3 citations · 12 across the 15 of their papers we have counts for
16 papers
Trust, but Verify: Rigorously Profiling Best-Effort High-Performance Computing for Digital Evolution
Matthew Andres Moreno, Santiago Rodriguez Papa, Charles Ofria +2
Developments in high-performance computing (HPC) technology continue to drastically increase quantities of available processing power. In the context of digital evolution, this exp…
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…
SPOOF: Simple Pixel Operations for Out-of-Distribution Fooling
Ankit Gupta, Christoph Adami, Emily Dolson
Deep neural networks (DNNs) excel across image recognition tasks, yet continue to exhibit overconfidence on inputs that bear no resemblance to natural images. Revisiting the "fooli…
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…
The Robustness of Structural Features in Species Interaction Networks
Sanaz Hasanzadeh Fard, Emily Dolson
Species interaction networks are a powerful tool for describing ecological communities; they typically contain nodes representing species, and edges representing interactions betwe…
Structured Downsampling for Fast, Memory-efficient Curation of Online Data Streams
Matthew Andres Moreno, Luis Zaman, Emily Dolson
Operations over data streams typically hinge on efficient mechanisms to aggregate or summarize history on a rolling basis. For high-volume data steams, it is critical to manage sta…
Trackable Agent-based Evolution Models at Wafer Scale
Matthew Andres Moreno, Connor Yang, Emily Dolson +1
Continuing improvements in computing hardware are poised to transform capabilities for in silico modeling of cross-scale phenomena underlying major open questions in evolutionary b…
Trackable Island-model Genetic Algorithms at Wafer Scale
Matthew Andres Moreno, Connor Yang, Emily Dolson +1
Emerging ML/AI hardware accelerators, like the 850,000 processor Cerebras Wafer-Scale Engine (WSE), hold great promise to scale up the capabilities of evolutionary computation. How…
A Guide to Tracking Phylogenies in Parallel and Distributed Agent-based Evolution Models
Matthew Andres Moreno, Anika Ranjan, Emily Dolson +1
Computer simulations are an important tool for studying the mechanics of biological evolution. In particular, in silico work with agent-based models provides an opportunity to coll…
Phylotrack: C++ and Python libraries for in silico phylogenetic tracking
Emily Dolson, Santiago Rodriguez-Papa, Matthew Andres Moreno
In silico evolution instantiates the processes of heredity, variation, and differential reproductive success (the three "ingredients" for evolution by natural selection) within dig…
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…
Analysis of Phylogeny Tracking Algorithms for Serial and Multiprocess Applications
Matthew Andres Moreno, Santiago Rodriguez Papa, Emily Dolson
Since the advent of modern bioinformatics, the challenging, multifaceted problem of reconstructing phylogenetic history from biological sequences has hatched perennial statistical…
Algorithms for Efficient, Compact Online Data Stream Curation
Matthew Andres Moreno, Santiago Rodriguez Papa, Emily Dolson
Data stream algorithms tackle operations on high-volume sequences of read-once data items. Data stream scenarios include inherently real-time systems like sensor networks and finan…
Phylogeny-informed fitness estimation
Alexander Lalejini, Matthew Andres Moreno, Jose Guadalupe Hernandez +1
Phylogenies (ancestry trees) depict the evolutionary history of an evolving population. In evolutionary computing, a phylogeny can reveal how an evolutionary algorithm steers a pop…