arXiv subjects

G. Matthew Fricke

Publications and source records attributed to G. Matthew Fricke.

6 recordsLinked to original sources

arXiv2026

M-CaStLe: Uncovering Local Causal Structures in Multivariate Space-Time Gridded Data

Causal graph discovery for space-time systems is challenging in high-dimensional gridded data, which often has many more grid cells than temporal observations per cell. The Causal Space-Time Stencil Learning (CaStLe) meta-algorithm was developed to address that niche under space-time locality and stationarity assumptions, but it is currently limited to univariate analyses. In this work, we present M-CaStLe. M-CaStLe generalizes the local embedding and parent-identification phases of CaStLe to jointly model local within-variable and cross-variable space-time causal structures in gridded data. Like CaStLe, by constraining candidate parents to a constant-size space-time neighborhood and pooling spatial replicates, M-CaStLe increases effective sample size to make discovery tractable in high-dimensional settings. We further decompose the resulting multivariate stencil graph into reaction and spatial graphs to aid interpretation in complex settings. We study M-CaStLe in four settings: a multivariate space-time vector autoregression benchmark with known ground truth, an advective-diffusive-reaction partial differential equation verification problem with derived physical reference structure, an atmospheric chemistry case study in a low-temporal-sample regime, and an El Niño Southern Oscillation study on reanalysis data, identifying phase-dependent ocean--atmosphere coupling. Across these settings, M-CaStLe more accurately recovers multivariate causal structure in controlled settings and identifies important physical dynamics in real-world case studies. Overall, M-CaStLe advances causal discovery for multivariate space-time systems while retaining interpretability at the grid level.

cs.LG↗

arXiv2025

Bigger is Faster in the Adaptive Immune Response

Zoonotic pathogens represent a growing global risk, yet the speed of adaptive immune activation across mammalian species remains poorly understood. Despite orders-of-magnitude differences in size and metabolic rate, we show that the time to initiate adaptive immunity is remarkably consistent across species. To understand this invariance, we analyse empirical data showing how the numbers and sizes of lymph nodes scale with body mass, finding that larger animals have both more and larger lymph nodes. Using scaling theory and our mathematical model, we show that larger lymph nodes enable faster search times, conferring an advantage to larger animals that otherwise face slower biological times. This enables mammals to maintain, or even accelerate, the time to initiate the adaptive immune response as body size increases. We validate our analysis in simulations and compare it to empirical data.

physics.bio-ph↗

arXiv2024

Assembly Theory and its Relationship with Computational Complexity

Assembly theory (AT) quantifies selection using the assembly equation and identifies complex objects that occur in abundance based on two measurements, assembly index and copy number, where the assembly index is the minimum number of joining operations necessary to construct an object from basic parts, and the copy number is how many instances of the given object(s) are observed. Together these define a quantity, called Assembly, which captures the amount of causation required to produce objects in abundance in an observed sample. This contrasts with the random generation of objects. Herein we describe how AT's focus on selection as the mechanism for generating complexity offers a distinct approach, and answers different questions, than computational complexity theory with its focus on minimum descriptions via compressibility. To explore formal differences between the two approaches, we show several simple and explicit mathematical examples demonstrating that the assembly index, itself only one piece of the theoretical framework of AT, is formally not equivalent to other commonly used complexity measures from computer science and information theory including Shannon entropy, Huffman encoding, and Lempel-Ziv-Welch compression. We also include proofs that assembly index is not in the same computational complexity class as these compression algorithms and discuss fundamental differences in the ontological basis of AT, and assembly index as a physical observable, which distinguish it from theoretical approaches to formalizing life that are unmoored from measurement.

cs.CC↗

arXiv2020

LoCUS: A multi-robot loss-tolerant algorithm for surveying volcanic plumes

Measurement of volcanic CO2 flux by a drone swarm poses special challenges. Drones must be able to follow gas concentration gradients while tolerating frequent drone loss. We present the LoCUS algorithm as a solution to this problem and prove its robustness. LoCUS relies on swarm coordination and self-healing to solve the task. As a point of contrast we also implement the MoBS algorithm, derived from previously published work, which allows drones to solve the task independently. We compare the effectiveness of these algorithms using drone simulations, and find that LoCUS provides a reliable and efficient solution to the volcano survey problem. Further, the novel data-structures and algorithms underpinning LoCUS have application in other areas of fault-tolerant algorithm research.

cs.DC↗

arXiv2018

The Swarmathon: An Autonomous Swarm Robotics Competition

The Swarmathon is a swarm robotics programming challenge that engages college students from minority-serving institutions in NASA's Journey to Mars. Teams compete by programming a group of robots to search for, pick up, and drop off resources in a collection zone. The Swarmathon produces prototypes for robot swarms that would collect resources on the surface of Mars. Robots operate completely autonomously with no global map, and each team's algorithm must be sufficiently flexible to effectively find resources from a variety of unknown distributions. The Swarmathon includes Physical and Virtual Competitions. Physical competitors test their algorithms on robots they build at their schools; they then upload their code to run autonomously on identical robots during the three day competition in an outdoor arena at Kennedy Space Center. Virtual competitors complete an identical challenge in simulation. Participants mentor local teams to compete in a separate High School Division. In the first 2 years, over 1,100 students participated. 63% of students were from underrepresented ethnic and racial groups. Participants had significant gains in both interest and core robotic competencies that were equivalent across gender and racial groups, suggesting that the Swarmathon is effectively educating a diverse population of future roboticists.

cs.MA↗

arXiv2018

Using RuleBuilder to graphically define and visualize BioNetGen-language patterns and reaction rules

RuleBuilder is a tool for drawing graphs that can be represented by the BioNetGen language (BNGL), which is used to formulate mathematical, rule-based models of biochemical systems. BNGL provides an intuitive plain-text, or string, representation of such systems, which is based on a graphical formalism. Reactions are defined in terms of graph-rewriting rules that specify the necessary intrinsic properties of the reactants, a transformation, and a rate law. Rules may also contain contextual constraints that restrict application of the rule. In some cases, the specification of contextual constraints can be verbose, making a rule difficult to read. RuleBuilder is designed to ease the task of reading and writing individual reaction rules, as well as individual BNGL patterns similar to those found in rules. The software assists in the reading of existing models by converting BNGL strings of interest into a graph-based representation composed of nodes and edges. RuleBuilder also enables the user to construct de novo a visual representation of BNGL strings using drawing tools available in its interface. As objects are added to the drawing canvas, the corresponding BNGL string is generated on the fly, and objects are similarly drawn on the fly as BNGL strings are entered into the application. RuleBuilder thus facilitates construction and interpretation of rule-based models.

q-bio.QM↗