The biological and biomedical communities have been developing highly
structured, rich data sets for representing, analyzing and integrating complex biomed-
ical knowledge on the semantic web. However, the complexity of the query languages
that have been developed to access these resources makes it diﬃcult for non-technical
users to explore the data sets that have been developed, limiting the utility and wide-
spread adoption of both the data sets and the query languages. We present VIQUEN,
a graphical query engine designed to allow users to express sophisticated queries, which
are then compiled into a more complex underlying query language. After the...
In this dissertation, I present three browsers that I have developed for the purpose
of exploring, understanding, and analyzing models, simulations, and ontologies in
biology and medicine. The ﬁrst browser visualizes multidimensional simulation data
as an animation. The second browser visualizes the equations of a complex model as
a network and puts structure and organization on top of equations and variables. The
third browser is an ontology viewer and editor, directly intended for the Foundational
Model of Anatomy (FMA), but applicable to other ontologies as well. This browser
has two contributions. First, it is a lightweight deliverable that lets someone...
To date there is a lack of a query processor that can access and manage spatial anatomical
knowledge for use in anatomy education and clinical practice. Such knowledge can derive from labeled
2D images that a spatial query processor can build into 3D models which can be reasoned with for
spatial information. In this case, the thorax is used as proof of concept. The processor can answer
questions like: 'Which structures are anterior to the heart?', thanks to spatial relations (e.g. anterior)
provided and defined by an anatomist and integrated into the system. A spatial-symbolic query engine is
Re, Chris; Brinkley, James F; Suciu, Dan
We describe a largely complete and efficient XQuery to SQL translation for XML publishing. Our translation supports the entire XQuery language, except for functions, if statements and upwards navigation axes. The system has three important properties. First, it preserves the correct XQuery semantics. This is accomplished by first translating XQuery into core-XQuery, using a complete XQuery implementation, Galax. Second, we optimize the resulting SQL queries. We develop a comprehensive framework for optimizing the XQuery to SQL translation, which is effective for a wide range of XQuery workloads. Third, our translation is platform independent. Our system achieves high degree of efficiency...
This study introduces new signal processing methods for extracting meaningful information from brain signals (functional magnetic resonance imaging and single unit recording) and proposes a content-based retrieval system for functional brain data. First, a new method that combines maximal overlapped discrete wavelet transforms (MODWT) and dynamic time warping (DTW) is presented as a solution for dynamically detecting the hemodynamic response from fMRI data. Second, a new method for neuron spike sorting is presented that uses the maximal overlap discrete wavelet transform and rotated principal component analysis. Third, a procedure to characterize firing patterns of neuron spikes from the human brain,...
Smith, Veronica S
Cortical stimulation mapping (CSM) studies have shown cortical locations for language function are highly variable from one subject to the next. Because no two cortical surfaces are alike and language is a higher order cognitive function, observed variability is attributable to a combination of functional and anatomical variation. If individual variation can be normalized, patterns of language organization may emerge that were heretofore hidden. In order to discover whether or not such patterns exist, computer-aided spatial normalization is required. Because CSM data has been collected on the cortical surface, we believe that a surface-based normalization method will provide more accurate...
Albright, Evan M
This thesis discusses two related topics, a system for generating scenes of 3-D anatomical structures, and the implementation of parallel algorithms for 3-D rendering. In an educational setting, 3-D scenes help students discover relationships between various anatomical structures. In a clinical environment, physicians can use 3-D scenes to examine how anatomical structures are effected by disease or injury.
In order for a scene generation system to be usable, scenes must be rendered as fast as possible. One approach to increase rendering performance is to use parallel algorithms to take advantage of multi-processor or multi-workstation architectures.
Jakobovits, Rex M
Hinshaw, Kevin P
Current medical imaging technology makes it possible to gather remarkably detailed three-dimensional data about an individual's anatomy. In domains ranging from education to clinical medicine, a common desire is the ability to examine selected structures from such volume datasets. This dissertation describes tools for performing the two key tasks in that process: reconstructing (or segmenting) specific structures from volume data and illustrating them in meaningful ways.
On the reconstruction side, this work offers new, in-depth analysis of two previously proposed methods for using shape knowledge to guide image segmentation. The ideas are generalized to create a 3D shape model, which is...