publications.knit

Refereed Publications

Skeleton Regression: A Graph-Based Approach to Estimation with Manifold Structure (2023)
Zeyu Wei*, Yen-Chi Chen.
To appear in Electronic Journal of Statistics

Detecting Clinically Relevant Topological Structures in Multiplexed Spatial Proteomics Imaging Using TopKAT (2024)
Sarah Samorodnitsky, Katie Campbell, Amarise Little, Wodan Ling, Ni Zhao, Yen-Chi Chen, Michael C Wu.
To appear in Patterns

Long-term effect estimation when combining clinical trial and observational follow-up datasets
Gang Cheng*, Yen-Chi Chen, Joseph M. Unger, Cathee Till, Ying-Qi Zhao.
To appear in Journal of American Statistical Association.

Data Harmonization Via Regularized Nonparametric Mixing Distribution Estimation
Steven Wilkins-Reeves*, Yen-Chi Chen, Kwun Chuen Gary Chan.
To appear in the Annals of Applied Statistics.

Mode and Ridge Estimation in Euclidean and Directional Product Spaces: A Mean Shift Approach
Yikun Zhang*, Yen-Chi Chen.
To appear in Journal of Computational and Graphical Statistics.

Modeling Missing at Random Neuropsychological Test Scores Using a Mixture of Binomial Product Experts
Daniel Suen*, Yen-Chi Chen.
Psychometrika 91 (2026): 223–246

Information criterion for approximation of unnormalized densities
Youngjun Choe, Yen-Chi Chen, Nick Terry.
PLOS ONE 20, no, 3 (2025): e0317430.

Bayesian Finite Mixtures of Ising Models
Zhen Miao*, Yen-Chi Chen, Adrian Dobra.
Metrika 88, no. 6 (2025): 777–809.

Skeleton Clustering: Dimension-Free Density-based Clustering
Zeyu Wei*, Yen-Chi Chen.
Journal of American Statistical Association 119, no. 546 (2024): 1124-1135.

Linear Convergence of the Subspace Constrained Mean Shift Algorithm: From Euclidean to Directional Data
Yikun Zhang*, Yen-Chi Chen.
Information and Inference: a Journal of the IMA 12, no. 1 (2023): 210-311.

Cognitive Aging with Dementia, Mild Cognitive Impairment, or No Impairment: A Comparison of Same- and Mixed-Sex Couples
Anthony Correro, Kathryn Gauthreaux, Jaime Perales-Puchalt, et. al.
Journal of Alzheimer’s Disease 92, no. 1 (2023): 109-128.

Statistical Inference with Local Optima
Yen-Chi Chen.
Journal of American Statistical Association 118, no. 543 (2023): 1940-1952.

SCONCE: A cosmic web finder for spherical and conic geometries
Yikun Zhang*, Rafael S. de Souza, Yen-Chi Chen.
Monthly Notices of the Royal Astronomical Society 517, no. 1 (2022): 1197-1217.

The emptiness inside: Finding gaps, valleys, and lacunae with geometric data analysis
Gabriella Contardo, David W. Hogg, Jason A.S. Hunt, Joshua E.G. Peek, Yen-Chi Chen.
The Astronomical Journal 164, no. 5 (2022): 226.

Limbic-predominant age-related TDP-43 encephalopathy (LATE): medical and pathological factors associated with comorbid hippocampal sclerosis
Kathryn M. Gauthreaux, Merilee A. Teylan, Yuriko Katsumata, et al.
Neurology 98, no. 14 (2022): e1422-e1433.

Pattern Graphs: a Graphical Approach to Nonmonotone Missing Data
Yen-Chi Chen.
Annals of Statistics 50, no. 1 (2022): 129-146. R-code: PG

Solution Manifold and Its Statistical Applications
Yen-Chi Chen.
Electronic Journal of Statistics 16, no. 1 (2022): 408-450.

Differences in Symptomatic Presentation and Cognitive Performance Among Participants With LATE-NC Compared to FTLD-TDP
Merilee A Teylan, Charles Mock, Kathryn Gauthreaux, et al.
Journal of Neuropathology & Experimental Neurology 80, no. 11 (2021): 1024-1032.

Kernel Smoothing, Mean Shift, and Their Learning Theory with Directional Data
Yikun Zhang*, Yen-Chi Chen.
Journal of Machine Learning Research 22, no. 154 (2021): 1-92. Python code: DirMS

Refined Mode-Clustering via the Gradient of Slope
Kunhui Zhang*, Yen-Chi Chen.
Stat 4, no. 2 (2021): 486-508.

A statistical framework for measuring the temporal stability of human mobility patterns
Zhihang Dong*, Yen-Chi Chen, Adrian Dobra.
Journal of Applied Statistics 48, no. 1 (2021): 105-123.

Concordance of Clinical Alzheimer Diagnosis and Neuropathological Features at Autopsy
Kathryn Gauthreaux, Tyler A. Bonnett, Lilah M. Besser et al.
Journal of Neuropathology & Experimental Neurology 79, no. 5 (2020): 465-473.

Factor Consistency of Neuropsychological Test Battery Versions in the NACC Uniform Data Set
Jessica E. Culhane*, Kwun C. G. Chan, Merilee A. Teylan et al.
Alzheimer disease and associated disorders 34, no. 2 (2020): 175..

Measuring Human Activity Spaces from GPS Data with Density Ranking and Summary Curves
Yen-Chi Chen, Adrian Dobra.
Annals of Applied Statistics 14, no. 1 (2020): 409-432. R-code: DR

Functional Summaries of Persistence Diagrams
Eric Berry, Yen-Chi Chen, Jessi Cisewski, Brittany Terese Fasy.
Journal of Applied and Computational Topology 4, no. 2 (2020): 211-262.

Estimating associations between antidepressant use and incident mild cognitive impairment in older adults with depression
Fang Han, Tyler Bonnett, Willa Brenowitz et al.
PLOS ONE 15, no. 1: e0227924.

Cognitive trajectory in mild cognitive impairment due to primary age-related tauopathy
Merilee Teylan, Charles Mock, Kathryn Gauthreaux et al.
Brain 143, no. 2 (2020): 611-621.

Oracle Importance Sampling for Stochastic Simulation Models
Yen-Chi Chen, Youngjun Choe.
Electronic Journal of Statistics 13, no. 2 (2019): 3386-3423.

Nonparametric Inference via Bootstrapping the Debiased Estimator
Gang Cheng*, Yen-Chi Chen.
Electronic Journal of Statistics 13, no. 1 (2019): 2194-2256.

Alignment between filaments and galaxy spins from the MaNGA integral-field survey
Alex Krolewski*, Shirley Ho, Yen-Chi Chen, P.F. Chan, Ananth Tenneti, Dmitry Bizyaev, Katarina Kraljic.
The Astrophysical Journal 876, no 1 (2019): 52

Detecting Galaxy-Filament Alignments in the Sloan Digital Sky Survey III
Yen-Chi Chen, Shirley Ho, Jonathan Blazek, Siyu He*, Rachel Mandelbaum, Peter Melchior, Sukhdeep Singh.
Monthly Notices of the Royal Astronomical Society 485, no 2 (2019): 2492-2504.

Clinical diagnoses among individuals with primary age-related tauopathy versus Alzheimers neuropathology
Merilee Teylan, Lilah M. Besser, John F. Crary et al.
Laboratory Investigation (2019): 1.

Generalized Cluster Trees and Singular Measures
Yen-Chi Chen.
The Annals of Statistics 47, no. 4 (2019): 2174-2203.

On the Use of Bootstrap with Variational Inference: Theory, Interpretation, and a Two-sample Test Example
Yen-Chi Chen, Y. Samuel Wang*, Elena Erosheva.
The Annals of Applied Statistics 12, no. 2 (2018): 846-876.

An Analysis Framework for Understanding the Origin of Nuclear Activity in Low-Power Radio Galaxies
Yen-Ting Lin, Hung-Jin Huang*, Yen-Chi Chen.
The Astronomical Journal 155, no. 5 (2018): 188.

Modal Regression using Kernel Density Estimation: a Review
Yen-Chi Chen.
Wiley Interdisciplinary Reviews: Computational Statistics 10, no. 4 (2018): e1431.

Size uniformity of animal cells is actively maintained by a p38 MAPK-dependent regulation of G1-length
Shixuan Liu*, Miriam Bracha Ginzberg, Nish Patel et al.
eLife 7, (2018): p.e26947.

The detection of the imprint of filaments on cosmic microwave background lensingg
Siyu He*, Shadab Alam, Simone Ferraro, Yen-Chi Chen, Shirley Ho.
Nature Astronomy 2, no. 5 (2018): 401.

Intrinsic Alignment in redMaPPer clusters – II. Radial alignment of satellites toward cluster centers
Hung-Jin Huang*, Rachel Mandelbaum, Peter E. Freeman, Yen-Chi Chen et al.
Monthly Notices of the Royal Astronomical Society 474, no. 4 (2017): 4772–4794.

A Tutorial on Kernel Density Estimation and Recent Advances
Yen-Chi Chen.
Biostatistics & Epidemiology 1, no. 1 (2017): 161-187.

Density Level Sets: Asymptotics, Inference, and Visualization
Yen-Chi Chen, Christopher R. Genovese, Larry Wasserman.
Journal of the American Statistical Association 112, (2017): 1684-1696. R-code: HDLV

GraphCom: A Multi-dimensional Measure of Graphic Complexity Applied to 131 Written Languages
Li-Yun Chang, Yen-Chi Chen, Charles Perfetti.
Behavior Research Methods 50, no. 1 (2017): 427–449.

Statistical Inference Using the Morse-Smale Complex
Yen-Chi Chen, Christopher R. Genovese, Larry Wasserman.
Electronic Journal of Statistics 11, no. 1 (2017): 1390-1433. R-code: MSHD

Detecting Effects of Filaments on Galaxy Properties in Sloan Digital Sky Survey III
Yen-Chi Chen, Shirley Ho, Rachel Mandelbaum et al.
Monthly Notices of the Royal Astronomical Society 466, no. 2 (2017): 1880-1893.

Confidence Sets for Density Trees
Jisu Kim*, Yen-Chi Chen, Sivaraman Balakrishnan, Alessandro Rinaldo, Larry Wasserman.
Advances in Neural Information Processing Systems 29 (NIPS 2016), 1831-1839.

Intrinsic Alignment in redMaPPer clusters I. Central Galaxy Alignment
Hung-Jin Huang*, Rachel Mandelbaum, Peter E. Freeman, Yen-Chi Chen et al.
Monthly Notices of the Royal Astronomical Society 463, no. 1 (2016): 222–244.

Cosmic Web Reconstruction through Density Ridges: Catalogue
Yen-Chi Chen, Shirley Ho, Jon Brinkmann et al.
Monthly Notices of the Royal Astronomical Society 461, no. 4 (2016): 3896–3909.

A Comprehensive Approach to Mode Clustering
Yen-Chi Chen, Christopher R. Genovese, Larry Wasserman.
Electronic Journal of Statistics 10, no. 1 (2016): 210-241. R-code: EMC

Non-parametric Modal Regression
Yen-Chi Chen, Christopher R. Genovese, Ryan J. Tibshirani, Larry Wasserman.
The Annals of Statistics 44, no. 2 (2016): 489–514. R-code: ModalRegression

Optimal Ridge Detection using Coverage Risk
Yen-Chi Chen, Christopher R. Genovese, Shirley Ho, Larry Wasserman.
Advances in Neural Information Processing Systems 28 (NIPS 2015), 316-324.

Investigating Galaxy-Filament Alignment in Hydrodynamic Simulations using Density Ridges
Yen-Chi Chen, Shirley Ho, Ananth Tenneti et al.
Monthly Notices of the Royal Astronomical Society 454, no. 3 (2015): 3341–3350.

Cosmic Web Reconstruction through Density Ridges: Method and Algorithm
Yen-Chi Chen, Shirley Ho, Peter E. Freeman, Christopher R. Genovese, Larry Wasserman.
Monthly Notices of the Royal Astronomical Society 454, no. 1 (2015): 1140–1156.

Asymptotic Theory for Density Ridges
Yen-Chi Chen, Christopher R. Genovese, Larry Wasserman.
The Annals of Statistics 43, no. 5 (2015): 1896–1928.

The Eleventh and Twelfth Data Releases of the Sloan Digital Sky Survey: Final Data from SDSS-III
Shadab Alam, Franco D. Albareti, Carlos Allende Prieto et al.
The Astrophysical Journal Supplement Series 219, no. 1 (2015): 12.

Preprints

Refereed Publications

Technical Reports