Research Output

2020

A Comprehensive Map of the Monocyte-Derived Dendritic Cell Transcriptional Network Engaged upon Innate Sensing of HIV

Johnson, J. S., De Veaux, N., Rives, A. W., Lahaye, X., Lucas, S. Y., Perot, B. P., Luka, M., Garcia-Paredes, V., Amon, L. M., Watters, A., Abdessalem, G., Aderem, A., Manel, N., Littman, D. R., Bonneau, R. & Ménager, M. M., Jan 21 2020, In : Cell Reports. 30, 3, p. 914-931.e9

Research output: Contribution to journalArticle

Open Access

Analysis of the gradient method with an Armijo–Wolfe line search on a class of non-smooth convex functions

Asl, A. & Overton, M. L., Mar 3 2020, In : Optimization Methods and Software. 35, 2, p. 223-242 20 p.

Research output: Contribution to journalArticle

A stable and effective learning strategy for trainable greedy decoding

Chen, Y., Li, V. O. K., Cho, K. & Bowman, S. R., Jan 1 2020, Proceedings of the 2018 Conference on Empirical Methods in Natural Language Processing, EMNLP 2018. Riloff, E., Chiang, D., Hockenmaier, J. & Tsujii, J. (eds.). Association for Computational Linguistics, p. 380-390 11 p. (Proceedings of the 2018 Conference on Empirical Methods in Natural Language Processing, EMNLP 2018).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

A truthful cardinal mechanism for one-sided matching

Abebe, R., Cole, R., Gkatzelis, V. & Hartline, J. D., 2020, 31st Annual ACM-SIAM Symposium on Discrete Algorithms, SODA 2020. Chawla, S. (ed.). Association for Computing Machinery, p. 2096-2113 18 p. (Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms; vol. 2020-January).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Attention-based CNN for KL Grade Classification: Data from the Osteoarthritis Initiative

Zhang, B., Tan, J., Cho, K., Chang, G. & Deniz, C. M., Apr 2020, ISBI 2020 - 2020 IEEE International Symposium on Biomedical Imaging. IEEE Computer Society, p. 731-735 5 p. 9098456. (Proceedings - International Symposium on Biomedical Imaging; vol. 2020-April).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Better together: Elements of successful scientific software development in a distributed collaborative community

RosettaCommons Consortium, May 1 2020, In : PLoS computational biology. 16, 5, e1007507.

Research output: Contribution to journalReview article

Open Access

Big Data Analytics and the Struggle for Equity in Health Care: The Promise and Perils

Ibrahim, S. A., Charlson, M. E. & Neill, D. B., Apr 1 2020, In : Health Equity. 4, 1, p. 99-101 3 p.

Research output: Contribution to journalReview article

Open Access

Bounds on Dimension Reduction in the Nuclear Norm

Regev, O. & Vidick, T., 2020, Lecture Notes in Mathematics. Springer, p. 279-299 21 p. (Lecture Notes in Mathematics; vol. 2266).

Research output: Chapter in Book/Report/Conference proceedingChapter

BugDoc: Algorithms to Debug Computational Processes

Lourenço, R., Freire, J. & Shasha, D., Jun 14 2020, SIGMOD 2020 - Proceedings of the 2020 ACM SIGMOD International Conference on Management of Data. Association for Computing Machinery, p. 463-478 16 p. (Proceedings of the ACM SIGMOD International Conference on Management of Data).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Open Access

BugDoc: A System for Debugging Computational Pipelines

Lourenço, R., Freire, J. & Shasha, D., Jun 14 2020, SIGMOD 2020 - Proceedings of the 2020 ACM SIGMOD International Conference on Management of Data. Association for Computing Machinery, p. 2733-2736 4 p. (Proceedings of the ACM SIGMOD International Conference on Management of Data).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Open Access

Can far memory improve job throughput?

Amaro, E., Branner-Augmon, C., Luo, Z., Ousterhout, A., Aguilera, M. K., Panda, A., Ratnasamy, S. & Shenker, S., Apr 15 2020, Proceedings of the 15th European Conference on Computer Systems, EuroSys 2020. Association for Computing Machinery, Inc, (Proceedings of the 15th European Conference on Computer Systems, EuroSys 2020).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Open Access

CDK7 Inhibition Potentiates Genome Instability Triggering Anti-tumor Immunity in Small Cell Lung Cancer

Zhang, H., Christensen, C. L., Dries, R., Oser, M. G., Deng, J., Diskin, B., Li, F., Pan, Y., Zhang, X., Yin, Y., Papadopoulos, E., Pyon, V., Thakurdin, C., Kwiatkowski, N., Jani, K., Rabin, A. R., Castro, D. M., Chen, T., Silver, H., Huang, Q. & 29 others, Bulatovic, M., Dowling, C. M., Sundberg, B., Leggett, A., Ranieri, M., Han, H., Li, S., Yang, A., Labbe, K. E., Almonte, C., Sviderskiy, V. O., Quinn, M., Donaghue, J., Wang, E. S., Zhang, T., He, Z., Velcheti, V., Hammerman, P. S., Freeman, G. J., Bonneau, R., Kaelin, W. G., Sutherland, K. D., Kersbergen, A., Aguirre, A. J., Yuan, G. C., Rothenberg, E., Miller, G., Gray, N. S. & Wong, K. K., Jan 13 2020, In : Cancer Cell. 37, 1, p. 37-54.e9

Research output: Contribution to journalArticle

Characterization of antibiotic resistance and host-microbiome interactions in the human upper respiratory tract during influenza infection

Zhang, L., Forst, C. V., Gordon, A., Gussin, G., Geber, A. B., Fernandez, P. J., Ding, T., Lashua, L., Wang, M., Balmaseda, A., Bonneau, R., Zhang, B. & Ghedin, E., Mar 17 2020, In : Microbiome. 8, 1, 39.

Research output: Contribution to journalArticle

Open Access

Characterizing chromatin landscape from aggregate and single-cell genomic assays using flexible duration modeling

Gabitto, M. I., Rasmussen, A., Wapinski, O., Allaway, K., Carriero, N., Fishell, G. J. & Bonneau, R., Dec 1 2020, In : Nature communications. 11, 1, 747.

Research output: Contribution to journalArticle

Open Access

Classification of the Molecular Defects Associated with Pathogenic Variants of the SLC6A8 Creatine Transporter

Salazar, M. D., Zelt, N. B., Saldivar, R., Kuntz, C. P., Chen, S., Penn, W. D., Bonneau, R., Koehler Leman, J. & Schlebach, J. P., Apr 7 2020, In : Biochemistry. 59, 13, p. 1367-1377 11 p.

Research output: Contribution to journalArticle

Classifier-agnostic saliency map extraction

Zolna, K., Geras, K. J. & Cho, K., Jul 2020, In : Computer Vision and Image Understanding. 196, 102969.

Research output: Contribution to journalArticle

Open Access

Clustering Complex Zeros of Triangular Systems of Polynomials

Imbach, R., Pouget, M. & Yap, C., 2020, (Accepted/In press) In : Mathematics in Computer Science.

Research output: Contribution to journalArticle

Computational limits don't fully explain human cognitive limitations

Davis, E. S. & Marcus, G. F., 2020, In : Behavioral and Brain Sciences. 43, e7.

Research output: Contribution to journalArticle

Conditional word embedding and hypothesis testing via bayes-by-backprop

Han, R., Spirling, A., Gill, M. & Cho, K., Jan 1 2020, Proceedings of the 2018 Conference on Empirical Methods in Natural Language Processing, EMNLP 2018. Riloff, E., Chiang, D., Hockenmaier, J. & Tsujii, J. (eds.). Association for Computational Linguistics, p. 4890-4895 6 p. (Proceedings of the 2018 Conference on Empirical Methods in Natural Language Processing, EMNLP 2018).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Open Access

Countering language drift via visual grounding

Lee, J., Cho, K. & Kiela, D., 2020, EMNLP-IJCNLP 2019 - 2019 Conference on Empirical Methods in Natural Language Processing and 9th International Joint Conference on Natural Language Processing, Proceedings of the Conference. Association for Computational Linguistics, p. 4385-4395 11 p. (EMNLP-IJCNLP 2019 - 2019 Conference on Empirical Methods in Natural Language Processing and 9th International Joint Conference on Natural Language Processing, Proceedings of the Conference).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Data-driven physiologic thresholds for iron deficiency associated with hematologic decline

Foy, B. H., Li, A., McClung, J. P., Ranganath, R. & Higgins, J. M., Mar 1 2020, In : American Journal of Hematology. 95, 3, p. 302-309 8 p.

Research output: Contribution to journalArticle

Decoupling strategy and generation in negotiation dialogues

He, H., Chen, D., Balakrishnan, A. & Liang, P., Jan 1 2020, Proceedings of the 2018 Conference on Empirical Methods in Natural Language Processing, EMNLP 2018. Riloff, E., Chiang, D., Hockenmaier, J. & Tsujii, J. (eds.). Association for Computational Linguistics, p. 2333-2343 11 p. (Proceedings of the 2018 Conference on Empirical Methods in Natural Language Processing, EMNLP 2018).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Deep learning models for electrocardiograms are susceptible to adversarial attack

Han, X., Hu, Y., Foschini, L., Chinitz, L., Jankelson, L. & Ranganath, R., Mar 1 2020, In : Nature Medicine. 26, 3, p. 360-363 4 p.

Research output: Contribution to journalLetter

Deep Neural Networks Improve Radiologists' Performance in Breast Cancer Screening

Wu, N., Phang, J., Park, J., Shen, Y., Huang, Z., Zorin, M., Jastrzebski, S., Fevry, T., Katsnelson, J., Kim, E., Wolfson, S., Parikh, U., Gaddam, S., Lin, L. L. Y., Ho, K., Weinstein, J. D., Reig, B., Gao, Y., Toth, H., Pysarenko, K. & 12 others, Lewin, A., Lee, J., Airola, K., Mema, E., Chung, S., Hwang, E., Samreen, N., Kim, S. G., Heacock, L., Moy, L., Cho, K. & Geras, K. J., Apr 2020, In : IEEE Transactions on Medical Imaging. 39, 4, p. 1184-1194 11 p., 8861376.

Research output: Contribution to journalArticle

Deterministic non-autoregressive neural sequence modeling by iterative refinement

Lee, J., Mansimov, E. & Cho, K., Jan 1 2020, Proceedings of the 2018 Conference on Empirical Methods in Natural Language Processing, EMNLP 2018. Riloff, E., Chiang, D., Hockenmaier, J. & Tsujii, J. (eds.). Association for Computational Linguistics, p. 1173-1182 10 p. (Proceedings of the 2018 Conference on Empirical Methods in Natural Language Processing, EMNLP 2018).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Dialogue natural language inference

Welleck, S., Weston, J., Szlam, A. & Cho, K., 2020, ACL 2019 - 57th Annual Meeting of the Association for Computational Linguistics, Proceedings of the Conference. Association for Computational Linguistics (ACL), p. 3731-3741 11 p. (ACL 2019 - 57th Annual Meeting of the Association for Computational Linguistics, Proceedings of the Conference).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Discrepancy-Based Theory and Algorithms for Forecasting Non-Stationary Time Series

Kuznetsov, V. & Mohri, M., Apr 1 2020, In : Annals of Mathematics and Artificial Intelligence. 88, 4, p. 367-399 33 p.

Research output: Contribution to journalArticle

Distributed Algorithms to Find Similar Time Series

Levchenko, O., Kolev, B., Yagoubi, D. E., Shasha, D., Palpanas, T., Valduriez, P., Akbarinia, R. & Masseglia, F., 2020, Machine Learning and Knowledge Discovery in Databases - European Conference, ECML PKDD 2019, Proceedings. Brefeld, U., Fromont, E., Hotho, A., Knobbe, A., Maathuis, M. & Robardet, C. (eds.). Springer, p. 781-785 5 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 11908 LNAI).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Dynamic meta-embeddings for improved sentence representations

Kiela, D., Wang, C. & Cho, K., Jan 1 2020, Proceedings of the 2018 Conference on Empirical Methods in Natural Language Processing, EMNLP 2018. Riloff, E., Chiang, D., Hockenmaier, J. & Tsujii, J. (eds.). Association for Computational Linguistics, p. 1466-1477 12 p. (Proceedings of the 2018 Conference on Empirical Methods in Natural Language Processing, EMNLP 2018).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Emergent linguistic phenomena in multi-agent communication games

Graesser, L., Cho, K. & Kiela, D., 2020, EMNLP-IJCNLP 2019 - 2019 Conference on Empirical Methods in Natural Language Processing and 9th International Joint Conference on Natural Language Processing, Proceedings of the Conference. Association for Computational Linguistics, p. 3700-3710 11 p. (EMNLP-IJCNLP 2019 - 2019 Conference on Empirical Methods in Natural Language Processing and 9th International Joint Conference on Natural Language Processing, Proceedings of the Conference).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Evaluating pretrained transformer models for citation recommendation

Nogueira, R., Jiang, Z., Cho, K. & Lin, J., 2020, In : CEUR Workshop Proceedings. 2591, p. 89-100 12 p.

Research output: Contribution to journalConference article

Evaluation of Combined Artificial Intelligence and Radiologist Assessment to Interpret Screening Mammograms

and the DM DREAM Consortium, Mar 2 2020, In : JAMA network open. 3, 3, p. e200265

Research output: Contribution to journalArticle

Open Access

Fast radix-32 approximate dfts for 1024-beam digital rf beamforming

Madanayake, A., Cintra, R. J., Akram, N., Ariyarathna, V., Mandal, S., Coutinho, V. A., Bayer, F. M., Coelho, D. & Rappaport, T. S., 2020, In : IEEE Access. 8, p. 96613-96627 15 p., 9093889.

Research output: Contribution to journalArticle

Open Access

Finding generalizable evidence by learning to convince Q&A models

Perez, E., Karamcheti, S., Fergus, R., Weston, J., Kiela, D. & Cho, K., 2020, EMNLP-IJCNLP 2019 - 2019 Conference on Empirical Methods in Natural Language Processing and 9th International Joint Conference on Natural Language Processing, Proceedings of the Conference. Association for Computational Linguistics, p. 2402-2411 10 p. (EMNLP-IJCNLP 2019 - 2019 Conference on Empirical Methods in Natural Language Processing and 9th International Joint Conference on Natural Language Processing, Proceedings of the Conference).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

First-order perturbation theory for eigenvalues and eigenvectors

Greenbaum, A., Li, R. C. & Overton, M. L., 2020, In : SIAM Review. 62, 2, p. 463-482 20 p.

Research output: Contribution to journalArticle

Open Access

Generating diverse translations with sentence codes

Shu, R., Nakayama, H. & Cho, K., 2020, ACL 2019 - 57th Annual Meeting of the Association for Computational Linguistics, Proceedings of the Conference. Association for Computational Linguistics (ACL), p. 1823-1827 5 p. (ACL 2019 - 57th Annual Meeting of the Association for Computational Linguistics, Proceedings of the Conference).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Gene regulatory network reconstruction using single-cell rna sequencing of barcoded genotypes in diverse environments

Jackson, C. A., Castro, D. M., Saldi, G. A., Bonneau, R. & Gresham, D., Jan 2020, In : eLife. 9, e51254.

Research output: Contribution to journalArticle

Open Access

Global Identifiability of Differential Models

Hong, H., Ovchinnikov, A., Pogudin, G. & Yap, C., Sep 1 2020, In : Communications on Pure and Applied Mathematics. 73, 9, p. 1831-1879 49 p.

Research output: Contribution to journalArticle

Grammar induction with neural language models: An unusual replication

Htut, P. M., Cho, K. & Bowman, S. R., Jan 1 2020, Proceedings of the 2018 Conference on Empirical Methods in Natural Language Processing, EMNLP 2018. Riloff, E., Chiang, D., Hockenmaier, J. & Tsujii, J. (eds.). Association for Computational Linguistics, p. 4998-5003 6 p. (Proceedings of the 2018 Conference on Empirical Methods in Natural Language Processing, EMNLP 2018).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Guest Editorial: Special Issue on Analytics for Local Events and News

Magdy, A., Zhou, X. & Neill, D. B., Apr 1 2020, In : GeoInformatica. 24, 2, p. 267-268 2 p.

Research output: Contribution to journalEditorial

Open Access

Identifying predictive causal factors from news streams

Balashankar, A., Chakraborty, S., Fraiberger, S. & Subramanian, L., 2020, EMNLP-IJCNLP 2019 - 2019 Conference on Empirical Methods in Natural Language Processing and 9th International Joint Conference on Natural Language Processing, Proceedings of the Conference. Association for Computational Linguistics, p. 2338-2348 11 p. (EMNLP-IJCNLP 2019 - 2019 Conference on Empirical Methods in Natural Language Processing and 9th International Joint Conference on Natural Language Processing, Proceedings of the Conference).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Improved zero-shot neural machine translation via ignoring spurious correlations

Gu, J., Wang, Y., Cho, K. & Li, V. O. K., 2020, ACL 2019 - 57th Annual Meeting of the Association for Computational Linguistics, Proceedings of the Conference. Association for Computational Linguistics (ACL), p. 1258-1268 11 p. (ACL 2019 - 57th Annual Meeting of the Association for Computational Linguistics, Proceedings of the Conference).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Inference of bacterial small RNA regulatory networks and integration with transcription factor-driven regulatory networks

Arrieta-Ortiz, M. L., Arrieta-Ortiz, M. L., Hafemeister, C., Shuster, B., Baliga, N. S., Bonneau, R., Bonneau, R., Bonneau, R. & Eichenberger, P., Jun 2020, In : mSystems. 5, 3, e00057-20.

Research output: Contribution to journalArticle

Open Access

Interleukin-17 Inhibition in Spondyloarthritis Is Associated With Subclinical Gut Microbiome Perturbations and a Distinctive Interleukin-25–Driven Intestinal Inflammation

Manasson, J., Wallach, D. S., Guggino, G., Stapylton, M., Badri, M. H., Solomon, G., Reddy, S. M., Coras, R., Aksenov, A. A., Jones, D. R., Girija, P. V., Neimann, A. L., Heguy, A., Segal, L. N., Dorrestein, P. C., Bonneau, R., Guma, M., Ciccia, F., Ubeda, C., Clemente, J. C. & 1 others, Scher, J. U., Apr 1 2020, In : Arthritis and Rheumatology. 72, 4, p. 645-657 13 p.

Research output: Contribution to journalArticle

Kymatio: Scattering transforms in python

Andreux, M., Angles, T., Exarchakis, G., Leonarduzzi, R., Rochette, G., Thiry, L., Zarka, J., Mallat, S., Andén, J., Belilovsky, E., Bruna, J., Lostanlen, V., Chaudhary, M., Hirn, M. J., Oyallon, E., Zhang, S., Cella, C. & Eickenberg, M., Jan 1 2020, In : Journal of Machine Learning Research. 21

Research output: Contribution to journalArticle

Local Reasoning for Global Graph Properties

Krishna, S., Summers, A. J. & Wies, T., 2020, Programming Languages and Systems- 29th European Symposium on Programming, ESOP 2020 held as Part of the European Joint Conferences on Theory and Practice of Software, ETAPS 2020, Proceedings. Müller, P. (ed.). Springer, p. 308-335 28 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 12075 LNCS).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Open Access

Macromolecular modeling and design in Rosetta: recent methods and frameworks

Leman, J. K., Weitzner, B. D., Lewis, S. M., Adolf-Bryfogle, J., Alam, N., Alford, R. F., Aprahamian, M., Baker, D., Barlow, K. A., Barth, P., Basanta, B., Bender, B. J., Blacklock, K., Bonet, J., Boyken, S. E., Bradley, P., Bystroff, C., Conway, P., Cooper, S., Correia, B. E. & 88 others, Coventry, B., Das, R., De Jong, R. M., DiMaio, F., Dsilva, L., Dunbrack, R., Ford, A. S., Frenz, B., Fu, D. Y., Geniesse, C., Goldschmidt, L., Gowthaman, R., Gray, J. J., Gront, D., Guffy, S., Horowitz, S., Huang, P. S., Huber, T., Jacobs, T. M., Jeliazkov, J. R., Johnson, D. K., Kappel, K., Karanicolas, J., Khakzad, H., Khar, K. R., Khare, S. D., Khatib, F., Khramushin, A., King, I. C., Kleffner, R., Koepnick, B., Kortemme, T., Kuenze, G., Kuhlman, B., Kuroda, D., Labonte, J. W., Lai, J. K., Lapidoth, G., Leaver-Fay, A., Lindert, S., Linsky, T., London, N., Lubin, J. H., Lyskov, S., Maguire, J., Malmström, L., Marcos, E., Marcu, O., Marze, N. A., Meiler, J., Moretti, R., Mulligan, V. K., Nerli, S., Norn, C., Ó’Conchúir, S., Ollikainen, N., Ovchinnikov, S., Pacella, M. S., Pan, X., Park, H., Pavlovicz, R. E., Pethe, M., Pierce, B. G., Pilla, K. B., Raveh, B., Renfrew, P. D., Burman, S. S. R., Rubenstein, A., Sauer, M. F., Scheck, A., Schief, W., Schueler-Furman, O., Sedan, Y., Sevy, A. M., Sgourakis, N. G., Shi, L., Siegel, J. B., Silva, D. A., Smith, S., Song, Y., Stein, A., Szegedy, M., Teets, F. D., Thyme, S. B., Wang, R. Y. R., Watkins, A., Zimmerman, L. & Bonneau, R., Jul 1 2020, In : Nature methods. 17, 7, p. 665-680 16 p.

Research output: Contribution to journalReview article

Meta-learning for low-resource neural machine translation

Gu, J., Wang, Y., Chen, Y., Cho, K. & Li, V. O. K., Jan 1 2020, Proceedings of the 2018 Conference on Empirical Methods in Natural Language Processing, EMNLP 2018. Riloff, E., Chiang, D., Hockenmaier, J. & Tsujii, J. (eds.). Association for Computational Linguistics, p. 3622-3631 10 p. (Proceedings of the 2018 Conference on Empirical Methods in Natural Language Processing, EMNLP 2018).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Multi-lingual common semantic space construction via cluster-consistent word embedding

Huang, L., Cho, K., Zhang, B., Ji, H. & Knight, K., Jan 1 2020, Proceedings of the 2018 Conference on Empirical Methods in Natural Language Processing, EMNLP 2018. Riloff, E., Chiang, D., Hockenmaier, J. & Tsujii, J. (eds.). Association for Computational Linguistics, p. 250-260 11 p. (Proceedings of the 2018 Conference on Empirical Methods in Natural Language Processing, EMNLP 2018).

Research output: Chapter in Book/Report/Conference proceedingConference contribution