OpenRaiser/Intern-Atlas huggingface dataset:
A Characterization of the DNA Data Storage Channel
Venue: arXiv cs.ET 2018
Year: 2018

Owing to its longevity and enormous information density, DNA, the molecule encoding biological information, has emerged as a promising archival storage medium. However, due to technological constraints, data can only be written onto many short DNA molecules that are stored in an unordered way, and can only be read by sampling from this DNA pool. Moreover, imperfections in writing (synthesis), reading (sequencing), storage, and handling of the DNA, in particular amplification via PCR, lead to a loss of DNA molecules and induce errors within the molecules. In order to design DNA storage systems, a qualitative and quantitative understanding of the errors and the loss of molecules is crucial. In this paper, we characterize those error probabilities by analyzing data from our own experiments as well as from experiments of two different groups. We find that errors within molecules are mainly due to synthesis and sequencing, while imperfections in handling and storage lead to a significant loss of sequences. The aim of our study is to help guide the design of future DNA data storage systems by providing a quantitative and qualitative understanding of the DNA data storage channel.
Learning Deep Generative Models of Graphs
Venue: arXiv cs.LG 2018
Year: 2018

Graphs are fundamental data structures which concisely capture the relational structure in many important real-world domains, such as knowledge graphs, physical and social interactions, language, and chemistry. Here we introduce a powerful new approach for learning generative models over graphs, which can capture both their structure and attributes. Our approach uses graph neural networks to express probabilistic dependencies among a graph's nodes and edges, and can, in principle, learn distributions over any arbitrary graph. In a series of experiments our results show that once trained, our models can generate good quality samples of both synthetic graphs as well as real molecular graphs, both unconditionally and conditioned on data. Compared to baselines that do not use graph-structured representations, our models often perform far better. We also explore key challenges of learning generative models of graphs, such as how to handle symmetries and ordering of elements during the graph generation process, and offer possible solutions. Our work is the first and most general approach for learning generative models over arbitrary graphs, and opens new directions for moving away from restrictions of vector- and sequence-like knowledge representations, toward more expressive and flexible relational data structures.
Expert Finding in Heterogeneous Bibliographic Networks with Locally-trained Embeddings
Venue: arXiv cs.IR 2018
Year: 2018

Expert finding is an important task in both industry and academia. It is challenging to rank candidates with appropriate expertise for various queries. In addition, different types of objects interact with one another, which naturally forms heterogeneous information networks. We study the task of expert finding in heterogeneous bibliographical networks based on two aspects: textual content analysis and authority ranking. Regarding the textual content analysis, we propose a new method for query expansion via locally-trained embedding learning with concept hierarchy as guidance, which is particularly tailored for specific queries with narrow semantic meanings. Compared with global embedding learning, locally-trained embedding learning projects the terms into a latent semantic space constrained on relevant topics, therefore it preserves more precise and subtle information for specific queries. Considering the candidate ranking, the heterogeneous information network structure, while being largely ignored in the previous studies of expert finding, provides additional information. Specifically, different types of interactions among objects play different roles. We propose a ranking algorithm to estimate the authority of objects in the network, treating each strongly-typed edge type individually. To demonstrate the effectiveness of the proposed framework, we apply the proposed method to a large-scale bibliographical dataset with over two million entries and one million researcher candidates. The experiment results show that the proposed framework outperforms existing methods for both general and specific queries.
Clocked Definitions in HOL
Venue: arXiv cs.LO 2018
Year: 2018

Many potentially non-terminating functions cannot be directly defined in a logic of total functions, such as HOL. A well-known solution to this is to define non-terminating functions using a clock that forces termination at a certain depth of evaluation. Such clocked definitions are often frowned upon and avoided, since the clock is perceived as extra clutter. In this short paper, we explain that there are different ways to add a clock, some less intrusive than others. Our contribution is a technique by which termination proofs are kept simple even when minimising the use of the clock mechanism. Our examples are definitions of semantic interpreters for programming languages, so called functional big-step semantics.
Robust Landmark Detection for Alignment of Mouse Brain Section Images
Venue: arXiv cs.CV 2018
Year: 2018

Brightfield and fluorescent imaging of whole brain sections are funda- mental tools of research in mouse brain study. As sectioning and imaging become more efficient, there is an increasing need to automate the post-processing of sec- tions for alignment and three dimensional visualization. There is a further need to facilitate the development of a digital atlas, i.e. a brain-wide map annotated with cell type and tract tracing data, which would allow the automatic registra- tion of images stacks to a common coordinate system. Currently, registration of slices requires manual identification of landmarks. In this work we describe the first steps in developing a semi-automated system to construct a histology at- las of mouse brainstem that combines atlas-guided annotation, landmark-based registration and atlas generation in an iterative framework. We describe an unsu- pervised approach for identifying and matching region and boundary landmarks, based on modelling texture. Experiments show that the detected landmarks corre- spond well with brain structures, and matching is robust under distortion. These results will serve as the basis for registration and atlas building.
A Bias Aware News Recommendation System
Venue: arXiv cs.IR 2018
Year: 2018

In this era of fake news and political polarization, it is desirable to have a system to enable users to access balanced news content. Current solutions focus on top down, server based approaches to decide whether a news article is fake or biased, and display only trusted news to the end users. In this paper, we follow a different approach to help the users make informed choices about which news they want to read, making users aware in real time of the bias in news articles they were browsing and recommending news articles from other sources on the same topic with different levels of bias. We use a recent Pew research report to collect news sources that readers with varying political inclinations prefer to read. We then scrape news articles on a variety of topics from these varied news sources. After this, we perform clustering to find similar topics of the articles, as well as calculate a bias score for each article. For a news article the user is currently reading, we display the bias score and also display other articles on the same topic, out of the previously collected articles, from different news sources. This we present to the user. This approach, we hope, would make it possible for users to access more balanced articles on given news topics. We present the implementation details of the system along with some preliminary results on news articles.
Generalized distance domination problems and their complexity on graphs of bounded mim-width
Venue: arXiv cs.CC 2018
Year: 2018

We generalize the family of $(σ, ρ)$-problems and locally checkable vertex partition problems to their distance versions, which naturally captures well-known problems such as distance-$r$ dominating set and distance-$r$ independent set. We show that these distance problems are XP parameterized by the structural parameter mim-width, and hence polynomial on graph classes where mim-width is bounded and quickly computable, such as $k$-trapezoid graphs, Dilworth $k$-graphs, (circular) permutation graphs, interval graphs and their complements, convex graphs and their complements, $k$-polygon graphs, circular arc graphs, complements of $d$-degenerate graphs, and $H$-graphs if given an $H$-representation. To supplement these findings, we show that many classes of (distance) $(σ, ρ)$-problems are W[1]-hard parameterized by mim-width + solution size.
Synchronization Strings: Efficient and Fast Deterministic Constructions over Small Alphabets
Venue: arXiv cs.IT 2018
Year: 2018

Synchronization strings are recently introduced by Haeupler and Shahrasbi (STOC 2017) in the study of codes for correcting insertion and deletion errors (insdel codes). They showed that for any parameter $\varepsilon>0$, synchronization strings of arbitrary length exist over an alphabet whose size depends only on $\varepsilon$. Specifically, they obtained an alphabet size of $O(\varepsilon^{-4})$, which left an open question on where the minimal size of such alphabets lies between $Ω(\varepsilon^{-1})$ and $O(\varepsilon^{-4})$. In this work, we partially bridge this gap by providing an improved lower bound of $Ω(\varepsilon^{-3/2})$, and an improved upper bound of $O(\varepsilon^{-2})$. We also provide fast explicit constructions of synchronization strings over small alphabets. Further, along the lines of previous work on similar combinatorial objects, we study the extremal question of the smallest possible alphabet size over which synchronization strings can exist for some constant $\varepsilon < 1$. We show that one can construct $\varepsilon$-synchronization strings over alphabets of size four while no such string exists over binary alphabets. This reduces the extremal question to whether synchronization strings exist over ternary alphabets.
Predicting antimicrobial drug consumption using web search data
Venue: arXiv cs.IR 2018
Year: 2018

Consumption of antimicrobial drugs, such as antibiotics, is linked with antimicrobial resistance. Surveillance of antimicrobial drug consumption is therefore an important element in dealing with antimicrobial resistance. Many countries lack sufficient surveillance systems. Usage of web mined data therefore has the potential to improve current surveillance methods. To this end, we study how well antimicrobial drug consumption can be predicted based on web search queries, compared to historical purchase data of antimicrobial drugs. We present two prediction models (linear Elastic Net, and non-linear Gaussian Processes), which we train and evaluate on almost 6 years of weekly antimicrobial drug consumption data from Denmark and web search data from Google Health Trends. We present a novel method of selecting web search queries by considering diseases and drugs linked to antimicrobials, as well as professional and layman descriptions of antimicrobial drugs, all of which we mine from the open web. We find that predictions based on web search data are marginally more erroneous but overall on a par with predictions based on purchases of antimicrobial drugs. This marginal difference corresponds to $<1$\% point mean absolute error in weekly usage. Best predictions are reported when combining both web search and purchase data. This study contributes a novel alternative solution to the real-life problem of predicting (and hence monitoring) antimicrobial drug consumption, which is particularly valuable in countries/states lacking centralised and timely surveillance systems.
Constrained hierarchical networked optimization for energy markets
Venue: arXiv cs.SY 2018
Year: 2018

In this paper, we propose a distributed control strategy for the design of an energy market. The method relies on a hierarchical structure of aggregators for the coordination of prosumers (agents which can produce and consume energy). The hierarchy reflects the voltage level separations of the electrical grid and allows aggregating prosumers in pools, while taking into account the grid operational constraints. To reach optimal coordination, the prosumers communicate their forecasted power profile to the upper level of the hierarchy. Each time the information crosses upwards a level of the hierarchy, it is first aggregated, both to strongly reduce the data flow and to preserve the privacy. In the first part of the paper, the decomposition algorithm, which is based on the alternating direction method of multipliers (ADMM), is presented. In the second part, we explore how the proposed algorithm scales with increasing number of prosumers and hierarchical levels, through extensive simulations based on randomly generated scenarios.
Random Access Schemes in Wireless Systems With Correlated User Activity
Venue: arXiv cs.IT 2018
Year: 2018

Traditional random access schemes are designed based on the aggregate process of user activation, which is created on the basis of independent activations of the users. However, in Machine-Type Communications (MTC), some users are likely to exhibit a high degree of correlation, e.g. because they observe the same physical phenomenon. This paves the way to devise access schemes that combine scheduling and random access, which is the topic of this work. The underlying idea is to schedule highly correlated users in such a way that their transmissions are less likely to result in a collision. To this end, we propose two greedy allocation algorithms. Both attempt to maximize the throughput using only pairwise correlations, but they rely on different assumptions about the higher-order dependencies. We show that both algorithms achieve higher throughput compared to the traditional random access schemes, suggesting that user correlation can be utilized effectively in access protocols for MTC.
Disconnected Cuts in Claw-free Graphs
Venue: arXiv cs.DS 2018
Year: 2018

A disconnected cut of a connected graph is a vertex cut that itself also induces a disconnected subgraph. The decision problem whether a graph has a disconnected cut is called Disconnected Cut. This problem is closely related to several homomorphism and contraction problems, and fits in an extensive line of research on vertex cuts with additional properties. It is known that Disconnected Cut is NP-hard on general graphs, while polynomial-time algorithms are known for several graph classes. However, the complexity of the problem on claw-free graphs remained an open question. Its connection to the complexity of the problem to contract a claw-free graph to the 4-vertex cycle $C_4$ led Ito et al. (TCS 2011) to explicitly ask to resolve this open question. We prove that Disconnected Cut is polynomial-time solvable on claw-free graphs, answering the question of Ito et al. The centerpiece of our result is a novel decomposition theorem for claw-free graphs of diameter 2, which we believe is of independent interest and expands the research line initiated by Chudnovsky and Seymour (JCTB 2007-2012) and Hermelin et al. (ICALP 2011). On our way to exploit this decomposition theorem, we characterize how disconnected cuts interact with certain cobipartite subgraphs, and prove two further novel algorithmic results, namely Disconnected Cut is polynomial-time solvable on circular-arc graphs and line graphs.
Sequential Outlier Detection based on Incremental Decision Trees
Venue: arXiv cs.LG 2018
Year: 2018

We introduce an online outlier detection algorithm to detect outliers in a sequentially observed data stream. For this purpose, we use a two-stage filtering and hedging approach. In the first stage, we construct a multi-modal probability density function to model the normal samples. In the second stage, given a new observation, we label it as an anomaly if the value of aforementioned density function is below a specified threshold at the newly observed point. In order to construct our multi-modal density function, we use an incremental decision tree to construct a set of subspaces of the observation space. We train a single component density function of the exponential family using the observations, which fall inside each subspace represented on the tree. These single component density functions are then adaptively combined to produce our multi-modal density function, which is shown to achieve the performance of the best convex combination of the density functions defined on the subspaces. As we observe more samples, our tree grows and produces more subspaces. As a result, our modeling power increases in time, while mitigating overfitting issues. In order to choose our threshold level to label the observations, we use an adaptive thresholding scheme. We show that our adaptive threshold level achieves the performance of the optimal pre-fixed threshold level, which knows the observation labels in hindsight. Our algorithm provides significant performance improvements over the state of the art in our wide set of experiments involving both synthetic as well as real data.
Set Theory-Based Safety Supervisory Control for Wind Turbines to Ensure Adequate Frequency Response
Venue: arXiv cs.SY 2018
Year: 2018

Inadequate frequency response can arise due to a high penetration of wind turbine generators (WTGs) and requires a frequency support function to be integrated in the WTG. The appropriate design for these controllers to ensure adequate response has not been investigated thoroughly. In this paper, a safety supervisory control (SSC) is proposed to synthesize the supportive modes in WTGs to guarantee performance. The concept, region of safety (ROS), is stated for safe switching synthesis. An optimization formula is proposed to calculate the largest ROS. By assuming a polynomial structure, the problem can be solved by a sum of squares program. A feasible result will generate a polynomial, the zero sublevel set of which represents the ROS and is employed as the safety supervisor. A decentralized communication architecture is proposed for small-scale systems. Moreover, a scheduling loop is suggested so that the supervisor updates its boundary with respect to the renewable penetration level to be robust with respect to variations in system inertia. The proposed controller is first verified on a single-machine three-phase nonlinear microgrid, and then implemented on the IEEE 39-bus system. Both results indicate that the proposed framework and control configuration can guarantee adequate response without excessive conservativeness.
Geodesic Obstacle Representation of Graphs
Venue: arXiv cs.CG 2018
Year: 2018

An obstacle representation of a graph is a mapping of the vertices onto points in the plane and a set of connected regions of the plane (called obstacles) such that the straight-line segment connecting the points corresponding to two vertices does not intersect any obstacles if and only if the vertices are adjacent in the graph. The obstacle representation and its plane variant (in which the resulting representation is a plane straight-line embedding of the graph) have been extensively studied with the main objective of minimizing the number of obstacles. Recently, Biedl and Mehrabi (GD 2017) studied grid obstacle representations of graphs in which the vertices of the graph are mapped onto the points in the plane while the straight-line segments representing the adjacency between the vertices is replaced by the $L_1$ (Manhattan) shortest paths in the plane that avoid obstacles. In this paper, we introduce the notion of geodesic obstacle representations of graphs with the main goal of providing a generalized model, which comes naturally when viewing line segments as shortest paths in the Euclidean plane. To this end, we extend the definition of obstacle representation by allowing some obstacles-avoiding shortest path between the corresponding points in the underlying metric space whenever the vertices are adjacent in the graph. We consider both general and plane variants of geodesic obstacle representations (in a similar sense to obstacle representations) under any polyhedral distance function in $\mathbb{R}^d$ as well as shortest path distances in graphs. Our results generalize and unify the notions of obstacle representations, plane obstacle representations and grid obstacle representations, leading to a number of questions on such embeddings.
A Large-Scale Multi-Institutional Evaluation of Advanced Discrimination Algorithms for Buried Threat Detection in Ground Penetrating Radar
Venue: arXiv cs.CV 2018
Year: 2018

In this paper we consider the development of algorithms for the automatic detection of buried threats using ground penetrating radar (GPR) measurements. GPR is one of the most studied and successful modalities for automatic buried threat detection (BTD), and a large variety of BTD algorithms have been proposed for it. Despite this, large-scale comparisons of GPR-based BTD algorithms are rare in the literature. In this work we report the results of a multi-institutional effort to develop advanced buried threat detection algorithms for a real-world GPR BTD system. The effort involved five institutions with substantial experience with the development of GPR-based BTD algorithms. In this paper we report the technical details of the advanced algorithms submitted by each institution, representing their latest technical advances, and many state-of-the-art GPR-based BTD algorithms. We also report the results of evaluating the algorithms from each institution on the large experimental dataset used for development. The experimental dataset comprised 120,000 m^2 of GPR data using surface area, from 13 different lanes across two US test sites. The data was collected using a vehicle-mounted GPR system, the variants of which have supplied data for numerous publications. Using these results, we identify the most successful and common processing strategies among the submitted algorithms, and make recommendations for GPR-based BTD algorithm design.
Mobile Edge Computing for Cellular-Connected UAV: Computation Offloading and Trajectory Optimization
Venue: arXiv cs.IT 2018
Year: 2018

This paper studies a new mobile edge computing (MEC) setup where an unmanned aerial vehicle (UAV) is served by cellular ground base stations (GBSs) for computation offloading. The UAV flies between a give pair of initial and final locations, during which it needs to accomplish certain computation tasks by offloading them to some selected GBSs along its trajectory for parallel execution. Under this setup, we aim to minimize the UAV's mission completion time by optimizing its trajectory jointly with the computation offloading scheduling, subject to the maximum speed constraint of the UAV, and the computation capacity constraints at GBSs. The joint UAV trajectory and computation offloading optimization problem is, however, non-convex and thus difficult to be solved optimally. To tackle this problem, we propose an efficient algorithm to obtain a high-quality suboptimal solution. Numerical results show that the proposed design significantly reduces the UAV's mission completion time, as compared to benchmark schemes.