Sivan Yogev

Discovering Motifs in Ranked Lists of DNA Sequences

Computational methods for discovery of sequence elements that are enriched in a target set compared with a background set are fundamental in molecular biology research. One example is the discovery of transcription factor binding motifs that are inferred from ChIP–chip (chromatin immuno-precipitation on a microarray) measurements. Several major challenges in sequence motif discovery still require consideration: (i) the need for a principled approach to partitioning the data into target and background sets; (ii) the lack of rigorous models and of an exact p-value for measuring motif enrichment; (iii) the need for an appropriate framework for accounting for motif multiplicity; (iv) the tendency, in many of the existing methods, to report presumably significant motifs even when applied to randomly generated data. In this paper we present a statistical framework for discovering enriched sequence elements in ranked lists that resolves these four issues. We demonstrate the implementation of this framework in a software application, termed DRIM (discovery of rank imbalanced motifs), which identifies sequence motifs in lists of ranked DNA sequences. We applied DRIM to ChIP–chip and CpG methylation data and obtained the following results. (i) Identification of 50 novel putative transcription factor (TF) binding sites in yeast ChIP–chip data. The biological function of some of them was further investigated to gain new insights on transcription regulation networks in yeast. For example, our discoveries enable the elucidation of the network of the TF ARO80. Another finding concerns a systematic TF binding enhancement to sequences containing CA repeats. (ii) Discovery of novel motifs in human cancer CpG methylation data. Remarkably, most of these motifs are similar to DNA sequence elements bound by the Polycomb complex that promotes histone methylation. Our findings thus support a model in which histone methylation and CpG methylation are mechanistically linked. Overall, we demonstrate that the statistical framework embodied in the DRIM software tool is highly effective for identifying regulatory sequence elements in a variety of applications ranging from expression and ChIP–chip to CpG methylation data. DRIM is publicly available at http://bioinfo.cs.technion.ac.il/drim.

Personalized recommendation of social software items based on social relations

We study personalized recommendation of social software items, including bookmarked web-pages, blog entries, and communities. We focus on recommendations that are derived from the users social network. Social network information is collected and aggregated across different data sources within our organization. At the core of our research is a comparison between recommendations that are based on the users familiarity network and his/her similarity network. We also examine the effect of adding explanations to each recommended item that show related people and their relationship to the user and to the item. Evaluation, based on an extensive user survey with 290 participants and a field study including 90 users, indicates superiority of the familiarity network as a basis for recommendations. In addition, an important instant effect of explanations is found - interest rate in recommended items increases when explanations are provided.

Beyond basic faceted search

This paper extends traditional faceted search to support richer information discovery tasks over more complex data models. Our first extension adds exible, dynamic business intelligence aggregations to the faceted application, enabling users to gain insight into their data that is far richer than just knowing the quantities of documents belonging to each facet. We see this capability as a step toward bringing OLAP capabilities, traditionally supported by databases over relational data, to the domain of free-text queries over metadata-rich content. Our second extension shows how one can efficiently extend a faceted search engine to support correlated facets - a more complex information model in which the values associated with a document across multiple facets are not independent. We show that by reducing the problem to a recently solved tree-indexing scenario, data with correlated facets can be efficiently indexed and retrieved

Social search and discovery using a unified approach

This research explores new ways to augment the search and discovery of relations between Web 2.0 entities using multiple types and sources of social information. Our goal is to allow the search for all object types such as documents, persons and tags, while retrieving related objects of all types. We implemented a social-search engine using a unified approach, where the search space is expanded to represent heterogeneous information objects that are interrelated by several relation types. Our solution is based on multifaceted search, which provides an efficient update mechanism for relations between objects, as well as efficient search over the heterogeneous data. We describe a social search engine positioned within a large enterprise, applied over social data gathered from several Web 2.0 applications. We conducted a large user study with over 600 people to evaluate the contribution of social data for search. Our results demonstrate the high precision of social search results and confirm the strong relationship of users and tags to the topics retrieved.

Social networks and discovery in the enterprise (SaND)

Traditional information discovery methods are based on content: documents, terms, and the relationships between them. In Web 2.0, people come into play as they create documents and tags in many forms. Personalized search, social graphs, content and people recommendation, are some of the tasks that can take advantage of this newly formed ecosystem. The Social Networks and Discovery (SaND) platform is an aggregation tool for information discovery and analysis over social data gathered from Web 2.0 applications in the enterprise. It leverages complex relationships between content and people as surfaced through the social applications to unleash the value of information. Its integrated index supports combining content-based analysis and people-based analysis over a rich data foundation. Enterprise social data is easily modeled and ingested into SaND, and can be further combined with data from external social applications. This demo will present three main functions provided by SaND: Social search: SaND supports search over the social data using a unified approach [1] in which all system entities (documents, people, tags) are searchable and retrievable (See Figure 1). The search UI enables the searcher to get a wider view on the query topic through results from all entity types, while uncovering the relationships between the on-screen entities. Entity recommendation: SaND can be utilized to recommend people and content for the searcher (Figure 2 shows the “Do You Know” widget for people recommendation). People are recommended according to their “social similarity” relations with the searcher, e.g. organizational and friending ties, similar tagging activity and more. Similarly, content that is related to people that are “socially related” to the searcher is recommended as valuable interesting data. Personalization: Search results are personalized by considering the relations of retrieved entities with the searcher. Entities are ranked according to their relevance to the query as well as according to their relationship strength with the searcher.

Efficient indexing of versioned document sequences

Many information systems keep multiple versions of documents. Examples include content management systems, version control systems (e.g. ClearCase, CVS), Wikis, and backup and archiving solutions. Often, it is desired to enable free-text search over such repositories, i.e. to enable submitting queries that may match any version of any document. We propose an indexing method that takes advantage of the inherent redundancy present in versioned documents by solving a variant of the multiple sequence alignment problem. The scheme produces an index that is much more compact than a standard index that treats each version independently. In experiments over publicly available versioned data, our method achieved compaction ratios of 81% as compared with standard indexing, while supporting the same retrieval capabilities.

Towards expressive exploratory search over entity-relationship data

In this paper we describe a novel approach for exploratory search over rich entity-relationship data that utilizes a unique combination of expressive, yet intuitive, query language, faceted search, and graph navigation. We describe an extended faceted search solution which allows to index, search, and browse rich entity-relationship data. We report experimental results of an evaluation study, using a benchmark of several of entity-relationship datasets, demonstrating that our exploratory approach is both effective and efficient compared to other existing approaches.

Exploratory search over social-medical data

In this demo we shall present the IBM Patient Empowerment System (PES), and more specifically, its social-medical discovery sub-system. Social and medical data are represented using entities and relationships and are explored using a combination of expressive, yet intuitive, query language, faceted search, and ER graph navigation. While this demonstration focuses on the healthcare domain, the underlining search technology is generic and can be utilized in many other domains. Therefore, this demo has two main contributions. First, we present a novel entity-relationship indexing and retrieval solution, and discuss its implementation challenges. Second, the demonstration depicts a practical entity-relationship discovery technology in a real domain setting within a real IBM system.

Entity oriented search and exploration for cultural heritage collections: the EU cultura project

In this paper we describe an entity oriented search and exploration system that we are developing for the EU Cultura project.

CULTURA: A Metadata-Rich Environment to Support the Enhanced Interrogation of Cultural Collections

The increased digitisation of cultural collections, and their availability on the World Wide Web, has made access to these valuable documents much easier than ever before. However, despite the increased availability of access to cultural archives, curators still struggle to instigate and enhance engagement with these resources. The CULTURA project is actively addressing this issue through the development of a metadata-driven personalisation environment for navigating cultural collections and instigating collaborations. The corpus agnostic CULTURA environment also supports a full spectrum of users: ranging from professional researchers seeking patterns in the data and trying to answer complex queries; to interested members of the public who need help navigating a vast collection of resources. This paper discusses the state of the art in this area and the various innovative approaches used in the CULTURA project, with a special focus on how the underlying metadata helps facilitate its semantically rich environment.