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2016

Learning multiagent communication with backpropagation

Sukhbaatar, S., Szlam, A. & Fergus, R., 2016, In : Advances in Neural Information Processing Systems. p. 2252-2260 9 p.

Research output: Contribution to journalArticle

Learning N-gram language models from uncertain data

Kuznetsov, V., Liao, H., Mohri, M., Riley, M. & Roark, B., 2016, In : Unknown Journal. 08-12-September-2016, p. 2323-2327 5 p.

Research output: Contribution to journalArticle

Mediator facilitates transcriptional activation and dynamic long-range contacts at the IgH locus during class switch recombination

Thomas-Claudepierre, A. S., Robert, I., Rocha, P. P., Raviram, R., Schiavo, E., Heyer, V., Bonneau, R., Luo, V. M., Reddy, J. K., Borggrefe, T., Skok, J. A. & Reina-San-Martin, B., 2016, In : Journal of Experimental Medicine. 213, 3, p. 303-312 10 p.

Research output: Contribution to journalArticle

MEsh arrangements for solid geometry

Zhou, Q., Grinspun, E., Zorin, D. & Jacobson, A., Jul 11 2016, In : ACM Transactions on Graphics. 35, 4, a39.

Research output: Contribution to journalArticle

Multi-way, multilingual neural machine translation

Firat, O., Cho, K., Sankaran, B., Yarman Vural, F. T. & Bengio, Y., Apr 21 2016, (Accepted/In press) In : Computer Speech and Language.

Research output: Contribution to journalArticle

Numerical investigation of Crouzeix's conjecture

Greenbaum, A. & Overton, M., Oct 18 2016, (Accepted/In press) In : Linear Algebra and Its Applications.

Research output: Contribution to journalArticle

On integrating a language model into neural machine translation

Gulcehre, C., Firat, O., Xu, K., Cho, K. & Bengio, Y., May 1 2016, (Accepted/In press) In : Computer Speech and Language.

Research output: Contribution to journalArticle

On the Length of a Random Minimum Spanning Tree

Cooper, C., Frieze, A., Ince, N., Janson, S. & Spencer, J., Jan 1 2016, In : Combinatorics Probability and Computing. 25, 1, p. 89-107 19 p.

Research output: Contribution to journalArticle

Open network interfaces for carrier networks

Panda, A., McCauley, J., Tootoonchian, A., Sherry, J., Koponen, T., Ratnasamy, S. & Shenker, S., Jan 1 2016, In : Computer Communication Review. 46, 1, p. 6-11 6 p.

Research output: Contribution to journalArticle

Optimistic bandit convex optimization

Mohri, M. & Yang, S., 2016, In : Advances in Neural Information Processing Systems. p. 2297-2305 9 p.

Research output: Contribution to journalArticle

Penalized Fast Subset Scanning

Speakman, S., Somanchi, S., McFowland, E. & Neill, D., Apr 2 2016, In : Journal of Computational and Graphical Statistics. 25, 2, p. 382-404 23 p.

Research output: Contribution to journalArticle

Planar minimization diagrams via subdivision with applications to anisotropic voronoi diagrams

Bennett, H., Papadopoulou, E. & Yap, C., 2016, In : Eurographics Symposium on Geometry Processing. 35, 5, p. 229-247 19 p.

Research output: Contribution to journalArticle

Planning, executing, and evaluating the winograd schema challenge

Morgenstern, L., Davis, E. & Ortiz, C. L., 2016, In : AI Magazine. 37, 1, p. 50-54 5 p.

Research output: Contribution to journalArticle

Polynomial root radius optimization with affine constraints

Eaton, J., Grundel, S., Gürbüzbalaban, M. & Overton, M., Nov 23 2016, (Accepted/In press) In : Mathematical Programming. p. 1-20 20 p.

Research output: Contribution to journalArticle

PPII Helical Peptidomimetics Templated by Cation–π Interactions

Craven, T. W., Bonneau, R. & Kirshenbaum, K., Oct 4 2016, In : ChemBioChem. p. 1824-1828 5 p.

Research output: Contribution to journalArticle

Preface

Kotsireas, I. S., Rump, S. M. & Yap, C., 2016, In : Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 9582, p. V-VI

Research output: Contribution to journalArticle

Probabilistic Belief Embedding for Large-Scale Knowledge Population

Fan, M., Zhou, Q., Abel, A., Zheng, T. F. & Grishman, R., Aug 8 2016, (Accepted/In press) In : Cognitive Computation. p. 1-16 16 p.

Research output: Contribution to journalArticle

Proposal on millimeter-wave channel modeling for 5G cellular system

Hur, S., Baek, S., Kim, B., Chang, Y., Molisch, A. F., Rappaport, T., Haneda, K. & Park, J., Apr 1 2016, In : IEEE Journal on Selected Topics in Signal Processing. 10, 3, p. 454-469 16 p., 7400962.

Research output: Contribution to journalArticle

Racemization barriers of atropisomeric 3,3′-bipyrroles: An experimental study with theoretical verification

Chatterjee, S., Butterfoss, G., Mandal, M., Paul, B., Gupta, S., Bonneau, R. & Jaisankar, P., 2016, In : RSC Advances. 6, 75, p. 71245-71249 5 p.

Research output: Contribution to journalArticle

Rates and mechanisms of bacterial mutagenesis from maximum-depth sequencing

Jee, J., Rasouly, A., Shamovsky, I., Akivis, Y., Steinman, S. R., Mishra, B. & Nudler, E., Jun 30 2016, In : Nature. 534, 7609, p. 693-696 4 p.

Research output: Contribution to journalArticle

Recursive SDN for carrier networks

McCauley, J., Liu, Z., Panda, A., Koponen, T., Raghavan, B., Rexford, J. & Shenker, S., Oct 1 2016, In : Computer Communication Review. 46, 4, p. 1-7 7 p.

Research output: Contribution to journalArticle

Rig animation with a tangible and modular input device

Glauser, O., Ma, W. C., Panozzo, D., Jacobson, A., Hilliges, O. & Sorkine-Hornung, O., Jul 11 2016, In : ACM Transactions on Graphics. 35, 4, a144.

Research output: Contribution to journalArticle

Robust classification of protein variation using structural modelling and large-scale data integration

Baugh, E. H., Simmons-Edler, R., Müller, C. L., Alford, R. F., Volfovsky, N., Lash, A. E. & Bonneau, R., Feb 28 2016, In : Nucleic Acids Research. 44, 6, p. 2501-2513 13 p.

Research output: Contribution to journalArticle

Scale-invariant directional alignment of surface parametrizations

Campen, M., Ibing, M., Ebke, H. C., Zorin, D. & Kobbelt, L., 2016, In : Eurographics Symposium on Geometry Processing. 35, 5, p. 1-10 10 p.

Research output: Contribution to journalArticle

Side-Chain Conformational Preferences Govern Protein-Protein Interactions

Watkins, A. M., Bonneau, R. & Arora, P., Aug 24 2016, In : Journal of the American Chemical Society. 138, 33, p. 10386-10389 4 p.

Research output: Contribution to journalArticle

Simulating heterogeneous tumor cell populations

Sundstrom, A., Bar-Sagi, D. & Mishra, B., Dec 1 2016, In : PLoS One. 11, 12, e0168984.

Research output: Contribution to journalArticle

Stereo matching by training a convolutional neural network to compare image patches

Žbontar, J. & LeCun, Y., Apr 1 2016, In : Journal of Machine Learning Research. 17

Research output: Contribution to journalArticle

Symbolic Quick Error Detection for Pre-Silicon and Post-Silicon Validation: Frequently Asked Questions

Singh, E., Lin, D., Barrett, C. & Mitra, S., Dec 1 2016, In : IEEE Design and Test. 33, 6, p. 55-62 8 p., 7511763.

Research output: Contribution to journalArticle

The list-decoding size of fourier-sparse Boolean functions

Haviv, I. & Regev, O., May 1 2016, In : ACM Transactions on Computation Theory. 8, 3, 10.

Research output: Contribution to journalArticle

The scope and limits of simulation in automated reasoning

Davis, E. & Marcus, G., Apr 1 2016, In : Artificial Intelligence. 233, p. 60-72 13 p.

Research output: Contribution to journalArticle

Threats from inside: Dynamic utility (Mis)alignments in an agent based model

Casey, W., Morales, J. A. & Mishra, B., Mar 1 2016, In : Journal of Wireless Mobile Networks, Ubiquitous Computing, and Dependable Applications. 7, 1, p. 97-117 21 p.

Research output: Contribution to journalArticle

Toward rational thermostabilization of Aspergillus oryzae cutinase: Insights into catalytic and structural stability

Shirke, A. N., Basore, D., Butterfoss, G. L., Bonneau, R., Bystroff, C. & Gross, R. A., Jan 1 2016, In : Proteins: Structure, Function and Genetics. 84, 1, p. 60-72 13 p.

Research output: Contribution to journalArticle

TRONCO: An R package for the inference of cancer progression models from heterogeneous genomic data

De Sano, L., Caravagna, G., Ramazzotti, D., Graudenzi, A., Mauri, G., Mishra, B. & Antoniotti, M., Jun 15 2016, In : Bioinformatics. 32, 12, p. 1911-1913 3 p.

Research output: Contribution to journalArticle

Tweeting identity? Ukrainian, Russian, and #Euromaidan

MacDuffee Metzger, M., Bonneau, R., Nagler, J. & Tucker, J. A., Feb 1 2016, In : Journal of Comparative Economics. 44, 1, p. 16-40 25 p.

Research output: Contribution to journalArticle

Upstart puzzles: Ice trap

Shasha, D., Jan 1 2016, In : Communications of the ACM. 59, 1, p. 136 1 p.

Research output: Contribution to journalArticle

Upstart puzzles: Sleep no more

Shasha, D., Apr 1 2016, In : Communications of the ACM. 59, 4, p. 96 1 p.

Research output: Contribution to journalArticle

Variational analysis of the Crouzeix ratio

Greenbaum, A., Lewis, A. S. & Overton, M., Nov 2 2016, (Accepted/In press) In : Mathematical Programming. p. 1-15 15 p.

Research output: Contribution to journalArticle

Youth Violence: What We Know and What We Need to Know

Bushman, B. J., Newman, K., Calvert, S. L., Downey, G., Dredze, M., Gottfredson, M., Jablonski, N. G., Masten, A. S., Morrill, C., Neill, D., Romer, D. & Webster, D. W., Jan 1 2016, In : American Psychologist. 71, 1, p. 17-39 23 p.

Research output: Contribution to journalArticle

2015

A disambiguation algorithm for weighted automata

Mohri, M. & Riley, M. D., Nov 29 2015, (Accepted/In press) In : Theoretical Computer Science.

Research output: Contribution to journalArticle

An efficient algorithm for computing the generalized null space decomposition

Guglielmi, N., Overton, M. L. & Stewart, G. W., Jan 1 2015, In : SIAM Journal on Matrix Analysis and Applications. 36, 1, p. 38-54 17 p.

Research output: Contribution to journalArticle

An efficient DPLL(T) solver for a theory of strings and regular expressions

Liang, T., Reynolds, A., Tsiskaridze, N., Tinelli, C., Barrett, C. & Deters, M., 2015, (Accepted/In press) In : Formal Methods in System Design. to appear.

Research output: Contribution to journalArticle

An experimentally supported model of the Bacillus subtilis global transcriptional regulatory network

Arrieta-Ortiz, M. L., Hafemeister, C., Bate, A. R., Chu, T., Greenfield, A., Shuster, B., Barry, S. N., Gallitto, M., Liu, B., Kacmarczyk, T., Santoriello, F., Chen, J., Rodrigues, C. D., Sato, T., Rudner, D. Z., Driks, A., Bonneau, R. & Eichenberger, P., Nov 1 2015, In : Molecular systems biology [electronic resource].. 11, 11, 839.

Research output: Contribution to journalArticle

An IL-23R/IL-22 Circuit Regulates Epithelial Serum Amyloid A to Promote Local Effector Th17 Responses

Sano, T., Huang, W., Hall, J. A., Yang, Y., Chen, A., Gavzy, S. J., Lee, J. Y., Ziel, J. W., Miraldi, E. R., Domingos, A. I., Bonneau, R. & Littman, D. R., Oct 8 2015, In : Cell. 163, 2, p. 381-393 13 p.

Research output: Contribution to journalArticle

An O (N) direct solver for integral equations on the plane

Corona, E., Martinsson, P. G. & Zorin, D., Mar 1 2015, In : Applied and Computational Harmonic Analysis. 38, 2, p. 284-317 34 p.

Research output: Contribution to journalArticle

A note on the stability of cut cells and cell merging

Berger, M., Jul 10 2015, In : Applied Numerical Mathematics. 96, p. 180-186 7 p.

Research output: Contribution to journalArticle

Beam steering in millimeter wave cellular networks

Barati, C. N., Hosseini, S. A., Rangan, S., Liu, P., Korakis, T., Panwar, S. & Rappaport, T., Mar 2015, (Accepted/In press) In : IEEE Transactions on Wireless Communications. Accepted.

Research output: Contribution to journalArticle

Boundary integral method for the flow of vesicles with viscosity contrast in three dimensions

Rahimian, A., Veerapaneni, S. K., Zorin, D. & Biros, G., 2015, In : Journal of Computational Physics. 298, p. 766-786 21 p.

Research output: Contribution to journalArticle

Breaking TADs: Insights into hierarchical genome organization

Rocha, P. P., Raviram, R., Bonneau, R. & Skok, J. A., Jun 1 2015, In : Epigenomics. 7, 4, p. 523-526 4 p.

Research output: Contribution to journalArticle

Certified computation of planar Morse-Smale complexes

Chattopadhyay, A., Vegter, G. & Yap, C., Jan 29 2015, (Accepted/In press) In : Journal of Symbolic Computation.

Research output: Contribution to journalArticle

Cohesin loss alters adult hematopoietic stem cell homeostasis, leading to myeloproliferative neoplasms

Mullenders, J., Aranda-Orgilles, B., Lhoumaud, P., Keller, M., Pae, J., Wang, K., Kayembe, C., Rocha, P. P., Raviram, R., Gong, Y., Premsrirut, P. K., Tsirigos, A., Bonneau, R., Skok, J. A., Cimmino, L., Hoehn, D. & Aifantis, I., 2015, In : Journal of Experimental Medicine. 212, 11, p. 1833-1850 18 p.

Research output: Contribution to journalArticle