STELLAR: Spatio-Temporal Environmental Learning with Latent Alignment and Refinement for Long-Tailed Species Distribution Modeling
Authors: Shufeng Kong, Tao Yu, Yuanyuan Wei, Caihua Liu, Junwen Bai, Yingheng Wang, Marc Grimson, Daniel Fink, +1 more
Organizations: School of Software Engineering, Sun Yat-sen University, Zhuhai, China · School of Computer Science and Artificial Intelligence, Foshan University, Foshan, China · Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA · Department of Computer Science, Cornell University, Ithaca, NY, USA · Cornell Lab of Ornithology, Ithaca, NY, USA
Abstract
Joint Species Distribution Modeling (JSDM) is a key enabler for biodiversity monitoring and conservation planning. However, accurate JSDM faces two coupled challenges: environmental drivers and species distributions are inherently spatio-temporal, while species co-occurrence patterns exhibit complex non-linear community structure and severe long-tail imbalance driven by rare species. Existing approaches often address these factors in isolation, learning from static covariates or neglecting the historical trajectories of dynamic community structure. To overcome these limitations, we propose STELLAR (Spatio-Temporal Environmental Learning with Latent Alignment and Refinement), a novel framework that learns a shared latent space where dynamic habitat context and community structure are optimized jointly. Our approach integrates three complementary components: (1) a Graph-Temporal Encoder that employs graph attention and recurrent units to aggregate spatial neighborhood effects and capture the co-evolving historical dynamics of environmental context and community structure; (2) a Context-Anchored Latent Alignment mechanism that structures the latent space using a label-activated mixture prior and supervised contrastive learning, actively clustering species based on shared environmental preferences; and (3) an Imbalance-Aware Decoupled Decoding module that utilizes Asymmetric Loss to focus learning on hard, rare species samples, preventing mode collapse in the long tail. Experiments on the large-scale eBird dataset, curated with domain experts, demonstrate that our framework significantly outperforms state-of-the-art baselines, particularly in predicting rare species and revealing interpretable species interactions.
Species Distribution Modelling (SDM) is essential for understanding how environmental conditions shape biodiversity, particularly for destructive pests such as the Desert Locust (Schistocerca gregaria), whose breeding dynamics are tightly coupled to rapidly evolving environmental conditions. Maxent has become the dominant method for presence-only data, but its reliance on a linear combination of hand chosen feature transforms limits its ability to capture the nonlinear, temporal relationships common in ecological monitoring, where covariates such as precipitation, soil moisture, and vegetation indices evolve meaningfully over time. Standard implementations flatten time-series covariates into independent features, discarding sequential structure that carries critical signal. We introduce RNN Maxent, an extension of the Maxent framework that replaces the fixed feature dictionary with a neural network, specifically a Gated Recurrent Unit (GRU), trained end to end via backpropagation. The approach preserves Maxent's presence only statistical foundations, background normalization, and probability calibration, differing only in that the nonlinearity is learned from data rather than fixed in advance. We apply RNN Maxent to map suitable habitat for the Desert Locust using 50 day environmental time series derived from ERA5 Land, MODIS, and Sentinel 3, maintaining a 7 day gap between covariates and presence records to yield forecasting behavior. Compared against standard Maxent, RNN Maxent improves performance across metrics (ROC AUC 0.862 std 0.036 vs. 0.792; F1 0.671 std 0.056 vs. 0.590).
Alessandro Grassi, Edoardo Kimani Bellotto, Wassim El Azami +2
Federated learning has emerged as a promising paradigm for spatio-temporal forecasting (STF), enabling collaborative model training without sharing raw observations. Existing federated STF methods primarily regard cross-client heterogeneity as an optimization challenge and mitigate it through personalized approaches. However, such heterogeneity fundamentally stems from diverse \emph{environmental conditions}, and these methods capture environment-specific forecasting patterns, hardly generalizing under environmental shifts. Our key insight is that the environmental diversity across federated clients should be exploited, as they provide \emph{complementary observations of the same underlying spatio-temporal system}. Based on this insight, we propose \method, a novel federated de-confounding framework that \textbf{treats clients as distinct causal environments}. \method leverages the client heterogeneity as distributed environmental evidence and learns a global prototype codebook to capture shared environmental regimes. We further derive a theoretical federated de-confounding bound that is linearly controlled by the averaged confounding strength. Extensive experiments demonstrate that \method consistently outperforms federated baselines, while providing transferable, interpretable, and communication-efficient environmental representations.
Recovering latent structure from count data has received considerable attention in network inference, particularly when one seeks both cross-group interactions and within-group similarity patterns in bipartite networks, which is widely used in ecology research. Such networks are often sparse and inherently imperfect in their detection. Existing models mainly focus on interaction recovery, while the induced similarity graphs are much less studied. Moreover, sparsity is often not controlled, and scale is unbalanced, leading to oversparse or poorly rescaled estimates with degrading structural recovery. To address these issues, we propose a framework for structured sparse nonnegative low-rank factorization with detection probability estimation. We impose nonconvex ℓ1/2 regularization on the latent similarity and connectivity structures to promote sparsity within-group similarity and cross-group connectivity with better relative scale. The resulting optimization problem is nonconvex and nonsmooth. To solve it, we develop an ADMM-based algorithm with adaptive penalization and scale-aware initialization and establish its asymptotic feasibility and KKT stationarity of cluster points under mild regularity conditions. Experiments on synthetic and real-world ecological datasets demonstrate improved recovery of latent factors and similarity/connectivity structure relative to existing baselines.