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Ilya Safro

Publications and source records attributed to Ilya Safro.

At least 91 records · Page 5Linked to original sources
arXiv2019

Relaxation-Based Coarsening for Multilevel Hypergraph Partitioning

Multilevel partitioning methods that are inspired by principles of multiscaling are the most powerful practical hypergraph partitioning solvers. Hypergraph partitioning has many applications in disciplines ranging from scientific computing to data science. In this paper we introduce the concept of algebraic distance on hypergraphs and demonstrate its use as an algorithmic component in the coarsening stage of multilevel hypergraph partitioning solvers. The algebraic distance is a vertex distance measure that extends hyperedge weights for capturing the local connectivity of vertices which is critical for hypergraph coarsening schemes. The practical effectiveness of the proposed measure and corresponding coarsening scheme is demonstrated through extensive computational experiments on a diverse set of problems. Finally, we propose a benchmark of hypergraph partitioning problems to compare the quality of other solvers.

cs.DM↗
arXiv2018

Large-Scale Validation of Hypothesis Generation Systems via Candidate Ranking

The first step of many research projects is to define and rank a short list of candidates for study. In the modern rapidity of scientific progress, some turn to automated hypothesis generation (HG) systems to aid this process. These systems can identify implicit or overlooked connections within a large scientific corpus, and while their importance grows alongside the pace of science, they lack thorough validation. Without any standard numerical evaluation method, many validate general-purpose HG systems by rediscovering a handful of historical findings, and some wishing to be more thorough may run laboratory experiments based on automatic suggestions. These methods are expensive, time consuming, and cannot scale. Thus, we present a numerical evaluation framework for the purpose of validating HG systems that leverages thousands of validation hypotheses. This method evaluates a HG system by its ability to rank hypotheses by plausibility; a process reminiscent of human candidate selection. Because HG systems do not produce a ranking criteria, specifically those that produce topic models, we additionally present novel metrics to quantify the plausibility of hypotheses given topic model system output. Finally, we demonstrate that our proposed validation method aligns with real-world research goals by deploying our method within Moliere, our recent topic-driven HG system, in order to automatically generate a set of candidate genes related to HIV-associated neurodegenerative disease (HAND). By performing laboratory experiments based on this candidate set, we discover a new connection between HAND and Dead Box RNA Helicase 3 (DDX3). Reproducibility: code, validation data, and results can be found at sybrandt.com/2018/validation.

cs.IR↗
arXiv2018

Spatio-temporal prediction of crimes using network analytic approach

It is quite evident that majority of the population lives in urban area today than in any time of the human history. This trend seems to increase in coming years. A study [5] says that nearly 80.7% of total population in USA stays in urban area. By 2030 nearly 60% of the population in the world will live in or move to cities. With the increase in urban population, it is important to keep an eye on criminal activities. By doing so, governments can enforce intelligent policing systems and hence many government agencies and local authorities have made the crime data publicly available. In this paper, we analyze Chicago city crime data fused with other social information sources using network analytic techniques to predict criminal activity for the next year. We observe that as we add more layers of data which represent different aspects of the society, the quality of prediction is improved. Our prediction models not just predict total number of crimes for the whole Chicago city, rather they predict number of crimes for all types of crimes and for different regions in City of Chicago.

stat.AP↗
arXiv2018

Are Abstracts Enough for Hypothesis Generation?

The potential for automatic hypothesis generation (HG) systems to improve research productivity keeps pace with the growing set of publicly available scientific information. But as data becomes easier to acquire, we must understand the effect different textual data sources have on our resulting hypotheses. Are abstracts enough for HG, or does it need full-text papers? How many papers does an HG system need to make valuable predictions? How sensitive is a general-purpose HG system to hyperparameter values or input quality? What effect does corpus size and document length have on HG results? To answer these questions we train multiple versions of knowledge network-based HG system, Moliere, on varying corpora in order to compare challenges and trade offs in terms of result quality and computational requirements. Moliere generalizes main principles of similar knowledge network-based HG systems and reinforces them with topic modeling components. The corpora include the abstract and full-text versions of PubMed Central, as well as iterative halves of MEDLINE, which allows us to compare the effect document length and count has on the results. We find that, quantitatively, corpora with a higher median document length result in marginally higher quality results, yet require substantially longer to process. However, qualitatively, full-length papers introduce a significant number of intruder terms to the resulting topics, which decreases human interpretability. Additionally, we find that the effect of document length is greater than that of document count, even if both sets contain only paper abstracts. Reproducibility: Our code and data are available at github.com/jsybran/moliere, and bit.ly/2GxghpM respectively.

cs.IR↗
arXiv2018

Community Detection Across Emerging Quantum Architectures

One of the roadmap plans for quantum computers is an integration within HPC ecosystems assigning them a role of accelerators for a variety of computationally hard tasks. However, in the near term, quantum hardware will be in a constant state of change. Heading towards solving real-world problems, we advocate development of portable, architecture-agnostic hybrid quantum-classical frameworks and demonstrate one for the community detection problem evaluated using quantum annealing and gate-based universal quantum computation paradigms.

quant-ph↗
arXiv2018

Optimal Installation for Electric Vehicle Wireless Charging Lanes

Range anxiety, the persistent worry about not having enough battery power to complete a trip, remains one of the major obstacles to widespread electric-vehicle adoption. As cities look to attract more users to adopt electric vehicles, the emergence of wireless in-motion car charging technology presents itself as a solution to range anxiety. For a limited budget, cities could face the decision problem of where to install these wireless charging units. With a heavy price tag, an installation without a careful study can lead to inefficient use of limited resources. In this work, we model the installation of wireless charging units as an integer programming problem. We use our basic formulation as a building block for different realistic scenarios, carry out experiments using real geospatial data, and compare our results to different heuristics.

math.OC↗
arXiv2018

Aggregative Coarsening for Multilevel Hypergraph Partitioning

Algorithms for many hypergraph problems, including partitioning, utilize multilevel frameworks to achieve a good trade-off between the performance and the quality of results. In this paper we introduce two novel aggregative coarsening schemes and incorporate them within state-of-the-art hypergraph partitioner Zoltan. Our coarsening schemes are inspired by the algebraic multigrid and stable matching approaches. We demonstrate the effectiveness of the developed schemes as a part of multilevel hypergraph partitioning framework on a wide range of problems.

cs.DS↗
arXiv2017

Detecting and monitoring foodborne illness outbreaks: Twitter communications and the 2015 U.S. Salmonella outbreak linked to imported cucumbers

This research uses Twitter, as a social media device, to track communications related to the 2015 U.S. foodborne illness outbreak linked to Salmonella in imported cucumbers from Mexico. The relevant Twitter data are analyzed in light of the timeline of the official announcements made by the Centers for Disease Control and Prevention (CDC). The largest number of registered tweets is associated with the period immediately following the CDC initial announcement and the official release of the first recall of cucumbers.

stat.AP↗
arXiv2017

MOLIERE: Automatic Biomedical Hypothesis Generation System

Hypothesis generation is becoming a crucial time-saving technique which allows biomedical researchers to quickly discover implicit connections between important concepts. Typically, these systems operate on domain-specific fractions of public medical data. MOLIERE, in contrast, utilizes information from over 24.5 million documents. At the heart of our approach lies a multi-modal and multi-relational network of biomedical objects extracted from several heterogeneous datasets from the National Center for Biotechnology Information (NCBI). These objects include but are not limited to scientific papers, keywords, genes, proteins, diseases, and diagnoses. We model hypotheses using Latent Dirichlet Allocation applied on abstracts found near shortest paths discovered within this network, and demonstrate the effectiveness of MOLIERE by performing hypothesis generation on historical data. Our network, implementation, and resulting data are all publicly available for the broad scientific community.

cs.IR↗
arXiv2017

Generating realistic scaled complex networks

Research on generative models is a central project in the emerging field of network science, and it studies how statistical patterns found in real networks could be generated by formal rules. Output from these generative models is then the basis for designing and evaluating computational methods on networks, and for verification and simulation studies. During the last two decades, a variety of models has been proposed with an ultimate goal of achieving comprehensive realism for the generated networks. In this study, we (a) introduce a new generator, termed ReCoN; (b) explore how ReCoN and some existing models can be fitted to an original network to produce a structurally similar replica, (c) use ReCoN to produce networks much larger than the original exemplar, and finally (d) discuss open problems and promising research directions. In a comparative experimental study, we find that ReCoN is often superior to many other state-of-the-art network generation methods. We argue that ReCoN is a scalable and effective tool for modeling a given network while preserving important properties at both micro- and macroscopic scales, and for scaling the exemplar data by orders of magnitude in size.

cs.SI↗
arXiv2016

Algebraic multigrid support vector machines

The support vector machine is a flexible optimization-based technique widely used for classification problems. In practice, its training part becomes computationally expensive on large-scale data sets because of such reasons as the complexity and number of iterations in parameter fitting methods, underlying optimization solvers, and nonlinearity of kernels. We introduce a fast multilevel framework for solving support vector machine models that is inspired by the algebraic multigrid. Significant improvement in the running has been achieved without any loss in the quality. The proposed technique is highly beneficial on imbalanced sets. We demonstrate computational results on publicly available and industrial data sets.

stat.ML↗
arXiv2016

Detecting and Summarizing Emergent Events in Microblogs and Social Media Streams by Dynamic Centralities

Methods for detecting and summarizing emergent keywords have been extensively studied since social media and microblogging activities have started to play an important role in data analysis and decision making. We present a system for monitoring emergent keywords and summarizing a document stream based on the dynamic semantic graphs of streaming documents. We introduce the notion of dynamic eigenvector centrality for ranking emergent keywords, and present an algorithm for summarizing emergent events that is based on the minimum weight set cover. We demonstrate our system with an analysis of streaming Twitter data related to public security events.

cs.SI↗
arXiv2016

A Multilevel Bilinear Programming Algorithm For the Vertex Separator Problem

The Vertex Separator Problem for a graph is to find the smallest collection of vertices whose removal breaks the graph into two disconnected subsets that satisfy specified size constraints. In the paper 10.1016/j.ejor.2014.05.042, the Vertex Separator Problem was formulated as a continuous (non-concave/non-convex) bilinear quadratic program. In this paper, we develop a more general continuous bilinear program which incorporates vertex weights, and which applies to the coarse graphs that are generated in a multilevel compression of the original Vertex Separator Problem. A Mountain Climbing Algorithm is used to find a stationary point of the continuous bilinear quadratic program, while second-order optimality conditions and perturbation techniques are used to escape from either a stationary point or a local maximizer. The algorithms for solving the continuous bilinear program are employed during the solution and refinement phases in a multilevel scheme. Computational results and comparisons demonstrate the advantage of the proposed algorithm.

cs.DS↗
arXiv2016

Multilevel Weighted Support Vector Machine for Classification on Healthcare Data with Missing Values

This work is motivated by the needs of predictive analytics on healthcare data as represented by Electronic Medical Records. Such data is invariably problematic: noisy, with missing entries, with imbalance in classes of interests, leading to serious bias in predictive modeling. Since standard data mining methods often produce poor performance measures, we argue for development of specialized techniques of data-preprocessing and classification. In this paper, we propose a new method to simultaneously classify large datasets and reduce the effects of missing values. It is based on a multilevel framework of the cost-sensitive SVM and the expected maximization imputation method for missing values, which relies on iterated regression analyses. We compare classification results of multilevel SVM-based algorithms on public benchmark datasets with imbalanced classes and missing values as well as real data in health applications, and show that our multilevel SVM-based method produces fast, and more accurate and robust classification results.

stat.ML↗
arXiv2016

Single- and Multi-level Network Sparsification by Algebraic Distance

Network sparsification methods play an important role in modern network analysis when fast estimation of computationally expensive properties (such as the diameter, centrality indices, and paths) is required. We propose a method of network sparsification that preserves a wide range of structural properties. Depending on the analysis goals, the method allows to distinguish between local and global range edges that can be filtered out during the sparsification. First we rank edges by their algebraic distances and then we sample them. We also introduce a multilevel framework for sparsification that can be used to control the sparsification process at various coarse-grained resolutions. Based primarily on the matrix-vector multiplications, our method is easily parallelized for different architectures.

cs.SI↗
arXiv2015

Fast Imbalanced Classification of Healthcare Data with Missing Values

In medical domain, data features often contain missing values. This can create serious bias in the predictive modeling. Typical standard data mining methods often produce poor performance measures. In this paper, we propose a new method to simultaneously classify large datasets and reduce the effects of missing values. The proposed method is based on a multilevel framework of the cost-sensitive SVM and the expected maximization imputation method for missing values, which relies on iterated regression analyses. We compare classification results of multilevel SVM-based algorithms on public benchmark datasets with imbalanced classes and missing values as well as real data in health applications, and show that our multilevel SVM-based method produces fast, and more accurate and robust classification results.

stat.ML↗