Hawkes processes are a class of past-dependent point processes, widely used in many applications such as seismology [Ogata, 1988], criminology [Olinde and Short, 2020] and neuroscience [Reynaud-Bouret et al., 2013] for their ability to capture complex dependence structures. In their multidimensional version [Ogata, 1988], Hawkes processes can model pairwise interactions between different types of events, allowing to recover a connectivity graph between different features. Originally developed by Hawkes [1971] in order to model self-exciting phenomena, where each event increases the probability of a new event occurring, many extensions have been proposed ever since. In particular, nonlinear Hawkes processes have been introduced notably to detect inhibiting interactions, when an event can decrease the probability of another one appearing. Hawkes processes with inhibition are notoriously more complicated to handle due to the loss of many properties of linear Hawkes processes such as the cluster representation and the branching structure of the process [Hawkes and Oakes, 1974]. Since the first article on nonlinear Hawkes processes [Brémaud and Massoulié, 1996] proving in particular their existence, many works have focused on inhibition in the past few years. Among them, limit theorems have been established in [Costa et al., 2020] while Duval et al. [2022] obtained mean-field results on the behaviour of two neuronal populations. Regarding statistical inference, in the frequentist setting we can mention the exact maximum likelihood procedure of Bonnet et al. [2023], the least-squares approach by Bacry et al. [2020] and the nonparametric approach based on Bernstein-type polynomials by Lemonnier and Vayatis [2014]. While the first one proposes an exact inference procedure, it is restricted to exponential kernels.

When studying ecosystems, hierarchical trees are often used to organize entities based on proximity criteria, such as the taxonomy in microbiology, social classes in geography, or product types in retail businesses, offering valuable insights into entity relationships. Despite their significance, current count-data models do not leverage this structured information. In particular, the widely used Poisson log-normal (PLN) model, known for its ability to model interactions between entities from count data, lacks the possibility to incorporate such hierarchical tree structures, limiting its applicability in domains characterized by such complexities. To address this matter, we introduce the PLN-Tree model as an extension of the PLN model, specifically designed for modeling hierarchical count data. By integrating structured variational inference techniques, we propose an adapted training procedure and establish identifiability results, enhancisng both theoretical foundations and practical interpretability. Additionally, we extend our framework to classification tasks as a preprocessing pipeline, showcasing its versatility. Experimental evaluations on synthetic datasets as well as real-world microbiome data demonstrate the superior performance of the PLN-Tree model in capturing hierarchical dependencies and providing valuable insights into complex data structures, showing the practical interest of knowledge graphs like the taxonomy in ecosystems modeling.

The Hawkes model is a point process observed on the real line, which generally corresponds to the time, where any previously encountered event has a direct influence on the chances of future events occurring. This past-dependent mathematical model was introduced in [1] and its first application was to model earthquakes occurrences [2, 3]. Since then, Hawkes processes have been widely used in various fields, for instance finance [4], social media [5, 6], epidemiology [7], sociology [8] and neuroscience [9]. The main advantage of Hawkes processes is their ability to model different kinds of relationships between phenomena through an unknown kernel or transfer function. The Hawkes model was originally introduced as a self-exciting point process where the appearance of an event increases the chances of another one triggering. Several estimation procedures have been proposed for the kernel function, both in parametric [2, 10, 11] and nonparametric [9, 12] frameworks. However, the inhibition setting, where the presence of an event decreases the chance of another occurring, has drawn less attention in the literature, although it can be of great interest in several fields, in particular in neuroscience [13]. In this inhibition context, the cluster representation [14] on which is based the construction of a self-exciting Hawkes process, is no longer valid.