Tootfinder

Day 5: Robin Wall Kimmerer
I'm taking these liberty of changing my hashtag and expanding the intent of this list to include all non-men, although Kimerer is a woman so I'll get to more gender diversity later... I've also started planning this out more and realized that I may continue a bit beyond 20...
In any case, Robin Wall Kimmerer is an Indigenous academic biologist and excellent non-fiction author whose work touches on Potawotomi philosophy, colonialism (including in academic spaces), and ideas for a better future. Anyone interested in ecology, conservation, or decolonization in North America will probably be impressed by her work and the rich connections she weaves between academic ecology and Indigenous knowledge offer a critical opportunity to expand your understanding of the world if like me you were raised deeply enmeshed in "Western" scientific tradition. I suppose a little background in skepticism helped prepare me to respect her writing, but I don't think that's essential.
I've only read "Braiding Sweetgrass," but "Gathering Moss" and her more recent "The Serviceberry" are high on my to-read list, despite my predilection for fiction. Kimmerer incorporates a backbone of fascinating anecdotes into "Braiding Sweetgrass" that makes it surprisingly easy reading for a work that's philosophical at its core. She also pulls off an impressive braided organization to the whole thing, weaving together disparate knowledges in a way that lets you see both their contradictions and their connections.
The one criticism I've seen of her work is that it's not sufficiently connected to other Indigenous philosophers & writers, and that it's perhaps too comfortable of a read for colonizers, and that seems valid to me, even though (perhaps because I am a colonizer) I still find her book important.
An excellent author in any case, and one doing concrete ideological work towards a better world.
#20AuthorsNoMen

Flexible metadata harvesting for ecology using large language models
Zehao Lu, Thijs L van der Plas, Parinaz Rashidi, W Daniel Kissling, Ioannis N Athanasiadis
https://arxiv.org/abs/2508.20115

Flexible metadata harvesting for ecology using large language models
Large, open datasets can accelerate ecological research, particularly by enabling researchers to develop new insights by reusing datasets from multiple sources. However, to find the most suitable datasets to combine and integrate, researchers must navigate diverse ecological and environmental data provider platforms with varying metadata availability and standards. To overcome this obstacle, we have developed a large language model (LLM)-based metadata harvester that flexibly extracts metadata …

Check out our just-published story by Chris Freimuth '25 M.Div. on the video interview series launched by the Yale Forum on Religion and Ecology! The interview series showcases the stories and pathways of alums working in religion and ecology. https://di…

Self-organized biodiversity and species abundance distribution patterns in ecosystems with higher-order interactions
Ju Kang, Yiyuan Niu, Yuanzhi Li, Chengjin Chu
https://arxiv.org/abs/2507.22287

Self-organized biodiversity and species abundance distribution patterns in ecosystems with higher-order interactions
Explaining the emergence of self-organized biodiversity and species abundance distribution patterns remians a fundamental challenge in ecology. While classical frameworks, such as neutral theory and models based on pairwise species interactions, have provided valuable insights, they often neglect higher-order interactions (HOIs), whose role in stabilizing ecological communities is increasingly recognized. Here, we extend the Generalized Lotka-Volterra framework to incorporate HOIs and demonstra…

Crosslisted article(s) found for cs.DB. https://arxiv.org/list/cs.DB/new
[1/1]:
- Flexible metadata harvesting for ecology using large language models
Zehao Lu, Thijs L van der Plas, Parinaz Rashidi, W Daniel Kissling, Ioannis N Athanasiadis

Human disturbances drive significant soil carbon loss in hyper-arid deserts, study reveals #desert

Human disturbances drive significant soil carbon loss in hyper-arid deserts, study reveals
A recent study led by Prof. Zeng Fanjiang from the Xinjiang Institute of Ecology and Geography of the Chinese Academy of Sciences has revealed concerning trends in soil organic carbon (SOC) loss due to prolonged human disturbance in hyper-arid desert ecosystems.

🇺🇦 #NowPlaying on #BBC6Music's #CerysMatthews
Marvin Gaye:
🎵 Mercy Mercy Me (The Ecology)
#MarvinGaye
https://rarerecordings.bandcamp.com/track/marvin-gaye-mercy-mercy-me
https://open.spotify.com/track/07sIFn6Weq7dfrBs6oMiRa

Chris Sawyer '75 M.Div. is a conservation leader and Chair Emeritus of the YDS Dean’s Advisory Council. In this episode of "Reflections on Religion and Ecology: Yale Alumni Speak from the Field" Chris joins host Mary Evelyn Tucker to reflect on a lifetime of faith-driven leadership in #landpreservation and community renewal.

Special Panel on Esotericism, Occultism, Magic, and Ecology at Southwest Popular/American Culture Association, Feb. 25-28, 2026, Albuquerque, New Mexico
https://ift.tt/9dRuT7Z
updated: Monday, October 27, 2025 - 10:52amfull name / name of organization: Southwest…
via Input 4 RELCFP

Generalized Stochastic Resilience for Early Warning Signals Based on Koopman Operator
Yuta Miyauchi, Masahiro Ikeda, Yoshinobu Kawahara
https://arxiv.org/abs/2508.19655 https://…

Generalized Stochastic Resilience for Early Warning Signals Based on Koopman Operator
Developing methods for detecting tipping phenomena at an early stage is an important problem in various fields such as ecology, medicine, and economics. A tipping phenomenon is characterized by a rapid transition resulting from the accumulation of small parameter changes and is known to be related to bifurcations of dynamical systems. However, few studies have examined how nonlinear properties near bifurcation points affect early warning signal (EWS) performance. In this study, we apply the Koo…

Population genetics in complex ecological communities
Shing Yan Li, Zhijie Feng, Akshit Goyal, Pankaj Mehta
https://arxiv.org/abs/2509.23977 https://arxiv.…

Population genetics in complex ecological communities
Ecological interactions can dramatically alter evolutionary outcomes in complex communities. Yet, the classic theoretical results of population genetics (e.g., Kimura's fixation formula) largely ignore ecological effects. Here, we address this shortcoming by using dynamical mean-field theory to integrate ecology into classical population genetics models. We show that ecological interactions between parents and mutants result in frequency-dependent selection and can be characterized by a single …

'Attacking the science': WA Ecology director slams Trump's climate policies • Washington State Standard
https://washingtonstatestandard.com/2025/10/04/attacking-the-science-wa-ecology-director-slams-trumps-climate-policies/

"Greenwashing at #Elsevier: A political ecology of corporate publishing"
https://doi.org/10.3998/jep.7482

Saccade crossing avoidance as a visual search strategy
Alex Szorkovszky, Rujeena Mathema, Pedro Lencastre, Pedro Lind, Anis Yazidi
https://arxiv.org/abs/2508.18404 https://

Saccade crossing avoidance as a visual search strategy
Although visual search appears largely random, several oculomotor biases exist such that the likelihoods of saccade directions and lengths depend on the previous scan path. Compared to the most recent fixations, the impact of the longer path history is more difficult to quantify. Using the step-selection framework commonly used in movement ecology, and analyzing data from 45-second viewings of "Where's Waldo"?, we report a new memory-dependent effect that also varies significantly between indiv…

Vendi Information Gain for Active Learning and its Application to Ecology
Quan Nguyen, Adji Bousso Dieng
https://arxiv.org/abs/2509.10390 https://arxiv.org…

Vendi Information Gain for Active Learning and its Application to Ecology
While monitoring biodiversity through camera traps has become an important endeavor for ecological research, identifying species in the captured image data remains a major bottleneck due to limited labeling resources. Active learning -- a machine learning paradigm that selects the most informative data to label and train a predictive model -- offers a promising solution, but typically focuses on uncertainty in the individual predictions without considering uncertainty across the entire dataset.…

MetaQuestion: A web application for expert knowledge elicitation addressing plant health and applied plant ecology
Robert Fontan, Christopher M. Perez, Ashish Adhikari, Romaric A. Mouafo-Tchinda, Aaron I. Plex Sul\'a, Jacobo Robledo, Berea A. Etherton, Manoj Choudhary, Muhammad Aqeel Sarwar, Zunaira Afzal Naveed, Karen A. Garrett
https://

MetaQuestion: A web application for expert knowledge elicitation addressing plant health and applied plant ecology
1. Expert knowledge elicitation provides information to characterize ecological systems and management options. Linking expert knowledge elicitation with a curated question catalog supports a community of practice for ongoing improvement of question quality. 2. The MetaQuestion web app we introduce here draws on the PlantQuest catalog of questions addressing applied plant ecology and management options, making the catalog available in a flexible form for organizers of expert knowledge elicita…

In monochrome you can't see the iridescence of the plastic films in the Polyform sculpture in front of the Human Ecology building it making it look like a glass cube with a stainless steel foam inside
#photo #photography

Identifiability of linear stochastic state-space models with application to ecology
Frederic Barraquand, Julien Gibaud
https://arxiv.org/abs/2508.08714 https://

Identifiability of linear stochastic state-space models with application to ecology
State-space models are dynamical systems defined by a latent and an observed process. In ecology, stochastic state-space models in discrete time are most often used to describe the imperfectly observed dynamics of population sizes or animal movement. However, several studies have observed identifiability issues when state-space models are fitted to simulated or real data, and it is not currently clear whether those are due to data limitations or more fundamental model non-identifiability. To in…

Video interview with Julia Johnson '18 M.Div. on faith, farming, and the sacredness of food systems. Part of the new series from the Yale Forum on Religion and Ecology on alums pursuing callings at the intersection of spiritual traditions and environmental stewardship. #ecotheology

The Final Frontier: Race, Ecology and Colonialism in Space Opera https://call-for-papers.sas.upenn.edu/cfp/2025/09/13/the-final-frontier-race-ecology-and-colonialism-in-space-opera

About three-quarters of fungi are “dark taxa” – species known only by their DNA sequence, as physical specimens have not been found.
https://www.theguardian.com/environment/2025/aug/15/biology-mycorrhizal-fungi-map-restoring-world-fore…

Bridging Farm Economics and Landscape Ecology for Global Sustainability through Hierarchical and Bayesian Optimization
Kevin Bradley Dsouza, Graham Alexander Watt, Yuri Leonenko, Juan Moreno-Cruz
https://arxiv.org/abs/2508.06386

Bridging Farm Economics and Landscape Ecology for Global Sustainability through Hierarchical and Bayesian Optimization
Agricultural landscapes face the dual challenge of sustaining food production while reversing biodiversity loss. Agri-environmental policies often fall short of delivering ecological functions such as landscape connectivity, in part due to a persistent disconnect between farm-level economic decisions and landscape-scale spatial planning. We introduce a novel hierarchical optimization framework that bridges this gap. First, an Ecological Intensification (EI) model determines the economically opt…

One of my dreams by now was to build an ecology on the moon and make it a comfortable place to live. "Homestuck" seemed to pale into insignificance alongside such thoughts.

The Living Library of Trees: Mapping Knowledge Ecology in the Arnold Arboretum
Johan Malmstedt, Giacomo Nanni, Dario Rodighiero
https://arxiv.org/abs/2509.00114 https://

The Living Library of Trees: Mapping Knowledge Ecology in the Arnold Arboretum
As biodiversity loss and climate change accelerate, botanical gardens serve as vital infrastructures for research, education, and conservation. This project focuses on the Arnold Arboretum of Harvard University, a 281-acre living museum founded in 1872 in Boston. Drawing on more than a century of curatorial data, the research combines historical analysis with computational methods to visualize the biographies of plants and people. The resulting platform reveals patterns of care and scientific o…

Diffusion-driven pattern formation in an opinion dynamical network model
Tim Mauch, Thilo Gross
https://arxiv.org/abs/2508.15377 https://arxiv.org/pdf/2508…

Diffusion-driven pattern formation in an opinion dynamical network model
The spatial organization of individuals and their interactions in communities are important factors known to preserve diversity in many complex systems. Inspired by metapopulation models from ecology, we study opinion formation using a network-based approach in which nodes represent communities of interacting agents holding one of two competing opinions, and links represent avenues of migration. Agents adapt to the dominant opinion within a community or migrate toward communities with similar v…

Spatiotemporal Determinants of Vector-Borne Disease Outbreaks
Bibandhan Poudyal, Gourab Ghoshal
https://arxiv.org/abs/2508.20318 https://arxiv.org/pdf/2508…

Spatiotemporal Determinants of Vector-Borne Disease Outbreaks
Vector-borne diseases arise from the coupled dynamics of human mobility and mosquito ecology, producing outbreaks shaped by both spatial distributions and temporal patterns of movement. Here we develop a coarse-grained hub--leaf reduction that isolates the universal principles governing epidemic vulnerability in interconnected populations. By deriving and analyzing the epidemic vulnerability equation, we show how human and vector population ratios, together with mobility parameters that regulat…

When using an old damaged shoulder bag stops being a matter of ecology, and starts being a matter of a "how much more will it manage" challenge.

Reaction enhancement by flux-limited chemotaxis
Jing An, Alexander Kiselev, Yao Yao
https://arxiv.org/abs/2508.13704 https://arxiv.org/pdf/2508.13704

Reaction enhancement by flux-limited chemotaxis
Chemotaxis plays a crucial role in a variety of processes in biology and ecology. Quite often it acts to improve efficiency of biological reactions; one example is the immune system signalling, where infected tissues release chemokines attracting monocytes to fight invading bacteria. Another example is reproduction, where eggs release pheromones that attract sperm. In this paper, we analyze a system of two reacting densities, one of which is chemotactic on another. Since the speed of any biolog…

“On labor and AI”
https://buttondown.com/practicaltips/archive/on-labor-and-ai/
“[M]aybe large numbers of us should come to a common conclusion that these bubble-boy charlatans shouldn’t just get to decide that the world’s economy (not to mention its ecology) sh…

On labor and AI
Happy Labor/Labour Day/bank holiday to you. Seems like a good day to talk about the elephant in the room again. The predominant storyline around labor, of...

Complex dynamic transformations and strange attractors in a tri-trophic predator-prey system
Ju Kang, Yiyuan Niu, Xin Wang
https://arxiv.org/abs/2508.18038 https://

Complex dynamic transformations and strange attractors in a tri-trophic predator-prey system
Understanding predator-prey interactions is a fundamental issue in ecology, and the complex dynamics they induce are highly significant for maintaining community stability and self-organising biodiversity. Here, we investigate complex dynamical behaviors and bifurcation structures in a tri-trophic food web comprising a basal prey, an intermediate predator, and an omnivorous top predator. By combining Jacobian analysis with Hopf bifurcation theory, we derive explicit stability conditions and ide…

Weekend #Plankton Factoid 🦠🦐
Plankton have #parasites, just like any other organism, but in some cases, this leads to improved feeding conditions. #Daphnia zooplankton must often feed on freshwater cy…

A Scalable Formula for the Moments of a Family of Self-Normalized Statistics
Haolin Zou, Heyuan Yao, Victor de la Pe\~na
https://arxiv.org/abs/2509.14428 https://

A Scalable Formula for the Moments of a Family of Self-Normalized Statistics
Following the student t-statistic, normalization has been a widely used method in statistic and other disciplines including economics, ecology and machine learning. We focus on statistics taking the form of a ratio over (some power of) the sample mean, the probabilistic features of which remain unknown. We develop a unified formula for the moments of these self-normalized statistics with non-negative observations, yielding closed-form expressions for several important cases. Moreover, the compl…

Applications of the Vendi score in genomic epidemiology
Bjarke Frost Nielsen, Amey P. Pasarkar, Qiqi Yang, Bryan T. Grenfell, Adji Bousso Dieng
https://arxiv.org/abs/2509.22520 …

Applications of the Vendi score in genomic epidemiology
The Vendi score (VS), a diversity metric recently conceived in the context of machine learning, with applications in a wide range of fields, has a few distinct advantages over the metrics commonly used in ecology. It is classification-independent, incorporates abundance information, and has a tunable sensitivity to rare/abundant types. Using rich COVID-19 sequence data as a paradigm, we develop methods for applying the VS to time-resolved sequence data. We show how the VS allows for characteriz…

Adding structure to generalized additive models, with applications in ecology
David L Miller, Ken Newman, Thomas Cornulier
https://arxiv.org/abs/2508.07915 https://

Adding structure to generalized additive models, with applications in ecology
Generalized additive models (GAMs) that connect a set of scalar covariates that map 1-1 to a response variable are commonly employed in ecological and other scientific disciplines. However, covariates are often inherently non-scalar, taking on multiple values for each observation of the response. They can sometimes have a temporal structure, e.g., a time series of temperature and precipitation measurements, or a spatial structure, e.g., multiple soil pH measurements made at nearby locations. Wh…

Fascinating article, from the island of Seil:
https://www.theguardian.com/environment/2025/aug/15/biology-mycorrhizal-fungi-map-restoring-world-forests

kabr-tools: Automated Framework for Multi-Species Behavioral Monitoring
Jenna Kline, Maksim Kholiavchenko, Samuel Stevens, Nina van Tiel, Alison Zhong, Namrata Banerji, Alec Sheets, Sowbaranika Balasubramaniam, Isla Duporge, Matthew Thompson, Elizabeth Campolongo, Jackson Miliko, Neil Rosser, Tanya Berger-Wolf, Charles V. Stewart, Daniel I. Rubenstein
https://

kabr-tools: Automated Framework for Multi-Species Behavioral Monitoring
A comprehensive understanding of animal behavior ecology depends on scalable approaches to quantify and interpret complex, multidimensional behavioral patterns. Traditional field observations are often limited in scope, time-consuming, and labor-intensive, hindering the assessment of behavioral responses across landscapes. To address this, we present kabr-tools (Kenyan Animal Behavior Recognition Tools), an open-source package for automated multi-species behavioral monitoring. This framework in…

Bio-Inspired Robotic Houbara: From Development to Field Deployment for Behavioral Studies
Lyes Saad Saoud, Irfan Hussain
https://arxiv.org/abs/2510.04692 https://

Bio-Inspired Robotic Houbara: From Development to Field Deployment for Behavioral Studies
Biomimetic intelligence and robotics are transforming field ecology by enabling lifelike robotic surrogates that interact naturally with animals under real world conditions. Studying avian behavior in the wild remains challenging due to the need for highly realistic morphology, durable outdoor operation, and intelligent perception that can adapt to uncontrolled environments. We present a next generation bio inspired robotic platform that replicates the morphology and visual appearance of the fe…

Replaced article(s) found for q-bio.QM. https://arxiv.org/list/q-bio.QM/new
[1/1]:
- Adding structure to generalized additive models, with applications in ecology
David L Miller, Ken Newman, Thomas Cornulier

Data Driven Discovery of Emergent Dynamics in Reaction Diffusion Systems from Sparse and Noisy Observations
Saumitra Dwivedi, Ricardo da Silva Torres, Ibrahim A. Hameed, Gunnar Tufte, Anniken Susanne T. Karlsen
https://arxiv.org/abs/2509.09278

Data Driven Discovery of Emergent Dynamics in Reaction Diffusion Systems from Sparse and Noisy Observations
Data-driven discovery of emergent dynamics is gaining popularity, particularly in the context of reaction-diffusion systems. These systems are widely studied across various fields, including neuroscience, ecology, epidemiology, and several other subject areas that deal with emergent dynamics. A current challenge in the discovery process relates to system identification when there is no prior knowledge of the underlying physics. We attempt to address this challenge by learning Soft Artificial Li…

The Lotka-Volterra Predator-Prey Model with Disturbance
Arhonefe Joseph Ogethakpo, Sunday Amaju Ojobor
https://arxiv.org/abs/2510.09628 https://arxiv.org/p…

The Lotka-Volterra Predator-Prey Model with Disturbance
The forces which drive growth, development, survival and change within an ecological system involving a predator and prey specie are not easily addressed in the field. To better understand the dynamics in the system, ecologists have turned to mathematical models. The predator-prey dynamics of rat and cat population in a given ecology is studied. The mathematical model proposed by Alfred J. Lotka and Vito Volterra called the Lotka-Volterra model for studying predator-prey dynamics is utilized. A…

A Single Index Approach to Integrated Species Distribution Modeling for Fisheries Abundance Data
Quan Vu, Francis K. C. Hui, A. H. Welsh, Samuel Muller, Eva Cantoni, Christopher R. Haak
https://arxiv.org/abs/2509.15379

A Single Index Approach to Integrated Species Distribution Modeling for Fisheries Abundance Data
In fisheries ecology, species abundance data are often collected by multiple surveys, each with unique characteristics. This article focuses on Atlantic sea scallop abundance data along the northeast coast of the United States, collected from two bottom trawl surveys which cover a larger spatial domain but have low catch efficiency, and a dredge survey which is more efficient but limited to domains where the species are believed to be present. To model such data, integrated species distribution…

In this episode of "Reflections on Religion and Ecology: Yale Alumni Speak from the Field," Stephen Blackmer '12 M.A.R.—forest conservationist, Episcopal priest (now former), and founder of Church of the Woods—joins host Tali Anisfeld for a deeply contemplative conversation on trees, prophecy, and spiritual communion with the Earth.
View the interview here:

🇺🇦 #NowPlaying on #BBC6Music's #TheHueyShow
Marvin Gaye:
🎵 Mercy Mercy Me (The Ecology)
#MarvinGaye
https://rarerecordings.bandcamp.com/track/marvin-gaye-mercy-mercy-me
https://open.spotify.com/track/3IDc87lrpEHWFBASmgTgFV

Stabilization of Age-Structured Competing Populations
Carina Veil, Miroslav Krsti\'c, Patrick McNamee, Oliver Sawodny
https://arxiv.org/abs/2507.23013 https://

Stabilization of Age-Structured Competing Populations
Age-structured models represent the dynamic behaviors of populations over time and result in integro-partial differential equations (IPDEs). Such processes arise in biotechnology, economics, demography, and other domains. Coupled age-structured IPDE population dynamics with two or more species occur in epidemiology and ecology, but have received little attention thus far. This work considers an exponentially unstable model of two competing predator populations, formally referred to in the liter…

Book Review: "Doughnut Economics"
#economics

Stabilizing by steering: Enhancing bacterial motility by non-uniform diffusiophoresis
Viet Sang Doan, Ali Nikkhah, Sangwoo Shin
https://arxiv.org/abs/2509.25770 https://

Stabilizing by steering: Enhancing bacterial motility by non-uniform diffusiophoresis
Bacteria are often required to navigate across confined spaces to reach desired destinations in biological and environmental systems, allowing critical functions in host-microbe symbiosis, infection, drug delivery, soil ecology, and soil bioremediation. While the canonical run-and-tumble motility is effective in finding targets under confinement, it may not represent the most ideal strategy due to the continuous monitoring of environmental cues and stochastic recorrection of their paths. Here, …

Generalized Taylor's Law for Dependent and Heterogeneous Heavy-Tailed Data
Pok Him Cheng, Joel E. Cohen, Hok Kan Ling, Sheung Chi Phillip Yam
https://arxiv.org/abs/2510.09562

Generalized Taylor's Law for Dependent and Heterogeneous Heavy-Tailed Data
Taylor's law, also known as fluctuation scaling in physics and the power-law variance function in statistics, is an empirical pattern widely observed across fields including ecology, physics, finance, and epidemiology. It states that the variance of a sample scales as a power function of the mean of the sample. We study generalizations of Taylor's law in the context of heavy-tailed distributions with infinite mean and variance. We establish the probabilistic limit and analyze the associated con…

Reproducibility and scientific interpretation in the age of AI: consilience in biological systematics, ecology, and molecular biology
Charles Morphy D. Santos, Luciana Campos Paulino, Michaella P. Andrade, Gabriel Tognella-Poccia, Jo\~ao Paulo Gois
https://arxiv.org/abs/2507.22942

Reproducibility and scientific interpretation in the age of AI: consilience in biological systematics, ecology, and molecular biology
Achieving complete reproducibility in science, particularly in research fields such as biodiversity, is challenging due to analytical choices, bias and interpretation. Here, we examine examples of reproducibility in biological systematics, ecology, and molecular biology. To mitigate the impact of interpretation and analytical choices, Artificial Intelligence (AI) has provided potential tools. In the present work, while emphasizing the need for methodological rigor and transparency, we acknowled…

The Final Frontier: Race, Ecology and Colonialism in Space Opera
https://ift.tt/7vMD8Zq
updated: Saturday, September 13, 2025 - 7:38pmfull name / name of organization: Mikail Boz and Cenk…
via Input 4 RELCFP

Computational approaches for virus host prediction: A review of methods and applications
Jiayu Shang, Cheng Peng, Jiaojiao Guan, Dehan Cai, Donglin Wang, Yanni Sun
https://arxiv.org/abs/2509.00349

Computational approaches for virus host prediction: A review of methods and applications
Accurate prediction of virus-host interactions is critical for understanding viral ecology and developing applications like phage therapy. However, the growing number of computational tools has created a complex landscape, making direct performance comparison challenging due to inconsistent benchmarks and varying usability. Here, we provide a systematic review and a rigorous benchmark of 27 virus-host prediction tools. We formulate the host prediction task into two primary frameworks, link pred…

Modelling phenology using ordered categorical generalized additive models
David L Miller
https://arxiv.org/abs/2508.07789 https://arxiv.org/pdf/2508.07789

Modelling phenology using ordered categorical generalized additive models
One form of data collected in ecology is phenological, describing the timing of life stages. It can be tempting to analyze such data using a continuous distribution or to model individual transitions via probit/logit models. Such simplifications can lead to incorrect inference in various ways, all of which stem from ignoring the natural structure of the data. This paper presents a flexible approach to modelling ordered categorical data using the popular R package `mgcv`. An example analysis of …

Replaced article(s) found for cs.DL. https://arxiv.org/list/cs.DL/new
[1/1]:
- Flexible metadata harvesting for ecology using large language models
Zehao Lu, Thijs L van der Plas, Parinaz Rashidi, W Daniel Kissling, Ioannis N Athanasiadis

Friend or Foe
Oleksandr Cherendichenko, Josephine Solowiej-Wedderburn, Laura M. Carroll, Eric Libby
https://arxiv.org/abs/2509.00123 https://arxiv.org/pdf/…

Friend or Foe
A fundamental challenge in microbial ecology is determining whether bacteria compete or cooperate in different environmental conditions. With recent advances in genome-scale metabolic models, we are now capable of simulating interactions between thousands of pairs of bacteria in thousands of different environmental settings at a scale infeasible experimentally. These approaches can generate tremendous amounts of data that can be exploited by state-of-the-art machine learning algorithms to uncov…

Cooperation in public goods game on regular lattices with agents changing interaction groups
Jaros{\l}aw Adam Miszczak
https://arxiv.org/abs/2510.03772 https://

Cooperation in public goods game on regular lattices with agents changing interaction groups
The emergence of cooperation in the groups of interacting agents is one of the most fascinating phenomena observed in many complex systems studied in social science and ecology, even in the situations where one would expect the agent to use a free-rider policy. This is especially surprising in the situation where no external mechanisms based on reputation or punishment are present. One of the possible explanations of this effect is the inhomogeneity of the various aspects of interactions, which…

Soil Texture Prediction with Bayesian Generalized Additive Models for Spatial Compositional Data
Joaqu\'in Mart\'inez-Minaya, Lore Zumeta-Olaskoaga, Dae-Jin Lee
https://arxiv.org/abs/2508.07708

Soil Texture Prediction with Bayesian Generalized Additive Models for Spatial Compositional Data
Compositional data (CoDa) plays an important role in many fields such as ecology, geology, or biology. The most widely used modeling approaches are based on the Dirichlet and the logistic-normal formulation under Aitchison geometry. Recent developments in the mathematical field on the simplex geometry allow to express the regression model in terms of coordinates and estimate its coefficients. Once the model is projected in the real space, we can employ a multivariate Gaussian regression to deal…

Tennyson 2026: Ecology, Landscape, Environment
https://ift.tt/hbTqv8D
updated: Monday, August 11, 2025 - 7:48amfull name / name of organization: Tennyson Society and…
via Input 4 RELCFP http…

🇺🇦 Auf radioeins läuft...
The Strokes feat. Eddie Vedder & Josh Homme:
🎵 Mercy Mercy Me (The Ecology)
#NowPlaying #TheStrokes #EddieVedder #JoshHomme
https://open.spotify.com/track/7BCQ4QUzY9F4wChjy1D40p

Density estimation for compositional data using nonparametric mixtures
Jiajin Xie, Yong Wang, Eduardo Garc\'ia-Portugu\'es
https://arxiv.org/abs/2510.07608 https://

Density estimation for compositional data using nonparametric mixtures
Compositional data, representing proportions constrained to the simplex, arise in diverse fields such as geosciences, ecology, genomics, and microbiome research. Existing nonparametric density estimation methods often rely on transformations, which may induce substantial bias near the simplex boundary. We propose a nonparametric mixture-based framework for density estimation on compositions. Nonparametric Dirichlet mixtures are employed to naturally accommodate boundary values, thereby avoiding…

Likelihood-based inference for the Gompertz model with Poisson errors
Paolo Onorati, Sofia Ruiz-Suarez, Radu Craiu
https://arxiv.org/abs/2510.06787 https://

Likelihood-based inference for the Gompertz model with Poisson errors
Population dynamics models play an important role in a number of fields, such as actuarial science, demography, and ecology. Statistical inference for these models can be difficult when, in addition to the process' inherent stochasticity, one also needs to account for sampling error. Ignoring the latter can lead to biases in the estimation, which in turn can produce erroneous conclusions about the system's behavior. The Gompertz model is widely used to infer population size dynamics, but a full…

Evaluating multi-season occupancy models with autocorrelation fitted to heterogeneous datasets
Andr\'e Lu\'is Luza, Didier Alard, Fr\'ed\'eric Barraquand
https://arxiv.org/abs/2510.08151

Evaluating multi-season occupancy models with autocorrelation fitted to heterogeneous datasets
Predicting species distributions using occupancy models accounting for imperfect detection is now commonplace in ecology. Recently, modelling spatial and temporal autocorrelation was proposed to alleviate the lack of replication in occupancy data, which often prevents model identifiability. However, how such models perform in highly heterogeneous datasets where missing or single-visit data dominates remains an open question. Motivated by an heterogeneous fine-scale butterfly occupancy dataset, …

Replaced article(s) found for q-bio.PE. https://arxiv.org/list/q-bio.PE/new
[1/1]:
- Vendi Information Gain for Active Learning and its Application to Ecology
Quan Nguyen, Adji Bousso Dieng

Transient Histories- Form (Aesthetics) and Relations (Ecology) in Sustainable Development
https://ift.tt/64PCBWs
updated: Friday, September 5, 2025 - 9:17amfull name / name of organization: Kristu Jayanti Deemed…
via Input 4 RELCFP

A multi-stage Bayesian approach to fit spatial point process models
Rachael Ren, Mevin B. Hooten, Toryn L. J. Schafer, Nicholas M. Calzada, Benjamin Hoose, Jamie N. Womble, Scott Gende
https://arxiv.org/abs/2508.02922

A multi-stage Bayesian approach to fit spatial point process models
Spatial point process (SPP) models are commonly used to analyze point pattern data, including presence-only data in ecology. Current methods for fitting these models are computationally expensive because they require numerical quadrature and algorithm supervision (i.e., tuning) in the Bayesian setting. We propose a flexible and efficient multi-stage recursive Bayesian approach to fitting SPP models that leverages parallel computing resources to estimate point process model coefficients and deri…

Temperature and Competition: Drivers in the Ecological Dynamics of Aedes Mosquitoes and Dengue Spread
Santiago Andr\'es Villamil Chac\'on, Mauricio Santos-Vega
https://arxiv.org/abs/2509.10785 …

Temperature and Competition: Drivers in the Ecological Dynamics of Aedes Mosquitoes and Dengue Spread
Dengue, a mosquito-borne viral disease common in tropical areas, is spread by Aedes aegypti and Aedes albopictus. Temperature changes driven by climate affect vector ecology and expand regions of species coexistence. The combined effect of temperature and larval competition on mosquito dynamics and dengue transmission is unclear. We built a deterministic model with temperature-dependent parameters to study larval-stage interactions, linked with a SEIR framework for human infection. We assessed …

Evolution du Principe d'Exclusion Comp\'etitive : Le r\^ole des math\'ematiques
Claude Lobry
https://arxiv.org/abs/2510.03158 https://arxiv.org…

Evolution du Principe d'Exclusion Compétitive : Le rôle des mathématiques
Everyone can see that over the last 150 years, theoretical ecology has become considerably more mathematical. But what is the nature of this phenomenon? Are mathematics applied, as in the use of statistical tests, for example, or are they involved, as in physics, where laws cannot be expressed without them? Through the history of the {\em Competitive Exclusion Principle} formulated at the very beginning of the 20th century by the naturalist Grinnell concerning the distribution of brown-backed c…