204 citations
Counting papers with at most 25 authors, so collaboration author lists do not stand in for the people here.
- National Institutes of HealthUS16 papers
- National Cancer InstituteUS6 papers
- University of WaterlooCA5 papers
- University of WashingtonUS4 papers
- East China Normal UniversityCN3 papers
- Universidad Nacional Autónoma de MéxicoMX3 papers
- University College LondonGB3 papers
- University of California San DiegoUS3 papers
- University of ZurichCH3 papers
- Allen Institute for Cell ScienceUS2 papers
- BioLegend (United States)US2 papers
- Broad InstituteUS2 papers
29 papers
The NIAID Discovery Portal: A Unified Search Engine for Infectious and Immune-Mediated Disease Datasets
Ginger Tsueng, Emily Bullen, Candice Czech +18
The NIAID Data Ecosystem Discovery Portal (https://data.niaid.nih.gov) provides a unified search interface for over 4 million datasets relevant to infectious and immune-mediated di…
Retrospective score tests versus prospective score tests for genetic association with case-control data
Yukun Liu, Pengfei Li, Lei Song +2
Since the seminal work by Prentice and Pyke (1979), the prospective logistic likelihood has become the standard method of analysis for retrospectively collected case-control data,…
Instability of inverse probability weighting methods and a remedy for non-ignorable missing data
Pengfei Li, Jing Qin, Yukun Liu
Inverse probability weighting (IPW) methods are commonly used to analyze non-ignorable missing data under the assumption of a logistic model for the missingness probability. Howeve…
Empirical likelihood meta analysis with publication bias correction under Copas-like selection model
Mengke Li, Yukun Liu, Pengfei Li +1
Meta analysis is commonly-used to synthesize multiple results from individual studies. However, its validation is usually threatened by publication bias and between-study heterogen…
A mixture distribution approach for assessing genetic impact from twin study
Zonghui Hu, Pengfei Li, Dean Follmann +1
This work was motivated by a twin study with the goal of assessing the genetic control of immune traits. We propose a mixture bivariate distribution to model twin data where the un…
The IBEX Imaging Knowledge-Base: A Community Resource Enabling Adoption and Development of Immunofluoresence Imaging Methods
Ziv Yaniv, Ifeanyichukwu U. Anidi, Leanne Arakkal +59
The iterative bleaching extends multiplexity (IBEX) Knowledge-Base is a central portal for researchers adopting IBEX and related 2D and 3D immunofluorescence imaging methods. The d…
Conformal predictive intervals in survival analysis: a re-sampling approach
Jing Qin, Jin Piao, Jing Ning +1
The distribution-free method of conformal prediction (Vovk et al, 2005) has gained considerable attention in computer science, machine learning, and statistics. Candes et al. (2023…
The IBEX Knowledge-Base: Achieving more together with open science
Andrea J. Radtke, Ifeanyichukwu Anidi, Leanne Arakkal +55
Iterative Bleaching Extends multipleXity (IBEX) is a versatile method for highly multiplexed imaging of diverse tissues. Based on open science principles, we created the IBEX Knowl…
Harmonizing the Generation and Pre-publication Stewardship of FAIR Image Data
Nikki Bialy, Frank Alber, Brenda Andrews +44
Alongside molecular insights into genes and proteins, biological imaging holds great promise for deepening scientific understanding of complex cellular systems and advancing predic…
Identifying factors associated with fast visual field progression in patients with ocular hypertension based on unsupervised machine learning
Xiaoqin Huang, Asma Poursoroush, Jian Sun +3
Purpose: To identify ocular hypertension (OHT) subtypes with different trends of visual field (VF) progression based on unsupervised machine learning and to discover factors associ…
Understanding metric-related pitfalls in image analysis validation
Annika Reinke, Minu D. Tizabi, Michael Baumgartner +75
Validation metrics are key for the reliable tracking of scientific progress and for bridging the current chasm between artificial intelligence (AI) research and its translation int…
Experiment-selector cross-validated targeted maximum likelihood estimator for hybrid RCT-external data studies
Lauren Eyler Dang, Jens Magelund Tarp, Trine Julie Abrahamsen +4
Augmenting a randomized controlled trial (RCT) with external data may increase power at the risk of introducing bias. To select and analyze the experiment (RCT alone or combined wi…
Mediation Analyses for the Effect of Antibodies in Vaccination
Michael P. Fay, Dean A. Follmann
We review standard mediation assumptions as they apply to identifying antibody effects in a randomized vaccine trial and propose new study designs to allow identification of an est…
Accurate Virus Identification with Interpretable Raman Signatures by Machine Learning
Jiarong Ye, Yin-Ting Yeh, Yuan Xue +16
Rapid identification of newly emerging or circulating viruses is an important first step toward managing the public health response to potential outbreaks. A portable virus capture…
Confidence Intervals for Prevalence Estimates from Complex Surveys with Imperfect Assays
Damon Bayer, Michael Fay, Barry Graubard
We present several related methods for creating confidence intervals to assess disease prevalence in variety of survey sampling settings. These include simple random samples with i…
PhenoTagger: A Hybrid Method for Phenotype Concept Recognition using Human Phenotype Ontology
Ling Luo, Shankai Yan, Po-Ting Lai +7
Automatic phenotype concept recognition from unstructured text remains a challenging task in biomedical text mining research. Previous works that address the task typically use dic…
A linear noise approximation for stochastic epidemic models fit to partially observed incidence counts
Jonathan Fintzi, Jon Wakefield, Vladimir N. Minin
Stochastic epidemic models (SEMs) fit to incidence data are critical to elucidating outbreak dynamics, shaping response strategies, and preparing for future epidemics. SEMs typical…
Test for homogeneity with unordered paired observations
Jiahua Chen, Pengfei Li, Jing Qin +1
In some applications, an experimental unit is composed of two distinct but related subunits. The response from such a unit is but we observe only $Y_1 = \min\{X_{1…
Practical Valid Inferences for the Two-Sample Binomial Problem
Michael P. Fay, Sally A. Hunsberger
Our interest is whether two binomial parameters differ, which parameter is larger, and by how much. This apparently simple problem was addressed by Fisher in the 1930's, and has be…
A Distance Map Regularized CNN for Cardiac Cine MR Image Segmentation
Shusil Dangi, Cristian Linte, Ziv Yaniv
Cardiac image segmentation is a critical process for generating personalized models of the heart and for quantifying cardiac performance parameters. Several convolutional neural ne…
Valid and Approximately Valid Confidence Intervals for Current Status Data
Sungwook Kim, Michael P. Fay, Michael A. Proschan
We introduce a new framework for creating point-wise confidence intervals for the distribution of event times for current status data. Existing methods are based on asymptotics. Ou…
Path integral approach to theories of diffusion-influenced reactions
Thorsten Prüstel, Martin Meier-Schellersheim
The path decomposition expansion represents the propagator of the irreversible reaction as a convolution of the first-passage, last-passage and rebinding time probability densities…
Quantum mechanical inspired factorization of the molecule pair propagator in theories of diffusion-influenced reactions
Thorsten Prüstel, Martin Meier-Schellersheim
Building on mathematical similarities between quantum mechanics and theories of diffusion-influenced reactions, we discuss how the propagator of a reacting molecule pair can be rep…
Combining isotonic regression and EM algorithm to predict genetic risk under monotonicity constraint
Jing Qin, Tanya P. Garcia, Yanyuan Ma +3
In certain genetic studies, clinicians and genetic counselors are interested in estimating the cumulative risk of a disease for individuals with and without a rare deleterious muta…