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Symbiosis in Digital Evolution: A Review and Future Directions

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Symbiosis in Digital Evolution: A Review and Future Directio...

2022 Conference on Artificial Life, ALIFE 2022

作者： Vostinar, Anya E. Skocelas, Katherine G. Lalejini, Alexander Zaman, Luis SymbuLab Carleton College Computer Science NorthfieldMN United States Digital Evolution Lab Michigan State University Department of Computer Science Program in Ecology Evolution and Biology BEACON Center for the Study of Evolution in Action East LansingMI United States ZE3 Lab University of Michigan Department of Ecology and Evolutionary Biology Center for the Study of Complex Systems Ann ArborMI United States

Testing the Inference Accuracy of Accelerator-Friendly Approximate Phylogeny Tracking

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Testing the Inference Accuracy of Accelerator-Friendly Appro...

2025 IEEE Symposium on Computational Intelligence in Artificial Life and Cooperative Intelligent systems, ALIFE-CIS 2025

作者： Moreno, Matthew Andres Ranjan, Anika Dolson, Emily Zaman, Luis University of Michigan Department of Ecology and Evolutionary Biology Ann Arbor United States Center for the Study of Complex Systems University of Michigan Ann Arbor United States Michigan Institute for Data and Ai in Society University of Michigan Ann Arbor United States Undergraduate Research Opportunities Program University of Michigan Ann Arbor United States Michigan State University Department of Computer Science and Engineering East Lansing United States Program in Ecology Evolution and Behavior Michigan State University East Lansing United States

ISBN: (纸本)9798331508371

Computer simulations are an important tool for studying the mechanics of biological evolution. In particular, agent-based approaches provide an opportunity to collect high-quality records of ancestry relationships. Such phylogenies can provide insight into evolutionary dynamics within these simulations. Previous work generally tracks lineages directly, yielding an exact phylogenetic record of evolutionary history. However, challenges exist in scaling direct ancestrytracking approaches to highly-distributed, many-processor evolution in silico. An alternative approach is to estimate phylogenetic history via noncoding annotations on digital genomes, akin to how bioinformaticians build phylogenies by assessing genetic similarities between organisms. Recent work has extended this 'hereditary stratigraphy' approach to support powerful hardware accelerator platforms, such as the Cerebras Wafer-Scale Engine. Although these second-generation 'surface'-based hereditary stratigraphy algorithms have demonstrated order-ofmagnitude speedups over first-generation 'column'-based algorithms, it remains unknown how they impact the accuracy of reconstructed phylogenies. To address this question, we assessed reconstruction accuracy under alternative configurations across a matrix of evolutionary conditions varying in selection pressure, spatial structure, and ecological dynamics. Encouragingly, we find that the second-generation approaches provide higher reconstruction quality across most surveyed conditions. © 2025 IEEE.

关键词： Biostratigraphy

Testing the Inference Accuracy of Accelerator-Friendly Approximate Phylogeny Tracking

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Testing the Inference Accuracy of Accelerator-Friendly Appro...

Computational Intelligence in Artificial Life and Cooperative Intelligent systems (ALIFE-CIS), IEEE Symposium on

作者： Matthew Andres Moreno Anika Ranjan Emily Dolson Luis Zaman Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor United States Center for the Study of Complex Systems University of Michigan Ann Arbor United States Michigan Institute for Data and AI in Society University of Michigan Ann Arbor United States Undergraduate Research Opportunities Program University of Michigan Ann Arbor United States Department of Computer Science and Engineering Michigan State University East Lansing United States Program in Ecology Evolution and Behavior Michigan State University East Lansing United States

ISBN: (数字)9798331508371

ISBN: (纸本)9798331508388

Computer simulations are an important tool for studying the mechanics of biological evolution. In particular, agent-based approaches provide an opportunity to collect high-quality records of ancestry relationships. Such phylogenies can provide insight into evolutionary dynamics within these simulations. Previous work generally tracks lineages directly, yielding an exact phylogenetic record of evolutionary history. However, challenges exist in scaling direct ancestrytracking approaches to highly-distributed, many-processor evolution in silico. An alternative approach is to estimate phylogenetic history via noncoding annotations on digital genomes, akin to how bioinformaticians build phylogenies by assessing genetic similarities between organisms. Recent work has extended this “hereditary stratigraphy” approach to support powerful hardware accelerator platforms, such as the Cerebras Wafer-Scale Engine. Although these second-generation “surface”-based hereditary stratigraphy algorithms have demonstrated order-ofmagnitude speedups over first-generation “column”-based algorithms, it remains unknown how they impact the accuracy of reconstructed phylogenies. To address this question, we assessed reconstruction accuracy under alternative configurations across a matrix of evolutionary conditions varying in selection pressure, spatial structure, and ecological dynamics. Encouragingly, we find that the second-generation approaches provide higher reconstruction quality across most surveyed conditions.

关键词： Surface reconstruction Accuracy Annotations Heuristic algorithms Computational modeling Biological system modeling Stratigraphy Phylogeny History Bars

Trackable Agent-based Evolution Models at Wafer Scale

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arXiv 2024年

作者： Moreno, Matthew Andres Yang, Connor Dolson, Emily Zaman, Luis Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor United States Center for the Study of Complex Systems University of Michigan Ann Arbor United States Michigan Institute for Data Science University of Michigan Ann Arbor United States Undergraduate Research Opportunities Program University of Michigan Ann Arbor United States Department of Computer Science and Engineering Michigan State University East Lansing United States Program in Ecology Evolution and Behavior Michigan State University East Lansing United States

Continuing improvements in computing hardware are poised to transform capabilities for in silico modeling of cross-scale phenomena underlying major open questions in evolutionary biology and artificial life, such as transitions in individuality, eco-evolutionary dynamics, and rare evolutionary events. Emerging ML/AI-oriented hardware accelerators, like the 850,000 processor Cerebras Wafer Scale Engine (WSE), hold particular promise. However, many practical challenges remain in conducting informative evolution experiments that efficiently utilize these platforms’ large processor counts. Here, we focus on the problem of extracting phylogenetic information from agent-based evolution on the WSE platform. This goal drove significant refinements to decentralized in silico phylogenetic tracking, reported here. These improvements yield order-of-magnitude performance improvements. We also present an asynchronous island-based genetic algorithm (GA) framework for WSE hardware. Emulated and on-hardware GA benchmarks with a simple tracking-enabled agent model clock upwards of 1 million generations a minute for population sizes reaching 16 million agents. This pace enables quadrillions of agent replication events a day. We validate phylogenetic reconstructions from these trials and demonstrate their suitability for inference of underlying evolutionary conditions. In particular, we demonstrate extraction, from wafer-scale simulation, of clear phylometric signals that differentiate runs with adaptive dynamics enabled versus disabled. Together, these benchmark and validation trials reflect strong potential for highly scalable agent-based evolution simulation that is both efficient and observable. Developed capabilities will bring entirely new classes of previously intractable research questions within reach, benefiting further explorations within the evolutionary biology and artificial life communities across a variety of emerging high-performance computing platforms. Copyright © 20

关键词： Genetic algorithms

A Guide to Tracking Phylogenies in Parallel and Distributed Agent-based Evolution Models

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arXiv 2024年

作者： Moreno, Matthew Andres Ranjan, Anika Dolson, Emily Zaman, Luis Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor United States Center for the Study of Complex Systems University of Michigan Ann Arbor United States Michigan Institute for Data and AI in Society University of Michigan Ann Arbor United States Undergraduate Research Opportunities Program University of Michigan Ann Arbor United States Department of Computer Science and Engineering Michigan State University East Lansing United States Program in Ecology Evolution and Behavior Michigan State University East Lansing United States

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 collect high-quality records of ancestry relationships among simulated agents. Such phylogenies can provide insight into evolutionary dynamics within these simulations. Existing work generally tracks lineages directly, yielding an exact phylogenetic record of evolutionary history. However, direct tracking can be inefficient for large-scale, many-processor evolutionary simulations. An alternate approach to extracting phylogenetic information from simulation that scales more favorably is post hoc estimation, akin to how bioinformaticians build phylogenies by assessing genetic similarities between organisms. Recently introduced "hereditary stratigraphy" algorithms provide means for efficient inference of phylogenetic history from non-coding annotations on simulated organisms' genomes. A number of options exist in configuring hereditary stratigraphy methodology, but no work has yet tested how they impact reconstruction quality. To address this question, we surveyed reconstruction accuracy under alternate configurations across a matrix of evolutionary conditions varying in selection pressure, spatial structure, and ecological dynamics. We synthesize results from these experiments to suggest a prescriptive system of best practices for work with hereditary stratigraphy, ultimately guiding researchers in choosing appropriate instrumentation for large-scale simulation studies. Copyright © 2024, The Authors. All rights reserved.

关键词： Biotic

Ecology, Spatial Structure, and Selection Pressure Induce Strong Signatures in Phylogenetic Structure

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arXiv 2024年

作者： Moreno, Matthew Andres Rodriguez-Papa, Santiago Dolson, Emily Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor United States Center for the Study of Complex Systems University of Michigan Ann Arbor United States Michigan Institute for Data Science University of Michigan Ann Arbor United States Department of Computer Science and Engineering Michigan State University East Lansing United States Program in Ecology Evolution and Behavior Michigan State University East Lansing United States

evolutionary dynamics are shaped by a variety of fundamental, generic drivers, including spatial structure, ecology, and selection pressure. These drivers impact the trajectory of evolution, and have been hypothesized to influence phylogenetic structure. For instance, they can help explain natural history, steer behavior of contemporary evolving populations, and influence efficacy of application-oriented evolutionary optimization. Likewise, in inquiry-oriented artificial life systems, these drivers constitute key building blocks for open-ended evolution. Here, we set out to assess (1) if spatial structure, ecology, and selection pressure leave detectable signatures in phylogenetic structure, (2) the extent, in particular, to which ecology can be detected and discerned in the presence of spatial structure, and (3) the extent to which these phylogenetic signatures generalize across evolutionary systems. To this end, we analyze phylogenies generated by manipulating spatial structure, ecology, and selection pressure within three computational models of varied scope and sophistication. We find that selection pressure, spatial structure, and ecology have characteristic effects on phylogenetic metrics, although these effects are complex and not always intuitive. Signatures have some consistency across systems when using equivalent taxonomic unit definitions (e.g., individual, genotype, species). Further, we find that sufficiently strong ecology can be detected in the presence of spatial structure. We also find that, while low-resolution phylogenetic reconstructions can bias some phylogenetic metrics, high-resolution reconstructions recapitulate them faithfully. Although our results suggest potential for evolutionary inference of spatial structure, ecology, and selection pressure through phylogenetic analysis, further methods development is needed to distinguish these drivers' phylometric signatures from each other and to appropriately normalize phylogenetic metrics. With s

关键词： Abiotic

Structured Downsampling for Fast, Memory-efficient Curation of Online Data Streams

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arXiv 2024年

作者： Moreno, Matthew Andres Zaman, Luis Dolson, Emily Department of Ecology and Evolutionary Biology Ann Arbor United States Center for the Study of Complex Systems Ann Arbor United States Michigan Institute for Data and AI in Society Ann Arbor United States University of Michigan Ann Arbor United States Department of Computer Science and Engineering East Lansing United States Program in Ecology Evolution and Behavior East Lansing United States Michigan State University East Lansing United States

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 state in a manner that is fast and memory efficient - particularly in resource-constrained or real-time contexts. Here, we address the problem of extracting a fixed-capacity, rolling subsample from a data stream. Specifically, we explore "data stream curation" strategies to fulfill requirements on the composition of sample time points retained. Our "DStream" suite of algorithms targets three temporal coverage criteria: (1) steady coverage, where retained samples should spread evenly across elapsed data stream history;(2) stretched coverage, where early data items should be proportionally favored;and (3) tilted coverage, where recent data items should be proportionally favored. For each algorithm, we prove worst-case bounds on rolling coverage quality. In contrast to previous work by Moreno, Rodriguez Papa, and Dolson (2024), which dynamically scales memory use to guarantee a specified level of coverage quality, here we focus on the more practical, application-driven case of maximizing coverage quality given a fixed memory capacity. As a core simplifying assumption, we restrict algorithm design to a single update operation: writing from the data stream to a calculated buffer site - with data never being read back, no metadata stored (e.g., sample timestamps), and data eviction occurring only implicitly via overwrite. Drawing only on primitive, low-level operations and ensuring full, overhead-free use of available memory, this "DStream" framework ideally suits domains that are resource-constrained (e.g., embedded systems), performance-critical (e.g., real-time), and fine-grained (e.g., individual data items as small as single bits or bytes). In particular, proposed power-of-two-based buffer layout schemes support O(1) data ingestion via concise bit-level operations. To further practical applica

关键词： Data streams

The context-specificity of virulence evolution revealed through evolutionary invasion analysis

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arXiv 2023年

作者： Surasinghe, Sudam Kabengele, Ketty Turner, Paul E. Brandon Ogbunugafor, C. Department of Ecology and Evolutionary Biology Yale University New HavenCT06520 United States Public Health Modeling Unit Yale School of Public Health New HavenCT06510 United States Microbiology Program Yale School of Medicine New HavenCT06510 United States Santa Fe Institute Santa FeNM87501 United States Vermont Complex Systems Center University of Vermont BurlingtonVT05405 United States

Models are often employed to integrate knowledge about epidemics across scales and simulate disease dynamics. While these approaches have played a central role in studying the mechanics underlying epidemics, we lack ways to reliably predict how the relationship between virulence (the harm to hosts caused by an infection) and transmission will evolve in certain virus-host contexts. In this study, we invoke evolutionary invasion analysis-a method used to identify the evolution of uninvadable strategies in dynamical systems-to examine how the virulence-transmission dichotomy can evolve in models of virus infections defined by different natural histories. We reveal that peculiar ecologies drive different evolved relationships between virulence and transmission. Specifically, we discover patterns of virulence evolution between epidemics of various kinds (SARS-CoV-2 and hepatitis C virus) and that varying definitions of virulence alter our predictions for how viruses will evolve. We discuss the findings in light of contemporary conversations in the public health sector around the possibility of predicting virus evolution and in more extensive theoretical discussions involving virulence evolution in emerging infectious diseases. © 2023, CC BY-NC-ND.

关键词： Transmissions

Fine-scale heterogeneity in population density predicts wave dynamics in dengue epidemics (vol 13, 996, 2022)

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NATURE COMMUNICATIONS 2022年第1期13卷 1-9页

作者： Romeo-Aznar, Victoria Picinini Freitas, Lais Goncalves Cruz, Oswaldo King, Aaron A. Pascual, Mercedes Department of Ecology and Evolution University of Chicago Chicago IL USA Departamento de Ecología Genética y Evolución and Instituto IEGEBA (CONICET-UBA) Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires Ciudad Universitaria Pabellón 2 C1428EHA Buenos Aires Argentina Mansueto Institute for Urban Innovation The University of Chicago Chicago IL USA Postgraduate Program of Epidemiology in Public Health - Escola Nacional de Saúde Pública Sergio Arouca - Fundação Oswaldo Cruz Rio de Janeiro Brazil Programa de Computação Científica - Fundação Oswaldo Cruz Rio de Janeiro Brazil Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor MI USA Center for the Study of Complex Systems University of Michigan Ann Arbor MI USA The Santa Fe Institute Santa Fe NM USA

The spread of dengue and other arboviruses constitutes an expanding global health threat. The extensive heterogeneity in population distribution and potential complexity of movement in megacities of low and middle-income countries challenges predictive modeling, even as its importance to disease spread is clearer than ever. Using surveillance data at fine resolution following the emergence of the DENV4 dengue serotype in Rio de Janeiro, we document a pattern in the size of successive epidemics that is invariant to the scale of spatial aggregation. This pattern emerges from the combined effect of herd immunity and seasonal transmission, and is strongly driven by variation in population density at sub-kilometer scales. It is apparent only when the landscape is stratified by population density and not by spatial proximity as has been common practice. Models that exploit this emergent simplicity should afford improved predictions of the local size of successive epidemic waves.

关键词： Computational models Dengue virus Ecological epidemiology Ecological modelling Epidemiology