Networks in the mind – what communities reveal about the structure of the lexicon

The mental lexicon stores words and information about words. The lexicon is seen by many researchers as a network, where lexical units are nodes and the different links between the units are connections. Based on the analysis of a word association network, in this article we show that different kinds of associative connections exist in the mental lexicon. Our analysis is based on a word association database from the agglutinative language Hungarian. We use communities – closely knit groups – of the lexicon to provide evidence for the existence and coexistence of different connections. We search for communities in the database using two different algorithms, enabling us to see the overlapping (a word belongs to multiple communities) and non-overlapping (a word belongs to only one community) community structures. Our results show that the network of the lexicon is organized by semantic, phonetic, syntactic and grammatical connections, but encyclopedic knowledge and individual experiences are also shaping the associative structure. We also show that words may be connected not just by one, but more types of connections at the same time

GRAPES-DD: exploiting decision diagrams for index-driven search in biological graph databases

BACKGROUND: Graphs are mathematical structures widely used for expressing relationships among elements when representing biomedical and biological information. On top of these representations, several analyses are performed. A common task is the search of one substructure within one graph, called target. The problem is referred to as one-to-one subgraph search, and it is known to be NP-complete. Heuristics and indexing techniques can be applied to facilitate the search. Indexing techniques are also exploited in the context of searching in a collection of target graphs, referred to as one-to-many subgraph problem. Filter-and-verification methods that use indexing approaches provide a fast pruning of target graphs or parts of them that do not contain the query. The expensive verification phase is then performed only on the subset of promising targets. Indexing strategies extract graph features at a sufficient granularity level for performing a powerful filtering step. Features are memorized in data structures allowing an efficient access. Indexing size, querying time and filtering power are key points for the development of efficient subgraph searching solutions.RESULTS: An existing approach, GRAPES, has been shown to have good performance in terms of speed-up for both one-to-one and one-to-many cases. However, it suffers in the size of the built index. For this reason, we propose GRAPES-DD, a modified version of GRAPES in which the indexing structure has been replaced with a Decision Diagram. Decision Diagrams are a broad class of data structures widely used to encode and manipulate functions efficiently. Experiments on biomedical structures and synthetic graphs have confirmed our expectation showing that GRAPES-DD has substantially reduced the memory utilization compared to GRAPES without worsening the searching time.CONCLUSION: The use of Decision Diagrams for searching in biochemical and biological graphs is completely new and potentially promising thanks to their ability to encode compactly sets by exploiting their structure and regularity, and to manipulate entire sets of elements at once, instead of exploring each single element explicitly. Search strategies based on Decision Diagram makes the indexing for biochemical graphs, and not only, more affordable allowing us to potentially deal with huge and ever growing collections of biochemical and biological structures