Now showing items 1-20 of 331

    • Rational curves over generalized complex numbers 

      Du, Juan; Goldman, Ron; Wang, Xuhui (2019)
      Complex rational curves have been used to represent circular splines as well as many classical curves including epicycloids, cardioids, Joukowski profiles, and the lemniscate of Bernoulli. Complex rational curves are known ...
    • Point-Based Policy Synthesis for POMDPs With Boolean and Quantitative Objectives 

      Wang, Yue; Chaudhuri, Swarat; Kavraki, Lydia E. (2019)
      Effectively planning robust executions under uncertainty is critical for building autonomous robots. Partially observable Markov decision processes (POMDPs) provide a standard framework for modeling many robot applications ...
    • Automated Abstraction of Manipulation Domains for Cost-Based Reactive Synthesis 

      He, Keliang; Lahijanian, Morteza; Kavraki, Lydia E.; Vardi, Moshe Y. (2019)
      When robotic manipulators perform high-level tasks in the presence of another agent, e.g., a human, they must have a strategy that considers possible interferences in order to guarantee task completion and efficient resource ...
    • Inference of species phylogenies from bi-allelic markers using pseudo-likelihood 

      Zhu, Jiafan; Nakhleh, Luay (2018)
      MOTIVATION: Phylogenetic networks represent reticulate evolutionary histories. Statistical methods for their inference under the multispecies coalescent have recently been developed. A particularly powerful approach uses ...
    • An incremental constraint-based framework for task and motion planning 

      Dantam, Neil T.; Kingston, Zachary K.; Chaudhuri, Swarat; Kavraki, Lydia E. (2018)
      We present a new constraint-based framework for task and motion planning (TMP). Our approach is extensible, probabilistically complete, and offers improved performance and generality compared with a similar, state-of-the-art ...
    • Maintaining and Enhancing Diversity of Sampled Protein Conformations in Robotics-Inspired Methods 

      Abella, Jayvee R.; Moll, Mark; Kavraki, Lydia E. (2018)
      The ability to efficiently sample structurally diverse protein conformations allows one to gain a high-level view of a protein's energy landscape. Algorithms from robot motion planning have been used for conformational ...
    • General Prediction of Peptide-MHC Binding Modes Using Incremental Docking: A Proof of Concept 

      Antunes, Dinler A.; Devaurs, Didier; Moll, Mark; Lizée, Gregory; Kavraki, Lydia E. (2018)
      The class I major histocompatibility complex (MHC) is capable of binding peptides derived from intracellular proteins and displaying them at the cell surface. The recognition of these peptide-MHC (pMHC) complexes by T-cells ...
    • Bayesian inference of phylogenetic networks from bi-allelic genetic markers 

      Zhu, Jiafan; Wen, Dingqiao; Yu, Yun; Meudt, Heidi M.; Nakhleh, Luay (2018)
      Phylogenetic networks are rooted, directed, acyclic graphs that model reticulate evolutionary histories. Recently, statistical methods were devised for inferring such networks from either gene tree estimates or the sequence ...
    • Matrilysin/MMP-7 Cleavage of Perlecan/HSPG2 Complexed with Semaphorin 3A Supports FAK-Mediated Stromal Invasion by Prostate Cancer Cells 

      Grindel, Brian J.; Martinez, Jerahme R.; Tellman, Tristen V.; Harrington, Daniel A.; Zafar, Hamim; Nakhleh, Luay; Chung, Leland W.; Farach-Carson, Mary C. (2018)
      Interrupting the interplay between cancer cells and extracellular matrix (ECM) is a strategy to halt tumor progression and stromal invasion. Perlecan/heparan sulfate proteoglycan 2 (HSPG2) is an extracellular proteoglycan ...
    • q-Blossoming for analytic functions 

      Goldman, Ron; Simeonov, Plamen (2018)
      We construct aᅠq-analog of the blossom for analytic functions, the analyticᅠq-blossom. Thisᅠq-analog also extends the notion ofᅠq-blossoming from polynomials to analytic functions. We then apply this analyticᅠq-blossom to ...
    • Efficacy of Novel Carbon Nanoparticle Antioxidant Therapy in a Severe Model of Reversible Middle Cerebral Artery Stroke in Acutely Hyperglycemic Rats 

      Fabian, Roderic H.; Derry, Paul J.; Rea, Harriett Charmaine; Dalmeida, William V.; Nilewski, Lizanne G.; Sikkema, William K.A.; Mandava, Pitchaiah; Tsai, Ah-Lim; Mendoza, Kimberly; Berka, Vladimir; Tour, James M.; Kent, Thomas A. (2018)
      INTRODUCTION: While oxidative stress can be measured during transient cerebral ischemia, antioxidant therapies for ischemic stroke have been clinically unsuccessful. Many antioxidants are limited in their range and/or ...
    • A Polynomial Blossom for the Askey–Wilson Operator 

      Simeonov, Plamen; Goldman, Ron (2018)
      We introduce a blossoming procedure for polynomials related to the Askey–Wilson operator. This new blossom is symmetric, multiaffine, and reduces to the complex representation of the polynomial on a certain diagonal. This ...
    • Platform-Independent Benchmarks for Task and Motion Planning 

      Lagriffoul, Fabien; Dantam, Neil T.; Garrett, Caelan; Akbari, Aliakbar; Srivastava, Siddharth; Kavraki, Lydia E. (2018)
      We present the first platform-independent evaluation method for task and motion planning (TAMP). Previously point, various problems have been used to test individual planners for specific aspects of TAMP. However, no common ...
    • Syzygies for translational surfaces 

      Wang, Haohao; Goldman, Ron (2018)
      A translational surface is a rational tensor product surface generated from two rational space curves by translating one curve along the other curve. Translational surfaces are invariant under rigid motions: translating ...
    • Quantitative comparison of adaptive sampling methods for protein dynamics 

      Hruska, Eugen; Abella, Jayvee R.; Nüske, Feliks; Kavraki, Lydia E.; Clementi, Cecilia (2018)
      Adaptive sampling methods, often used in combination with Markov state models, are becoming increasingly popular for speeding up rare events in simulation such as molecular dynamics (MD) without biasing the system dynamics. ...
    • Revealing Unknown Protein Structures Using Computational Conformational Sampling Guided by Experimental Hydrogen-Exchange Data 

      Devaurs, Didier; Antunes, Dinler A.; Kavraki, Lydia E. (2018)
      Both experimental and computational methods are available to gather information about a protein's conformational space and interpret changes in protein structure. However, experimentally observing and computationally ...
    • SiFit: inferring tumor trees from single-cell sequencing data under finite-sites models 

      Zafar, Hamim; Tzen, Anthony; Navin, Nicholas; Chen, Ken; Nakhleh, Luay (2017-09-19)
      Abstract Single-cell sequencing enables the inference of tumor phylogenies that provide insights on intra-tumor heterogeneity and evolutionary trajectories. Recently introduced methods perform this task under ...
    • A review of parameters and heuristics for guiding metabolic pathfinding 

      Kim, Sarah M; Peña, Matthew I; Moll, Mark; Bennett, George N; Kavraki, Lydia E (2017-09-15)
      Abstract Recent developments in metabolic engineering have led to the successful biosynthesis of valuable products, such as the precursor of the antimalarial compound, artemisinin, and opioid precursor, ...
    • Atlas + X: Sampling-based Planners on Constraint Manifolds 

      Voss, Caleb; Moll, Mark; Kavraki, Lydia E. (2017-06-14)
      Sampling-based planners struggle when the valid configurations are constrained to an implicit manifold. Special planners have been proposed for this problem recently. Our new framework is decoupled from any particular ...
    • Parallel Flow-Sensitive Points-to Analysis 

      Zhao, Jisheng; Burke, Michael G.; Sarkar, Vivek (2017-02-01)
      Points-to analysis is a fundamental requirement for many program analyses, optimizations, and debugging/verification tools. However, finding an effective balance between performance, scalability and precision in points-to ...