The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Data Mining - Concepts and Techniques.

We will review some of the major results in random graphs and some of the more challenging open problems. We will cover algorithmic and structural questions. We will touch on newer models, including those related to the WWW.

Random graphs

In most natural and engineered systems, a set of entities interact with each other in complicated patterns that can encompass multiple types of relationships, change in time, and include other types of complications Such systems include multiple subsystems and layers of connectivity, and it is important to take such "multilayer" features into account to try to improve our understanding of complex systems Consequently, it is necessary to generalize "traditional" network theory by developing (and validating) a framework and associated tools to study multilayer systems in a comprehensive fashion The origins of such efforts date back several decades and arose in multiple disciplines, and now the study of multilayer networks has become one of the most important directions in network science In this paper, we discuss the history of multilayer networks (and related concepts) and review the exploding body of work on such networks To unify the disparate terminology in the large body of recent work, we discuss a general framework for multilayer networks, construct a dictionary of terminology to relate the numerous existing concepts to each other, and provide a thorough discussion that compares, contrasts, and translates between related notions such as multilayer networks, multiplex networks, interdependent networks, networks of networks, and many others We also survey and discuss existing data sets that can be represented as multilayer networks We review attempts to generalize single-layer-network diagnostics to multilayer networks We also discuss the rapidly expanding research on multilayer-network models and notions like community structure, connected components, tensor decompositions, and various types of dynamical processes on multilayer networks We conclude with a summary and an outlook

Multilayer Networks

The Grid 2: Blueprint for a New Computing Infrastructure

Geolocation of Internet hosts enables a new class of location-aware applications. Previous measurement-based approaches use reference hosts, called landmarks, with a well-known geographic location to provide the location estimation of a target host. This leads to a discrete space of answers, limiting the number of possible location estimates to the number of adopted landmarks. In contrast, we propose Constraint-Based Geolocation (CBG), which infers the geographic location of Internet hosts using multilateration with distance constraints to establish a continuous space of answers instead of a discrete one. However, to use multilateration in the Internet, the geographic distances from the landmarks to the target host have to be estimated based on delay measurements between these hosts. This is a challenging problem because the relationship between network delay and geographic distance in the Internet is perturbed by many factors, including queueing delays and the absence of great-circle paths between hosts. CBG accurately transforms delay measurements to geographic distance constraints, and then uses multilateration to infer the geolocation of the target host. Our experimental results show that CBG outperforms previous geolocation techniques. Moreover, in contrast to previous approaches, our method is able to assign a confidence region to each given location estimate. This allows a location-aware application to assess whether the location estimate is sufficiently accurate for its needs.

Constraint-based geolocation of internet hosts

We present a novel and complete tool-set for evaluating the delivery quality of MPEG video transmissions in simulations of a network environment. This tool-set is based on the EvalVid framework. We extend the connecting interfaces of EvalVid to replace its simple error simulation model by a more general network simulator like NS2. With this combination, researchers and practitioners in general can analyze through simulation the performance of real video streams, i.e. taking into account the video semantics, under a large range of network scenarios. To demonstrate the usefulness of our new tool-set, we point out that it enables the investigation of the relationship between two popular objective metrics for Quality of Service (QoS) assessment of video quality delivery: the PSNR (Peak Signal to Noise Ratio) and the fraction of decodable frames. The results show that the fraction of decodable frames reflects well the behavior of the PSNR metric, while being less time-consuming. Therefore, the fraction of decodable frames can be an alternative metric to objectively assess through simulations the delivery quality of transmission in a network of publicly available video trace files.

An Evaluation Framework for More Realistic Simulations of MPEG Video Transmission

Geolocation of Internet hosts enables a diverse and interesting new class of location-aware applications. Previous measurement-based approaches use reference hosts, called landmarks, with a well-known geographic location to provide the location estimation of a target host. This leads to a discrete space of answers, limiting the number of possible location estimates to the number of adopted landmarks. In contrast, we propose Constraint-Based Geolocation (CBG), which infers the geographic location of Internet hosts using multilateration with distance constraints, thus establishing a continuous space of answers instead of a discrete one. CBG accurately transforms delay measurements to geographic distance constraints, and then uses multilateration to infer the geolocation of the target host. Our experimental results show that CBG outperforms the previous measurement-based geolocation techniques. Moreover, in contrast to previous approaches, our method is able to assign a confidence region to each given location estimate. This allows a location-aware application to assess whether the location estimate is sufficiently accurate for its needs.

/pdf/constraint-based-geolocation-of-internet-hosts-3n1h4uot7g.pdf

Indiscriminated packet discards strongly degrade the quality perceived by end users of MPEG video transmissions. This paper investigates different Quality of Service (QoS) schemes and the tradeoffs of jointly adopting such schemes to improve the delivery quality of an MPEG stream. From an analytical model, we evaluate the impact of frame losses on the quality of MPEG streams and on the waste of network resources. Our assessment considers issues such as the use of redundancy by applying a Forward Error Correction (FEC) scheme to tolerate losses, the changing of the compression factor in MPEG encoding, the unequal protection of MPEG frames in a Differentiated Services environment, and how to evaluate the impact of network losses onto application quality. Results provide predicted bounds on the quality to be expected by end users as well as guidelines on how to take the best advantage from the joint adoption of the investigated QoS schemes.

Joint Adoption of QoS Schemes for MPEG Streams

We present the algebraic representation and basic algorithms for MultiAspect Graphs (MAGs). A MAG is a structure capable of representing multilayer and time-varying networks, as well as higher-order networks, while also having the property of being isomorphic to a directed graph. In particular, we show that, as a consequence of the properties associated with the MAG structure, a MAG can be represented in matrix form. Moreover, we also show that any possible MAG function (algorithm) can be obtained from this matrix-based representation. This is an important theoretical result since it paves the way for adapting well-known graph algorithms for application in MAGs. We present a set of basic MAG algorithms, constructed from well-known graph algorithms, such as degree computing, Breadth First Search (BFS), and Depth First Search (DFS). These algorithms adapted to the MAG context can be used as primitives for building other more sophisticated MAG algorithms. Therefore, such examples can be seen as guidelines on how to properly derive MAG algorithms from basic algorithms on directed graphs. We also make available Python implementations of all the algorithms presented in this paper.

/pdf/multiaspect-graphs-algebraic-representation-and-algorithms-1vjx4leahp.pdf

Artur Ziviani

Papers

Constraint-based geolocation of internet hosts

An Evaluation Framework for More Realistic Simulations of MPEG Video Transmission

Constraint-based geolocation of internet hosts

Joint Adoption of QoS Schemes for MPEG Streams

MultiAspect Graphs: Algebraic Representation and Algorithms