Mozzamil Mohammed, Mohammed AY Mohammed, Abdallah Alsammani, Mohamed Bakheet, Cang Hui, Pietro Landi
Carnivores interact with herbivores to indirectly impact plant populations, creating trophic cascades within plant-herbivore-carnivore systems. We developed and analyzed a food chain model to gain a mechanistic understanding of the critical roles carnivores play in ecosystems where plants face intense herbivory. Our model incorporates key factors such as seed production rates, seed germination probabilities, local plant interactions, herbivory rates, and carnivore predation rates. In the absence of carnivores, herbivores significantly reduce plant densities, often driving plants to extinction under high herbivory rates. However, the presence of carnivores suppresses herbivore populations, allowing plants to recover from herbivore pressure. We found that plant densities increase with carnivore predation rates, highlighting top-down effects and underscoring the importance of conserving carnivores in ecosystems where plants are at high risk of extinction from herbivory. Our results also show that carnivore density increases with seed-production rates, while herbivore density remains constant, indicating that plants benefit carnivores more than herbivores. This increase in carnivore density driven by high seed-production rates reflects bottom-up effects in the system. Overall, our study demonstrates that plants, herbivores, and carnivores can coexist even under intense predation stress. It suggests that carnivores play a crucial role in regulating plant and herbivore populations, with significant potential for maintaining biodiversity within ecosystems.
{"title":"Coexistence via trophic cascade in plant-herbivore-carnivore systems under intense predation pressure","authors":"Mozzamil Mohammed, Mohammed AY Mohammed, Abdallah Alsammani, Mohamed Bakheet, Cang Hui, Pietro Landi","doi":"arxiv-2408.04862","DOIUrl":"https://doi.org/arxiv-2408.04862","url":null,"abstract":"Carnivores interact with herbivores to indirectly impact plant populations,\u0000creating trophic cascades within plant-herbivore-carnivore systems. We\u0000developed and analyzed a food chain model to gain a mechanistic understanding\u0000of the critical roles carnivores play in ecosystems where plants face intense\u0000herbivory. Our model incorporates key factors such as seed production rates,\u0000seed germination probabilities, local plant interactions, herbivory rates, and\u0000carnivore predation rates. In the absence of carnivores, herbivores\u0000significantly reduce plant densities, often driving plants to extinction under\u0000high herbivory rates. However, the presence of carnivores suppresses herbivore\u0000populations, allowing plants to recover from herbivore pressure. We found that\u0000plant densities increase with carnivore predation rates, highlighting top-down\u0000effects and underscoring the importance of conserving carnivores in ecosystems\u0000where plants are at high risk of extinction from herbivory. Our results also\u0000show that carnivore density increases with seed-production rates, while\u0000herbivore density remains constant, indicating that plants benefit carnivores\u0000more than herbivores. This increase in carnivore density driven by high\u0000seed-production rates reflects bottom-up effects in the system. Overall, our\u0000study demonstrates that plants, herbivores, and carnivores can coexist even\u0000under intense predation stress. It suggests that carnivores play a crucial role\u0000in regulating plant and herbivore populations, with significant potential for\u0000maintaining biodiversity within ecosystems.","PeriodicalId":501044,"journal":{"name":"arXiv - QuanBio - Populations and Evolution","volume":"84 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141945585","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Heroes are people who perform costly altruistic acts. Few people turn out to be heroes, but most people spontaneously honor heroes overtly by commenting, applauding, or enthusiastically celebrating their deeds. This behavior seems odd from an individual fitness optimization perspective. The best strategy should be to rely on others to invest time and effort in celebrations. To explain the universal propensity to pay tribute, we propose that public admiration is a way for admirers to signal that they are committed to the same values as the hero. We show that the emergence of heroic acts is an expected side-effect of this propensity.
{"title":"Why Honor Heroes? Praise as a Social Signal","authors":"Jean-Louis Dessalles","doi":"arxiv-2408.08893","DOIUrl":"https://doi.org/arxiv-2408.08893","url":null,"abstract":"Heroes are people who perform costly altruistic acts. Few people turn out to\u0000be heroes, but most people spontaneously honor heroes overtly by commenting,\u0000applauding, or enthusiastically celebrating their deeds. This behavior seems\u0000odd from an individual fitness optimization perspective. The best strategy\u0000should be to rely on others to invest time and effort in celebrations. To\u0000explain the universal propensity to pay tribute, we propose that public\u0000admiration is a way for admirers to signal that they are committed to the same\u0000values as the hero. We show that the emergence of heroic acts is an expected\u0000side-effect of this propensity.","PeriodicalId":501044,"journal":{"name":"arXiv - QuanBio - Populations and Evolution","volume":"46 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142204425","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Francesca Rovida, Marino Faccini, Carla Molina Grané, Irene Cassaniti, Sabrina Senatore, Eva Rossetti, Giuditta Scardina, Manuela Piazza, Giulia Campanini, Daniele Lilleri, Stefania Paolucci, Guglielmo Ferrari, Antonio Piralla, Francesco Defilippo, Davide Lelli, Ana Moreno, Luigi Vezzosi, Federica Attanasi, Soresini Marzia, Barozzi Manuela, Lorenzo Cerutti, Stefano Paglia, Angelo Regazzetti, Maurilia Marcacci, Guido Di Donato, Marco Farioli, Mattia Manica, Piero Poletti, Antonio Lavazza, Maira Bonini, Stefano Merler, Fausto Baldanti, Danilo Cereda, Lombardy Dengue network
Introduction. Here we reported the virological, entomological and epidemiological characteristics of the large autochthonous outbreak of dengue (DENV) occurred in a small village of the Lombardy region (Northern Italy) during summer 2023. Methods. After the diagnosis of the first autochthonous case on 18 August 2023, public health measures, including epidemiological investigation and vector control measures, were carried out. A serological screening for DENV antibodies detection was offered to the population. In the case of positive DENV IgM, a second sample was collected to detect DENV RNA and verify seroconversion. Entomological and epidemiological investigations were also performed. A modeling analysis was conducted to estimate the dengue generation time, transmission potential, distance of transmission, and assess diagnostic delays. Results. Overall, 416 subjects participated to the screening program and 20 were identified as DENV-1 cases (15 confirmed and 5 probable). In addition, DENV-1 infection was diagnosed in 24 symptomatic subjects referred to the local Emergency Room Department for suggestive symptoms and 1 case was identified through blood donation screening. The average generation time was estimated to be 18.3 days (95% CI: 13.1-23.5 days). R0 was estimated at 1.31 (95% CI: 0.76-1.98); 90% of transmission occurred within 500m. Entomological investigations performed in 46 pools of mosquitoes revealed the presence of only one positive pool for DENV-1. Discussion. This report highlights the importance of synergic surveillance, including virological, entomological and public health measures to control the spread of arboviral infections.
{"title":"The 2023 Dengue Outbreak in Lombardy, Italy: A One-Health Perspective","authors":"Francesca Rovida, Marino Faccini, Carla Molina Grané, Irene Cassaniti, Sabrina Senatore, Eva Rossetti, Giuditta Scardina, Manuela Piazza, Giulia Campanini, Daniele Lilleri, Stefania Paolucci, Guglielmo Ferrari, Antonio Piralla, Francesco Defilippo, Davide Lelli, Ana Moreno, Luigi Vezzosi, Federica Attanasi, Soresini Marzia, Barozzi Manuela, Lorenzo Cerutti, Stefano Paglia, Angelo Regazzetti, Maurilia Marcacci, Guido Di Donato, Marco Farioli, Mattia Manica, Piero Poletti, Antonio Lavazza, Maira Bonini, Stefano Merler, Fausto Baldanti, Danilo Cereda, Lombardy Dengue network","doi":"arxiv-2408.04768","DOIUrl":"https://doi.org/arxiv-2408.04768","url":null,"abstract":"Introduction. Here we reported the virological, entomological and\u0000epidemiological characteristics of the large autochthonous outbreak of dengue\u0000(DENV) occurred in a small village of the Lombardy region (Northern Italy)\u0000during summer 2023. Methods. After the diagnosis of the first autochthonous case on 18 August\u00002023, public health measures, including epidemiological investigation and\u0000vector control measures, were carried out. A serological screening for DENV\u0000antibodies detection was offered to the population. In the case of positive\u0000DENV IgM, a second sample was collected to detect DENV RNA and verify\u0000seroconversion. Entomological and epidemiological investigations were also\u0000performed. A modeling analysis was conducted to estimate the dengue generation\u0000time, transmission potential, distance of transmission, and assess diagnostic\u0000delays. Results. Overall, 416 subjects participated to the screening program and 20\u0000were identified as DENV-1 cases (15 confirmed and 5 probable). In addition,\u0000DENV-1 infection was diagnosed in 24 symptomatic subjects referred to the local\u0000Emergency Room Department for suggestive symptoms and 1 case was identified\u0000through blood donation screening. The average generation time was estimated to\u0000be 18.3 days (95% CI: 13.1-23.5 days). R0 was estimated at 1.31 (95% CI:\u00000.76-1.98); 90% of transmission occurred within 500m. Entomological\u0000investigations performed in 46 pools of mosquitoes revealed the presence of\u0000only one positive pool for DENV-1. Discussion. This report highlights the importance of synergic surveillance,\u0000including virological, entomological and public health measures to control the\u0000spread of arboviral infections.","PeriodicalId":501044,"journal":{"name":"arXiv - QuanBio - Populations and Evolution","volume":"93 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141945512","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
We demonstrate a graphical map, a new correspondence between circular electrical networks and circular planar split systems. When restricted to the planar circular electrical case, this graphical map finds the split system associated uniquely to the Kalmanson resistance distance of the dual network, matching the induced split system familiar from phylogenetics. This is extended to compactifications of the respective spaces, taking cactus networks to the newly defined compactified split systems. The graphical map preserves both components and cactus structure, allowing an elegant enumeration of induced phylogenetic split systems.
{"title":"Compactifications of phylogenetic systems and electrical networks","authors":"Satyan L. Devadoss, Stefan Forcey","doi":"arxiv-2408.03431","DOIUrl":"https://doi.org/arxiv-2408.03431","url":null,"abstract":"We demonstrate a graphical map, a new correspondence between circular\u0000electrical networks and circular planar split systems. When restricted to the\u0000planar circular electrical case, this graphical map finds the split system\u0000associated uniquely to the Kalmanson resistance distance of the dual network,\u0000matching the induced split system familiar from phylogenetics. This is extended\u0000to compactifications of the respective spaces, taking cactus networks to the\u0000newly defined compactified split systems. The graphical map preserves both\u0000components and cactus structure, allowing an elegant enumeration of induced\u0000phylogenetic split systems.","PeriodicalId":501044,"journal":{"name":"arXiv - QuanBio - Populations and Evolution","volume":"49 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141945588","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
From the proliferative mechanisms generating neurons from progenitor cells to neuron migration and synaptic connection formation, several vicissitudes culminate in the mature brain. Both component loss and gain remain ubiquitous during brain development. For example, rodent brains lose over half of their initial neurons and synapses during healthy development. The role of deleterious steps in network ontogeny remains unclear, yet it is unlikely these costly processes are random. Like neurogenesis and synaptogenesis, synaptic pruning and neuron death likely evolved to support complex, efficient computations. In order to incorporate both component loss and gain in describing neuronal networks, we propose an algorithm where a directed network evolves through the selective deletion of less-connected nodes (neurons) and edges (synapses). Resulting in networks that display scale-invariant degree distributions, provided the network is predominantly feed-forward. Scale-invariance offers several advantages in biological networks: scalability, resistance to random deletions, and strong connectivity with parsimonious wiring. Whilst our algorithm is not intended to be a realistic model of neuronal network formation, our results suggest selective deletion is an adaptive mechanism contributing to more stable and efficient networks. This process aligns with observed decreasing pruning rates in animal studies, resulting in higher synapse preservation. Our overall findings have broader implications for network science. Scale-invariance in degree distributions was demonstrated in growing preferential attachment networks and observed empirically. Our preferential detachment algorithm offers an alternative mechanism for generating such networks, suggesting that both mechanisms may be part of a broader class of algorithms resulting in scale-free networks.
{"title":"Selective pruning and neuronal death generate heavy-tail network connectivity","authors":"Rodrigo Siqueira Kazu, Kleber Neves, Bruno Mota","doi":"arxiv-2408.02625","DOIUrl":"https://doi.org/arxiv-2408.02625","url":null,"abstract":"From the proliferative mechanisms generating neurons from progenitor cells to\u0000neuron migration and synaptic connection formation, several vicissitudes\u0000culminate in the mature brain. Both component loss and gain remain ubiquitous\u0000during brain development. For example, rodent brains lose over half of their\u0000initial neurons and synapses during healthy development. The role of\u0000deleterious steps in network ontogeny remains unclear, yet it is unlikely these\u0000costly processes are random. Like neurogenesis and synaptogenesis, synaptic\u0000pruning and neuron death likely evolved to support complex, efficient\u0000computations. In order to incorporate both component loss and gain in\u0000describing neuronal networks, we propose an algorithm where a directed network\u0000evolves through the selective deletion of less-connected nodes (neurons) and\u0000edges (synapses). Resulting in networks that display scale-invariant degree\u0000distributions, provided the network is predominantly feed-forward.\u0000Scale-invariance offers several advantages in biological networks: scalability,\u0000resistance to random deletions, and strong connectivity with parsimonious\u0000wiring. Whilst our algorithm is not intended to be a realistic model of\u0000neuronal network formation, our results suggest selective deletion is an\u0000adaptive mechanism contributing to more stable and efficient networks. This\u0000process aligns with observed decreasing pruning rates in animal studies,\u0000resulting in higher synapse preservation. Our overall findings have broader\u0000implications for network science. Scale-invariance in degree distributions was\u0000demonstrated in growing preferential attachment networks and observed\u0000empirically. Our preferential detachment algorithm offers an alternative\u0000mechanism for generating such networks, suggesting that both mechanisms may be\u0000part of a broader class of algorithms resulting in scale-free networks.","PeriodicalId":501044,"journal":{"name":"arXiv - QuanBio - Populations and Evolution","volume":"6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141945514","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jimmy Calvo-Monge, Baltazar Espinoza, Fabio Sanchez
In this study, we couple a population dynamics model with a model for optimal foraging to study the interdependence between individual-level cost-benefits and population-scale dynamics. Specifically, we study the logistic growth model, which provides insights into population dynamics under resource limitations. Unlike exponential growth, the logistic model incorporates the concept of carrying capacity, thus offering a more realistic depiction of biological populations as they near environmental limits. We aim to study the impact of individual-level incentives driving behavioral responses in a dynamic environment. Specifically, explore the coupled dynamics between population density and individuals' foraging times. Our results yield insights into the effects of population size on individuals' optimal foraging efforts, which impacts the population's size.
{"title":"Interplay between Foraging Choices and Population Growth Dynamics","authors":"Jimmy Calvo-Monge, Baltazar Espinoza, Fabio Sanchez","doi":"arxiv-2408.02552","DOIUrl":"https://doi.org/arxiv-2408.02552","url":null,"abstract":"In this study, we couple a population dynamics model with a model for optimal\u0000foraging to study the interdependence between individual-level cost-benefits\u0000and population-scale dynamics. Specifically, we study the logistic growth\u0000model, which provides insights into population dynamics under resource\u0000limitations. Unlike exponential growth, the logistic model incorporates the\u0000concept of carrying capacity, thus offering a more realistic depiction of\u0000biological populations as they near environmental limits. We aim to study the\u0000impact of individual-level incentives driving behavioral responses in a dynamic\u0000environment. Specifically, explore the coupled dynamics between population\u0000density and individuals' foraging times. Our results yield insights into the\u0000effects of population size on individuals' optimal foraging efforts, which\u0000impacts the population's size.","PeriodicalId":501044,"journal":{"name":"arXiv - QuanBio - Populations and Evolution","volume":"39 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141945649","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Andrea Iglesias Ramas, Samuele Pio Lipani, Rosalind J. Allen
Population genetics lies at the heart of evolutionary theory. This topic forms part of many biological science curricula but is rarely taught to physics students. Since physicists are becoming increasingly interested in biological evolution, we aim to provide a brief introduction to population genetics, written for physicists. We start with two background chapters: chapter 1 provides a brief historical introduction to the topic, while chapter 2 provides some essential biological background. We begin our main content with chapter 3 which discusses the key concepts behind Darwinian natural selection and Mendelian inheritance. Chapter 4 covers the basics of how variation is maintained in populations, while chapter 5 discusses mutation and selection. In chapter 6 we discuss stochastic effects in population genetics using the Wright-Fisher model as our example, and finally we offer concluding thoughts and references to excellent textbooks in chapter 7.
{"title":"Population genetics: an introduction for physicists","authors":"Andrea Iglesias Ramas, Samuele Pio Lipani, Rosalind J. Allen","doi":"arxiv-2408.02650","DOIUrl":"https://doi.org/arxiv-2408.02650","url":null,"abstract":"Population genetics lies at the heart of evolutionary theory. This topic\u0000forms part of many biological science curricula but is rarely taught to physics\u0000students. Since physicists are becoming increasingly interested in biological\u0000evolution, we aim to provide a brief introduction to population genetics,\u0000written for physicists. We start with two background chapters: chapter 1\u0000provides a brief historical introduction to the topic, while chapter 2 provides\u0000some essential biological background. We begin our main content with chapter 3\u0000which discusses the key concepts behind Darwinian natural selection and\u0000Mendelian inheritance. Chapter 4 covers the basics of how variation is\u0000maintained in populations, while chapter 5 discusses mutation and selection. In\u0000chapter 6 we discuss stochastic effects in population genetics using the\u0000Wright-Fisher model as our example, and finally we offer concluding thoughts\u0000and references to excellent textbooks in chapter 7.","PeriodicalId":501044,"journal":{"name":"arXiv - QuanBio - Populations and Evolution","volume":"25 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141945589","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Kevin Godin-Dubois, Sylvain Cussat-Blanc, Yves Duthen
To tackle the challenge of producing tractable phylogenetic trees in contexts where complete information is available, we introduce APOGeT: an online, pluggable, clustering algorithm for a stream of genomes. It is designed to run alongside a given experimental protocol with minimal interactions and integration effort. From the genomic flow, it extracts and displays species' boundaries and dynamics. Starting with a light introduction to the core idea of this classification we discuss the requirements on the genomes and the underlying processes of building species' identities and managing hybridism. Though stemming from an ALife experimental setting, APOGeT ought not be limited to this field but could be used by (and benefit from) a broader audience.
{"title":"APOGeT: Automated Phylogeny over Geological Time-scales","authors":"Kevin Godin-Dubois, Sylvain Cussat-Blanc, Yves Duthen","doi":"arxiv-2407.21412","DOIUrl":"https://doi.org/arxiv-2407.21412","url":null,"abstract":"To tackle the challenge of producing tractable phylogenetic trees in contexts\u0000where complete information is available, we introduce APOGeT: an online,\u0000pluggable, clustering algorithm for a stream of genomes. It is designed to run\u0000alongside a given experimental protocol with minimal interactions and\u0000integration effort. From the genomic flow, it extracts and displays species'\u0000boundaries and dynamics. Starting with a light introduction to the core idea of\u0000this classification we discuss the requirements on the genomes and the\u0000underlying processes of building species' identities and managing hybridism.\u0000Though stemming from an ALife experimental setting, APOGeT ought not be limited\u0000to this field but could be used by (and benefit from) a broader audience.","PeriodicalId":501044,"journal":{"name":"arXiv - QuanBio - Populations and Evolution","volume":"13 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141872716","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mridul Khurana, Arka Daw, M. Maruf, Josef C. Uyeda, Wasila Dahdul, Caleb Charpentier, Yasin Bakış, Henry L. Bart Jr., Paula M. Mabee, Hilmar Lapp, James P. Balhoff, Wei-Lun Chao, Charles Stewart, Tanya Berger-Wolf, Anuj Karpatne
A central problem in biology is to understand how organisms evolve and adapt to their environment by acquiring variations in the observable characteristics or traits of species across the tree of life. With the growing availability of large-scale image repositories in biology and recent advances in generative modeling, there is an opportunity to accelerate the discovery of evolutionary traits automatically from images. Toward this goal, we introduce Phylo-Diffusion, a novel framework for conditioning diffusion models with phylogenetic knowledge represented in the form of HIERarchical Embeddings (HIER-Embeds). We also propose two new experiments for perturbing the embedding space of Phylo-Diffusion: trait masking and trait swapping, inspired by counterpart experiments of gene knockout and gene editing/swapping. Our work represents a novel methodological advance in generative modeling to structure the embedding space of diffusion models using tree-based knowledge. Our work also opens a new chapter of research in evolutionary biology by using generative models to visualize evolutionary changes directly from images. We empirically demonstrate the usefulness of Phylo-Diffusion in capturing meaningful trait variations for fishes and birds, revealing novel insights about the biological mechanisms of their evolution.
{"title":"Hierarchical Conditioning of Diffusion Models Using Tree-of-Life for Studying Species Evolution","authors":"Mridul Khurana, Arka Daw, M. Maruf, Josef C. Uyeda, Wasila Dahdul, Caleb Charpentier, Yasin Bakış, Henry L. Bart Jr., Paula M. Mabee, Hilmar Lapp, James P. Balhoff, Wei-Lun Chao, Charles Stewart, Tanya Berger-Wolf, Anuj Karpatne","doi":"arxiv-2408.00160","DOIUrl":"https://doi.org/arxiv-2408.00160","url":null,"abstract":"A central problem in biology is to understand how organisms evolve and adapt\u0000to their environment by acquiring variations in the observable characteristics\u0000or traits of species across the tree of life. With the growing availability of\u0000large-scale image repositories in biology and recent advances in generative\u0000modeling, there is an opportunity to accelerate the discovery of evolutionary\u0000traits automatically from images. Toward this goal, we introduce\u0000Phylo-Diffusion, a novel framework for conditioning diffusion models with\u0000phylogenetic knowledge represented in the form of HIERarchical Embeddings\u0000(HIER-Embeds). We also propose two new experiments for perturbing the embedding\u0000space of Phylo-Diffusion: trait masking and trait swapping, inspired by\u0000counterpart experiments of gene knockout and gene editing/swapping. Our work\u0000represents a novel methodological advance in generative modeling to structure\u0000the embedding space of diffusion models using tree-based knowledge. Our work\u0000also opens a new chapter of research in evolutionary biology by using\u0000generative models to visualize evolutionary changes directly from images. We\u0000empirically demonstrate the usefulness of Phylo-Diffusion in capturing\u0000meaningful trait variations for fishes and birds, revealing novel insights\u0000about the biological mechanisms of their evolution.","PeriodicalId":501044,"journal":{"name":"arXiv - QuanBio - Populations and Evolution","volume":"185 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141881277","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
This study investigates the spatial integration of agent-based models (ABMs) and compartmental models in infectious disease modeling, presenting a novel hybrid approach and studying its implications. ABMs, characterized by individual agent interactions and decision-making, offer detailed insights but are computationally intensive for large populations. Compartmental models, based on differential equations, provide population-level dynamics but lack granular detail. Our hybrid model aims to balance the granularity of ABMs with the computational efficiency of compartmental models, offering a more nuanced understanding of disease spread in diverse scenarios, including large populations. We developed a custom ABM and a compartmental model, analyzing their infectious disease dynamics separately before integrating them into a hybrid model. This integration involved spatial coupling of discrete and continuous populations and evaluating the consistency of disease dynamics at the macro scale. Our key objectives were to assess the effect of model hybridization on resulting infection dynamics, and to quantify computational cost savings of the hybrid approach over the ABM. We show that the hybrid approach can significantly reduce computational costs, but is sensitive to between-model differences, highlighting that model equivalence is a crucial component of hybrid modeling approaches. The code is available at http://github.com/iebos/hybrid_model1.
{"title":"Integrating Agent-Based and Compartmental Models for Infectious Disease Modeling: A Novel Hybrid Approach","authors":"Inan Bostanci, Tim Conrad","doi":"arxiv-2407.20993","DOIUrl":"https://doi.org/arxiv-2407.20993","url":null,"abstract":"This study investigates the spatial integration of agent-based models (ABMs)\u0000and compartmental models in infectious disease modeling, presenting a novel\u0000hybrid approach and studying its implications. ABMs, characterized by\u0000individual agent interactions and decision-making, offer detailed insights but\u0000are computationally intensive for large populations. Compartmental models,\u0000based on differential equations, provide population-level dynamics but lack\u0000granular detail. Our hybrid model aims to balance the granularity of ABMs with\u0000the computational efficiency of compartmental models, offering a more nuanced\u0000understanding of disease spread in diverse scenarios, including large\u0000populations. We developed a custom ABM and a compartmental model, analyzing\u0000their infectious disease dynamics separately before integrating them into a\u0000hybrid model. This integration involved spatial coupling of discrete and\u0000continuous populations and evaluating the consistency of disease dynamics at\u0000the macro scale. Our key objectives were to assess the effect of model\u0000hybridization on resulting infection dynamics, and to quantify computational\u0000cost savings of the hybrid approach over the ABM. We show that the hybrid\u0000approach can significantly reduce computational costs, but is sensitive to\u0000between-model differences, highlighting that model equivalence is a crucial\u0000component of hybrid modeling approaches. The code is available at\u0000http://github.com/iebos/hybrid_model1.","PeriodicalId":501044,"journal":{"name":"arXiv - QuanBio - Populations and Evolution","volume":"31 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141872717","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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