SIA: A Scalable Interoperable Annotation Server for Biomedical Named Entities

Recent years showed a strong increase in biomedical sciences and an inherent increase in publication volume. Extraction of specific information from these sources requires highly sophisticated text mining and information extraction tools. However, the integration of freely available tools into customized workflows is often cumbersome and difficult. We describe SIA (Scalable Interoperable Annotation Server), our contribution to the BeCalm-Technical interoperability and performance of annotation servers (BeCalm-TIPS) task, a scalable, extensible, and robust annotation service. The system currently covers six named entity types (i.e., Chemicals, Diseases, Genes, miRNA, Mutations, and Organisms) and is freely available under Apache 2.0 license at https://github.com/Erechtheus/sia.

Sharing Hash Codes for Multiple Purposes

Locality sensitive hashing (LSH) is a powerful tool for sublinear-time approximate nearest neighbor search, and a variety of hashing schemes have been proposed for different dissimilarity measures. However, hash codes significantly depend on the dissimilarity, which prohibits users from adjusting the dissimilarity at query time. In this paper, we propose {multiple purpose LSH (mp-LSH) which shares the hash codes for different dissimilarities. mp-LSH supports L2, cosine, and inner product dissimilarities, and their corresponding weighted sums, where the weights can be adjusted at query time. It also allows us to modify the importance of pre-defined groups of features. Thus, mp-LSH enables us, for example, to retrieve similar items to a query with the user preference taken into account, to find a similar material to a query with some properties (stability, utility, etc.) optimized, and to turn on or off a part of multi-modal information (brightness, color, audio, text, etc.) in image/video retrieval. We theoretically and empirically analyze the performance of three variants of mp-LSH, and demonstrate their usefulness on real-world data sets.