Esther Galbrun

Sara Si-Moussi, Esther Galbrun, Mickael Hedde et al.

There is no much doubt that biotic interactions shape community assembly and ultimately the spatial co-variations between species. There is a hope that the signal of these biotic interactions can be observed and retrieved by investigating the spatial associations between species while accounting for the direct effects of the environment. By definition, biotic interactions can be both symmetric and asymmetric. Yet, most models that attempt to retrieve species associations from co-occurrence or co-abundance data internally assume symmetric relationships between species. Here, we propose and validate a machine-learning framework able to retrieve bidirectional associations by analyzing species community and environmental data. Our framework (1) models pairwise species associations as directed influences from a source to a target species, parameterized with two species-specific latent embeddings: the effect of the source species on the community, and the response of the target species to the community; and (2) jointly fits these associations within a multi-species conditional generative model with different modes of interactions between environmental drivers and biotic associations. Using both simulated and empirical data, we demonstrate the ability of our framework to recover known asymmetric and symmetric associations and highlight the properties of the learned association networks. By comparing our approach to other existing models such as joint species distribution models and probabilistic graphical models, we show its superior capacity at retrieving symmetric and asymmetric interactions. The framework is intuitive, modular and broadly applicable across various taxonomic groups.

Maiju Karjalainen, Esther Galbrun, Pauli Miettinen

Redescription mining is a data analysis technique that has found applications in diverse fields. The most used redescription mining approaches involve two phases: finding matching pairs among data attributes and extending the pairs. This process is relatively efficient when the number of attributes remains limited and when the attributes are Boolean, but becomes almost intractable when the data consist of many numerical attributes. In this paper, we present new algorithms that perform the matching and extension orders of magnitude faster than the existing approaches. Our algorithms are based on locality-sensitive hashing with a tailored approach to handle the discretisation of numerical attributes as used in redescription mining.

Erwan Bourrand, Luis Galárraga, Esther Galbrun et al.

We are interested in understanding the underlying generation process for long sequences of symbolic events. To do so, we propose COSSU, an algorithm to mine small and meaningful sets of sequential rules. The rules are selected using an MDL-inspired criterion that favors compactness and relies on a novel rule-based encoding scheme for sequences. Our evaluation shows that COSSU can successfully retrieve relevant sets of closed sequential rules from a long sequence. Such rules constitute an interpretable model that exhibits competitive accuracy for the tasks of next-element prediction and classification.

Esther Galbrun

This is about the Minimum Description Length (MDL) principle applied to pattern mining. The length of this description is kept to the minimum. Mining patterns is a core task in data analysis and, beyond issues of efficient enumeration, the selection of patterns constitutes a major challenge. The MDL principle, a model selection method grounded in information theory, has been applied to pattern mining with the aim to obtain compact high-quality sets of patterns. After giving an outline of relevant concepts from information theory and coding, as well as of work on the theory behind the MDL and similar principles, we review MDL-based methods for mining various types of data and patterns. Finally, we open a discussion on some issues regarding these methods, and highlight currently active related data analysis problems.