Lamiae Azizi

Mohamed Mouhajir, Limei Wang, El Houcine Bergou et al.

Graph-based representations are widely used in protein modeling, yet many existing approaches rely primarily on sequence adjacency or geometric proximity, which only partially reflect the principles governing protein folding. Proteins instead adopt complex three-dimensional conformations organized around secondary structure elements, such as $α$-helices and $β$-sheets, which encode recurring local motifs and stabilizing hydrogen-bond interactions. In this work, we introduce a secondary-structure-aware graph neural network for protein representation learning. Residue-level node representations are augmented with secondary structure assignments, and graph edges are constructed from hydrogen-bond interactions filtered by their energetic strength. This design enables the model to capture both local structural context and long-range couplings that are central to protein stability and function. We evaluate the proposed approach on commonly used protein benchmarks and observe consistent improvements over existing graph-based methods. In addition, the resulting graph representations offer enhanced biological interpretability, as the learned connectivity aligns with established structural motifs. These findings suggest that incorporating secondary structure and energy-filtered hydrogen-bond topology provides an effective inductive bias for protein representation learning. The code is released at https://github.com/mohamedmohamed2021/SSProNet

Simon Luo, Feng Zhou, Lamiae Azizi et al.

We present the Additive Poisson Process (APP), a novel framework that can model the higher-order interaction effects of the intensity functions in stochastic processes using lower dimensional projections. Our model combines the techniques in information geometry to model higher-order interactions on a statistical manifold and in generalized additive models to use lower-dimensional projections to overcome the effects from the curse of dimensionality. Our approach solves a convex optimization problem by minimizing the KL divergence from a sample distribution in lower dimensional projections to the distribution modeled by an intensity function in the stochastic process. Our empirical results show that our model is able to use samples observed in the lower dimensional space to estimate the higher-order intensity function with extremely sparse observations.

Steven Y. K. Wong, Jennifer Chan, Lamiae Azizi et al.

We consider the problem of neural network training in a time-varying context. Machine learning algorithms have excelled in problems that do not change over time. However, problems encountered in financial markets are often time-varying. We propose the online early stopping algorithm and show that a neural network trained using this algorithm can track a function changing with unknown dynamics. We compare the proposed algorithm to current approaches on predicting monthly U.S. stock returns and show its superiority. We also show that prominent factors (such as the size and momentum effects) and industry indicators, exhibit time varying stock return predictiveness. We find that during market distress, industry indicators experience an increase in importance at the expense of firm level features. This indicates that industries play a role in explaining stock returns during periods of heightened risk.

Nick James, Max Menzies, Lamiae Azizi et al.

This paper proposes a new method for determining similarity and anomalies between time series, most practically effective in large collections of (likely related) time series, by measuring distances between structural breaks within such a collection. We introduce a class of \emph{semi-metric} distance measures, which we term \emph{MJ distances}. These semi-metrics provide an advantage over existing options such as the Hausdorff and Wasserstein metrics. We prove they have desirable properties, including better sensitivity to outliers, while experiments on simulated data demonstrate that they uncover similarity within collections of time series more effectively. Semi-metrics carry a potential disadvantage: without the triangle inequality, they may not satisfy a "transitivity property of closeness." We analyse this failure with proof and introduce an computational method to investigate, in which we demonstrate that our semi-metrics violate transitivity infrequently and mildly. Finally, we apply our methods to cryptocurrency and measles data, introducing a judicious application of eigenvalue analysis.

Simon Luo, Lamiae Azizi, Mahito Sugiyama

We present a novel blind source separation (BSS) method, called information geometric blind source separation (IGBSS). Our formulation is based on the log-linear model equipped with a hierarchically structured sample space, which has theoretical guarantees to uniquely recover a set of source signals by minimizing the KL divergence from a set of mixed signals. Source signals, received signals, and mixing matrices are realized as different layers in our hierarchical sample space. Our empirical results have demonstrated on images and time series data that our approach is superior to well established techniques and is able to separate signals with complex interactions.