Fused Lasso Improves Accuracy of Co-occurrence Network Inference in Grouped Samples
This work addresses the challenge of capturing dynamic microbial associations in microbiome research, though it is incremental as it adapts an existing machine learning method to a new domain.
The study tackled the problem of inferring microbial co-occurrence networks across different environmental niches by proposing the fuser algorithm, which achieved comparable performance within homogeneous environments and reduced test error in cross-environment scenarios compared to baseline methods.
Co-occurrence network inference algorithms have significantly advanced our understanding of microbiome communities. However, these algorithms typically analyze microbial associations within samples collected from a single environmental niche, often capturing only static snapshots rather than dynamic microbial processes. Previous studies have commonly grouped samples from different environmental niches together without fully considering how microbial communities adapt their associations when faced with varying ecological conditions. Our study addresses this limitation by explicitly investigating both spatial and temporal dynamics of microbial communities. We analyzed publicly available microbiome abundance data across multiple locations and time points, to evaluate algorithm performance in predicting microbial associations using our proposed Same-All Cross-validation (SAC) framework. SAC evaluates algorithms in two distinct scenarios: training and testing within the same environmental niche (Same), and training and testing on combined data from multiple environmental niches (All). To overcome the limitations of conventional algorithms, we propose fuser, an algorithm that, while not entirely new in machine learning, is novel for microbiome community network inference. It retains subsample-specific signals while simultaneously sharing relevant information across environments during training. Unlike standard approaches that infer a single generalized network from combined data, fuser generates distinct, environment-specific predictive networks. Our results demonstrate that fuser achieves comparable predictive performance to existing algorithms such as glmnet when evaluated within homogeneous environments (Same), and notably reduces test error compared to baseline algorithms in cross-environment (All) scenarios.