Pairwise causal discovery in biochemical networks: A survey on directionality inference within complex networks from stationary observations

Metabolic networks map complex biochemical reactions within organisms, which is crucial for understanding cellular processes and metabolite flow. This study focuses on inferring the directionality of interactions in metabolomics networks. Given the challenge of using steady-state data, we benchmark various methods, including statistical scores and neural network approaches, on synthetic yet realistic biological models. Our findings highlight the relative success of a few methods in some cases where the interaction mechanism is known, whereas other methods show limited effectiveness.