Charles Ofria
Current Organizations / Institutes
The organizations/institutes from the scholar's latest article
Previous Organizations / Institutes
The organizations / institutes from the scholar's other articles in the past ten years
Research Subjects
Charles Ofria has a total of 135 co-authors. Here are the top co-authors by number of shared publications:
- Emily Dolson
Department of Computer Science and Engineering, Michigan State University, East Lansing, Michigan, United States
22 shared publications - Richard E. Lenski
Department of Microbiology, Genetics, and Immunology, Michigan State University
20 shared publications Philip K. McKinley
Michigan State University, East Lansing, MI, USA
14 shared publicationsRobert T. Pennock
BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, Michigan, United States of America
13 shared publicationsJeff Clune
University of Wyoming, Laramie, WY, USA & Universidad Politecnica de Valéncia, Valencia, Spain
12 shared publications- Alexander Lalejini
Grand Valley State University
11 shared publications
Latest Publications
- 3 June 2026
- Published by Springer Nature
- p. 305-327
Tips on Effective Theory and Practice of Genetic Programming
- 3 June 2026
- Published by Springer Nature
- p. 305-327
Tips on Effective Theory and Practice of Genetic Programming
- Open Access
- 13 July 2025
- Published by Association for Computing Machinery (ACM)
- p. 970-979
A comparison of tournament and lexicase selection paradigms in regression problems: error-based fitness versus correlation fitness
- 13 July 2025
- Published by Association for Computing Machinery (ACM)
- p. 970-979
Open AccessA comparison of tournament and lexicase selection paradigms in regression problems: error-based fitness versus correlation fitness
- 28 February 2025
- Published by Springer Nature
- p. 395-411
Using Lineage Age to Augment Search Space Exploration in Lexicase Selection
- 28 February 2025
- Published by Springer Nature
- p. 395-411
Using Lineage Age to Augment Search Space Exploration in Lexicase Selection
- 2 December 2024
- Published by MIT Press in Evolutionary Computation
- Vol. 32 (4) , 307-337
Informed Down-Sampled Lexicase Selection: Identifying Productive Training Cases for Efficient Problem Solving
Genetic Programming (GP) often uses large training sets and requires all individuals to be evaluated on all training cases during selection. Random down-sampled lexicase selection evaluates individuals on only a random subset of the training cases, allowing for more individuals to be explored with the same number of program executions. However, sampling randomly can exclude important cases from the down-sample for a number of generations, while cases that measure the same behavior (synonymous cases) may be overused. In this work, we introduce Informed Down-Sampled Lexicase Selection. This method leverages population statistics to build down-samples that contain more distinct and therefore informative training cases. Through an empirical investigation across two different GP systems (PushGP and Grammar-Guided GP), we find that informed down-sampling significantly outperforms random down-sampling on a set of contemporary program synthesis benchmark problems. Through an analysis of the created down-samples, we find that important training cases are included in the down-sample consistently across independent evolutionary runs and systems. We hypothesize that this improvement can be attributed to the ability of Informed Down-Sampled Lexicase Selection to maintain more specialist individuals over the course of evolution, while still benefiting from reduced per-evaluation costs.
- 2 December 2024
- Published by MIT Press in Evolutionary Computation
- Vol. 32 (4) , 307-337
Informed Down-Sampled Lexicase Selection: Identifying Productive Training Cases for Efficient Problem Solving
Genetic Programming (GP) often uses large training sets and requires all individuals to be evaluated on all training cases during selection. Random down-sampled lexicase selection evaluates individuals on only a random subset of the training cases, allowing for more individuals to be explored with the same number of program executions. However, sampling randomly can exclude important cases from the down-sample for a number of generations, while cases that measure the same behavior (synonymous cases) may be overused. In this work, we introduce Informed Down-Sampled Lexicase Selection. This method leverages population statistics to build down-samples that contain more distinct and therefore informative training cases. Through an empirical investigation across two different GP systems (PushGP and Grammar-Guided GP), we find that informed down-sampling significantly outperforms random down-sampling on a set of contemporary program synthesis benchmark problems. Through an analysis of the created down-samples, we find that important training cases are included in the down-sample consistently across independent evolutionary runs and systems. We hypothesize that this improvement can be attributed to the ability of Informed Down-Sampled Lexicase Selection to maintain more specialist individuals over the course of evolution, while still benefiting from reduced per-evaluation costs.
- Open Access
- 14 July 2024
- Published by Association for Computing Machinery (ACM)
- p. 25-26
Improving Lexicase Selection with Informed Down-Sampling
This short paper presents the main findings of our work titled Informed Down-Sampled Lexicase Selection: Identifying Productive Training Cases for Efficient Problem Solving, which was recently published in the Evolutionary Computation Journal. In this work, we introduce informed down-sampled lexicase selection to dynamically build diverse subsets of training cases during evolution using population statistics. We evaluate our method on a set of program synthesis problems in two genetic programming systems and find that informed down-sampling improves performance in both systems compared to random down-sampling when using lexicase selection. Additionally, we investigate the constructed down-samples and find that informed down-sampling can identify important training cases and does so across different evolutionary runs and systems.
- 14 July 2024
- Published by Association for Computing Machinery (ACM)
- p. 25-26
Open AccessImproving Lexicase Selection with Informed Down-Sampling
This short paper presents the main findings of our work titled Informed Down-Sampled Lexicase Selection: Identifying Productive Training Cases for Efficient Problem Solving, which was recently published in the Evolutionary Computation Journal. In this work, we introduce informed down-sampled lexicase selection to dynamically build diverse subsets of training cases during evolution using population statistics. We evaluate our method on a set of program synthesis problems in two genetic programming systems and find that informed down-sampling improves performance in both systems compared to random down-sampling when using lexicase selection. Additionally, we investigate the constructed down-samples and find that informed down-sampling can identify important training cases and does so across different evolutionary runs and systems.
- Open Access
- 2 June 2024
- Published by The Open Journal in Journal of Open Source Software
- Vol. 9 (98) , 6617
Empirical: A scientific software library for research, education, and public engagement
- 2 June 2024
- Published by The Open Journal in Journal of Open Source Software
- Vol. 9 (98) , 6617
Open AccessEmpirical: A scientific software library for research, education, and public engagement
- Open Access
Reduced selection during sweeps lead to adaptive momentum on rugged landscapes
: Evolutionary theory seeks to explain the remarkable diversity and adaptability of life on Earth. Current theory offers substantial explanatory power, but it overlooks important transient dynamics that are prominent only when populations are outside equilibrium, such as during selective sweeps. We identify a dynamic that we call “adaptive momentum” whereby lineages with a selective advantage can temporarily sustain more deleterious mutations. This reduction in the strength of purifying selection allows populations to explore fitness valleys that are usually too costly to enter, potentially leading to the discovery of otherwise inaccessible fitness peaks. Using mathematical and agent-based simulations, we demonstrate adaptive momentum and show how periods of disequilibrium become windows of enhanced adaptation. Genetic exploration can occur during these windows without requiring mechanisms such as changing environments or complex landscapes. Adaptive momentum provides a simple potential explanation for bursts of rapid evolution observed in nature, including in pathogens such as SARS-CoV-2 and cancers. (152 words)
Open AccessReduced selection during sweeps lead to adaptive momentum on rugged landscapes
: Evolutionary theory seeks to explain the remarkable diversity and adaptability of life on Earth. Current theory offers substantial explanatory power, but it overlooks important transient dynamics that are prominent only when populations are outside equilibrium, such as during selective sweeps. We identify a dynamic that we call “adaptive momentum” whereby lineages with a selective advantage can temporarily sustain more deleterious mutations. This reduction in the strength of purifying selection allows populations to explore fitness valleys that are usually too costly to enter, potentially leading to the discovery of otherwise inaccessible fitness peaks. Using mathematical and agent-based simulations, we demonstrate adaptive momentum and show how periods of disequilibrium become windows of enhanced adaptation. Genetic exploration can occur during these windows without requiring mechanisms such as changing environments or complex landscapes. Adaptive momentum provides a simple potential explanation for bursts of rapid evolution observed in nature, including in pathogens such as SARS-CoV-2 and cancers. (152 words)
- Open Access
Informed Down-Sampled Lexicase Selection: Identifying productive training cases for efficient problem solving
Genetic Programming (GP) often uses large training sets and requires all individuals to be evaluated on all training cases during selection. Random down-sampled lexicase selection evaluates individuals on only a random subset of the training cases allowing for more individuals to be explored with the same amount of program executions. However, creating a down-sample randomly might exclude important cases from the current down-sample for a number of generations, while cases that measure the same behavior (synonymous cases) may be overused despite their redundancy. In this work, we introduce Informed Down-Sampled Lexicase Selection. This method leverages population statistics to build down-samples that contain more distinct and therefore informative training cases. Through an empirical investigation across two different GP systems (PushGP and Grammar-Guided GP), we find that informed down-sampling significantly outperforms random down-sampling on a set of contemporary program synthesis benchmark problems. Through an analysis of the created down-samples, we find that important training cases are included in the down-sample consistently across independent evolutionary runs and systems. We hypothesize that this improvement can be attributed to the ability of Informed Down-Sampled Lexicase Selection to maintain more specialist individuals over the course of evolution, while also benefiting from reduced per-evaluation costs.
Open AccessInformed Down-Sampled Lexicase Selection: Identifying productive training cases for efficient problem solving
Genetic Programming (GP) often uses large training sets and requires all individuals to be evaluated on all training cases during selection. Random down-sampled lexicase selection evaluates individuals on only a random subset of the training cases allowing for more individuals to be explored with the same amount of program executions. However, creating a down-sample randomly might exclude important cases from the current down-sample for a number of generations, while cases that measure the same behavior (synonymous cases) may be overused despite their redundancy. In this work, we introduce Informed Down-Sampled Lexicase Selection. This method leverages population statistics to build down-samples that contain more distinct and therefore informative training cases. Through an empirical investigation across two different GP systems (PushGP and Grammar-Guided GP), we find that informed down-sampling significantly outperforms random down-sampling on a set of contemporary program synthesis benchmark problems. Through an analysis of the created down-samples, we find that important training cases are included in the down-sample consistently across independent evolutionary runs and systems. We hypothesize that this improvement can be attributed to the ability of Informed Down-Sampled Lexicase Selection to maintain more specialist individuals over the course of evolution, while also benefiting from reduced per-evaluation costs.
- Open Access
A suite of diagnostic metrics for characterizing selection schemes
Benchmark suites are crucial for assessing the performance of evolutionary algorithms, but the constituent problems are often too complex to provide clear intuition about an algorithm's strengths and weaknesses. To address this gap, we introduce DOSSIER ("Diagnostic Overview of Selection Schemes In Evolutionary Runs"), a diagnostic suite initially composed of eight handcrafted metrics. These metrics are designed to empirically measure specific capacities for exploitation, exploration, and their interactions. We consider exploitation both with and without constraints, and we divide exploration into two aspects: diversity exploration (the ability to simultaneously explore multiple pathways) and valley-crossing exploration (the ability to cross wider and wider fitness valleys). We apply DOSSIER to six popular selection schemes: truncation, tournament, fitness sharing, lexicase, nondominated sorting, and novelty search. Our results confirm that simple schemes (e.g., tournament and truncation) emphasized exploitation. For more sophisticated schemes, however, our diagnostics revealed interesting dynamics. Lexicase selection performed moderately well across all diagnostics that did not incorporate valley crossing, but faltered dramatically whenever valleys were present, performing worse than even random search. Fitness sharing was the only scheme to effectively contend with valley crossing but it struggled with the other diagnostics. Our study highlights the utility of using diagnostics to gain nuanced insights into selection scheme characteristics, which can inform the design of new selection methods.
Open AccessA suite of diagnostic metrics for characterizing selection schemes
Benchmark suites are crucial for assessing the performance of evolutionary algorithms, but the constituent problems are often too complex to provide clear intuition about an algorithm's strengths and weaknesses. To address this gap, we introduce DOSSIER ("Diagnostic Overview of Selection Schemes In Evolutionary Runs"), a diagnostic suite initially composed of eight handcrafted metrics. These metrics are designed to empirically measure specific capacities for exploitation, exploration, and their interactions. We consider exploitation both with and without constraints, and we divide exploration into two aspects: diversity exploration (the ability to simultaneously explore multiple pathways) and valley-crossing exploration (the ability to cross wider and wider fitness valleys). We apply DOSSIER to six popular selection schemes: truncation, tournament, fitness sharing, lexicase, nondominated sorting, and novelty search. Our results confirm that simple schemes (e.g., tournament and truncation) emphasized exploitation. For more sophisticated schemes, however, our diagnostics revealed interesting dynamics. Lexicase selection performed moderately well across all diagnostics that did not incorporate valley crossing, but faltered dramatically whenever valleys were present, performing worse than even random search. Fitness sharing was the only scheme to effectively contend with valley crossing but it struggled with the other diagnostics. Our study highlights the utility of using diagnostics to gain nuanced insights into selection scheme characteristics, which can inform the design of new selection methods.
- Open Access
- 15 July 2023
- Published by Association for Computing Machinery (ACM)
- p. 35-36
Tag Affinity Criteria Influence Adaptive Evolution
- 15 July 2023
- Published by Association for Computing Machinery (ACM)
- p. 35-36
Open AccessTag Affinity Criteria Influence Adaptive Evolution