# Publications

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##### 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