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)

Social Network Analysis

KEGG(Kyoto Encyclopedia of Genes and Genomes)〔和文〕 (特集 ゲノム医学の現在と未来--基礎と臨床) -- (データベース)

Matrix Factorization Techniques for Recommender Systems

In the real world, a realistic setting for computer vision or multimedia recognition problems is that we have some classes containing lots of training data and many classes contain a small amount of training data. Therefore, how to use frequent classes to help learning rare classes for which it is harder to collect the training data is an open question. Learning with Shared Information is an emerging topic in machine learning, computer vision and multimedia analysis. There are different level of components that can be shared during concept modeling and machine learning stages, such as sharing generic object parts, sharing attributes, sharing transformations, sharing regularization parameters and sharing training examples, etc. Regarding the specific methods, multi-task learning, transfer learning and deep learning can be seen as using different strategies to share information. These learning with shared information methods are very effective in solving real-world large-scale problems. This special issue aims at gathering the recent advances in learning with shared information methods and their applications in computer vision and multimedia analysis. Both state-of-the-art works, as well as literature reviews, are welcome for submission. Papers addressing interesting real-world computer vision and multimedia applications are especially encouraged. Topics of interest include, but are not limited to:  • Multi-task learning or transfer learning for large-scale computer vision and multimedia analysis • Deep learning for large-scale computer vision and multimedia analysis • Multi-modal approach for large-scale computer vision and multimedia analysis • Different sharing strategies, e.g., sharing generic object parts, sharing attributes, sharing transformations, sharing regularization parameters and sharing training examples, • Real-world computer vision and multimedia applications based on learning with shared information, e.g., event detection, object recognition, object detection, action recognition, human head pose estimation, object tracking, location-based services, semantic indexing. • New datasets and metrics to evaluate the benefit of the proposed sharing ability for the specific computer vision or multimedia problem. • Survey papers regarding the topic of learning with shared information.  Authors who are unsure whether their planned submission is in scope may contact the guest editors prior to the submission deadline with an abstract, in order to receive feedback.

IEEE transactions on pattern analysis and machine intelligence

Serious concerns on privacy protection in social networks have been raised in recent years; however, research in this area is still in its infancy. The problem is challenging due to the diversity and complexity of graph data, on which an adversary can use many types of background knowledge to conduct an attack. One popular type of attacks as studied by pioneer work [2] is the use of embedding subgraphs. We follow this line of work and identify two realistic targets of attacks, namely, NodeInfo and LinkInfo. Our investigations show that k-isomorphism, or anonymization by forming k pairwise isomorphic subgraphs, is both sufficient and necessary for the protection. The problem is shown to be NP-hard. We devise a number of techniques to enhance the anonymization efficiency while retaining the data utility. A compound vertex ID mechanism is also introduced for privacy preservation over multiple data releases. The satisfactory performance on a number of real datasets, including HEP-Th, EUemail and LiveJournal, illustrates that the high symmetry of social networks is very helpful in mitigating the difficulty of the problem.

/pdf/k-isomorphism-privacy-preserving-network-publication-against-1xktb3hpxo.pdf

K-isomorphism: privacy preserving network publication against structural attacks

Graph clustering, also known as community detection, is a long-standing problem in data mining. However, with the proliferation of rich attribute information available for objects in real-world graphs, how to leverage structural and attribute information for clustering attributed graphs becomes a new challenge. Most existing works take a distance-based approach. They proposed various distance measures to combine structural and attribute information. In this paper, we consider an alternative view and propose a model-based approach to attributed graph clustering. We develop a Bayesian probabilistic model for attributed graphs. The model provides a principled and natural framework for capturing both structural and attribute aspects of a graph, while avoiding the artificial design of a distance measure. Clustering with the proposed model can be transformed into a probabilistic inference problem, for which we devise an efficient variational algorithm. Experimental results on large real-world datasets demonstrate that our method significantly outperforms the state-of-art distance-based attributed graph clustering method.

/pdf/a-model-based-approach-to-attributed-graph-clustering-2jstb13u7d.pdf

A model-based approach to attributed graph clustering

The k-truss is a type of cohesive subgraphs proposed recently for the study of networks. While the problem of computing most cohesive subgraphs is NP-hard, there exists a polynomial time algorithm for computing k-truss. Compared with k-core which is also efficient to compute, k-truss represents the "core" of a k-core that keeps the key information of, while filtering out less important information from, the k-core. However, existing algorithms for computing k-truss are inefficient for handling today's massive networks. We first improve the existing in-memory algorithm for computing k-truss in networks of moderate size. Then, we propose two I/O-efficient algorithms to handle massive networks that cannot fit in main memory. Our experiments on real datasets verify the efficiency of our algorithms and the value of k-truss.

/pdf/truss-decomposition-in-massive-networks-c8c12o8avh.pdf

Truss decomposition in massive networks

Graphs are prevalently used to model the relationships between objects in various domains. With the increasing usage of graph databases, it has become more and more demanding to efficiently process graph queries. Querying graph databases is costly since it involves subgraph isomorphism testing, which is an NP-complete problem. In recent years, some effective graph indexes have been proposed to first obtain a candidate answer set by filtering part of the false results and then perform verification on each candidate by checking subgraph isomorphism. Query performance is improved since the number of subgraph isomorphism tests is reduced. However, candidate verification is still inevitable, which can be expensive when the size of the candidate answer set is large. In this paper, we propose a novel indexing technique that constructs a nested inverted-index, called FG-index, based on the set of Frequent subGraphs (FGs). Given a graph query that is an FG in the database, FG-index returns the exact set of query answers without performing candidate verification. When the query is an infrequent graph, FG-index produces a candidate answer set which is close to the exact answer set. Since an infrequent graph means the graph occurs in only a small number of graphs in the database, the number of subgraph isomorphism tests is small. To ensure that the index fits into the main memory, we propose a new notion of δ-Tolerance Closed Frequent Graphs (δ-TCFGs), which allows us to flexibly tune the size of the index in a parameterized way. Our extensive experiments verify that query processing using FG-index is orders of magnitude more efficient than using the state-of-the-art graph index.

/pdf/fg-index-towards-verification-free-query-processing-on-graph-3551z10uja.pdf

Fg-index: towards verification-free query processing on graph databases

The k-core of a graph is the largest subgraph in which every vertex is connected to at least k other vertices within the subgraph. Core decomposition finds the k-core of the graph for every possible k. Past studies have shown important applications of core decomposition such as in the study of the properties of large networks (e.g., sustainability, connectivity, centrality, etc.), for solving NP-hard problems efficiently in real networks (e.g., maximum clique finding, densest subgraph approximation, etc.), and for large-scale network fingerprinting and visualization. The k-core is a well accepted concept partly because there exists a simple and efficient algorithm for core decomposition, by recursively removing the lowest degree vertices and their incident edges. However, this algorithm requires random access to the graph and hence assumes the entire graph can be kept in main memory. Nevertheless, real-world networks such as online social networks have become exceedingly large in recent years and still keep growing at a steady rate. In this paper, we propose the first external-memory algorithm for core decomposition in massive graphs. When the memory is large enough to hold the graph, our algorithm achieves comparable performance as the in-memory algorithm. When the graph is too large to be kept in the memory, our algorithm requires only O(k max ) scans of the graph, where k max is the largest core number of the graph. We demonstrate the efficiency of our algorithm on real networks with up to 52.9 million vertices and 1.65 billion edges.

/pdf/efficient-core-decomposition-in-massive-networks-58kls9agof.pdf

James Cheng

Papers

K-isomorphism: privacy preserving network publication against structural attacks

A model-based approach to attributed graph clustering

Truss decomposition in massive networks

Fg-index: towards verification-free query processing on graph databases

Efficient core decomposition in massive networks