Publications
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2023 (1)
A. Mikalsen, J. Zola (2023)
Coriolis: Enabling Metagenomic Classification on Lightweight Mobile Devices.
Bioinformatics 39
doi bibtex @ARTICLE{Mikalsen2023,
author = {Mikalsen, A. and Zola, J.},
title = {Coriolis: Enabling Metagenomic Classification on Lightweight Mobile Devices},
journal = {Bioinformatics},
volume = {39},
year = 2023,
doi = {10.1093/bioinformatics/btad243},
note = {Proceedings of ISMB 2023}
}
2022 (3)
J. Niu, J. Zola, A.E. Sariyuce (2022)
Counting Induced 6-Cycles in Bipartite Graphs. In
International Conference on Parallel Processing (ICPP).
bibtex @INPROCEEDINGS{Niu2022,
author = {Niu, J. and Zola, J. and Sariyuce, A.E.},
title = {Counting Induced 6-Cycles in Bipartite Graphs},
booktitle = {International Conference on Parallel Processing (ICPP)},
year = 2022
}
B.O. Turkkan, T. Dai, T. Kosar, C. Chen, M.F. Bulut, J. Zola, D. Sow (2022)
GreenABR: Energy‐Aware Adaptive Bitrate Streaming with
Deep Reinforcement Learning. In
ACM Multimedia Systems Conference (MMSys).
bibtex @INPROCEEDINGS{Turkkan2022,
author = {Turkkan, B.O. and Dai, T. and Kosar, T. and Chen, C. and
Bulut, M.F. and Zola, J. and Sow, D.},
title = {GreenABR: Energy‐Aware Adaptive Bitrate Streaming with
Deep Reinforcement Learning},
booktitle = {ACM Multimedia Systems Conference (MMSys)},
year = 2022
}
V. Zheng, A.E. Sariyuce, J. Zola (2022)
Identifying Taxonomic Units in Metagenomic DNA Streams on
Mobile Devices.
IEEE/ACM Transactions on Computational Biology and
Bioinformatics doi bibtex @ARTICLE{Zheng2022,
author = {Zheng, V. and Sariyuce, A.E. and Zola, J.},
title = {Identifying Taxonomic Units in Metagenomic DNA Streams on
Mobile Devices},
journal = {IEEE/ACM Transactions on Computational Biology and
Bioinformatics},
year = 2022,
doi = {10.1109/TCBB.2022.3172661}
}
2021 (2)
S. Mullin, J. Zola, R. Lee, J. Hu, B. MacKenzie, A. Brickman, G. Anaya, S. Sinha, A. Li, P.L. Elkin (2021)
Longitudinal K-Means Approaches to Clustering and
Analyzing EHR Opioid Use Trajectories for Clinical
Subtypes.
Journal of Biomedical Informatics 122
doi web bibtex @ARTICLE{Mullin2021,
author = {Mullin, S. and Zola, J. and Lee, R. and Hu, J. and
MacKenzie, B. and Brickman, A. and Anaya, G. and Sinha,
S. and Li, A. and Elkin, P.L.},
title = {Longitudinal K-Means Approaches to Clustering and
Analyzing EHR Opioid Use Trajectories for Clinical
Subtypes},
journal = {Journal of Biomedical Informatics},
volume = {122},
year = 2021,
doi = {10.1016/j.jbi.2021.103889},
url = {http://www.jzola.org/papers/mullin_jbmi2021.pdf}
}
N. Juneja, J. Zola, V. Chandola, O. Wodo (2021)
Graph-based Strategy for Establishing Morphology
Similarity. In
International Conference on Scientific and Statistical
Database Management (SSDBM). pp. 169–180.
doi bibtex @INPROCEEDINGS{Juneja2021,
author = {Juneja, N. and Zola, J. and Chandola, V. and Wodo, O.},
title = {Graph-based Strategy for Establishing Morphology
Similarity},
booktitle = {International Conference on Scientific and Statistical
Database Management (SSDBM)},
pages = {169--180},
year = 2021,
doi = {10.1145/3468791.3468819}
}
2020 (3)
V. Zheng, A.E. Sariyuce, J. Zola (2020)
Identifying Taxonomic Units in Metagenomic DNA Streams. In
International Workshop on Data Mining in Bioinformatics
(BIOKDD).
doi bibtex @INPROCEEDINGS{Zheng2020,
author = {Zheng, V. and Sariyuce, A.E. and Zola, J.},
title = {Identifying Taxonomic Units in Metagenomic DNA Streams},
booktitle = {International Workshop on Data Mining in Bioinformatics
(BIOKDD)},
year = 2020,
doi = {10.1101/2020.08.21.261313}
}
M.M. Javanmard, Z. Ahmad, J. Zola, R. Pouchet, R. Harrison (2020)
Efficient Execution of Dynamic Programming Algorithms on
Apache Spark. In
IEEE Cluster.
doi bibtex @INPROCEEDINGS{Javanmard2020,
author = {Javanmard, M.M. and Ahmad, Z. and Zola, J. and Pouchet,
L.-N., Chowdhury, R. and Harrison, R.},
title = {Efficient Execution of Dynamic Programming Algorithms on
Apache Spark},
booktitle = {IEEE Cluster},
year = 2020,
doi = {10.1109/CLUSTER49012.2020.00044}
}
F. Schoeneman, V. Chandola, N. Napp, O. Wodo, J. Zola (2020)
Learning Manifolds from Dynamic Process Data.
MDPI Algorithms 13 (30)
doi bibtex @ARTICLE{Schoeneman2020,
author = {Schoeneman, F. and Chandola, V. and Napp, N. and Wodo,
O. and Zola, J.},
title = {Learning Manifolds from Dynamic Process Data},
journal = {MDPI Algorithms},
volume = 13,
number = 30,
year = 2020,
doi = {10.3390/a13020030}
}
2019 (1)
F. Schoeneman, J. Zola (2019)
Solving All-Pairs Shortest-Paths Problem in Large Graphs
Using Apache Spark. In
International Conference on Parallel Processing (ICPP).
doi bibtex @INPROCEEDINGS{Schoeneman2019,
author = {Schoeneman, F. and Zola, J.},
title = {Solving All-Pairs Shortest-Paths Problem in Large Graphs
Using Apache Spark},
booktitle = {International Conference on Parallel Processing (ICPP)},
year = 2019,
doi = {10.1145/3337821.3337852},
archivePrefix = {arXiv},
eprint = {1902.04446},
primaryClass = {cs.DC}
}
2018 (7)
J. Zola, N. Fillmore, R. Samudrala, N. Mushi, M. Brophy, N. Do (2018)
Bayesian Network Model of Multiple Myeloma Patients Based
on Pharmaceutical Records.
bibtex @MISC{Zola2018,
author = {Zola, J. and Fillmore, N. and Samudrala, R. and Mushi,
N. and Brophy, M. and Do, N.},
title = {Bayesian Network Model of Multiple Myeloma Patients Based
on Pharmaceutical Records},
year = 2018,
note = {Extended Abstract, 30th Anniversary AACR Conference on
Convergence: Artificial Intelligence, Big Data, and
Prediction in Cancer}
}
P. Du, A. Zebrowski, J. Zola, B. Ganapathysubramanian, O. Wodo (2018)
Microstructure Design Using Graphs.
Nature Computational Materials 4 (50)
doi bibtex @ARTICLE{Du2018,
author = {Du, P. and Zebrowski, A. and Zola, J. and
Ganapathysubramanian, B. and Wodo, O.},
title = {Microstructure Design Using Graphs},
journal = {Nature Computational Materials},
volume = 4,
number = 50,
year = 2018,
doi = {10.1038/s41524-018-0108-5}
}
M. Blanton, A.R. Kang, S. Karan, J. Zola (2018)
Privacy Preserving Analytics on Distributed Medical Data.
bibtex @MISC{Blanton2018,
author = {Blanton, M. and Kang, A.R. and Karan, S. and Zola, J.},
title = {Privacy Preserving Analytics on Distributed Medical Data},
year = 2018,
archivePrefix = {arXiv},
eprint = {1806.06477},
primaryClass = {cs-CR}
}
S. Karan, M. Eichhorn, B. Hurlburt, G. Iraci, J. Zola (2018)
Fast Counting in Machine Learning Applications. In
Uncertainty in Artificial Intelligence (UAI).
bibtex @INPROCEEDINGS{Karan2018,
author = {Karan, S. and Eichhorn, M. and Hurlburt, B. and Iraci,
G. and Zola, J.},
title = {Fast Counting in Machine Learning Applications},
booktitle = {Uncertainty in Artificial Intelligence (UAI)},
year = 2018,
archivePrefix = {arXiv},
eprint = {1804.04640},
primaryClass = {stat-ML}
}
F. Schoeneman, V. Chandola, N. Napp, O. Wodo, J. Zola (2018)
Entropy-Isomap: Manifold Learning for High-dimensional
Dynamic Processes. In
IEEE International Conference on Big Data (IEEE BigData). pp. 1655–1660.
doi bibtex @INPROCEEDINGS{Schoeneman2018a,
author = {Schoeneman, F. and Chandola, V. and Napp, N. and Wodo,
O. and Zola, J.},
title = {Entropy-Isomap: Manifold Learning for High-dimensional
Dynamic Processes},
booktitle = {IEEE International Conference on Big Data (IEEE BigData)},
pages = {1655–1660},
year = 2018,
doi = {10.1109/BigData.2018.8622454},
archivePrefix = {arXiv},
eprint = {1802.06823},
primaryClass = {stat-ML}
}
F. Schoeneman, J. Zola (2018)
Scalable Manifold Learning for Big Data with Apache Spark. In
IEEE International Conference on Big Data (IEEE BigData). pp. 272-281.
doi bibtex @INPROCEEDINGS{Schoeneman2018b,
author = {Schoeneman, F. and Zola, J.},
title = {Scalable Manifold Learning for Big Data with Apache Spark},
booktitle = {IEEE International Conference on Big Data (IEEE BigData)},
pages = {272-281},
year = 2018,
doi = {10.1109/BigData.2018.8622617},
archivePrefix = {arXiv},
eprint = {1802.06823},
primaryClass = {cs.DC, cs.LG}
}
S. Ko, L. Sassoubre, J. Zola (2018)
Applications and Challenges of Real-time Mobile DNA
Analysis. In
International Workshop on Mobile Computing Systems and
Applications (HotMobile). pp. 1-6.
doi bibtex @INPROCEEDINGS{Ko2018,
author = {Ko, S. and Sassoubre, L. and Zola, J.},
title = {Applications and Challenges of Real-time Mobile DNA
Analysis},
booktitle = {International Workshop on Mobile Computing Systems and
Applications (HotMobile)},
pages = {1-6},
year = 2018,
doi = {10.1145/3177102.3177114},
archivePrefix = {arXiv},
eprint = {1711.07370},
primaryClass = {cs-CE}
}
2017 (2)
S. Karan, J. Zola (2017)
Scalable Exact Parent Sets Identification in Bayesian
Networks Learning with Apache Spark. In
IEEE International Conference on High Performance
Computing, Data, and Analytics (HiPC). pp. 33-41.
doi bibtex @INPROCEEDINGS{Karan2017,
author = {Karan, S. and Zola, J.},
title = {Scalable Exact Parent Sets Identification in Bayesian
Networks Learning with Apache Spark},
booktitle = {IEEE International Conference on High Performance
Computing, Data, and Analytics (HiPC)},
pages = {33-41},
year = 2017,
doi = {10.1109/HiPC.2017.00014},
archivePrefix = {arXiv},
eprint = {1705.06390},
primaryClass = {cs-AI}
}
F. Schoeneman, S. Mahapatra, V. Chandola, N. Napp, J. Zola (2017)
Error Metrics for Learning Reliable Manifolds from
Streaming Data. In
SIAM International Conference on Data Mining (SDM). pp. 750-758.
bibtex @INPROCEEDINGS{Schoeneman2017,
author = {Schoeneman, F. and Mahapatra, S. and Chandola, V. and
Napp, N. and Zola, J.},
title = {Error Metrics for Learning Reliable Manifolds from
Streaming Data},
booktitle = {SIAM International Conference on Data Mining (SDM)},
pages = {750-758},
year = 2017,
archivePrefix = {arXiv},
eprint = {1611.04067},
primaryClass = {stat-ML}
}
2016 (1)
S. Karan, J. Zola (2016)
Exact Structure Learning of Bayesian Networks by Optimal
Path Extension. In
IEEE International Conference on Big Data (IEEE BigData). pp. 48-55.
doi bibtex @INPROCEEDINGS{Karan2016,
author = {Karan, S. and Zola, J.},
title = {Exact Structure Learning of Bayesian Networks by Optimal
Path Extension},
booktitle = {IEEE International Conference on Big Data (IEEE BigData)},
pages = {48-55},
year = 2016,
doi = {10.1109/BigData.2016.7840588},
archivePrefix = {arXiv},
eprint = {1608.02682},
primaryClass = {cs-AI}
}
2015 (3)
O. Wodo, J. Zola, B.S.S. Pokuri, P. Du, B. Ganapathysubramanian (2015)
Automated, High Throughput Exploration of
Process-structure-property Relationships Using the MapReduce
Paradigm.
Materials Discovery 1 pp. 21–28.
doi bibtex @ARTICLE{Wodo2015,
author = {Wodo, O. and Zola, J. and Pokuri, B.S.S. and Du, P. and
Ganapathysubramanian, B.},
title = {Automated, High Throughput Exploration of
Process-structure-property Relationships Using the MapReduce
Paradigm},
journal = {Materials Discovery},
year = 2015,
volume = 1,
pages = {21--28},
doi = {10.1016/j.md.2015.12.001}
}
N. Clauvelin, P. Lo, O.I. Kulaeva, E.V. Nizovtseva, J. Diaz-Montes, J. Zola, M. Parashar, V.M. Studitsky, W.K. Olson (2015)
Nucleosome Positioning and Composition Modulate In Silico
Chromatin Flexibility.
Journal of Physics: Condensed Matter 27 (6) pp. 064112.
doi bibtex @ARTICLE{Clauvelin2015,
author = {Clauvelin, N. and Lo, P. and Kulaeva, O.I. and Nizovtseva,
E.V. and Diaz-Montes, J. and Zola, J. and Parashar, M. and
Studitsky, V.M. and Olson, W.K.},
title = {Nucleosome Positioning and Composition Modulate In Silico
Chromatin Flexibility},
journal = {Journal of Physics: Condensed Matter},
year = 2015,
volume = 27,
number = 6,
pages = 064112,
doi = {10.1088/0953-8984/27/6/064112}
}
S.K. Samudrala, J. Zola, S. Aluru, B. Ganapathysubramanian (2015)
Parallel Framework for Dimensionality Reduction of
Large-Scale Datasets.
Scientific Programming doi bibtex @ARTICLE{Samudrala2015,
author = {Samudrala, S.K. and Zola, J. and Aluru, S. and
Ganapathysubramanian, B.},
title = {Parallel Framework for Dimensionality Reduction of
Large-Scale Datasets},
journal = {Scientific Programming},
year = 2015,
doi = {10.1155/2015/180214}
}
Selected SCoRe Posters