O. A. von Lilienfeld, R. Ramakrishanan, M., A. Knoll. Fourier Series of Atomic Radial Distribution Functions: A Molecular Fingerprint for Machine Learning Models of Quantum Chemical Properties, In International Journal of Quantum Chemistry, Wiley Online Library, 2015.
We introduce a fingerprint representation of molecules based on a Fourier series of atomic radial distribution functions. This fingerprint is unique (except for chirality), continuous, and differentiable with respect to atomic coordinates and nuclear charges. It is invariant with respect to translation, rotation, and nuclear permutation, and requires no pre-conceived knowledge about chemical bonding, topology, or electronic orbitals. As such it meets many important criteria for a good molecular representation, suggesting its usefulness for machine learning models of molecular properties trained across chemical compound space. To assess the performance of this new descriptor we have trained machine learning models of molecular enthalpies of atomization for training sets with up to 10 k organic molecules, drawn at random from a published set of 134 k organic molecules with an average atomization enthalpy of over 1770 kcal/mol. We validate the descriptor on all remaining molecules of the 134 k set. For a training set of 10k molecules the fingerprint descriptor achieves a mean absolute error of 8.0 kcal/mol, respectively. This is slightly worse than the performance attained using the Coulomb matrix, another popular alternative, reaching 6.2 kcal/mol for the same training and test sets.
S. Liu, D. Maljovec, Bei Wang, P. T. Bremer, V. Pascucci. Visualizing High-Dimensional Data: Advances in the Past Decade, In State of The Art Report, Eurographics Conference on Visualization (EuroVis), 2015.
S. Liu, Bei Wang, J. J. Thiagarajan, P. T. Bremer, V. Pascucci.
Visual Exploration of High-Dimensional Data through Subspace Analysis and Dynamic Projections, In Computer Graphics Forum, Vol. 34, No. 3, Wiley-Blackwell, pp. 271--280. June, 2015.
CIBC. Note: map3d: Interactive scientific visualization tool for bioengineering data. Scientific Computing and Imaging Institute (SCI), Download from: http://www.sci.utah.edu/cibc/software.html, 2015.
s-CorrPlot: An Interactive Scatterplot for Exploring Correlation, In Journal of Computational and Graphical Statistics, 2015.
Disjunctive Normal Shape and Appearance Priors with Applications to Image Segmentation, In Lecture Notes in Computer Science, Springer International Publishing, pp. 703--710. 2015.
The use of appearance and shape priors in image segmentation is known to improve accuracy; however, existing techniques have several drawbacks. Active shape and appearance models require landmark points and assume unimodal shape and appearance distributions. Level set based shape priors are limited to global shape similarity. In this paper, we present a novel shape and appearance priors for image segmentation based on an implicit parametric shape representation called disjunctive normal shape model (DNSM). DNSM is formed by disjunction of conjunctions of half-spaces defined by discriminants. We learn shape and appearance statistics at varying spatial scales using nonparametric density estimation. Our method can generate a rich set of shape variations by locally combining training shapes. Additionally, by studying the intensity and texture statistics around each discriminant of our shape model, we construct a local appearance probability map. Experiments carried out on both medical and natural image datasets show the potential of the proposed method.
SCI Institute. Note: NCR Toolset: A collection of software tools for the reconstruction and visualization of neural circuitry from electron microscopy data. Scientific Computing and Imaging Institute (SCI). Download from: http://www.sci.utah.edu/software.html, 2015.
Geographical datasets are ubiquitous in oceanography. While map-based visualizations are useful for many different domains, they can suffer from cluttering and overplotting issues when used for multivariate data sets. As a result, spatial data exploration in oceanography has often been restricted to multiple maps showing various depths or time intervals. This lack of interactive exploration often hinders efforts to expose correlations between properties of oceanographic features, specifically currents. OceanPaths provides powerful interaction and exploration methods for spatial, multivariate oceanography datasets to remedy these situations. Fundamentally, our method allows users to define pathways, typically following currents, along which the variation of the high-dimensional data can be plotted efficiently. We present a case study conducted by domain experts to underscore the usefulness of OceanPaths in uncovering trends and correlations in oceanographic data sets.
Entropy-based particle correspondence for shape populations, In International Journal of Computer Assisted Radiology and Surgery, Springer, pp. 1-12. December, 2015.I. OguzI, J. Cates, M. Datar, B. Paniagua, T. Fletcher, C. Vachet, M. Styner, R. Whitaker.
Statistical shape analysis of anatomical structures plays an important role in many medical image analysis applications such as understanding the structural changes in anatomy in various stages of growth or disease. Establishing accurate correspondence across object populations is essential for such statistical shape analysis studies.
In this paper, we present an entropy-based correspondence framework for computing point-based correspondence among populations of surfaces in a groupwise manner. This robust framework is parameterization-free and computationally efficient. We review the core principles of this method as well as various extensions to deal effectively with surfaces of complex geometry and application-driven correspondence metrics.
We apply our method to synthetic and biological datasets to illustrate the concepts proposed and compare the performance of our framework to existing techniques.
Through the numerous extensions and variations presented here, we create a very flexible framework that can effectively handle objects of various topologies, multi-object complexes, open surfaces, and objects of complex geometry such as high-curvature regions or extremely thin features.
Poor scar formation after ablation is associated with atrial fibrillation recurrence, In Journal of Interventional Cardiac Electrophysiology, Vol. 44, No. 3, pp. 247-256. December, 2015.B.R. Parmar, T.R. Jarrett, E.G. Kholmovski, N. Hu, D. Parker, R.S. MacLeod, N.F. Marrouche, R. Ranjan.
Patients routinely undergo ablation for atrial fibrillation (AF) but the recurrence rate remains high. We explored in this study whether poor scar formation as seen on late-gadolinium enhancement magnetic resonance imaging (LGE-MRI) correlates with AF recurrence following ablation.
We retrospectively identified 94 consecutive patients who underwent their initial ablation for AF at our institution and had pre-procedural magnetic resonance angiography (MRA) merged with left atrial (LA) anatomy in an electroanatomic mapping (EAM) system, ablated areas marked intraprocedurally in EAM, 3-month post-ablation LGE-MRI for assessment of scar, and minimum of 3-months of clinical follow-up. Ablated area was quantified retrospectively in EAM and scarred area was quantified in the 3-month post-ablation LGE-MRI.
With the mean follow-up of 336 days, 26 out of 94 patients had AF recurrence. Age, hypertension, and heart failure were not associated with AF recurrence, but LA size and difference between EAM ablated area and LGE-MRI scar area was associated with higher AF recurrence. For each percent higher difference between EAM ablated area and LGE-MRI scar area, there was a 7–9 % higher AF recurrence (p values 0.001–0.003) depending on the multivariate analysis.
In AF ablation, poor scar formation as seen on LGE-MRI was associated with AF recurrence. Improved mapping and ablation techniques are necessary to achieve the desired LA scar and reduce AF recurrence.
Developing Uintah’s Runtime System For Forthcoming Architectures, Subtitled Refereed paper presented at the RESPA 15 Workshop at SuperComputing 2015 Austin Texas, SCI Institute, 2015.B. Peterson, N. Xiao, J. Holmen, S. Chaganti, A. Pakki, J. Schmidt, D. Sunderland, A. Humphrey, M. Berzins.
J. M. Phillips, Bei Wang, Y. Zheng. Geometric Inference on Kernel Density Estimates, In CoRR, Vol. abs/1307.7760, 2015.
S. Pujol, W. Wells, C. Pierpaoli, C. Brun, J. Gee, G. Cheng, B. Vemuri, O. Commowick, S. Prima, A. Stamm, M. Goubran, A. Khan, T. Peters, P. Neher, K. H. Maier-Hein, Y. Shi, A. Tristan-Vega, G. Veni, R. Whitaker, M. Styner, C.F. Westin, S. Gouttard, I. Norton, L. Chauvin, H. Mamata, G. Gerig, A. Nabavi, A. Golby,, R. Kikinis.
The DTI Challenge: Toward Standardized Evaluation of Diffusion Tensor Imaging Tractography for Neurosurgery, In Journal of Neuroimaging, Wiley, August, 2015.
M. Raj, M. Mirzargar, R. Kirby, R. Whitaker, J. Preston. Evaluating Alignment of Shapes by Ensemble Visualization, In IEEE Computer Graphics and Applications, IEEE, 2015.
The visualization of variability in 3D shapes or surfaces, which is a type of ensemble uncertainty visualization for volume data, provides a means of understanding the underlying distribution for a collection or ensemble of surfaces. While ensemble visualization for surfaces is already described in the literature, we conduct an expert-based evaluation in a particular medical imaging application: the construction of atlases or templates from a population of images. In this work, we extend contour boxplots to 3D, allowing us to evaluate it against an enumeration-style visualization of the ensemble members and also other conventional visualizations used by atlas builders, namely examining the atlas image and the corresponding images/data provided as part of the construction process. We present feedback from domain experts on the efficacy of contour boxplots compared to other modalities when used as part of the atlas construction and analysis stages of their work.
A novel implicit parametric shape model is proposed for segmentation and analysis of medical images. Functions representing the shape of an object can be approximated as a union of N polytopes. Each polytope is obtained by the intersection of M half-spaces. The shape function can be approximated as a disjunction of conjunctions, using the disjunctive normal form. The shape model is initialized using seed points defined by the user. We define a cost function based on the Chan-Vese energy functional. The model is differentiable, hence, gradient based optimization algorithms are used to find the model parameters.
D. Reed, M. Berzins, R. Lucas, S. Matsuoka, R. Pennington, V. Sarkar, V. Taylor.
DOE Advanced Scientific Computing Advisory Committee (ASCAC) Report: Exascale Computing Initiative Review, Note: DOE Report, 2015.
DOI: DOI 10.2172/1222712
H. J.V. Rutherford, G. Gerig, S. Gouttard, M. N. Potenza, L. C. Mayes. Investigating maternal brain structure and its relationship to substance use and motivational systems, In Yale Journal of Biology and Medicine, in print, 2015.
Substance use during pregnancy and the postpartum period may have significant implications for both mother and the developing child. However, the neurobiological basis of the impact of substance use on parenting is less well understood. Here we examined the impact of maternal substance use on cortical gray matter (GM) and white matter volumes, and whether this was associated with individual differences in motivational systems of behavioral activation and inhibition. Mothers were included in the substance-using group if any addictive substance was used during pregnancy and/or in the immediate postpartum period (within 3 months of delivery). GM volume was reduced in substance-using mothers compared to non-substance-using mothers, particularly in frontal brain regions. In substance-using mothers, we also found that frontal GM was negatively correlated with levels of behavioral activation (i.e., the motivation to approach rewarding stimuli). This effect was absent in non-substance-using mothers. Taken together, these findings indicate a reduction in GM volume is associated with substance use, and that frontal GM volumetric differences may be related to approach motivation in substance-using mothers.