Ali Hariri

Ali Hariri, Álvaro Arroyo, Alessio Gravina et al.

ChebNet, one of the earliest spectral GNNs, has largely been overshadowed by Message Passing Neural Networks (MPNNs), which gained popularity for their simplicity and effectiveness in capturing local graph structure. Despite their success, MPNNs are limited in their ability to capture long-range dependencies between nodes. This has led researchers to adapt MPNNs through rewiring or make use of Graph Transformers, which compromises the computational efficiency that characterized early spatial message-passing architectures, and typically disregards the graph structure. Almost a decade after its original introduction, we revisit ChebNet to shed light on its ability to model distant node interactions. We find that out-of-box, ChebNet already shows competitive advantages relative to classical MPNNs and GTs on long-range benchmarks, while maintaining good scalability properties for high-order polynomials. However, we uncover that this polynomial expansion leads ChebNet to an unstable regime during training. To address this limitation, we cast ChebNet as a stable and non-dissipative dynamical system, which we coin Stable-ChebNet. Our Stable-ChebNet model allows for stable information propagation, and has controllable dynamics which do not require the use of eigendecompositions, positional encodings, or graph rewiring. Across several benchmarks, Stable-ChebNet achieves near state-of-the-art performance.

Aditya Sengar, Ali Hariri, Daniel Probst et al.

Generating diverse, all-atom conformational ensembles of dynamic proteins such as G-protein-coupled receptors (GPCRs) is critical for understanding their function, yet most generative models simplify atomic detail or ignore conformational diversity altogether. We present latent diffusion for full protein generation (LD-FPG), a framework that constructs complete all-atom protein structures, including every side-chain heavy atom, directly from molecular dynamics (MD) trajectories. LD-FPG employs a Chebyshev graph neural network (ChebNet) to obtain low-dimensional latent embeddings of protein conformations, which are processed using three pooling strategies: blind, sequential and residue-based. A diffusion model trained on these latent representations generates new samples that a decoder, optionally regularized by dihedral-angle losses, maps back to Cartesian coordinates. Using D2R-MD, a 2-microsecond MD trajectory (12 000 frames) of the human dopamine D2 receptor in a membrane environment, the sequential and residue-based pooling strategy reproduces the reference ensemble with high structural fidelity (all-atom lDDT of approximately 0.7; C-alpha-lDDT of approximately 0.8) and recovers backbone and side-chain dihedral-angle distributions with a Jensen-Shannon divergence of less than 0.03 compared to the MD data. LD-FPG thereby offers a practical route to system-specific, all-atom ensemble generation for large proteins, providing a promising tool for structure-based therapeutic design on complex, dynamic targets. The D2R-MD dataset and our implementation are freely available to facilitate further research.

Pierre-Gabriel Berlureau, Ali Hariri, Victor Kawasaki-Borruat et al.

Graph Neural Networks (GNNs) often struggle to propagate information across long distances due to oversmoothing and oversquashing. Existing remedies such as graph transformers or rewiring typically incur high computational cost or require altering the graph structure. We introduce a Bakry-Emery graph Laplacian that integrates diffusion and advection through a learnable node-wise potential, inducing task-dependent propagation dynamics without modifying topology. This operator has a well-behaved spectral decomposition and acts as a drop-in replacement for standard Laplacians in spectral GNNs. Building on this insight, we develop mu-ChebNet, a spectral architecture that jointly learns the potential and Chebyshev filters, effectively bridging message-passing adaptivity and spectral efficiency. Our theoretical analysis shows how the potential modulates the spectrum, enabling control of key graph properties. Empirically, mu-ChebNet delivers consistent gains on synthetic long-range reasoning tasks, as well as real-world benchmarks, while offering an interpretable routing field that reveals how information flows through the graph. This establishes the Bakry-Emery Laplacian as a principled and efficient foundation for adaptive spectral graph learning.

Ali Hariri, Darya Dyachkova, Sergei Gleyzer

Accurate and fast simulation of particle physics processes is crucial for the high-energy physics community. Simulating particle interactions with detectors is both time consuming and computationally expensive. With the proton-proton collision energy of 13 TeV, the Large Hadron Collider is uniquely positioned to detect and measure the rare phenomena that can shape our knowledge of new interactions. The High-Luminosity Large Hadron Collider (HL-LHC) upgrade will put a significant strain on the computing infrastructure due to increased event rate and levels of pile-up. Simulation of high-energy physics collisions needs to be significantly faster without sacrificing the physics accuracy. Machine learning approaches can offer faster solutions, while maintaining a high level of fidelity. We discuss a graph generative model that provides effective reconstruction of LHC events, paving the way for full detector level fast simulation for HL-LHC.

Ali Hariri, Kamran Alipour, Yash Mantri et al.

Low fluence illumination sources can facilitate clinical transition of photoacoustic imaging because they are rugged, portable, affordable, and safe. However, these sources also decrease image quality due to their low fluence. Here, we propose a denoising method using a multi-level wavelet-convolutional neural network to map low fluence illumination source images to its corresponding high fluence excitation map. Quantitative and qualitative results show a significant potential to remove the background noise and preserve the structures of target. Substantial improvements up to 2.20, 2.25, and 4.3-fold for PSNR, SSIM, and CNR metrics were observed, respectively. We also observed enhanced contrast (up to 1.76-fold) in an in vivo application using our proposed methods. We suggest that this tool can improve the value of such sources in photoacoustic imaging.