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Understanding how species are distributed across landscapes over time is a fundamental question in biodiversity research. Unfortunately, most species distribution models only target a single species at a time, despite strong ecological…
There is no much doubt that biotic interactions shape community assembly and ultimately the spatial co-variations between species. There is a hope that the signal of these biotic interactions can be observed and retrieved by investigating…
The potential effects of conservation actions on threatened species can be predicted using ensemble ecosystem models by forecasting populations with and without intervention. These model ensembles commonly assume stable coexistence of…
In fisheries ecology, species abundance data are often collected by multiple surveys, each with unique characteristics. This article is motivated by a dataset of Atlantic sea scallop abundance records along the northeast coast of the United…
Climate change poses an extreme threat to biodiversity, making it imperative to efficiently model the geographical range of different species. The availability of large-scale remote sensing images and environmental data has facilitated the…
Joint Species Distribution Models are essential for understanding how ecological drivers shape species communities. However, most existing approaches are limited by rigid parametric distributions for count data and the inability to model…
We address an important problem in ecology called Species Distribution Modeling (SDM), whose goal is to predict whether a species exists at a certain position on Earth. In particular, we tackle a challenging version of this task, where we…
Earthworms are key drivers of soil function, influencing organic matter turnover, nutrient cycling, and soil structure. Understanding the environmental controls on their distribution is essential for predicting the impacts of land use and…
Species distribution models (SDMs) are widely used to predict species' geographic distributions, serving as critical tools for ecological research and conservation planning. Typically, SDMs relate species occurrences to environmental…
This paper describes a deep-SDM framework, MALPOLON. Written in Python and built upon the PyTorch library, this framework aims to facilitate training and inferences of deep species distribution models (deep-SDM) and sharing for users with…
Accurately identifying spatial patterns of species distribution is crucial for scientific insight and societal benefit, aiding our understanding of species fluctuations. The increasing quantity and quality of ecological datasets present…
We introduce Latent Space Distribution Matching (LSDM), a novel framework for semi-supervised generative modeling of conditional distributions. LSDM operates in two stages: (i) learning a low-dimensional latent space from both paired and…
Networks are useful representations of many systems with interacting entities, such as social, biological and physical systems. Characterizing the meso-scale organization, i.e. the community structure, is an important problem in network…
Understanding the relative contributions of environmental, spatial, and temporal processes in shaping species distribution is a central objective in ecology. Bayesian species distribution models (SDMs) offer a flexible framework for this…
A major challenge for community ecology is using spatio-temporal data to infer parameters of dynamical models without conducting laborious experiments. We present a novel framework from statistical physics -- Maximum Caliber -- to…
Understanding species-habitat associations is fundamental to ecological sciences and for species conservation. Consequently, various statistical approaches have been designed to infer species-habitat associations. Due to their conceptual…
In systems biomedicine, an experimenter encounters different potential sources of variation in data such as individual samples, multiple experimental conditions, and multi-variable network-level responses. In multiparametric cytometry,…
A wide range of studies in population genetics have employed the sample frequency spectrum (SFS), a summary statistic which describes the distribution of mutant alleles at a polymorphic site in a sample of DNA sequences. In particular,…
Continuous space species distribution models (SDMs) have a long-standing history as a valuable tool in ecological statistical analysis. Geostatistical and preferential models are both common models in ecology. Geostatistical models are…
Species distribution models (SDMs) are key tools in ecology, conservation and management of natural resources. They are commonly trained by scientific survey data but, since surveys are expensive, there is a need for complementary sources…