Research Output 1966 2019

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2019

Adaptation based on generalized discrepancy

Cortes, C., Mohri, M. & Medina, A. M., Jan 1 2019, In : Journal of Machine Learning Research. 20, p. 1-30 30 p.

Research output: Contribution to journalArticle

Discrepancy
Convex optimization
Training Samples
Convex Optimization
Theoretical Analysis

An oculus rift assessment of dynamic balance by head mobility in a virtual park scene: A pilot study

Lubetzky, A., Hujsak, B. D., Fu, G. & Perlin, K., Jan 1 2019, In : Motor Control. 23, 1, p. 127-142 16 p.

Research output: Contribution to journalArticle

Head
Head Movements
Biomechanical Phenomena

CAVE: Making collective virtual narrative

Layng, K., Perlin, K., Herscher, S., Brenner, C. & Meduri, T., Aug 1 2019, In : Leonardo. 52, 4, p. 349-356 8 p.

Research output: Contribution to journalArticle

Theaters
Virtual reality

Change surfaces for expressive multidimensional changepoints and counterfactual prediction

Herlands, W., Neill, D., Nickisch, H. & Wilson, A. G., Jun 1 2019, In : Journal of Machine Learning Research. 20

Research output: Contribution to journalArticle

Change Point
Prediction
Gaussian Process
Change-point Model
Posterior Mean

Characterization of Transcriptional Regulatory Networks that Promote and Restrict Identities and Functions of Intestinal Innate Lymphoid Cells

Pokrovskii, M., Hall, J. A., Ochayon, D. E., Yi, R., Chaimowitz, N. S., Seelamneni, H., Carriero, N., Watters, A., Waggoner, S. N., Littman, D. R., Bonneau, R. & Miraldi, E. R., Jul 16 2019, In : Immunity. 51, 1, p. 185-197.e6

Research output: Contribution to journalArticle

Gene Regulatory Networks
Homeostasis
Transcription Factors
Genome
Lymphocytes

Conditional Molecular Design with Deep Generative Models

Kang, S. & Cho, K., Jan 28 2019, In : Journal of Chemical Information and Modeling. 59, 1, p. 43-52 10 p.

Research output: Contribution to journalArticle

Molecules
drug
learning
performance
Learning systems

Deformation capture via soft and stretchable sensor arrays

Glauser, O., Panozzo, D., Hilliges, O. & Sorkine-Hornung, O., Apr 1 2019, In : ACM Transactions on Graphics. 38, 2, 16.

Research output: Contribution to journalArticle

Open Access
Sensor arrays
Hardware
Pipelines
Fabrication
Geometry

Elites tweet to get feet off the streets: Measuring regime social media strategies during protest

Munger, K., Bonneau, R., Nagler, J. & Tucker, J., Oct 1 2019, In : Political Science Research and Methods. 7, 4, p. 815-834 20 p.

Research output: Contribution to journalArticle

Open Access
social media
protest
elite
regime
twitter

Existential monadic second order logic on random rooted trees

Holroyd, A. E., Levy, A., Podder, M. & Spencer, J., Jan 1 2019, In : Discrete Mathematics. 342, 1, p. 152-167 16 p.

Research output: Contribution to journalArticle

Monadic Second-order Logic
Random Trees
Rooted Trees
Coloring
Finiteness

Exploiting high millimeter wave bands for military communications, applications, and design

Harvey, J. F., Steer, M. B. & Rappaport, T., Jan 1 2019, In : IEEE Access. 7, p. 52350-52359 10 p., 8692347.

Research output: Contribution to journalArticle

Military communications
Millimeter waves
Communication
Local area networks
Telecommunication networks

Fast Subgraph Matching Strategies Based on Pattern-Only Heuristics

Aparo, A., Bonnici, V., Micale, G., Ferro, A., Shasha, D., Pulvirenti, A. & Giugno, R., Mar 1 2019, In : Interdisciplinary Sciences: Computational Life Sciences. 11, 1, p. 21-32 12 p.

Research output: Contribution to journalArticle

Heuristic algorithms
Experiments
Heuristics

Feature Preserving Octree-Based Hexahedral Meshing

Gao, X., Shen, H. & Panozzo, D., Jan 1 2019, In : Computer Graphics Forum. 38, 5, p. 135-149 15 p.

Research output: Contribution to journalArticle

Scaffolds
Computer aided design
Tuning
Pipelines
Statistics

For Whom the Bot Tolls: A Neural Networks Approach to Measuring Political Orientation of Twitter Bots in Russia

Stukal, D., Sanovich, S., Tucker, J. & Bonneau, R., Apr 1 2019, In : SAGE Open. 9, 2

Research output: Contribution to journalArticle

Open Access
twitter
political attitude
neural network
Russia
social media

High-definition spatial transcriptomics for in situ tissue profiling

Vickovic, S., Eraslan, G., Salmén, F., Klughammer, J., Stenbeck, L., Schapiro, D., Äijö, T., Bonneau, R., Bergenstråhle, L., Navarro, J. F., Gould, J., Griffin, G. K., Borg, Å., Ronaghi, M., Frisén, J., Lundeberg, J., Regev, A. & Ståhl, P. L., Oct 1 2019, In : Nature methods. 16, 10, p. 987-990 4 p.

Research output: Contribution to journalArticle

Tissue
Spatial Analysis
Brain
RNA
Breast Neoplasms

Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells

Miraldi, E. R., Pokrovskii, M., Watters, A., Castro, D. M., De Veaux, N., Hall, J. A., Lee, J. Y., Ciofani, M., Madar, A., Carriero, N., Littman, D. R. & Bonneau, R., Mar 1 2019, In : Genome Research. 29, 3, p. 449-463 15 p.

Research output: Contribution to journalArticle

Open Access
Th17 Cells
Gene Regulatory Networks
Transposases
Chromatin
Transcription Factors

Millimeter-wave base station diversity for 5G coordinated multipoint (CoMP) applications

MacCartney, G. R. & Rappaport, T., Jul 1 2019, In : IEEE Transactions on Wireless Communications. 18, 7, p. 3395-3410 16 p., 8705688.

Research output: Contribution to journalArticle

Millimeter Wave
Millimeter waves
Base stations
Interference
Fading

Multi-study inference of regulatory networks for more accurate models of gene regulation

Castro, D. M., de Veaux, N. R., Miraldi, E. R. & Bonneau, R., Jan 1 2019, In : PLoS Computational Biology. 15, 1, e1006591.

Research output: Contribution to journalArticle

Gene Regulation
Regulatory Networks
Gene expression
gene
Genes

Network Walking charts transcriptional dynamics of nitrogen signaling by integrating validated and predicted genome-wide interactions

Brooks, M. D., Cirrone, J., Pasquino, A. V., Alvarez, J. M., Swift, J., Mittal, S., Juang, C. L., Varala, K., Gutiérrez, R. A., Krouk, G., Shasha, D. & Coruzzi, G., Dec 1 2019, In : Nature Communications. 10, 1, 1569.

Research output: Contribution to journalArticle

Open Access
walking
genome
charts
Walking
Transcription Factors

On the origin of biomolecular networks

Janwa, H., Massey, S. E., Velev, J. & Mishra, B., Jan 1 2019, In : Frontiers in Genetics. 10, APR, 240.

Research output: Contribution to journalArticle

Open Access
Gene Duplication
Game Theory
Horizontal Gene Transfer
Symbiosis
Essential Genes

Poly-spline finite-element method

Schneider, T., Dumas, J., Gao, X., Botsch, M., Panozzo, D. & Zorin, D., Jan 1 2019, In : ACM Transactions on Graphics. 38, 3, 19.

Research output: Contribution to journalArticle

Poisson equation
Splines
Partial differential equations
Stars
Pipelines

QCD-aware recursive neural networks for jet physics

Louppe, G., Cho, K., Becot, C. & Cranmer, K., Jan 1 2019, In : Journal of High Energy Physics. 2019, 1, 57.

Research output: Contribution to journalArticle

quantum chromodynamics
physics
sentences
momentum
machine learning

Relative deviation learning bounds and generalization with unbounded loss functions

Cortes, C., Greenberg, S. & Mohri, M., Jan 1 2019, (Accepted/In press) In : Annals of Mathematics and Artificial Intelligence.

Research output: Contribution to journalArticle

Loss Function
Deviation
Weighting
Moment
Learning

Robust regularization of topology optimization problems with a posteriori error estimators

Ovchinnikov, G. V., Zorin, D. & Oseledets, I. V., Feb 1 2019, In : Russian Journal of Numerical Analysis and Mathematical Modelling. 34, 1, p. 57-69 13 p.

Research output: Contribution to journalArticle

A Posteriori Error Estimators
Topology Optimization
Shape optimization
Finite Element Discretization
Regularization

SIAN: software for structural identifiability analysis of ODE models

Hong, H., Ovchinnikov, A., Pogudin, G. & Yap, C., Aug 15 2019, In : Bioinformatics (Oxford, England). 35, 16, p. 2873-2874 2 p.

Research output: Contribution to journalArticle

Identifiability
Bioinformatics
Ordinary differential equations
Structural analysis
Software

Some complexity results for stateful network verification

Alpernas, K., Panda, A., Rabinovich, A., Sagiv, M., Shenker, S., Shoham, S. & Velner, Y., Jan 1 2019, (Accepted/In press) In : Formal Methods in System Design.

Research output: Contribution to journalArticle

Safety
Firewall
Servers
Switches
Polynomials

Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis

Maniatis, S., Äijö, T., Vickovic, S., Braine, C., Kang, K., Mollbrink, A., Fagegaltier, D., Andrusivová, Ž., Saarenpää, S., Saiz-Castro, G., Cuevas, M., Watters, A., Lundeberg, J., Bonneau, R. & Phatnani, H., Apr 5 2019, In : Science. 364, 6435, p. 89-93 5 p.

Research output: Contribution to journalArticle

Molecular Pathology
Amyotrophic Lateral Sclerosis
Motor Neurons
Spinal Cord
Nerve Degeneration

Spurious valleys in one-hidden-layer neural network optimization landscapes

Venturi, L., Bandeira, A. & Bruna Estrach, J., Aug 1 2019, In : Journal of Machine Learning Research. 20

Research output: Contribution to journalArticle

Network Optimization
Neural Networks
Neural networks
Data Distribution
Gradient Descent Method

Tatonnement beyond gross substitutes? Gradient descent to the rescue

Cheung, Y. K., Cole, R. & Devanur, N. R., Jan 1 2019, In : Games and Economic Behavior.

Research output: Contribution to journalArticle

Gradient
Substitute
Tatonnement
Buyers
Rate of convergence

Thermoresponsive Protein-Engineered Coiled-Coil Hydrogel for Sustained Small Molecule Release

Hill, L. K., Meleties, M., Katyal, P., Xie, X., Delgado-Fukushima, E., Jihad, T., Liu, C. F., O'Neill, S., Tu, R. S., Renfrew, P. D., Bonneau, R., Wadghiri, Y. Z. & Montclare, J., Jan 1 2019, (Accepted/In press) In : Biomacromolecules.

Research output: Contribution to journalArticle

Hydrogel
Hydrogels
Proteins
Molecules
Curcumin

Thoughts on load distribution and the role of programmable switches

McCauley, J., Krishnamurthy, A., Panda, A. & Shenker, S., Jan 1 2019, In : Computer Communication Review. 49, 1, p. 18-23 6 p.

Research output: Contribution to journalArticle

Switching networks
Switches
Hardware

Towards region-specific propagation of protein functions

Koo, D. C. E. & Bonneau, R., May 15 2019, In : Bioinformatics (Oxford, England). 35, 10, p. 1737-1744 8 p.

Research output: Contribution to journalArticle

Open Access
Propagation
Proteins
Protein
Molecular Sequence Annotation
Prediction

Twenty-five years of information extraction

Grishman, R., Jan 1 2019, (Accepted/In press) In : Natural Language Engineering.

Research output: Contribution to journalArticle

information content
Neural networks
neural network
Processing
evaluation

VersionClimber: Version Upgrades without Tears

Pradal, C., Cohen-Boulakia, S., Valduriez, P. & Shasha, D., Sep 1 2019, In : Computing in Science and Engineering. 21, 5, p. 87-93 7 p., 8798946.

Research output: Contribution to journalArticle

Application programs
Virtual reality
Linux
Open Access
social media
politician
citizen
twitter
political agenda

Wireless communications and applications above 100 GHz: Opportunities and challenges for 6g and beyond

Rappaport, T., Xing, Y., Kanhere, O., Ju, S., Madanayake, A., Mandal, S., Alkhateeb, A. & Trichopoulos, G. C., Jan 1 2019, In : IEEE Access. 7, p. 78729-78757 29 p., 8732419.

Research output: Contribution to journalArticle

Open Access
Communication
Signal processing
Imaging techniques
Smart antennas
Array processing
2018

Airburst-Generated Tsunamis

Berger, M. & Goodman, J., Apr 1 2018, In : Pure and Applied Geophysics. 175, 4, p. 1525-1543 19 p.

Research output: Contribution to journalArticle

Tsunamis
asteroids
tsunami
shallow water
Asteroids

Airway microbiota is associated with upregulation of the PI3K pathway in lung cancer

Tsay, J. C. J., Wu, B. G., Badri, M. H., Clemente, J. C., Shen, N., Meyn, P., Li, Y., Yie, T. A., Lhakhang, T., Olsen, E., Murthy, V., Michaud, G., Sulaiman, I., Tsirigos, A., Heguy, A., Pass, H., Weiden, M. D., Rom, W. N., Sterman, D. H., Bonneau, R. & 2 others, Blaser, M. J. & Segal, L. N., Nov 1 2018, In : American Journal of Respiratory and Critical Care Medicine. 198, 9, p. 1188-1198 11 p.

Research output: Contribution to journalArticle

1-Phosphatidylinositol 4-Kinase
Microbiota
Lung Neoplasms
Mitogen-Activated Protein Kinase 6
Up-Regulation

A model-based embedding technique for segmenting customers

Jagabathula, S., Subramanian, L. & Venkataraman, A., Sep 1 2018, In : Operations Research. 66, 5, p. 1247-1267 21 p.

Research output: Contribution to journalArticle

Learning systems
Marketing
Recovery
Statistical Models
Latent class

An adaptive geometric search algorithm for macromolecular scaffold selection

Jiang, T., Renfrew, P. D., Drew, K., Youngs, N., Butterfoss, G., Bonneau, R. & Shasha, D., Sep 1 2018, In : Protein engineering, design & selection : PEDS. 31, 9, p. 345-354 10 p.

Research output: Contribution to journalArticle

Open Access
Scaffolds (biology)
Scaffolds
Proteins
Peptidomimetics
Catalytic Domain

Analog Approximate-FFT 8/16-Beam Algorithms, Architectures and CMOS Circuits for 5G Beamforming MIMO Transceivers

Ariyarathna, V., Madanayake, A., Tang, X., Coelho, D., Cintra, R. J., Belostotski, L., Mandal, S. & Rappaport, T., May 1 2018, (Accepted/In press) In : IEEE Journal on Emerging and Selected Topics in Circuits and Systems.

Research output: Contribution to journalArticle

Beamforming
Transceivers
Fast Fourier transforms
Millimeter waves
Bandwidth

Analysis of 3D genomic interactions identifies candidate host genes that transposable elements potentially regulate

Raviram, R., Rocha, P. P., Luo, V. M., Swanzey, E., Miraldi, E. R., Chuong, E. B., Feschotte, C., Bonneau, R. & Skok, J. A., Dec 13 2018, In : Genome Biology. 19, 1, 216.

Research output: Contribution to journalArticle

DNA Transposable Elements
transposons
genomics
genome
Genome

Analytical Framework of Hybrid Beamforming in Multi-Cell Millimeter-Wave Systems

Sun, S., Rappaport, T., Shafi, M. & Tataria, H., Sep 13 2018, (Accepted/In press) In : IEEE Transactions on Wireless Communications.

Research output: Contribution to journalArticle

Millimeter Wave
Beamforming
Millimeter waves
Cell
Base stations

An ODE-based wall model for turbulent flow simulations

Berger, M. & Aftosmis, M. J., Jan 1 2018, In : AIAA Journal. 56, 2, p. 700-714 15 p.

Research output: Contribution to journalArticle

Flow simulation
Turbulent flow
Viscosity
Pressure gradient
Ordinary differential equations

A Novel Domain Assembly Routine for Creating Full-Length Models of Membrane Proteins from Known Domain Structures

Koehler Leman, J. & Bonneau, R., Apr 3 2018, In : Biochemistry. 57, 13, p. 1939-1944 6 p.

Research output: Contribution to journalArticle

Membrane Proteins
Membranes
Computational methods
Hand
Protein Domains

Antibiotic-induced acceleration of type 1 diabetes alters maturation of innate intestinal immunity

Zhang, X. S., Li, J., Krautkramer, K. A., Badri, M., Battaglia, T., Borbet, T. C., Koh, H., Ng, S., Sibley, R. A., Li, Y., Pathmasiri, W., Jindal, S., Shields-Cutler, R. R., Hillmann, B., Al-Ghalith, G. A., Ruiz, V. E., Livanos, A., Van‘t Wout, A. B., Nagalingam, N., Rogers, A. B. & 9 others, Sumner, S. J., Knights, D., Denu, J. M., Li, H., Ruggles, K. V., Bonneau, R., Williamson, R. A., Rauch, M. & Blaser, M. J., Jul 24 2018, In : eLife. 7, e37816.

Research output: Contribution to journalArticle

Medical problems
Type 1 Diabetes Mellitus
Innate Immunity
Anti-Bacterial Agents
Gene expression

A parametric class of composites with a large achievable range of effective elastic properties

Ostanin, I., Ovchinnikov, G., Tozoni, D. C. & Zorin, D., Sep 1 2018, In : Journal of the Mechanics and Physics of Solids. 118, p. 204-217 14 p.

Research output: Contribution to journalArticle

Metamaterials
Poisson ratio
elastic properties
composite materials
Composite materials

Approximating the nash social welfare with indivisible items

Cole, R. & Gkatzelis, V., Jan 1 2018, In : SIAM Journal on Computing. 47, 3, p. 1211-1236 26 p.

Research output: Contribution to journalArticle

Indivisible
Welfare
Fractional
Valuation
Approximation algorithms

A probabilistic approach to discovering dynamic full-brain functional connectivity patterns

Manning, J. R., Zhu, X., Willke, T. L., Ranganath, R., Stachenfeld, K., Hasson, U., Blei, D. M. & Norman, K. A., Jan 1 2018, (Accepted/In press) In : NeuroImage.

Research output: Contribution to journalArticle

Statistical Factor Analysis
Brain
Magnetic Resonance Imaging
Television
Neuroimaging

A quantitative perceptual model for tactile roughness

Tymms, C., Gardner, E. P. & Zorin, D., Nov 1 2018, In : ACM Transactions on Graphics. 37, 5, 168.

Research output: Contribution to journalArticle

Surface roughness
Geometry
Drawing (graphics)
Textures
Printing

Axis-aligned height-field block decomposition of 3D shapes

Muntoni, A., Livesu, M., Scateni, R., Sheffer, A. & Panozzo, D., Nov 1 2018, In : ACM Transactions on Graphics. 37, 5, 169.

Research output: Contribution to journalArticle

Decomposition
Fabrication
Constrained optimization
Sorting
Geometry