Research

My research interests include spectral graph theory and algorithms, fast and scalable solvers for large-scale sparse linear systems and optimization, adaptive numerical methods for graph Laplacians. I also design and apply machine learning and data mining techniques for network analysis (e.g. on protein interaction networks, sports networks, and social networks).

google scholar page

SELECTED PUBLICATIONS:

New Precondtioners for Graph Laplacian Systems:

Solving Graph Laplacians via Multilevel Sparsifiers

Xiaozhe Hu, Junyuan Lin*

*Corresponding Author

SIAM J. Sci. Comput., S378-S400 (2023) 

Full Text: https://epubs.siam.org/doi/abs/10.1137/22M1503932

An example of spanning positive subgraph preconditioner
cover.mp4
Finding 1/2-approximated path cover

An Adaptive Algebraic Multigrid Method Based on Path Cover

Xiaozhe Hu, Junyuan Lin*, Ludmil Zikatanov

*Corresponding Author

SIAM J. Sci. Comput., 41(5), S220–S241. (2019)

Full Text: https://epubs.siam.org/doi/abs/10.1137/18M1194493  

Awarded Best Student Paper at the 15th Copper Mountain Conference on Iterative Methods

Fast Solvers for Clustering Biology Networks:

kNN Graph Construction: the Overlap Method

Random-Walk Based Approximate k-Nearest Neighbors Algorithm for Diffusion State Distance

Lenore J. Cowen, Xiaozhe Hu, Junyuan Lin, Yue Shen, Kaiyi Wu

International Conference on Large-Scale Scientific Computing, Volume 13127, pp 3-15 (2021)

Full Text: https://link.springer.com/chapter/10.1007/978-3-030-97549-4_1  

Invited paper

Assessment of network module identification across complex diseases

Sarvenaz Choobdar, Mehmet E Ahsen, Jake Crawford, Mattia Tomasoni, David Lamparter, Junyuan Lin, Ben Hescott, Xiaozhe Hu, Johnathan Mercer, Ted Natoli, Rajiv Narayan, The DREAM Module Identification Challenge Consortium, Aravind Subramanian, Jitao D. Zhang, Gustavo Stolovitzky, Zoltan Kutalik, Kasper Lage, Donna K Slonim, Julio Saez-Rodriguez, Lenore J. Cowen, Sven Bergmann, Daniel Marbach

Nature Methods, volume 16, pages 843–852 (2019) 

Full Text: https://www.nature.com/articles/s41592-019-0509-5 

Histograms of pairwise distance distributions using shortest path metric (left) vs. using the diffusion state distance metric (right)

Computing the Diffusion State Distance on Graphs via Algebraic Multigrid and Random Projections

Junyuan Lin, Lenore J. Cowen, Ben Hescott, Xiaozhe Hu

Numer Linear Algebra Appl. 2018; e2156.

Full Text: doi.org/10.1002/nla.2156 (PDF)

A Double Spectral Approach to DREAM 11 Subchallenge 3

Jake Crawford, Junyuan Lin, Xiaozhe Hu, Ben Hescott, Donna Slonim, Lenore J. Cowen

2017 Sage Bionetworks, 7 Oct. 2016 Published. Web. 

Full Text: syn7349492

Awarded Best Performer in 2016 Disease Module Identification DREAM Challenge

Team Tusk (Jake Crawford, Junyuan Lin, Xiaozhe Hu, Ben Hescott, Donna Slonim, Lenore J. Cowen) ranked No.1 in 2016 Disease Module Identification DREAM Challenge

Text Mining and Knowledge Graphs:

Hate speech and hate crimes: a data-driven study of evolving discourse around marginalized groups

Malvina Bozhidarova, Jonathn Chang, Aaishah Ale-Rasool, Yuxiang Liu, Chongyao Ma, Andrea L Bertozzi, P Jeffrey Brantingham, Junyuan Lin, Sanjukta Krishnagopal 


2023 IEEE International Conference on Big Data 

Full Text: https://ieeexplore.ieee.org/abstract/document/10386312/

The knowledge graph ontology for hate speech and hate crime datasets


Hierarchical clustering of QAnon-related topics from BERTopic 


Knowledge Graphs of the QAnon Twitter Network

Clay Adams, Malvina Bozhidarova, James Chen, Andrew Gao, Zhengtong Liu, J. Hunter Priniski, Junyuan Lin, Rishi Sonthalia, Andrea L. Bertozzi, P. Jeffrey Brantingham


2022 IEEE International Conference on Big Data 

Full Text: https://ieeexplore.ieee.org/abstract/document/10021128

An Analysis of COVID-19 Knowledge Graph Construction and Applications

Dominic Flocco, Bryce Palmer-Toy, Ruixiao Wang, Hongyu Zhu, Rishi Sonthalia, Junyuan Lin, Andrea L. Bertozzi, P. Jeffrey Brantingham


2021 IEEE International Conference on Big Data 

Full Text: https://ieeexplore.ieee.org/abstract/document/9671479

General structure of knowledge graph with an underlying social network of tweets at the center and external information and tweet attributes surrounding the network


Fast Statistical Ranking Algorithms:

Potential Voter Profile 

Algebraic Multigrid for Least Squares Problems on Graphs with Applications to HodgeRank

Charles Colley, Junyuan Lin, Xiaozhe Hu, Shuchin Aeron

2017 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW)

Full Text: doi: 10.1109/IPDPSW.2017.163 (PDF)

Contagion Modelling:

plane_emo20s.mp4
Plane Evacuation Simulation with Emotion Factor

A Particle Swarm Optimization Model of Emergency Airplane Evacuations with Emotion

Junyuan Lin, Timothy Lucas

Applied Math Journal Networks and Heterogeneous Media, Volume 10, Issue 3, (2015): 631-646.

Full Text: doi: 10.3934/nhm.2015.10.631 (PDF)

SOFTWARE PACKAGE:

     Authors: Xiaozhe Hu, Junyuan Lin and Ludmil Zikantonov

Link: https://github.com/XiaozheHu/Multilevel_Subgraph_Preconditioner

Reference: An Adaptive Algebraic Multigrid Method Based on Path Cover


Authors: Dominic Flocco, Bryce Palmer-Toy, Ruixiao Wang, Hongyu Zhu, Rishi Sonthalia, Junyuan Lin, Andrea L. Bertozzi, P. Jeffrey Brantingham

Link: https://github.com/dominicflocco/Twitter-COVID-19-Knowledge-Graph

Reference: An Analysis of COVID-19 Knowledge Graph Construction and Applications


Authors: Clay Adams, Malvina Bozhidarova, James Chen, Andrew Gao, Zhengtong Liu, J. Hunter Priniski, Junyuan Lin, Rishi Sonthalia, Andrea L. Bertozzi, P. Jeffrey Brantingham

Link: https://github.com/rsonthal/kg-twitter-reu

Reference: Knowledge Graphs of the QAnon Twitter Network


Authors: Malvina Bozhidarova, Jonathn Chang, Aaishah Ale-Rasool, Yuxiang Liu, Chongyao Ma, Andrea L Bertozzi, P Jeffrey Brantingham, Junyuan Lin, Sanjukta Krishnagopal 

Link: https://github.com/jimliu01/kg-twitter-hate-crimes

Reference: Hate speech and hate crimes: a data-driven study of evolving discourse around marginalized groups


POSTERS:

Presented at: 

2019 Joint Mathematics Meetings (JMM), Baltimore, MD.

2018 MAA MATHFEST, Denver, CO.

2017 SIAM Annual Meeting, AWM workshop, Pittsburgh, PA.

2017 Computational Aspects of Biological Information, Microsoft Research, Cambridge, MA.

Data Intensive Studies Center Fall 2017 Symposium, Tufts University, Medford, MA.

Applied Math Days 2017, Rensselaer Polytechnic Institute, Troy, NY.

Graduate Student Research Symposium, Tufts University, Medford, MA.

Presented at MAA Undergraduate Poster Session, 2014 Joint Mathematics Meetings, Baltimore, MD. (Outstanding Poster Winner)