Jian Peng

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Research Output

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Conference contribution
2020

Efficient contextualized representation: Language model pruning for sequence labeling

Liu, L., Ren, X., Shang, J., Gu, X., Peng, J. & Han, J., 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. 1215-1225 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

EMRQA: A large corpus for question answering on electronic medical records

Pampari, A., Raghavan, P., Liang, J. & Peng, J., 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. 2357-2368 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

Evolutionary context-integrated deep sequence modeling for protein engineering

Luo, Y., Vo, L., Ding, H., Su, Y., Liu, Y., Qian, W. W., Zhao, H. & Peng, J., Jan 1 2020, Research in Computational Molecular Biology - 24th Annual International Conference, RECOMB 2020, Proceedings. Schwartz, R. (ed.). Springer, p. 261-263 3 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 12074 LNBI).

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

SemRegex: A semantics-based approach for generating regular expressions from natural language specifications

Zhong, Z., Guo, J., Yang, W., Peng, J., Xie, T., Lou, J. G., Liu, T. & Zhang, D., 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. 1608-1618 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

2019

A gradual, semi-discrete approach to generative network training via explicit wasserstein minimization

Chen, Y., Telgarsky, M., Zhang, C., Bailey, B., Hsu, D. & Peng, J., Jan 1 2019, 36th International Conference on Machine Learning, ICML 2019. International Machine Learning Society (IMLS), p. 1845-1858 14 p. (36th International Conference on Machine Learning, ICML 2019; vol. 2019-June).

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

HetespaceyWalk: A heterogeneous Spacey random walk for heterogeneous information network embedding

He, Y., Song, Y., Li, J., Ji, C., Peng, J. & Peng, H., Nov 3 2019, CIKM 2019 - Proceedings of the 28th ACM International Conference on Information and Knowledge Management. Association for Computing Machinery, p. 639-648 10 p. (International Conference on Information and Knowledge Management, Proceedings).

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

Open Access

Quantite Stein variational gradient descent for batch Bayesian optimization

Gong, C., Peng, J. & Liu, Q., Jan 1 2019, 36th International Conference on Machine Learning, ICML 2019. International Machine Learning Society (IMLS), p. 4212-4221 10 p. (36th International Conference on Machine Learning, ICML 2019; vol. 2019-June).

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

REINAM: Reinforcement learning for input-grammar inference

Wu, Z., Johnson, E., Yang, W., Bastani, O., Song, D., Peng, J. & Xie, T., Aug 12 2019, ESEC/FSE 2019 - Proceedings of the 2019 27th ACM Joint Meeting European Software Engineering Conference and Symposium on the Foundations of Software Engineering. Apel, S., Dumas, M., Russo, A. & Pfahl, D. (eds.). Association for Computing Machinery, Inc, p. 488-498 11 p. (ESEC/FSE 2019 - Proceedings of the 2019 27th ACM Joint Meeting European Software Engineering Conference and Symposium on the Foundations of Software Engineering).

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

Similarity modeling on heterogeneous networks via automatic path discovery

Yang, C., Liu, M., He, F., Zhang, X., Peng, J. & Han, J., Jan 1 2019, Machine Learning and Knowledge Discovery in Databases - European Conference, ECML PKDD 2018, Proceedings. Bonchi, F., Berlingerio, M., Gärtner, T., Hurley, N. & Ifrim, G. (eds.). Springer-Verlag Berlin Heidelberg, p. 37-54 18 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 11052 LNAI).

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

Stochastic variance reduction for deep Q-iearning

Zhao, W. Y. & Peng, J., Jan 1 2019, 18th International Conference on Autonomous Agents and Multiagent Systems, AAMAS 2019. International Foundation for Autonomous Agents and Multiagent Systems (IFAAMAS), p. 2318-2320 3 p. (Proceedings of the International Joint Conference on Autonomous Agents and Multiagent Systems, AAMAS; vol. 4).

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

2018

Deciphering signaling specificity with deep neural networks

Luo, Y., Ma, J., Liu, Y., Ye, Q., Ideker, T. & Peng, J., Jan 1 2018, Research in Computational Molecular Biology - 22nd Annual International Conference, RECOMB 2018, Proceedings. Raphael, B. J. (ed.). Springer-Verlag Berlin Heidelberg, p. 266-268 3 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 10812 LNBI).

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

Efficient localized inference for large graphical models

Chen, J., Peng, J. & Liu, Q., Jan 1 2018, Proceedings of the 27th International Joint Conference on Artificial Intelligence, IJCAI 2018. Lang, J. (ed.). International Joint Conferences on Artificial Intelligence, p. 4987-4993 7 p. (IJCAI International Joint Conference on Artificial Intelligence; vol. 2018-July).

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

Empower sequence labeling with task-aware neural language model

Liu, L., Shang, J., Ren, X., Xu, F. F., Gui, H., Peng, J. & Han, J., Jan 1 2018, 32nd AAAI Conference on Artificial Intelligence, AAAI 2018. AAAI Press, p. 5253-5260 8 p. (32nd AAAI Conference on Artificial Intelligence, AAAI 2018).

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

Energy-efficient amortized inference with cascaded deep classifiers

Guan, J., Liu, Y., Liu, Q. & Peng, J., Jan 1 2018, Proceedings of the 27th International Joint Conference on Artificial Intelligence, IJCAI 2018. Lang, J. (ed.). International Joint Conferences on Artificial Intelligence, p. 2184-2190 7 p. (IJCAI International Joint Conference on Artificial Intelligence; vol. 2018-July).

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

Open Access

Generalizable visualization of mega-scale single-cell data

Cho, H., Berger, B. & Peng, J., Jan 1 2018, Research in Computational Molecular Biology - 22nd Annual International Conference, RECOMB 2018, Proceedings. Raphael, B. J. (ed.). Springer-Verlag Berlin Heidelberg, p. 251-253 3 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 10812 LNBI).

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

Learning to explore via meta-policy gradient

Xu, T., Liu, Q., Zhao, L. & Peng, J., Jan 1 2018, 35th International Conference on Machine Learning, ICML 2018. Dy, J. & Krause, A. (eds.). International Machine Learning Society (IMLS), p. 8686-8706 21 p. (35th International Conference on Machine Learning, ICML 2018; vol. 12).

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

2017

A network integration approach for drug-target interaction prediction and computational drug repositioning from heterogeneous information

Luo, Y., Zhao, X., Zhou, J., Yang, J., Zhang, Y., Kuang, W., Peng, J., Chen, L. & Zeng, J., Jan 1 2017, Research in Computational Molecular Biology - 21st Annual International Conference, RECOMB 2017, Proceedings. Sahinalp, S. C. (ed.). Springer-Verlag Berlin Heidelberg, p. 383-384 2 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 10229 LNCS).

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

ProSNet: Integrating homology with molecular networks for protein function prediction

Wang, S., Qu, M. & Peng, J., Jan 1 2017, PACIFIC SYMPOSIUM ON BIOCOMPUTING 2017. Altman, R. B., Murray, T., Klein, T. E., Dunker, A. K., Ritchie, M. D. & Hunter, L. (eds.). 212679 ed. World Scientific Publishing Co. Pte Ltd, p. 27-38 12 p. (Pacific Symposium on Biocomputing, 2017; no. 212679).

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

2016

DPClass: An effective but concise discriminative patterns-based classification framework

Shang, J., Tong, W., Peng, J. & Han, J., Jan 1 2016, 16th SIAM International Conference on Data Mining 2016, SDM 2016. Venkatasubramanian, S. C. & Meira, W. (eds.). Society for Industrial and Applied Mathematics Publications, p. 567-575 9 p. (16th SIAM International Conference on Data Mining 2016, SDM 2016).

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

Exploiting temporal divergence of topic distributions for event detection

Zhu, R., Zhang, A., Peng, J. & Zhai, C., Jan 1 2016, Proceedings - 2016 IEEE International Conference on Big Data, Big Data 2016. Institute of Electrical and Electronics Engineers Inc., p. 164-171 8 p. 7840602

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

MACFP: Maximal approximate consecutive frequent pattern mining under edit distance

Shang, J., Peng, J. & Han, J., Jan 1 2016, 16th SIAM International Conference on Data Mining 2016, SDM 2016. Venkatasubramanian, S. C. & Meira, W. (eds.). Society for Industrial and Applied Mathematics Publications, p. 558-566 9 p. (16th SIAM International Conference on Data Mining 2016, SDM 2016).

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

2015

Bermuda: De novo assembly of transcripts with new insights for handling uneven coverage

Tang, Q., Wang, S., Peng, J., Ma, J. & Xu, J., Sep 9 2015, BCB 2015 - 6th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics. Association for Computing Machinery, Inc, p. 166-175 10 p. (BCB 2015 - 6th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics).

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

Diffusion component analysis: Unraveling functional topology in biological networks

Cho, H., Berger, B. & Peng, J., Jan 1 2015, Research in Computational Molecular Biology - 19th Annual International Conference, RECOMB 2015, Proceedings. Przytycka, T. M. (ed.). Springer-Verlag, p. 62-64 3 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 9029).

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

Estimating the partition function by discriminance sampling

Liu, Q., Ihler, A., Peng, J. & Fisher, J., 2015, Uncertainty in Artificial Intelligence - Proceedings of the 31st Conference, UAI 2015. AUAI Press, p. 514-522 9 p.

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

Exact hybrid covariance thresholding for joint graphical lasso

Tang, Q., Yang, C., Peng, J. & Xu, J., Jan 1 2015, Machine Learning and Knowledge Discovery in Databases - European Conference, ECML PKDD 2015. Costa, V. S., Soares, C., Appice, A., Appice, A., Rodrigues, P. P., Costa, V. S., Soares, C., Gama, J., Jorge, A., Rodrigues, P. P., Gama, J., Costa, V. S., Jorge, A., Appice, A., Rodrigues, P. P., Gama, J., Appice, A., Soares, C., Jorge, A., Gama, J., Rodrigues, P. P., Costa, V. S., Soares, C. & Jorge, A. (eds.). Springer-Verlag, p. 593-607 15 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 9285).

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

2014

HapTree: A novel bayesian framework for single individual polyplotyping using NGS data

Berger, E., Yorukoglu, D., Peng, J. & Berger, B., Jan 1 2014, Research in Computational Molecular Biology - 18th Annual International Conference, RECOMB 2014, Proceedings. Springer-Verlag, p. 18-19 2 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 8394 LNBI).

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

2012

Tightening fractional covering upper bounds on the partition function for high-order region graphs

Hazan, T., Peng, J. & Shashua, A., Dec 1 2012, Uncertainty in Artificial Intelligence - Proceedings of the 28th Conference, UAI 2012. p. 356-366 11 p. (Uncertainty in Artificial Intelligence - Proceedings of the 28th Conference, UAI 2012).

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

Variational inference for crowdsourcing

Liu, Q., Peng, J. & Ihler, A., Dec 1 2012, Advances in Neural Information Processing Systems 25: 26th Annual Conference on Neural Information Processing Systems 2012, NIPS 2012. p. 692-700 9 p. (Advances in Neural Information Processing Systems; vol. 1).

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

2011

Convex max-product algorithms for continuous MRFs with applications to protein folding

Peng, J., Hazan, T., McAllester, D. & Urtasun, R., Oct 7 2011, Proceedings of the 28th International Conference on Machine Learning, ICML 2011. p. 729-736 8 p. (Proceedings of the 28th International Conference on Machine Learning, ICML 2011).

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

2010

Protein 8-class secondary structure prediction using conditional neural fields

Wang, Z., Zhao, F., Peng, J. & Xu, J., Dec 1 2010, Proceedings - 2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010. p. 109-114 6 p. 5706547. (Proceedings - 2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010).

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

2009

A probabilistic graphical model for ab initio folding

Zhao, F., Peng, J., De Bartolo, J., Freed, K. F., Sosnick, T. R. & Xu, J., Jul 17 2009, Research in Computational Molecular Biology - 13th Annual International Conference, RECOMB 2009, Proceedings. p. 59-73 15 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 5541 LNBI).

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

Boosting protein threading accuracy

Peng, J. & Xu, J., Jul 20 2009, Research in Computational Molecular Biology - 13th Annual International Conference, RECOMB 2009, Proceedings. p. 31-45 15 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 5541 LNBI).

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

Conditional neural fields

Peng, J., Bo, L. & Xu, J., Dec 1 2009, Advances in Neural Information Processing Systems 22 - Proceedings of the 2009 Conference. p. 1419-1427 9 p. (Advances in Neural Information Processing Systems 22 - Proceedings of the 2009 Conference).

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