96 citations · 113 across the 12 of their papers we have counts for
16 papers
Multi-objective Bayesian inference in an agent-based model of zebrafish patterns via topological data analysis
Yue Liu, Alexandria Volkening
Spatial patterns arising from the collective behavior of individual agents are present across biological systems. While agent-based models offer a natural framework for uncovering…
Quantifying topological features and irregularities in zebrafish patterns using the sweeping-plane filtration
Nour Khoudari, John Nardini, Alexandria Volkening
Complex patterns emerge across a wide range of biological systems. While such patterns often exhibit remarkable robustness, variation and irregularity exist at multiple scales and…
Enhancing generalizability of model discovery across parameter space with multi-experiment equation learning (ME-EQL)
Maria-Veronica Ciocanel, John T. Nardini, Kevin B. Flores +3
Agent-based modeling (ABM) is a powerful tool for understanding self-organizing biological systems, but it is computationally intensive and often not analytically tractable. Equati…
How time and pollster history affect U.S. election forecasts under a compartmental modeling approach
Ryan Branstetter, Samuel Chian, Joseph Cromp +8
In the months leading up to political elections in the United States, forecasts are widespread and take on multiple forms, including projections of what party will win the popular…
Methods for quantifying self-organization in biology: a forward-looking survey and tutorial
Alexandria Volkening
From flocking birds to schooling fish, organisms interact to form collective dynamics across the natural world. Self-organization is present at smaller scales as well: cells intera…
Linking discrete and continuous models of cell birth and migration
W. Duncan Martinson, Alexandria Volkening, Markus Schmidtchen +2
Self-organisation of individuals within large collectives occurs throughout biology. Mathematical models can help elucidate the individual-level mechanisms behind these dynamics, b…
Quantifying different modeling frameworks using topological data analysis: a case study with zebrafish patterns
Electa Cleveland, Angela Zhu, Bjorn Sandstede +1
Mathematical models come in many forms across biological applications. In the case of complex, spatial dynamics and pattern formation, stochastic models also face two main challeng…
Topological Data Analysis of Spatial Patterning in Heterogeneous Cell Populations: Clustering and Sorting with Varying Cell-Cell Adhesion
Dhananjay Bhaskar, William Y. Zhang, Alexandria Volkening +2
Different cell types aggregate and sort into hierarchical architectures during the formation of animal tissues. The resulting spatial organization depends (in part) on the strength…
A primer on data-driven modeling of complex social systems
Alexandria Volkening
Traffic jams on roadways, echo chambers on social media, crowds of moving pedestrians, and opinion dynamics during elections are all complex social systems. These applications may…
How do classroom-turnover times depend on lecture-hall size?
Joseph Benson, Mariya Bessonov, Korana Burke +4
Academic spaces in colleges and universities span classrooms for 10 students to lecture halls that hold over 600 people. During the break between consecutive classes, students from…
What's math got to do with patterns in fish?
Blake Shirman, Alexandria Volkening
When you think of fish, what comes to mind? Maybe you think of pet goldfish, movie characters like Dory or Nemo, or trout in a local river. One of the things that all of these fish…
Modeling stripe formation on growing zebrafish tailfins
Alexandria Volkening, Madeline R Abbott, Dorothy Catey +4
As zebrafish develop, black and gold stripes form across their skin due to the interactions of brightly colored pigment cells. These characteristic patterns emerge on the growing f…
Topological data analysis of zebrafish patterns
Melissa R. McGuirl, Alexandria Volkening, Björn Sandstede
Self-organized pattern behavior is ubiquitous throughout nature, from fish schooling to collective cell dynamics during organism development. Qualitatively these patterns display i…
Forecasting elections using compartmental models of infection
Alexandria Volkening, Daniel F. Linder, Mason A. Porter +1
Forecasting elections -- a challenging, high-stakes problem -- is the subject of much uncertainty, subjectivity, and media scrutiny. To shed light on this process, we develop a met…
Noise-induced tipping under periodic forcing: preferred tipping phase in a non-adiabatic forcing regime
Yuxin Chen, John Gemmer, Mary Silber +1
We consider a periodically-forced 1-D Langevin equation that possesses two stable periodic solutions in the absence of noise. We ask the question: is there a most likely noise-indu…
Emergence of Anti-Cancer Drug Resistance: Exploring the Importance of the Microenvironmental Niche via a Spatial Model
Jana L. Gevertz, Zahra Aminzare, Kerri-Ann Norton +3
Practically, all chemotherapeutic agents lead to drug resistance. Clinically, it is a challenge to determine whether resistance arises prior to, or as a result of, cancer therapy.…