Synonymous relationships among biomedical terms are extensively annotated within specialized terminologies, implying that synonymy is important for practical computational applications within this field. It remains unclear, however, whether text mining actually benefits from documented synonymy and whether existing biomedical thesauri provide adequate coverage of these linguistic relationships....

Biomedical computing applications often follow a computational pipeline: experimental data or image acquisition, mathematical modeling, geometric modeling (segmentation, mesh generation), material modeling, numerical approximation (finite element analysis, linear solvers, nonlinear optimization), visualization (of the geometric model, material model, and solutions), and validation. An important...

Biomedicine is an impressively fast developing, interdisciplinary field of research. To control the growing volumes of biomedical data, ontologies are increasingly used as common organization structures. Biomedical ontologies describe domain knowledge in a formal, computationally accessible way. They serve as controlled vocabularies and background knowledge in applications dealing with the inte...

This paper presents a probabilistic model for resolution of non-pronominal anaphora in biomedical texts. The model seeks to find the antecedents of anaphoric expressions, both coreferent and associative ones, and also to identify discourse-new expressions. We consider only the noun phrases referring to biomedical entities. The model reaches state-of-the art performance: 5669% precision and 54-6...

The traditional shell chicken chorioallantoic membrane (CAM) model has been used extensively in cancer research to study tumor growth and angiogenesis. Here we present a combined in vivo tumor spheroid and shell-less CAM three-dimensional model for use in quantitative and qualitative analysis. With this model, the angiogenic and tumorigenic environments can be generated locally without exogenou...