Data-driven Science - 2021

Cooley, M., Greene, C. S., Issac, D., Pividori, M., & Sullivan, B. D. (2021). Parameterized algorithms for identifying gene co-expression modules via weighted clique decomposition. SIAM Conference on Applied and Computational Discrete Algorithms (ACDA21), 111–122. https://doi.org/10.1137/1.9781611976830.11

Pividori, M., Lu, S., Li, B., Su, C., Johnson, M. E., Wei, W.-Q., … Greene, C. S. (2021). Projecting genetic associations through gene expression patterns highlights disease etiology and drug mechanisms. BioRxiv. https://doi.org/10.1101/2021.07.05.450786

Goodrich, T. D., Horton, E., & Sullivan, B. D. (2021). An Updated Experimental Evaluation of Graph Bipartization Methods. ACM Journal of Experimental Algorithmics, 26. https://doi.org/10.1145/3467968

Mizutani, Y., Staker, A., & Sullivan, B. D. (2021). Sparse dominating sets and balanced neighborhood partitioning. ArXiv. Retrieved from http://www.scopus.com/inward/record.url?eid=2-s2.0-85121833484&partnerID=MN8TOARS

Du, H., Ferrari, M. M., Heitsch, C., Hurley, F., Mennicke, C. V., Sullivan, B. D., & Xu, B. (2021). Secondary Structure Ensemble Analysis via Community Detection. In Association for Women in Mathematics Series (Vol. 22, pp. 55–81). https://doi.org/10.1007/978-3-030-57129-0_4

Cooley, M., Greene, C. S., Issac, D., Pividori, M., & Sullivan, B. D. (2021). Parameterized algorithms for identifying gene co-expression modules via weighted clique decomposition. ArXiv. Retrieved from http://www.scopus.com/inward/record.url?eid=2-s2.0-85108789587&partnerID=MN8TOARS

Breen-McKay, M., Lavallee, B., & Sullivan, B. D. (2021). Hardness of the Generalized Coloring Numbers. ArXiv. Retrieved from http://www.scopus.com/inward/record.url?eid=2-s2.0-85121786987&partnerID=MN8TOARS

Ul Mustafa, N., Xu, Y., Shen, X., & Solihin, Y. (2021). Seeds of SEED: New Security Challenges for Persistent Memory. 2021 INTERNATIONAL SYMPOSIUM ON SECURE AND PRIVATE EXECUTION ENVIRONMENT DESIGN (SEED 2021), pp. 83–88. https://doi.org/10.1109/SEED51797.2021.00020

Guan, H., Chaudhary, U., Xu, Y., Ning, L., Zhang, L., & Shen, X. (2021). Recurrent Neural Networks Meet Context-Free Grammar: Two Birds with One Stone. 2021 21ST IEEE INTERNATIONAL CONFERENCE ON DATA MINING (ICDM 2021), pp. 1078–1083. https://doi.org/10.1109/ICDM51629.2021.00125

Verma, G., Emani, M., Liao, C., Lin, P.-H., Vanderbruggen, T., Shen, X., & Chapman, B. (2021). HPCFAIR: Enabling FAIR AI for HPC Applications. PROCEEDINGS OF THE WORKSHOP ON MACHINE LEARNING IN HIGH PERFORMANCE COMPUTING ENVIRONMENTS (MLHPC 2021), pp. 58–68. https://doi.org/10.1109/MLHPC54614.2021.00011

Liao, C., Lin, P.-H., Verma, G., Vanderbruggen, T., Emani, M., Nan, Z., & Shen, X. (2021). HPC Ontology: Towards a Unified Ontology for Managing Training Datasets and AI Models for High-Performance Computing. PROCEEDINGS OF THE WORKSHOP ON MACHINE LEARNING IN HIGH PERFORMANCE COMPUTING ENVIRONMENTS (MLHPC 2021), pp. 69–80. https://doi.org/10.1109/MLHPC54614.2021.00012

Tan, J., Chen, Y., Liu, Z., Ren, B., Song, S. L., Shen, X., & Liu, X. (2021). Toward Efficient Interactions between Python and Native Libraries. PROCEEDINGS OF THE 29TH ACM JOINT MEETING ON EUROPEAN SOFTWARE ENGINEERING CONFERENCE AND SYMPOSIUM ON THE FOUNDATIONS OF SOFTWARE ENGINEERING (ESEC/FSE '21), pp. 1117–1128. https://doi.org/10.1145/3468264.3468541

Yang, S., Shen, X., & Lim, S.-H. (2021). Revisit the Scalability of Deep Auto-Regressive Models for Graph Generation. 2021 INTERNATIONAL JOINT CONFERENCE ON NEURAL NETWORKS (IJCNN). https://doi.org/10.1109/IJCNN52387.2021.9534206

Zhang, G., Xu, Y., Shen, X., & Dillig, I. (2021). UDF to SQL Translation through Compositional Lazy Inductive Synthesis. PROCEEDINGS OF THE ACM ON PROGRAMMING LANGUAGES-PACMPL, 5(OOPSLA). https://doi.org/10.1145/3485489

Shen, X., Zhang, G., Dea, I., Andow, S., Arroyo-Fang, E., Gafter, N., … Yang, S. (2021). Coarsening Optimization for Differentiable Programming. PROCEEDINGS OF THE ACM ON PROGRAMMING LANGUAGES-PACMPL, 5(OOPSLA). https://doi.org/10.1145/3485507

Zhao, P., Niu, W., Yuan, G., Cai, Y., Sung, H.-H., Liu, S., … Lin, X. (2021). Brief Industry Paper: Towards Real-Time 3D Object Detection for Autonomous Vehicles with Pruning Search. 2021 IEEE 27TH REAL-TIME AND EMBEDDED TECHNOLOGY AND APPLICATIONS SYMPOSIUM (RTAS 2021), pp. 425–428. https://doi.org/10.1109/RTAS52030.2021.00043

Agrawal, A., Fu, W., Chen, D., Shen, X., & Menzies, T. (2021). How to "DODGE" Complex Software Analytics. IEEE TRANSACTIONS ON SOFTWARE ENGINEERING, 47(10), 2182–2194. https://doi.org/10.1109/TSE.2019.2945020

Ye, C., Xu, Y., Shen, X., Liao, X., Jin, H., & Solihin, Y. (2021). Supporting Legacy Libraries on Non-Volatile Memory: A User-Transparent Approach. 2021 ACM/IEEE 48TH ANNUAL INTERNATIONAL SYMPOSIUM ON COMPUTER ARCHITECTURE (ISCA 2021), pp. 443–455. https://doi.org/10.1109/ISCA52012.2021.00042

Zhang, F., Pan, Z., Zhou, Y., Zhai, J., Shen, X., Mutlu, O., & Du, X. (2021). G-TADOC: Enabling Efficient GPU-Based Text Analytics without Decompression. 2021 IEEE 37TH INTERNATIONAL CONFERENCE ON DATA ENGINEERING (ICDE 2021), pp. 1679–1690. https://doi.org/10.1109/ICDE51399.2021.00148

Ye, C., Xu, Y., Shen, X., Liao, X., Jin, H., & Solihin, Y. (2021). Hardware-Based Address-Centric Acceleration of Key-Value Store. 2021 27TH IEEE INTERNATIONAL SYMPOSIUM ON HIGH-PERFORMANCE COMPUTER ARCHITECTURE (HPCA 2021), pp. 736–748. https://doi.org/10.1109/HPCA51647.2021.00067

Guan, H., Liu, S., Ma, X., Niu, W., Ren, B., Shen, X., … Zhao, P. (2021). CoCoPIE: Enabling Real-Time AI on Off-the-Shelf Mobile Devices via Compression-Compilation Co-Design. COMMUNICATIONS OF THE ACM, 64(6), 62–68. https://doi.org/10.1145/3418297

Hollis, A. N., Smith, R. C., & Wilson, A. G. (2021). SURROGATE BASED MUTUAL INFORMATION APPROXIMATION AND OPTIMIZATION FOR URBAN SOURCE LOCALIZATION. INTERNATIONAL JOURNAL FOR UNCERTAINTY QUANTIFICATION, 11(5), 39–55. https://doi.org/10.1615/Int.J.UncertaintyQuantification.2021034400

Zhang, L., Guan, H., Ding, Y., Shen, X., & Krim, H. (2021). Reuse-centric k-means configuration. INFORMATION SYSTEMS, 100. https://doi.org/10.1016/j.is.2021.101787

Sun, X., Xie, L., Shah, S. U., & Shen, X. (2021). A Machine Learning Based Ensemble Forecasting Optimization Algorithm for Preseason Prediction of Atlantic Hurricane Activity. ATMOSPHERE, 12(4). https://doi.org/10.3390/atmos12040522

Wendelberger, L. J., Reich, B. J., & Wilson, A. G. (2021). Multi-model penalized regression. STATISTICAL ANALYSIS AND DATA MINING, 14(6), 698–722. https://doi.org/10.1002/sam.11496

Cahoon, J., Sanborn, K., & Wilson, A. (2021). Practical reliability growth modeling. Quality and Reliability Engineering International. https://doi.org/10.1002/qre.2822

Zhang, F., Zhai, J., Shen, X., Wang, D., Chen, Z., Mutlu, O., … Du, X. (2021). TADOC: Text analytics directly on compression. VLDB JOURNAL, 30(2), 163–188. https://doi.org/10.1007/s00778-020-00636-3

Guan, H., Shen, X., & Krim, H. (2021). An Automatic Synthesizer of Advising Tools for High Performance Computing. IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS, 32(2), 330–341. https://doi.org/10.1109/TPDS.2020.3018636

Kun, J., Michael P. O'Brien, Pilipczuk, M., & Sullivan, B. D. (2021). Polynomial Treedepth Bounds in Linear Colorings. ALGORITHMICA, 83(1), 361–386. https://doi.org/10.1007/s00453-020-00760-0