic relationship the interface exhibits. Furthermore, in a user study, we evaluated the perceived affect and workload and recorded the EEG signals of our participants as they interacted with our custom-built, iterative explanatory interface to build personalized recommendation systems. We found that systems for perceptually driven iterative tasks with greater explanatory efficacy are characterized by statistically significant hemispheric differences in neural signals with 62.4% accuracy, indicating the feasibility of neural correlates as a measure of explanatory efficacy. These findings are beneficial for researchers who aim to study the circular ecosystem of the human-artificial intelligence partnership.