Topological network alignment uncovers biological function and phylogeny

Sequence comparison and alignment has had an enormous impact on our understanding of evolution, biology, and disease. Comparison and alignment of biological networks will likely have a similar impact. Existing network alignments use information external to the networks, such as sequence, because no good algorithm for purely topological alignment has yet been devised. In this paper, we present a novel algorithm based solely on network topology, that can be used to align any two networks. We apply it to biological networks to produce by far the most complete topological alignments of biological networks to date. We demonstrate that both species phylogeny and detailed biological function of individual proteins can be extracted from our alignments. Topology-based alignments have the potential to provide a completely new, independent source of phylogenetic information. Our alignment of the protein-protein interaction networks of two very different species--yeast and human--indicate that even distant species share a surprising amount of network topology with each other, suggesting broad similarities in internal cellular wiring across all life on Earth.Comment: Algorithm explained in more details. Additional analysis adde

On the Effect of Semantically Enriched Context Models on Software Modularization

Many of the existing approaches for program comprehension rely on the linguistic information found in source code, such as identifier names and comments. Semantic clustering is one such technique for modularization of the system that relies on the informal semantics of the program, encoded in the vocabulary used in the source code. Treating the source code as a collection of tokens loses the semantic information embedded within the identifiers. We try to overcome this problem by introducing context models for source code identifiers to obtain a semantic kernel, which can be used for both deriving the topics that run through the system as well as their clustering. In the first model, we abstract an identifier to its type representation and build on this notion of context to construct contextual vector representation of the source code. The second notion of context is defined based on the flow of data between identifiers to represent a module as a dependency graph where the nodes correspond to identifiers and the edges represent the data dependencies between pairs of identifiers. We have applied our approach to 10 medium-sized open source Java projects, and show that by introducing contexts for identifiers, the quality of the modularization of the software systems is improved. Both of the context models give results that are superior to the plain vector representation of documents. In some cases, the authoritativeness of decompositions is improved by 67%. Furthermore, a more detailed evaluation of our approach on JEdit, an open source editor, demonstrates that inferred topics through performing topic analysis on the contextual representations are more meaningful compared to the plain representation of the documents. The proposed approach in introducing a context model for source code identifiers paves the way for building tools that support developers in program comprehension tasks such as application and domain concept location, software modularization and topic analysis

Extracting tag hierarchies

Tagging items with descriptive annotations or keywords is a very natural way to compress and highlight information about the properties of the given entity. Over the years several methods have been proposed for extracting a hierarchy between the tags for systems with a "flat", egalitarian organization of the tags, which is very common when the tags correspond to free words given by numerous independent people. Here we present a complete framework for automated tag hierarchy extraction based on tag occurrence statistics. Along with proposing new algorithms, we are also introducing different quality measures enabling the detailed comparison of competing approaches from different aspects. Furthermore, we set up a synthetic, computer generated benchmark providing a versatile tool for testing, with a couple of tunable parameters capable of generating a wide range of test beds. Beside the computer generated input we also use real data in our studies, including a biological example with a pre-defined hierarchy between the tags. The encouraging similarity between the pre-defined and reconstructed hierarchy, as well as the seemingly meaningful hierarchies obtained for other real systems indicate that tag hierarchy extraction is a very promising direction for further research with a great potential for practical applications.Comment: 25 pages with 21 pages of supporting information, 25 figure

Ontology-Based Quality Evaluation of Value Generalization Hierarchies for Data Anonymization

In privacy-preserving data publishing, approaches using Value Generalization Hierarchies (VGHs) form an important class of anonymization algorithms. VGHs play a key role in the utility of published datasets as they dictate how the anonymization of the data occurs. For categorical attributes, it is imperative to preserve the semantics of the original data in order to achieve a higher utility. Despite this, semantics have not being formally considered in the specification of VGHs. Moreover, there are no methods that allow the users to assess the quality of their VGH. In this paper, we propose a measurement scheme, based on ontologies, to quantitatively evaluate the quality of VGHs, in terms of semantic consistency and taxonomic organization, with the aim of producing higher-quality anonymizations. We demonstrate, through a case study, how our evaluation scheme can be used to compare the quality of multiple VGHs and can help to identify faulty VGHs.Comment: 18 pages, 7 figures, presented in the Privacy in Statistical Databases Conference 2014 (Ibiza, Spain

Document generality: its computation for ranking

The increased variety of information makes it critical to retrieve documents which are not only relevant but also broad enough to cover as many different aspects of a certain topic as possible. The increased variety of users also makes it critical to retrieve documents that are jargon free and easy-to-understand rather than the specific technical materials. In this paper, we propose a new concept namely document generality computation. Generality of document is of fundamental importance to information retrieval. Document generality is the state or quality of docu- ment being general. We compute document general- ity based on a domain-ontology method that analyzes scope and semantic cohesion of concepts appeared in the text. For test purposes, our proposed approach is then applied to improving the performance of doc- ument ranking in bio-medical information retrieval. The retrieved documents are re-ranked by a combined score of similarity and the closeness of documents’ generality to that of a query. The experiments have shown that our method can work on a large scale bio-medical text corpus OHSUMED (Hersh, Buckley, Leone & Hickam 1994), which is a subset of MEDLINE collection containing of 348,566 medical journal references and 101 test queries, with an encouraging performance