The development of efficient machine learning models for molecular systems representation is becoming crucial in scientific research. We introduce TensorNet, an innovative O(3)-equivariant message-passing neural network architecture that leverages Cartesian tensor representations. By using Cartesian tensor atomic embeddings, feature mixing is simplified through matrix product operations. Furthermore, the cost-effective decomposition of these tensors into rotation group irreducible representations allows for the separate processing of scalars, vectors, and tensors when necessary. Compared to higher-rank spherical tensor models, TensorNet demonstrates state-of-the-art performance with significantly fewer parameters. For small molecule potential energies, this can be achieved even with a single interaction layer. As a result of all these properties, the model's computational cost is substantially decreased. Moreover, the accurate prediction of vector and tensor molecular quantities on top of potential energies and forces is possible. In summary, TensorNet's framework opens up a new space for the design of state-of-the-art equivariant models.

Kernel design is a pivotal but challenging aspect of time series analysis, especially in the context of small datasets. In recent years, Reservoir Computing (RC) has emerged as a powerful tool to compare time series based on the underlying dynamics of the generating process rather than the observed data. However, the performance of RC highly depends on the hyperparameter setting, which is hard to interpret and costly to optimize because of the recurrent nature of RC. Here, we present a new kernel for time series based on the recently established equivalence between reservoir dynamics and Nonlinear Vector AutoRegressive (NVAR) processes. The kernel is non-recurrent and depends on a small set of meaningful hyperparameters, for which we suggest an effective heuristic. We demonstrate excellent performance on a wide range of real-world classification tasks, both in terms of accuracy and speed. This further advances the understanding of RC representation learning models and extends the typical use of the NVAR framework to kernel design and representation of real-world time series data.

Models that rely solely on pairwise relationships often fail to capture the complete statistical structure of the complex multivariate data found in diverse domains, such as socio-economic, ecological, or biomedical systems. Non-trivial dependencies between groups of more than two variables can play a significant role in the analysis and modelling of such systems, yet extracting such high-order interactions from data remains challenging. Here, we introduce a hierarchy of d-order interaction measures, increasingly inclusive of possible factorisations of the joint probability distribution, and define non-parametric, kernel-based tests to establish systematically the statistical significance of d-order interactions. We also establish mathematical links with lattice theory, which elucidate the derivation of the interaction measures and their composite permutation tests; clarify the connection of simplicial complexes with kernel matrix centring; and provide a means to enhance computational efficiency. We illustrate our results numerically with validations on synthetic data, and through an application to neuroimaging data.

Phylogenetic inference, grounded in molecular evolution models, is essential for understanding the evolutionary relationships in biological data. Accounting for the uncertainty of phylogenetic tree variables, which include tree topologies and evolutionary distances on branches, is crucial for accurately inferring species relationships from molecular data and tasks requiring variable marginalization. Variational Bayesian methods are key to developing scalable, practical models; however, it remains challenging to conduct phylogenetic inference without restricting the combinatorially vast number of possible tree topologies. In this work, we introduce a novel, fully differentiable formulation of phylogenetic inference that leverages a unique representation of topological distributions in continuous geometric spaces. Through practical considerations on design spaces and control variates for gradient estimations, our approach, GeoPhy, enables variational inference without limiting the topological candidates. In experiments using real benchmark datasets, GeoPhy significantly outperformed other approximate Bayesian methods that considered whole topologies.

Since the proposal of transformers (Vaswani et al., 2017), these models have been limited to bounded input lengths, because of their need to attend to every token in the input. In this work, we propose Unlimiformer: a general approach that wraps any existing pretrained encoder-decoder transformer, and offloads the cross-attention computation to a single k-nearest-neighbor (kNN) index, while the returned kNN distances are the attention dot-product scores. This kNN index can be kept on either the GPU or CPU memory and queried in sub-linear time; this way, we can index practically unlimited input sequences, while every attention head in every decoder layer retrieves its top-k keys, instead of attending to every key. We evaluate Unlimiformer on several long-document and book-summarization benchmarks, showing that it can process even 500k token-long inputs from the BookSum dataset, without any input truncation at test time. We demonstrate that Unlimiformer improves pretrained models such as BART (Lewis et al., 2020a) and Longformer (Beltagy et al., 2020) by extending them to unlimited inputs without additional learned weights and without modifying their code. Our code and models are publicly available, and support LLaMA-2 as well2.