Mining Images in Biomedical Publications: Detection and Analysis of Gel Diagrams

Authors of biomedical publications use gel images to report experimental results such as protein-protein interactions or protein expressions under different conditions. Gel images offer a concise way to communicate such findings, not all of which need to be explicitly discussed in the article text. This fact together with the abundance of gel images and their shared common patterns makes them prime candidates for automated image mining and parsing. We introduce an approach for the detection of gel images, and present a workflow to analyze them. We are able to detect gel segments and panels at high accuracy, and present preliminary results for the identification of gene names in these images. While we cannot provide a complete solution at this point, we present evidence that this kind of image mining is feasible.Comment: arXiv admin note: substantial text overlap with arXiv:1209.148

A Survey of Word Reordering in Statistical Machine Translation: Computational Models and Language Phenomena

Word reordering is one of the most difficult aspects of statistical machine translation (SMT), and an important factor of its quality and efficiency. Despite the vast amount of research published to date, the interest of the community in this problem has not decreased, and no single method appears to be strongly dominant across language pairs. Instead, the choice of the optimal approach for a new translation task still seems to be mostly driven by empirical trials. To orientate the reader in this vast and complex research area, we present a comprehensive survey of word reordering viewed as a statistical modeling challenge and as a natural language phenomenon. The survey describes in detail how word reordering is modeled within different string-based and tree-based SMT frameworks and as a stand-alone task, including systematic overviews of the literature in advanced reordering modeling. We then question why some approaches are more successful than others in different language pairs. We argue that, besides measuring the amount of reordering, it is important to understand which kinds of reordering occur in a given language pair. To this end, we conduct a qualitative analysis of word reordering phenomena in a diverse sample of language pairs, based on a large collection of linguistic knowledge. Empirical results in the SMT literature are shown to support the hypothesis that a few linguistic facts can be very useful to anticipate the reordering characteristics of a language pair and to select the SMT framework that best suits them.Comment: 44 pages, to appear in Computational Linguistic