Interpretability of Graph Neural Networks to Assert Effects of Global Change Drivers on Ecological Networks

Pollinators play a crucial role for plant reproduction, either in natural ecosystem or in human-modified landscape. Global change drivers,including climate change or land use modifications, can alter the plant-pollinator interactions. To assert the potential influence of global change drivers on pollination, large-scale interactions, climate and land use data are required. While recent machine learning methods, such as graph neural networks (GNNs), allow the analysis of such datasets, interpreting their results can be challenging. We explore existing methods for interpreting GNNs in order to highlight the effects of various environmental covariates on pollination network connectivity. A large simulation study is performed to confirm whether these methods can detect the interactive effect between a covariate and a genus of plant on connectivity, and whether the application of debiasing techniques influences the estimation of these effects. An application on the Spipoll dataset, with and without accounting for sampling effects, highlights the potential impact of land use on network connectivity and shows that accounting for sampling effects partially alters the estimation of these effects.

HyperSBINN: A Hypernetwork-Enhanced Systems Biology-Informed Neural Network for Efficient Drug Cardiosafety Assessment

Mathematical modeling in systems toxicology enables a comprehensive understanding of the effects of pharmaceutical substances on cardiac health. However, the complexity of these models limits their widespread application in early drug discovery. In this paper, we introduce a novel approach to solving parameterized models of cardiac action potentials by combining meta-learning techniques with Systems Biology-Informed Neural Networks (SBINNs). The proposed method, HyperSBINN, effectively addresses the challenge of predicting the effects of various compounds at different concentrations on cardiac action potentials, outperforming traditional differential equation solvers in speed. Our model efficiently handles scenarios with limited data and complex parameterized differential equations. The HyperSBINN model demonstrates robust performance in predicting APD90 values, indicating its potential as a reliable tool for modeling cardiac electrophysiology and aiding in preclinical drug development. This framework represents an advancement in computational modeling, offering a scalable and efficient solution for simulating and understanding complex biological systems.

Bipartite Graph Variational Auto-Encoder with Fair Latent Representation to Account for Sampling Bias in Ecological Networks

We propose a method to represent bipartite networks using graph embeddings tailored to tackle the challenges of studying ecological networks, such as the ones linking plants and pollinators, where many covariates need to be accounted for, in particular to control for sampling bias. We adapt the variational graph auto-encoder approach to the bipartite case, which enables us to generate embeddings in a latent space where the two sets of nodes are positioned based on their probability of connection. We translate the fairness framework commonly considered in sociology in order to address sampling bias in ecology. By incorporating the Hilbert-Schmidt independence criterion (HSIC) as an additional penalty term in the loss we optimize, we ensure that the structure of the latent space is independent of continuous variables, which are related to the sampling process. Finally, we show how our approach can change our understanding of ecological networks when applied to the Spipoll data set, a citizen science monitoring program of plant-pollinator interactions to which many observers contribute, making it prone to sampling bias.