Reviewerly/exHarmony huggingface dataset:
Fast and Effective Biomedical Entity Linking Using a Dual Encoder

Biomedical entity linking is the task of identifying mentions of biomedical concepts in text documents and mapping them to canonical entities in a target thesaurus. Recent advancements in entity linking using BERT-based models follow a retrieve and rerank paradigm, where the candidate entities are first selected using a retriever model, and then the retrieved candidates are ranked by a reranker model. While this paradigm produces state-of-the-art results, they are slow both at training and test time as they can process only one mention at a time. To mitigate these issues, we propose a BERT-based dual encoder model that resolves multiple mentions in a document in one shot. We show that our proposed model is multiple times faster than existing BERT-based models while being competitive in accuracy for biomedical entity linking. Additionally, we modify our dual encoder model for end-to-end biomedical entity linking that performs both mention span detection and entity disambiguation and out-performs two recently proposed models.
Improving Transformation-based Defenses against Adversarial Examples with First-order Perturbations

Deep neural networks have been successfully applied in various machine learning tasks. However, studies show that neural networks are susceptible to adversarial attacks. This exposes a potential threat to neural network-based intelligent systems. We observe that the probability of the correct result outputted by the neural network increases by applying small first-order perturbations generated for non-predicted class labels to adversarial examples. Based on this observation, we propose a method for counteracting adversarial perturbations to improve adversarial robustness. In the proposed method, we randomly select a number of class labels and generate small first-order perturbations for these selected labels. The generated perturbations are added together and then clamped onto a specified space. The obtained perturbation is finally added to the adversarial example to counteract the adversarial perturbation contained in the example. The proposed method is applied at inference time and does not require retraining or finetuning the model. We experimentally validate the proposed method on CIFAR-10 and CIFAR-100. The results demonstrate that our method effectively improves the defense performance of several transformation-based defense methods, especially against strong adversarial examples generated using more iterations.
Remote Creation of Quantum Coherence via Indefinite Causal Order

Quantum coherence is a prime resource in quantum computing and quantum communication. Quantum coherence of an arbitrary qubit state can be created at a remote location using maximally entangled state, local operation and classical communication. However, if there is a noisy channel acting on one side of the shared resource, then, it is not possible to create perfect quantum coherence remotely. Here, we present a method for the creation of quantum coherence at a remote location via the use of entangled state and indefinite causal order. We show this specifically for the superposition of two completely depolarizing channels, two partially depolarizing channels and one completely depolarizing channel along with a unitary operator. We find that when the indefinite causal order of channels act on one-half of the entangled pair, then the shared state looses entanglement, but can retain non-zero quantum discord. This finding may have some interesting applications on its own where discord can be consumed as a resource. Our results suggest that the indefinite causal order along with a tiny amount of quantum discord can act as a resource in creating non-zero quantum coherence in the absence of entanglement.
Analysis of Convolutional Decoder for Image Caption Generation

Recently Convolutional Neural Networks have been proposed for Sequence Modelling tasks such as Image Caption Generation. However, unlike Recurrent Neural Networks, the performance of Convolutional Neural Networks as Decoders for Image Caption Generation has not been extensively studied. In this work, we analyse various aspects of Convolutional Neural Network based Decoders such as Network complexity and depth, use of Data Augmentation, Attention mechanism, length of sentences used during training, etc on performance of the model. We perform experiments using Flickr8k and Flickr30k image captioning datasets and observe that unlike Recurrent Neural Network based Decoder, Convolutional Decoder for Image Captioning does not generally benefit from increase in network depth, in the form of stacked Convolutional Layers, and also the use of Data Augmentation techniques. In addition, use of Attention mechanism also provides limited performance gains with Convolutional Decoder. Furthermore, we observe that Convolutional Decoders show performance comparable with Recurrent Decoders only when trained using sentences of smaller length which contain up to 15 words but they have limitations when trained using higher sentence lengths which suggests that Convolutional Decoders may not be able to model long-term dependencies efficiently. In addition, the Convolutional Decoder usually performs poorly on CIDEr evaluation metric as compared to Recurrent Decoder.
Formal Verification of Authenticated, Append-Only Skip Lists in Agda: Extended Version

Authenticated Append-Only Skiplists (AAOSLs) enable maintenance and querying of an authenticated log (such as a blockchain) without requiring any single party to store or verify the entire log, or to trust another party regarding its contents. AAOSLs can help to enable efficient dynamic participation (e.g., in consensus) and reduce storage overhead. In this paper, we formalize an AAOSL originally described by Maniatis and Baker, and prove its key correctness properties. Our model and proofs are machine checked in Agda. Our proofs apply to a generalization of the original construction and provide confidence that instances of this generalization can be used in practice. Our formalization effort has also yielded some simplifications and optimizations.
Continual Developmental Neurosimulation Using Embodied Computational Agents

There is much to learn through synthesis of Developmental Biology, Cognitive Science and Computational Modeling. Our path forward is to present a design for developmentally-inspired learning agents based on Braitenberg Vehicles. Using these agents to exemplify the embodied nature of computational autonomy, we move closer to modeling embodied experience and morphogenetic growth as components of cognitive developmental capacity. We consider biological and cognitive development which influence the generation of adult phenotypes and the contingency of available developmental pathways. Continual developmental neurosimulation allows us to consider the role of developmental trajectories in bridging the related phenomena of nervous system morphogenesis, developmental learning, and plasticity. Being closely tied to continual learning, our approach is tightly integrated with developmental embodiment, and can be implemented using a type of agent called developmental Braitenberg Vehicles (dBVs). This phenotype is characterized in terms of developmental timing: with distinct morphogenetic, critical, and acquisition (developmental learning) periods. These properties produce emergent connectivity with shifting weights and adaptive network topologies in the context of developmental processes and spatially-dependent embodiment in training neural networks. We further propose that network morphogenesis can be accomplished using a genetic algorithmic approach, while developmental learning can be implemented using a number of computational methodologies. This approach provides a blueprint for adaptive agent behavior that might result from a developmental approach. In conclusion, we will consider agent learning and development at different timescales. The development, evolution, and learning in an embodied agent-based approach is key to an integrative view of biologically-inspired intelligence.
Joint Coding and Scheduling Optimization for Distributed Learning over Wireless Edge Networks

Unlike theoretical distributed learning (DL), DL over wireless edge networks faces the inherent dynamics/uncertainty of wireless connections and edge nodes, making DL less efficient or even inapplicable under the highly dynamic wireless edge networks (e.g., using mmW interfaces). This article addresses these problems by leveraging recent advances in coded computing and the deep dueling neural network architecture. By introducing coded structures/redundancy, a distributed learning task can be completed without waiting for straggling nodes. Unlike conventional coded computing that only optimizes the code structure, coded distributed learning over the wireless edge also requires to optimize the selection/scheduling of wireless edge nodes with heterogeneous connections, computing capability, and straggling effects. However, even neglecting the aforementioned dynamics/uncertainty, the resulting joint optimization of coding and scheduling to minimize the distributed learning time turns out to be NP-hard. To tackle this and to account for the dynamics and uncertainty of wireless connections and edge nodes, we reformulate the problem as a Markov Decision Process and then design a novel deep reinforcement learning algorithm that employs the deep dueling neural network architecture to find the jointly optimal coding scheme and the best set of edge nodes for different learning tasks without explicit information about the wireless environment and edge nodes' straggling parameters. Simulations show that the proposed framework reduces the average learning delay in wireless edge computing up to 66% compared with other DL approaches. The jointly optimal framework in this article is also applicable to any distributed learning scheme with heterogeneous and uncertain computing nodes.
Artificial neural network as a universal model of nonlinear dynamical systems

We suggest a universal map capable to recover a behavior of a wide range of dynamical systems given by ODEs. The map is built as an artificial neural network whose weights encode a modeled system. We assume that ODEs are known and prepare training datasets using the equations directly without computing numerical time series. Parameter variations are taken into account in the course of training so that the network model captures bifurcation scenarios of the modeled system. Theoretical benefit from this approach is that the universal model admits using common mathematical methods without needing to develop a unique theory for each particular dynamical equations. Form the practical point of view the developed method can be considered as an alternative numerical method for solving dynamical ODEs suitable for running on contemporary neural network specific hardware. We consider the Lorenz system, the Roessler system and also Hindmarch-Rose neuron. For these three examples the network model is created and its dynamics is compared with ordinary numerical solutions. High similarity is observed for visual images of attractors, power spectra, bifurcation diagrams and Lyapunov exponents.
Matroid Secretary Is Equivalent to Contention Resolution

We show that the matroid secretary problem is equivalent to correlated contention resolution in the online random-order model. Specifically, the matroid secretary conjecture is true if and only if every matroid admits an online random-order contention resolution scheme which, given an arbitrary (possibly correlated) prior distribution over subsets of the ground set, matches the balance ratio of the best offline scheme for that distribution up to a constant. We refer to such a scheme as universal. Our result indicates that the core challenge of the matroid secretary problem lies in resolving contention for positively correlated inputs, in particular when the positive correlation is benign in as much as offline contention resolution is concerned. Our result builds on our previous work which establishes one direction of this equivalence, namely that the secretary conjecture implies universal random-order contention resolution, as well as a weak converse, which derives a matroid secretary algorithm from a random-order contention resolution scheme with only partial knowledge of the distribution. It is this weak converse that we strengthen in this paper: We show that universal random-order contention resolution for matroids, in the usual setting of a fully known prior distribution, suffices to resolve the matroid secretary conjecture in the affirmative. Our proof is the composition of three reductions. First, we use duality arguments to reduce the matroid secretary problem to the matroid prophet secretary problem with arbitrarily correlated distributions. Second, we introduce a generalization of contention resolution we term labeled contention resolution, to which we reduce the correlated matroid prophet secretary problem. Finally, we combine duplication of elements with limiting arguments to reduce labeled contention resolution to classical contention resolution.
New Separations Results for External Information

We obtain new separation results for the two-party external information complexity of boolean functions. The external information complexity of a function $f(x,y)$ is the minimum amount of information a two-party protocol computing $f$ must reveal to an outside observer about the input. We obtain the following results: 1. We prove an exponential separation between external and internal information complexity, which is the best possible; previously no separation was known. 2. We prove a near-quadratic separation between amortized zero-error communication complexity and external information complexity for total functions, disproving a conjecture of \cite{Bravermansurvey}. 3. We prove a matching upper showing that our separation result is tight.
Anomalicious: Automated Detection of Anomalous and Potentially Malicious Commits on GitHub

Security is critical to the adoption of open source software (OSS), yet few automated solutions currently exist to help detect and prevent malicious contributions from infecting open source repositories. On GitHub, a primary host of OSS, repositories contain not only code but also a wealth of commit-related and contextual metadata - what if this metadata could be used to automatically identify malicious OSS contributions? In this work, we show how to use only commit logs and repository metadata to automatically detect anomalous and potentially malicious commits. We identify and evaluate several relevant factors which can be automatically computed from this data, such as the modification of sensitive files, outlier change properties, or a lack of trust in the commit's author. Our tool, Anomalicious, automatically computes these factors and considers them holistically using a rule-based decision model. In an evaluation on a data set of 15 malware-infected repositories, Anomalicious showed promising results and identified 53.33% of malicious commits, while flagging less than 1% of commits for most repositories. Additionally, the tool found other interesting anomalies that are not related to malicious commits in an analysis of repositories with no known malicious commits.
Can You Fix My Neural Network? Real-Time Adaptive Waveform Synthesis for Resilient Wireless Signal Classification

Thanks to its capability of classifying complex phenomena without explicit modeling, deep learning (DL) has been demonstrated to be a key enabler of Wireless Signal Classification (WSC). Although DL can achieve a very high accuracy under certain conditions, recent research has unveiled that the wireless channel can disrupt the features learned by the DL model during training, thus drastically reducing the classification performance in real-world live settings. Since retraining classifiers is cumbersome after deployment, existing work has leveraged the usage of carefully-tailored Finite Impulse Response (FIR) filters that, when applied at the transmitter's side, can restore the features that are lost because of the the channel actions, i.e., waveform synthesis. However, these approaches compute FIRs using offline optimization strategies, which limits their efficacy in highly-dynamic channel settings. In this paper, we improve the state of the art by proposing Chares, a Deep Reinforcement Learning (DRL)-based framework for channel-resilient adaptive waveform synthesis. Chares adapts to new and unseen channel conditions by optimally computing through DRL the FIRs in real-time. Chares is a DRL agent whose architecture is-based upon the Twin Delayed Deep Deterministic Policy Gradients (TD3), which requires minimal feedback from the receiver and explores a continuous action space. Chares has been extensively evaluated on two well-known datasets. We have also evaluated the real-time latency of Chares with an implementation on field-programmable gate array (FPGA). Results show that Chares increases the accuracy up to 4.1x when no waveform synthesis is performed, by 1.9x with respect to existing work, and can compute new actions within 41us.
Real-time RGBD-based Extended Body Pose Estimation

We present a system for real-time RGBD-based estimation of 3D human pose. We use parametric 3D deformable human mesh model (SMPL-X) as a representation and focus on the real-time estimation of parameters for the body pose, hands pose and facial expression from Kinect Azure RGB-D camera. We train estimators of body pose and facial expression parameters. Both estimators use previously published landmark extractors as input and custom annotated datasets for supervision, while hand pose is estimated directly by a previously published method. We combine the predictions of those estimators into a temporally-smooth human pose. We train the facial expression extractor on a large talking face dataset, which we annotate with facial expression parameters. For the body pose we collect and annotate a dataset of 56 people captured from a rig of 5 Kinect Azure RGB-D cameras and use it together with a large motion capture AMASS dataset. Our RGB-D body pose model outperforms the state-of-the-art RGB-only methods and works on the same level of accuracy compared to a slower RGB-D optimization-based solution. The combined system runs at 30 FPS on a server with a single GPU. The code will be available at https://saic-violet.github.io/rgbd-kinect-pose
Graph Convolutional Embeddings for Recommender Systems

Modern recommender systems (RS) work by processing a number of signals that can be inferred from large sets of user-item interaction data. The main signal to analyze stems from the raw matrix that represents interactions. However, we can increase the performance of RS by considering other kinds of signals like the context of interactions, which could be, for example, the time or date of the interaction, the user location, or sequential data corresponding to the historical interactions of the user with the system. These complex, context-based interaction signals are characterized by a rich relational structure that can be represented by a multi-partite graph. Graph Convolutional Networks (GCNs) have been used successfully in collaborative filtering with simple user-item interaction data. In this work, we generalize the use of GCNs for N-partite graphs by considering N multiple context dimensions and propose a simple way for their seamless integration in modern deep learning RS architectures. More specifically, we define a graph convolutional embedding layer for N-partite graphs that processes user-item-context interactions, and constructs node embeddings by leveraging their relational structure. Experiments on several datasets from recommender systems to drug re-purposing show the benefits of the introduced GCN embedding layer by measuring the performance of different context-enriched tasks.
Tor circuit fingerprinting defenses using adaptive padding

Online anonymity and privacy has been based on confusing the adversary by creating indistinguishable network elements. Tor is the largest and most widely deployed anonymity system, designed against realistic modern adversaries. Recently, researchers have managed to fingerprint Tor's circuits -- and hence the type of underlying traffic -- simply by capturing and analyzing traffic traces. In this work, we study the circuit fingerprinting problem, isolating it from website fingerprinting, and revisit previous findings in this model, showing that accurate attacks are possible even when the application-layer traffic is identical. We then proceed to incrementally create defenses against circuit fingerprinting, using a generic adaptive padding framework for Tor based on WTF-PAD. We present a simple defense which delays a fraction of the traffic, as well as a more advanced one which can effectively hide onion service circuits with zero delays. We thoroughly evaluate both defenses, both analytically and experimentally, discovering new subtle fingerprints, but also showing the effectiveness of our defenses.
Parsing Indonesian Sentence into Abstract Meaning Representation using Machine Learning Approach

Abstract Meaning Representation (AMR) provides many information of a sentence such as semantic relations, coreferences, and named entity relation in one representation. However, research on AMR parsing for Indonesian sentence is fairly limited. In this paper, we develop a system that aims to parse an Indonesian sentence using a machine learning approach. Based on Zhang et al. work, our system consists of three steps: pair prediction, label prediction, and graph construction. Pair prediction uses dependency parsing component to get the edges between the words for the AMR. The result of pair prediction is passed to the label prediction process which used a supervised learning algorithm to predict the label between the edges of the AMR. We used simple sentence dataset that is gathered from articles and news article sentences. Our model achieved the SMATCH score of 0.820 for simple sentence test data.
Analysis of User Preferences for Robot Motions in Immersive Telepresence

This paper considers how the motions of a telepresence robot moving autonomously affect a person immersed in the robot through a head-mounted display. In particular, we explore the preference, comfort, and naturalness of elements of piecewise linear paths compared to the same elements on a smooth path. In a user study, thirty-six subjects watched panoramic videos of three different paths through a simulated museum in virtual reality and responded to questionnaires regarding each path. Preference for a particular path was influenced the most by comfort, forward speed, and characteristics of the turns. Preference was also strongly associated with the users' perceived naturalness, which was primarily determined by the ability to see salient objects, the distance to the walls and objects, as well as the turns. Participants favored the paths that had a one meter per second forward speed and rated the path with the least amount of turns as the most comfortable