Computer Sciences Commons^™

Data Assimilation And Prognostic Whole Ice Sheet Modelling With The Variationally Derived, Higher Order, Open Source, And Fully Parallel Ice Sheet Model Varglas, Douglas John Brinkerhoff, Jesse Johnson

Computer Science Faculty Publications

We introduce a novel, higher order, finite element

ice sheet model called VarGlaS (Variational Glacier Simulator),

which is built on the finite element framework FEniCS.

Contrary to standard procedure in ice sheet modelling, Var-

GlaS formulates ice sheet motion as the minimization of an

energy functional, conferring advantages such as a consistent

platform for making numerical approximations, a coherent

relationship between motion and heat generation, and implicit

boundary treatment. VarGlaS also solves the equations

of enthalpy rather than temperature, avoiding the solution of

a contact problem. Rather than include a lengthy model spinup

procedure, VarGlaS possesses an automated framework

for …

Integration Schemas For Constraint Answer Set Programming: A Case Study, Marcello Balduccini, Yuliya Lierler

Computer Science Faculty Publications

Recently, researchers in answer set programming and constraint programming spent significant efforts in the development of hybrid languages and solving algorithms combining the strengths of these traditionally separate fields. These efforts resulted in a new research area: constraint answer set programming (CASP). CASP languages and systems proved to be largely successful at providing efficient solutions to problems involving hybrid reasoning tasks, such as scheduling problems with elements of planning. Yet, the development of CASP systems is difficult, requiring non-trivial expertise in multiple areas. This suggests a need for a study identifying general development principles of hybrid systems. Once these principles …

Insights Into Spatial Sensitivities Of Ice Mass Response To Environmental Change From The Searise Ice Sheet Modeling Project I : Antarctica, Sophie Nowicki, Robert A. Bindschadler, Ayako Abe-Ouchi, Andy Aschwanden, Ed Bueler, Hyeungu Choi, Jim Fastook, Glen Granzow, Ralf Greve, Gail Gutowski, Ute Herzfeld, Charles Jackson, Jesse Johnson, Constantine Khroulev, Eric Larour, Anders Levermann, William Lipscomb, Maria A. Martin, Mathieu Morlighem, Byron R. Parizek, David Pollard, Stephen F. Price, Diandong Ren, Eric Rignot, Fuyuki Saito, Tatsuru Sato, Hakime Seddik, Helene Seroussi, Kunio Takahashi, Ryan Walker, Wei Li Wang

Computer Science Faculty Publications

Atmospheric, oceanic, and subglacial forcing scenarios from the Sea-level Response tovIce Sheet Evolution (SeaRISE) project are applied to six three-dimensional thermomechanical ice-sheet models to assess Antarctic ice sheet sensitivity over a 500 year timescale and to inform future modeling and field studies. Results indicate (i) growth with warming, except within low-latitude basins (where inland thickening is outpaced by marginal thinning); (ii) mass loss with enhanced sliding (with basins dominated by high driving stresses affected more than basins with low-surface-slope streaming ice); and (iii) mass loss with enhanced ice shelf melting (with changes in West Antarctica dominating the signal due to …

Insights Into Spatial Sensitivities Of Ice Mass Response To Environmental Change From The Searise Ice Sheet Modeling Project Ii : Greenland, Sophie Nowicki, Robert A. Bindschadler, Ayako Abe-Ouchi, Andy Aschwanden, Ed Bueler, Hyeungu Choi, Jim Fastook, Glen Granzow, Ralf Greve, Gail Gutowski, Ute Herzfeld, Charles Jackson, Jesse Johnson, Constantine Khroulev, Eric Larour, Anders Levermann, William Lipscomb, Maria A. Martin, Mathieu Morlighem, Byron R. Parizek, David Pollard, Stephen Price, Diandong Ren, Eric Rignot, Fuyuki Saito, Tatsuru Sato, Hakime Seddik, Helene Seroussi, Kunio Takahashi, Ryan Walker, Wei Li Wang

Computer Science Faculty Publications

The Sea-level Response to Ice Sheet Evolution (SeaRISE) effort explores the sensitivity of the current generation of ice sheet models to external forcing to gain insight into the potential future contribution to sea level from the Greenland and Antarctic ice sheets. All participating models simulated the ice sheet response to three types of external forcings: a change in oceanic condition, a warmer atmospheric environment, and enhanced basal lubrication. Here an analysis of the spatial response of the Greenland ice sheet is presented, and the impact of model physics and spin-up on the projections is explored. Although the modeled responses are …

Mebook: A Novel Device Using Video Self-Modeling To Enhance Literacy Among Children With Asd, Nchuaobah Ukaobah, Ju Shen, Sen-Ching S. Cheung

Computer Science Faculty Publications

The aim is to build a video application, MEBOOK, to overlay features of the protagonist on the face of the reader and replace the scene background with animated video pertinent to the story.

Ice-Sheet Model Sensitivities To Environmental Forcing And Their Use In Projecting Future Sea Level (The Searise Project), Robert A. Bindschadler, Sophie Nowicki, Ayako Abe-Ouchi, Andy Aschwanden, Hyeungu Choi, Jim Fastook, Glen Granzow, Ralf Greve, Gail Gutowski, Ute Herzfeld, Charles Jackson, Jesse Johnson, Constantine Khroulev, Anders Levermann, William H. Lipscomb, Maria A. Martin, Mathieu Morlighem, Byron R. Parizek, David Pollard, Stephen F. Price, Diandong Ren, Fuyuki Saito, Tatsuru Sato, Hakime Seddik, Helene Seroussi, Kunio Takahashi, Ryan Walker, Wei Li Wang

Computer Science Faculty Publications

Ten ice-sheet models are used to study sensitivity of the Greenland and Antarctic ice sheets to prescribed changes of surface mass balance, sub-ice-shelf melting and basal sliding. Results exhibit a large range in projected contributions to sea-level change. In most cases, the ice volume above flotation lost is linearly dependent on the strength of the forcing. Combinations of forcings can be closely approximated by linearly summing the contributions from single forcing experiments, suggesting that nonlinear feedbacks are modest. Our models indicate that Greenland is more sensitive than Antarctica to likely atmospheric changes in temperature and precipitation, while Antarctica is more …

Blackops: Increasing Confidence In Variant Detection Through Mappability Filtering, Christopher R. Cabanski, Matthew D. Wilkerson, Matthew Soloway, Joel S. Parker, Jinze Liu, Jan F. Prins, J. S. Marron, Charles M. Perou, D. Neil Hayes

Computer Science Faculty Publications

Identifying variants using high-throughput sequencing data is currently a challenge because true biological variants can be indistinguishable from technical artifacts. One source of technical artifact results from incorrectly aligning experimentally observed sequences to their true genomic origin (‘mismapping’) and inferring differences in mismapped sequences to be true variants. We developed BlackOPs, an open-source tool that simulates experimental RNA-seq and DNA whole exome sequences derived from the reference genome, aligns these sequences by custom parameters, detects variants and outputs a blacklist of positions and alleles caused by mismapping. Blacklists contain thousands of artifact variants that are indistinguishable from true variants and, …

Diffsplice: The Genome-Wide Detection Of Differential Splicing Events With Rna-Seq, Yin Hu, Yan Huang, Ying Du, Christian F. Orellana, Darshan Singh, Amy R. Johnson, Anaïs Monroy, Pei-Fen Kuan, Scott M. Hammond, Liza M. Hammond, Scott H. Randell, Derek Y. Chiang, D. Neil Hayes, Corbin Jones, Yufeng Liu, Jan F. Prins, Jinze Liu

Computer Science Faculty Publications

The RNA transcriptome varies in response to cellular differentiation as well as environmental factors, and can be characterized by the diversity and abundance of transcript isoforms. Differential transcription analysis, the detection of differences between the transcriptomes of different cells, may improve understanding of cell differentiation and development and enable the identification of biomarkers that classify disease types. The availability of high-throughput short-read RNA sequencing technologies provides in-depth sampling of the transcriptome, making it possible to accurately detect the differences between transcriptomes. In this article, we present a new method for the detection and visualization of differential transcription. Our approach does …

Fuel Efficient Computation In Passive Self-Assembly, Robert Schweller, Michael Sherman

Computer Science Faculty Publications

In this paper we show that passive self-assembly in the context of the tile self-assembly model is capable of performing fuel efficient, universal computation. The tile self-assembly model is a premiere model of self-assembly in which particles are modeled by four-sided squares with glue types assigned to each tile edge. The assembly process is driven by positive and negative force interactions between glue types, allowing for tile assemblies floating in the plane to combine and break apart over time. We refer to this type of assembly model as passive in that the constituent parts remain unchanged throughout the assembly process …

A Method For Identifying Personalized Representations In Web Archives, Mat Kelly, Justin F. Brunelle, Michele C. Weigle, Michael L. Nelson

Computer Science Faculty Publications

Web resources are becoming increasingly personalized — two different users clicking on the same link at the same time can see content customized for each individual user. These changes result in multiple representations of a resource that cannot be canonicalized in Web archives. We identify characteristics of this problem by presenting a potential solution to generalize personalized representations in archives. We also present our proof-of-concept prototype that analyzes WARC (Web ARChive) format files, inserts metadata establishing relationships, and provides archive users the ability to navigate on the additional dimension of environment variables in a modified Wayback Machine.

The 6th Computational Structural Bioinformatics Workshop Introduction, Jing He, Amarda Shehu, Nurit Haspel, Brian Chen

Computer Science Faculty Publications

No abstract provided.

Estimating Loop Length From Cryoem Images At Medium Resolutions, Andrew Mcknight, Dong Si, Kamal Al Nasr, Andrey Chemikov, Nikos Chrisochoides, Jing He

Computer Science Faculty Publications

Background: De novo protein modeling approaches utilize 3-dimensional (3D) images derived from electron cryomicroscopy (CryoEM) experiments. The skeleton connecting two secondary structures such as α-helices represent the loop in the 3D image. The accuracy of the skeleton and of the detected secondary structures are critical in De novo modeling. It is important to measure the length along the skeleton accurately since the length can be used as a constraint in modeling the protein.

Results: We have developed a novel computational geometric approach to derive a simplified curve in order to estimate the loop length along the skeleton. The method was …

Image-Level And Group-Level Models For Drosophila Gene Expression Pattern Annotation, Quian Sun, Sherin Muckatira, Lei Yuan, Shuiwang Ji, Stuart Newfeld, Sudhir Kumar, Jieping Ye

Computer Science Faculty Publications

Background: Drosophila melanogaster has been established as a model organism for investigating the developmental gene interactions. The spatio-temporal gene expression patterns of Drosophila melanogaster can be visualized by in situ hybridization and documented as digital images. Automated and efficient tools for analyzing these expression images will provide biological insights into the gene functions, interactions, and networks. To facilitate pattern recognition and comparison, many web-based resources have been created to conduct comparative analysis based on the body part keywords and the associated images. With the fast accumulation of images from high-throughput techniques, manual inspection of images will impose a serious impediment …

Computational Genetic Neuroanatomy Of The Developing Mouse Brain: Dimensionality Reduction, Visualization, And Clustering, Shuiwang Ji

Computer Science Faculty Publications

Background: The structured organization of cells in the brain plays a key role in its functional efficiency. This delicate organization is the consequence of unique molecular identity of each cell gradually established by precise spatiotemporal gene expression control during development. Currently, studies on the molecular-structural association are beginning to reveal how the spatiotemporal gene expression patterns are related to cellular differentiation and structural development.

Results: In this article, we aim at a global, data-driven study of the relationship between gene expressions and neuroanatomy in the developing mouse brain. To enable visual explorations of the high-dimensional data, we map the in …

Dinosolve: A Protein Disulfide Bonding Prediction Server Using Context-Based Features To Enhance Prediction Accuracy, Ashraf Yaseen, Yaohang Li

Computer Science Faculty Publications

Background: Disulfide bonds play an important role in protein folding and structure stability. Accurately predicting disulfide bonds from protein sequences is important for modeling the structural and functional characteristics of many proteins.

Methods: In this work, we introduce an approach of enhancing disulfide bonding prediction accuracy by taking advantage of context-based features. We firstly derive the first-order and second-order mean-force potentials according to the amino acid environment around the cysteine residues from large number of cysteine samples. The mean-force potentials are integrated as context-based scores to estimate the favorability of a cysteine residue in disulfide bonding state as well as …

A Mesh Generation And Machine Learning Framework For Drosophila Gene Expression Pattern Image Analysis, Wenlu Zhang, Daming Feng, Rongjian Li, Andrey Chernikov, Nikos Chrisochoides, Christopher Osgood, Charlotte Konikoff, Stuart Newfeld, Sudhir Kumar, Shuiwang Ji

Computer Science Faculty Publications

Background: Multicellular organisms consist of cells of many different types that are established during development. Each type of cell is characterized by the unique combination of expressed gene products as a result of spatiotemporal gene regulation. Currently, a fundamental challenge in regulatory biology is to elucidate the gene expression controls that generate the complex body plans during development. Recent advances in high-throughput biotechnologies have generated spatiotemporal expression patterns for thousands of genes in the model organism fruit fly Drosophila melanogaster. Existing qualitative methods enhanced by a quantitative analysis based on computational tools we present in this paper would provide …

Convergence Analysis Of Markov Chain Monte Carlo Linear Solvers Using Ulam--Von Neumann Algorithm, Hao Ji, Michael Mascagni, Yaohang Li

Computer Science Faculty Publications

The convergence of Markov chain--based Monte Carlo linear solvers using the Ulam--von Neumann algorithm for a linear system of the form x = Hx + b is investigated in this paper. We analyze the convergence of the Monte Carlo solver based on the original Ulam--von Neumann algorithm under the conditions that ||H|| < 1 as well as ρ(H) < 1, where ρ(H) is the spectral radius of H. We find that although the Monte Carlo solver is based on sampling the Neumann series, the convergence of Neumann series is not a sufficient condition for the convergence of the Monte Carlo solver. Actually, properties of H are not the only factors determining the convergence of the Monte Carlo solver; the underlying transition probability matrix plays an important role. An improper selection of the transition matrix may result in divergence even though the condition ||H|| <1 holds. However, if the condition ||H|| < 1 is satisfied, we show that there always exist certain transition matrices that guarantee convergence of the Monte Carlo solver. On the other hand, if ρ(H) <1 but ||H|| ≥ 1, the Monte Carlo linear solver may or may not converge. In particular, if the row sum ∑ n/j= 1|H_ij > 1 for every row in H or, more generally, ρ(H⁺) >1, where H⁺ is the nonnegative matrix where H+_ij = |H_ij|, we show that transition matrices leading to convergence of the Monte Carlo solver do not exist. Finally, given …

Conformational Sampling In Template Free Protein Loop Structure Modeling: An Overview, Yaohang Li

Computer Science Faculty Publications

Accurately modeling protein loops is an important step to predict three-dimensional structures as well as to understand functions of many proteins. Because of their high flexibility, modeling the three-dimensional structures of loops is difficult and is usually treated as a "mini protein folding problem" under geometric constraints. In the past decade, there has been remarkable progress in template-free loop structure modeling due to advances of computational methods as well as stably increasing number of known structures available in PDB. This mini review provides an overview on the recent computational approaches for loop structure modeling. In particular, we focus on the …

Intensity-Based Skeletonization Of Cryoem Gray-Scale Images Using A True Segmentation-Free Algorithm, Kamal Al Nasr, Chunmei Liu, Mugizi Rwebangira, Legand Burge, Jing He

Computer Science Faculty Publications

Cryo-electron microscopy is an experimental technique that is able to produce 3D gray-scale images of protein molecules. In contrast to other experimental techniques, cryo-electron microscopy is capable of visualizing large molecular complexes such as viruses and ribosomes. At medium resolution, the positions of the atoms are not visible and the process cannot proceed. The medium-resolution images produced by cryo-electron microscopy are used to derive the atomic structure of the proteins in de novo modeling. The skeletons of the 3D gray-scale images are used to interpret important information that is helpful in de novo modeling. Unfortunately, not all features of the …

Gpu-Optimized Code For Long-Term Simulations Of Beam-Beam Effects In Colliders, Y. Roblin, V. Morozov, B. Terzić, M. Aturban, D. Ranjan, M. Zubair

Computer Science Faculty Publications

We report on the development of the new code for long-term simulation of beam-beam effects in particle colliders. The underlying physical model relies on a matrix-based arbitrary-order symplectic particle tracking for beam transport and the Bassetti-Erskine approximation for beam-beam interaction. The computations are accelerated through a parallel implementation on a hybrid GPU/CPU platform. With the new code, a previously computationally prohibitive long-term simulations become tractable. We use the new code to model the proposed medium-energy electron-ion collider (MEIC) at Jefferson Lab.

A Technical Framework For Resource Synchronization, Martin Klein, Robert Sanderson, Herbert Van De Sompel, Simeon Warner, Bernhard Haslhofer, Carl Lagoze, Michael L. Nelson

Computer Science Faculty Publications

This is the second paper in D-Lib Magazine about the ResourceSync effort conducted by the National Information Standards Organization (NISO) and the Open Archives Initiative (OAI). The first part provided a perspective on the resource synchronization problem and introduced a template that organized possible components of a resource synchronization framework in a modular manner. This paper details a technical framework devised using that template.

Warcreate And Wail: Warc, Wayback, And Heritrix Made Easy, Mat Kelly, Michael L. Nelson, Michele C. Weigle

Computer Science Faculty Publications

[First slide]

The Problem

Institutional Tools, Personal Archivists

• ON YOUR MACHINE

-Complex to Operate

-Require Infrastructure

• DELEGATED TO INSTITUTIONS

-$$$

-Lose original perspective

• Locale content tailoring (DC vs. San Francisco)
• Observation Medium (PC web browser vs. Crawler)

3dme: 3d Media Express From Rgb-D Images, Tam Nguyen, Lusong Li, Jun Tan, Shuicheng Yan

Computer Science Faculty Publications

Considering the continuously increasing availability and accessibility of 3D media and the depth camera such as Kinect, we demonstrate an innovative 3D media system called 3DME. The objective of this demo is three-fold.

First, the demo exhibits the creation of 3D images from RGB-D images. Second, 3DME allows a user to insert impressive effects to the produced 3D content. Last but not least, our demo is one of the first attempts toward advertising with 3D content.

Hi, Magic Closet, Tell Me What To Wear!, Si Liu, Tam Nguyen, Jiashi Feng, Meng Wang, Shuicheng Yan

Computer Science Faculty Publications

In this demo, we present a practical system, "magic closet," for automatic occasion-oriented clothing pairing. Given a user-input occasion, e.g., wedding or shopping, the magic closet intelligently and automatically pairs the user-specified reference clothing (upper body or lower body) with the most suitable one from online shops. Two key criteria are explicitly considered for the magic closet system. One criterion is to dress properly, e.g., compared to suit pants, it is more decent to wear a cocktail dress for a banquet occasion. The other criterion is to dress aesthetically, e.g., a red T-shirt matches better with white pants than with …

Sense Beauty Via Face, Dressing, And/Or Voice, Tam Nguyen, Si Liu, Bingbing Ni, Jun Tan, Yong Rui, Shuicheng Yan

Computer Science Faculty Publications

Discovering the secret of beauty has been the pursuit of artists and philosophers for centuries. Nowadays, the computational model for beauty estimation has been actively explored in computer science community, yet with the focus mainly on facial features. In this work, we perform a comprehensive study of female attractiveness conveyed by single/multiple modalities of cues, i.e., face, dressing, and/or voice, and aim to uncover how different modalities individually and collectively affect the human sense of beauty. To this end, we collect the first Multi-Modality Beauty (M²B) dataset in the world for female attractiveness study, which is thoroughly annotated …

Constraint Answer Set Programming, Yuliya Lierler

Computer Science Faculty Publications

Constraint answer set programming (CASP) is a novel, promising direction of research whose roots go back to propositional satisfiability (SAT). SAT solvers are efficient tools for solving boolean constraint satisfaction problems that arise in different areas of computer science, including software and hardware verification. Some constraints are more naturally expressed by non-boolean constructs. Satisfiability modulo theories (SMT) extends boolean satisfiability by the integration of non-boolean symbols defined by a background theory in another formalism, such as a constraint processing language. Answer set programming (ASP) extends computational methods of SAT in yet another way, inspired by ideas from knowledge representation, logic …

Improving Stem Education In Research: Preliminary Report On The Development Of A Computer-Assisted Student-Mentor Research Community, David A. Rios, Artem Chebotko, Christine Reilly, Ralph Carlson, Emmett Tomai, Amy A. Weimer, Nicholas Weimer, Thomas Pearson, Francis Andoh-Baidoo, Robert Winkle, David Ammons, Joanne Rampersad-Ammons

Computer Science Faculty Publications

Research education in STEM disciplines currently suffers from 1) The inability to feasibly collect highly detailed data on both the student’s and mentor’s activities; 2) The lack of tools to assist students and mentors in organizing and managing their research activities and environments; and 3) The inability to correlate a student’s assessment results with their actual research activities. Together these three problems act to impede both the improvement and educational quality of student research experiences. We propose a computer-assisted student-mentor research community as a solution to these problems. Within this community setting, students and their mentors are provided tools to …

Online Bottleneck Matching, Barbara Anthony, Christine Chung

Computer Science Faculty Publications

No abstract provided.

A Novel Dataset-Similarity-Aware Approach For Evaluating Stability Of Software Metric Selection Techniques, Taghi M. Khoshgoftaar, Huanjing Wang, Randall Wald, Amri Napolitano

Computer Science Faculty Publications

Software metric (feature) selection is an important preprocessing step before building software defect prediction models. Although much research has been done analyzing the classification performance of feature selection methods, fewer works have focused on their stability (robustness). Stability is important because feature selection methods which reliably produce the same results despite changes to the data are more trustworthy. Of the papers studying stability, most either compare the features chosen from different random subsamples of the dataset or compare each random subsample with the original dataset. These either result in an unknown degree of overlap between the subsamples, or comparing datasets …

Representing First-Order Causal Theories By Logic Programs, Paolo Ferrarris, Joohyung Lee, Yuliya Lierler, Vladimir Lifschitz, Fangkai Yang

Computer Science Faculty Publications

Nonmonotonic causal logic, introduced by McCain and Turner (McCain, N. and Turner, H. 1997. Causal theories of action and change. In Proceedings of National Conference on Artificial Intelligence (AAAI), Stanford, CA, 460–465) became the basis for the semantics of several expressive action languages. McCain's embedding of definite propositional causal theories into logic programming paved the way to the use of answer set solvers for answering queries about actions described in such languages. In this paper we extend this embedding to nondefinite theories and to the first-order causal logic.