Now showing items 1-20 of 51

    • Present but Unreachable: Reducing Persistentlatent Secrets in HotSpot JVM 

      Pridgen, Adam; Garfinkel, Simson L.; Wallach, Dan S. (2017)
      Applications that manage sensitive secrets, including cryptographic keys, are typically engineered to overwrite the secrets in memory once they’re no longer necessary, offering an important defense against forensic attacks ...
    • Reasoning about Strategies: on the Satisfiability Problem 

      Mogavero, Fabio; Murano, Aniello; Perelli, Giuseppe; Vardi, Moshe Y. (2017)
      Strategy Logic (SL, for short) has been introduced by Mogavero, Murano, and Vardi as a useful formalism for reasoning explicitly about strategies, as first-order objects, in multi-agent concurrent games. This logic turns ...
    • Performance Analysis and Optimization of a Hybrid Seismic Imaging Application 

      Paul, Sri Raj; Araya-Polo, Mauricio; Mellor-Crummey, John; Hohl, Detlef (2016)
      Applications to process seismic data are computationally expensive and, therefore, employ scalable parallel systems to produce timely results. Here we describe our experiences of using performance analysis tools to gain ...
    • Bayesian Inference of Reticulate Phylogenies under the Multispecies Network Coalescent 

      Wen, Dingqiao; Yu, Yun; Nakhleh, Luay (2016)
      The multispecies coalescent (MSC) is a statistical framework that models how gene genealogies grow within the branches of a species tree. The field of computational phylogenetics has witnessed an explosion in the development ...
    • Deep imaging in scattering media with selective plane illumination microscopy 

      Pediredla, Adithya Kumar; Zhang, Shizheng; Avants, Ben; Ye, Fan; Nagayama, Shin; Chen, Ziying; Kemere, Caleb; Robinson, Jacob T.; Veeraraghavan, Ashok (2016)
      In most biological tissues, light scattering due to small differences in refractive index limits the depth of optical imaging systems. Two-photon microscopy (2PM), which significantly reduces the scattering of the excitation ...
    • Inferring Atmospheric Particulate Matter Concentrations from Chinese Social Media Data 

      Tao, Zhu; Kokas, Aynne; Zhang, Rui; Cohan, Daniel S.; Wallach, Dan (2016)
      Although studies have increasingly linked air pollution to specific health outcomes, less well understood is how public perceptions of air quality respond to changing pollutant levels. The growing availability of air ...
    • Monovar: single-nucleotide variant detection in single cells 

      Zafar, Hamim; Wang, Yong; Nakhleh, Luay; Navin, Nicholas; Chen, Ken (2016)
      Current variant callers are not suitable for single-cell DNA sequencing, as they do not account for allelic dropout, false-positive errors and coverage nonuniformity. We developed Monovar (https://bitbucket.org/hamimzafa ...
    • Structure-guided selection of specificity determining positions in the human Kinome 

      Moll, Mark; Finn, Paul W; Kavraki, Lydia E (2016)
      Abstract Background The human kinome contains many important drug targets. It is well-known that inhibitors of protein kinases bind with very different selectivity profiles. ...
    • From Error to Error: Why Voters Could not Cast a Ballot and Verify Their Vote With Helios, Prêt à Voter, and Scantegrity II 

      Acemyan, Claudia Z.; Kortum, Philip; Byrne, Michael D.; Wallach, Dan S. (2015)
      The aim of this paper is to identify user errors, and the related potential design deficiencies, that contributed to participants failing to vote cast and vote verify across three end-to-end voting systems: Helios, Prêt à ...
    • Meniscus-Mask Lithography for Fabrication of Narrow Nanowires 

      Abramova, Vera; Slesarev, Alexander S.; Tour, James M. (2015)
      We demonstrate the efficiency of meniscus-mask lithography (MML) for fabrication of precisely positioned nanowires in a variety of materials. Si, SiO2, Au, Cr, W, Ti, TiO2, and Al nanowires are fabricated and characterized. ...
    • The Mason Test: A Defense Against Sybil Attacks in Wireless Networks Without Trusted Authorities 

      Liu, Yue; Bild, David R.; Dick, Robert P.; Mao, Z. Morley; Wallach, Dan S. (2015)
      Wireless networks are vulnerable to Sybil attacks, in which a malicious node poses as many identities in order to gain disproportionate influence. Many defenses based on spatial variability of wireless channels exist, but ...
    • Drug Target Optimization in Chronic Myeloid Leukemia Using Innovative Computational Platform 

      Chuang, Ryan; Hall, Benjamin A.; Benque, David; Cook, Byron; Ishtiaq, Samin; Piterman, Nir; Taylor, Alex; Vardi, Moshe; Koschmieder, Steffen; Gottgens, Berthold; Fisher, Jasmin (2015)
      Chronic Myeloid Leukemia (CML) represents a paradigm for the wider cancer field. Despite the fact that tyrosine kinase inhibitors have established targeted molecular therapy in CML, patients often face the risk of developing ...
    • Non-intrusive Persistence with a Backend NVM Controller 

      Pu, Libei; Doshi, Kshitij; Giles, Ellis; Varman, Peter (2015)
      By providing instruction-grained access to vast amounts of persistent data with ordinary loads and stores, byte-addressable storage class memory (SCM) has the potential to revolutionize system architecture. We describe a ...
    • Transaction local aliasing in storage class memory 

      Giles, Ellis; Doshi, Kshitij; Varman, Peter (2015)
      This paper describes a lightweight software library to solve the challenges [6], [3], [1], [5], [2] of programming storage class memory (SCM). It provides primitives to demarcate failure-atomic code regions. SCM loads and ...
    • Understanding the challenges of protein flexibility in drug design 

      Antunes, Dinler A.; Devaurs, Didier; Kavraki, Lydia E. (2015)
      Introduction: Protein–ligand interactions play key roles in various metabolic pathways, and the proteins involved in these interactions represent major targets for drug discovery. Molecular docking is widely used to predict ...
    • On computing minimal independent support and its applications to sampling and counting 

      Ivrii, Alexander; Malik, Sharad; Meel, Kuldeep S.; Vardi, Moshe Y. (2015)
      Constrained sampling and counting are two fundamental problems arising in domains ranging from artificial intelligence and security, to hardware and software testing. Recent approaches to approximate solutions for these ...
    • A maximum pseudo-likelihood approach for phylogenetic networks 

      Yu, Yun; Nakhleh, Luay (2015)
      Abstract Background Several phylogenomic analyses have recently demonstrated the need to account simultaneously for incomplete lineage sorting (ILS) and hybridization when ...
    • Relentful Strategic Reasoning in 1 Alternating-Time Temporal Logic 

      Mogavero, Fabio; Murano, Aniello; Vardi, Moshe Y. (2014)
      Temporal logics are a well investigated formalism for the specification, verification, and synthesis of reactive systems. Within this family, Alternating-Time Temporal Logic (ATL , for short) has been introduced as a ...
    • Mechanism of Graphene Oxide Formation 

      Dimiev, Ayrat M.; Tour, James M. (2014)
      Despite intensive research, the mechanism of graphene oxide (GO) formation remains unclear. The role of interfacial interactions between solid graphite and the liquid reaction medium, and transport of the oxidizing agent ...
    • An HMM-Based Comparative Genomic Framework for Detecting Introgression in Eukaryotes 

      Liu, Kevin J.; Dai, Jingxuan; Truong, Kathy; Song, Ying; Kohn, Michael H.; Nakhleh, Luay (2014)
      One outcome of interspecific hybridization and subsequent effects of evolutionary forces is introgression, which is the integration of genetic material from one species into the genome of an individual in another species. ...