6 papers
PhyloFrame: A DataFrame-based Library for Fast, Flexible Phylogenetic Computation
Matthew Andres Moreno, Jeet Sukumaran, Luis Zaman +1
PhyloFrame is a Python library for phylogenetic computation targeting the gap between specialist, compiler-optimized operations and flexible, script-based workflows -- with emphasi…
Case Study of Novelty, Complexity, and Adaptation in a Multicellular System
Matthew Andres Moreno, Santiago Rodriguez Papa, Charles Ofria
Continuing generation of novelty, complexity, and adaptation are well-established as core aspects of open-ended evolution. However, it has yet to be firmly established to what exte…
A Scalable Trie Building Algorithm for High-Throughput Phyloanalysis of Wafer-Scale Digital Evolution Experiments
Vivaan Singhvi, Joey Wagner, Emily Dolson +2
Agent-based simulation platforms play a key role in enabling fast-to-run evolution experiments that can be precisely controlled and observed in detail. Availability of high-resolut…
Extending a Phylogeny-based Method for Detecting Signatures of Multi-level Selection for Applications in Artificial Life
Matthew Andres Moreno, Sanaz Hasanzadeh Fard, Luis Zaman +1
Multilevel selection occurs when short-term individual-level reproductive interests conflict with longer-term group-level fitness effects. Detecting and quantifying this phenomenon…
Downstream: efficient cross-platform algorithms for fixed-capacity stream downsampling
Connor Yang, Joey Wagner, Emily Dolson +2
Due to ongoing accrual over long durations, a defining characteristic of real-world data streams is the requirement for rolling, often real-time, mechanisms to coarsen or summarize…
Ecology, Spatial Structure, and Selection Pressure Induce Strong Signatures in Phylogenetic Structure
Matthew Andres Moreno, Santiago Rodriguez-Papa, Emily Dolson
Evolutionary dynamics are shaped by a variety of fundamental, generic drivers, including spatial structure, ecology, and selection pressure. These drivers impact the trajectory of…