Multi-Criteria Decision Making (MCDM) aims at modelling expert preferences and assisting decision makers in identifying options best accommodating expert criteria. An instance of MCDM model, the Choquet integral is widely used in real-world applications, due to its ability to capture interactions between criteria while retaining interpretability. Aimed at a better scalability and modularity, hierarchical Choquet integrals involve intermediate aggregations of the interacting criteria, at the cost of a more complex elicitation. The paper presents a machine learning-based approach for the automatic identification of hierarchical MCDM models, composed of 2-additive Choquet integral aggregators and of marginal utility functions on the raw features from data reflecting expert preferences. The proposed NEUR-HCI framework relies on a specific neural architecture, enforcing by design the Choquet model constraints and supporting its end-to-end training. The empirical validation of NEUR-HCI on real-world and artificial benchmarks demonstrates the merits of the approach compared to state-of-art baselines.