35 citations · 63 across the 23 of their papers we have counts for
24 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…
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…
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…
Methods to Estimate Cryptic Sequence Complexity
Matthew Andres Moreno
Complexity is a signature quality of interest in artificial life systems. Alongside other dimensions of assessment, it is common to quantify genome sites that contribute to fitness…
DendroPy 5: a mature Python library for phylogenetic computing
Matthew Andres Moreno, Mark T. Holder, Jeet Sukumaran
Contemporary bioinformatics has seen in profound new visibility into the composition, structure, and history of the natural world around us. Arguably, the central pillar of bioinfo…
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…
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…
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…
Runtime phylogenetic analysis enables extreme subsampling for test-based problems
Alexander Lalejini, Marcos Sanson, Jack Garbus +2
A phylogeny describes the evolutionary history of an evolving population. Evolutionary search algorithms can perfectly track the ancestry of candidate solutions, illuminating a pop…
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…
Best-Effort Communication Improves Performance and Scales Robustly on Conventional Hardware
Matthew Andres Moreno, Charles Ofria
Here, we test the performance and scalability of fully-asynchronous, best-effort communication on existing, commercially-available HPC hardware. A first set of experiments tested w…
Matchmaker, Matchmaker, Make Me a Match: Geometric, Variational, and Evolutionary Implications of Criteria for Tag Affinity
Matthew Andres Moreno, Alexander Lalejini, Charles Ofria
Genetic programming and artificial life systems commonly employ tag-matching schemes to determine interactions between model components. However, the implications of criteria used…
SignalGP-Lite: Event Driven Genetic Programming Library for Large-Scale Artificial Life Applications
Matthew Andres Moreno, Santiago Rodriguez Papa, Alexander Lalejini +1
Event-driven genetic programming representations have been shown to outperform traditional imperative representations on interaction-intensive problems. The event-driven approach o…
Conduit: A C++ Library for Best-effort High Performance Computing
Matthew Andres Moreno, Santiago Rodriguez Papa, Charles Ofria
Developing software to effectively take advantage of growth in parallel and distributed processing capacity poses significant challenges. Traditional programming techniques allow a…
Exploring Evolved Multicellular Life Histories in a Open-Ended Digital Evolution System
Matthew Andres Moreno, Charles Ofria
Evolutionary transitions occur when previously-independent replicating entities unite to form more complex individuals. Such transitions have profoundly shaped natural evolutionary…
Tag-based regulation of modules in genetic programming improves context-dependent problem solving
Alexander Lalejini, Matthew Andres Moreno, Charles Ofria
We introduce and experimentally demonstrate the utility of tag-based genetic regulation, a new genetic programming (GP) technique that allows programs to dynamically adjust which c…