Computational Entomology: Algorithms, Models, and Digital Insect Colonies

What Evidence Connects Physiology With Collective Foraging?

The physiology of forager hydration and variation among harvester ant (Pogonomyrmex barbatus) colonies in collective foraging behavior (Friedman, Greene & Gordon, 2019) reports that hydrated harvester ant foragers made more trips than unhydrated nestmates, with hydration and desiccation responses varying among colonies. Gene expression variation in the brains of harvester ant foragers is associated with collective behavior (Friedman et al., 2020) reports associations between brain gene expression and collective behavior. An association between expression and colony behavior does not alone establish a causal molecular mechanism.

How Can Models Explain Colony Behavior?

A single-pheromone model accounts for empirical patterns of ant colony foraging previously modeled using two pheromones (Saund & Friedman, 2023) shows that a single-pheromone model can account for empirical patterns previously addressed with more complex pheromone models. Computational Complexity and Energetics of the Ant Stack (Friedman, 2025) studies a particular Ant Stack framework. Its computational and energy analysis concerns that biomimetic architecture and its assumptions.

Which Software Projects Are Relevant?

BeeStack: An Evidence-Typed Scaffold for Whole-Colony Honeybee Simulation (Friedman & Chambers, 2026) presents a scaffold for honeybee simulation with explicit evidence distinctions. Ento-Linguistics: Language, Ambiguity, and Scientific Communication in Entomology (Friedman & Chambers, 2026) concerns language and scientific communication in entomology. COGANT: Deterministic Codebase-to-GNN Translation (Friedman, 2026) describes codebase-to-GNN translation; it is a computational tool rather than an empirical insect model.

Project repositories include BeeStack, Ento-Linguistics, MetaInformAnt, and Active_InferAnts. Their implementation and validation scopes differ; consult the project documentation before choosing one.

What Does Neurogenomics Add?

The Role of Dopamine in the Collective Regulation of Foraging in Harvester Ants (Friedman et al., 2018) reports experiments on dopamine and foraging in harvester ants. Behavioral, physiological, and transcriptomic variation among colonies of the red harvester ant (Pogonomyrmex barbatus) (Friedman, 2019) brings together behavioral, physiological, and transcriptomic variation among colonies. Combining these measurements can motivate models, but a calibrated prediction from molecular measurements to whole-colony behavior requires its own validation.

How Should Biological and Engineering Claims Be Compared?

A simulation that reproduces a behavioral pattern is evidence about that model under its tested conditions. It does not establish that insects implement the same algorithm or that a related robotic system will behave reliably. Compare the model assumptions, measured outputs, negative controls, and available code before transferring a result to another setting.

References

1. Friedman, Daniel A.; Greene, Michael J.; Gordon, Deborah M. 2019. The physiology of forager hydration and variation among harvester ant (Pogonomyrmex barbatus) colonies in collective foraging behavior. Scientific Reports. Publication source.
2. Friedman, Daniel Ari; York, Ryan Alexander; Hilliard, Austin Travis; Gordon, Deborah M. 2020. Gene expression variation in the brains of harvester ant foragers is associated with collective behavior. Communications Biology. Publication source.
3. Saund, Eric; Friedman, Daniel Ari. 2023. A single-pheromone model accounts for empirical patterns of ant colony foraging previously modeled using two pheromones. Cognitive Systems Research. Publication source.
4. Friedman, Daniel. 2025. Computational Complexity and Energetics of the Ant Stack. Zenodo. Publication source.
5. Friedman, Daniel Ari; Chambers, Tucker Cahill. 2026. BeeStack: An Evidence-Typed Scaffold for Whole-Colony Honeybee Simulation. Zenodo. Publication source.
6. Friedman, Daniel Ari; Chambers, Tucker Cahill. 2026. Ento-Linguistics: Language, Ambiguity, and Scientific Communication in Entomology. Zenodo. Publication source.
7. Friedman, Daniel Ari. 2026. COGANT: Deterministic Codebase-to-GNN Translation. Zenodo. Publication source.
8. Friedman, Daniel A.; Pilko, Anna; Skowronska-Krawczyk, Dorota; Krasinska, Karolina; Parker, Jacqueline W.; Hirsh, Jay; Gordon, Deborah M. 2018. The Role of Dopamine in the Collective Regulation of Foraging in Harvester Ants. iScience. Publication source.
9. Friedman, Daniel Ari. 2019. Behavioral, physiological, and transcriptomic variation among colonies of the red harvester ant (Pogonomyrmex barbatus). Stanford University. Publication source.