arXiv subjects

Zakaria Elabid

Publications and source records attributed to Zakaria Elabid.

5 recordsLinked to original sources

arXiv2026

MANDALA: An E(3)-Equivariant Graph Neural Network Framework for Learning Electronic-Structure Operators with Observable Guidance

Electronic-structure calculations based on Kohn-Sham density functional theory remain indispensable in computational materials science and chemistry. Their computational cost, however, limits accessible system sizes and simulation times. At the same time, conventional machine-learning interatomic potentials (MLIPs), which are becoming the workhorse of large-scale materials modeling, usually target only energies and forces. They therefore leave out the quantum-operator-level information required to reconstruct band structures, densities of states, spatial charge distributions, and other electronic observables. \texttt{Mandala} fills this methodological gap. It is a modular software framework for learning block-sparse electronic-structure matrices with E(3)-equivariant graph neural networks. The framework is built around a unified representation of atom-resolved Hamiltonian, overlap, and density matrices, together with reusable abstractions for basis conversion, sparse block handling, irreducible representation mapping, graph construction, model definition, and training. This design allows \texttt{Mandala} to support heterogeneous chemical compositions, a wide range of neural architecture variants within one workflow, and multiple electronic-structure backends. \texttt{Mandala} evaluates selected observables directly from the predicted operators, including band energy, electron count, density of states, and band structure. This connects electronic-structure learning and observable-guided modeling while retaining a representation tied to quantum-mechanical operators rather than only scalar or vector targets as in MLIPs. In this form, \texttt{Mandala} is intended to complement atomistic interatomic potential workflows by resolving electronic structure and operator-derived observables within one scalable implementation.

cond-mat.mtrl-sci↗

arXiv2026

Molecules Meet Language: Confound-Aware Representation Learning and Chemical Property Steering in Transformer-VAE Latent Spaces

Molecular generative models often assume meaningful latent geometry, but apparent property predictability can reflect sequence-level shortcuts rather than chemical organization. We study this issue in an unsupervised autoregressive Transformer-VAE trained on SELFIES. After training, we freeze the model, fit linear probes to RDKit descriptors, and use the probe weights as candidate global steering directions. To separate chemical signal from SELFIES artifacts, we introduce a confound-aware evaluation based on residualization, confound-direction alignment analysis, and decoded-molecule traversal. This is necessary because SELFIES length, branch tokens, ring tokens, and token entropy are strongly encoded in the latent space. Under this confound-aware evaluation, we find robust monotonic steering for cLogP, FractionCSP3, HeavyAtomCount, TPSA, BertzCT, and HBA. Nonlinear probes further show that some properties admit stable global directions, while others are better described by local latent gradients. Overall, our results show that chemically meaningful steering can emerge in entangled molecular latent spaces, but only when validated through decoded molecules and controlled for representation-level confounds.

cs.LG↗

arXiv2024

TG-PhyNN: An Enhanced Physically-Aware Graph Neural Network framework for forecasting Spatio-Temporal Data

Accurately forecasting dynamic processes on graphs, such as traffic flow or disease spread, remains a challenge. While Graph Neural Networks (GNNs) excel at modeling and forecasting spatio-temporal data, they often lack the ability to directly incorporate underlying physical laws. This work presents TG-PhyNN, a novel Temporal Graph Physics-Informed Neural Network framework. TG-PhyNN leverages the power of GNNs for graph-based modeling while simultaneously incorporating physical constraints as a guiding principle during training. This is achieved through a two-step prediction strategy that enables the calculation of physical equation derivatives within the GNN architecture. Our findings demonstrate that TG-PhyNN significantly outperforms traditional forecasting models (e.g., GRU, LSTM, GAT) on real-world spatio-temporal datasets like PedalMe (traffic flow), COVID-19 spread, and Chickenpox outbreaks. These datasets are all governed by well-defined physical principles, which TG-PhyNN effectively exploits to offer more reliable and accurate forecasts in various domains where physical processes govern the dynamics of data. This paves the way for improved forecasting in areas like traffic flow prediction, disease outbreak prediction, and potentially other fields where physics plays a crucial role.

cs.LG↗

arXiv2024

Knowledge-Based Convolutional Neural Network for the Simulation and Prediction of Two-Phase Darcy Flows

Physics-informed neural networks (PINNs) have gained significant prominence as a powerful tool in the field of scientific computing and simulations. Their ability to seamlessly integrate physical principles into deep learning architectures has revolutionized the approaches to solving complex problems in physics and engineering. However, a persistent challenge faced by mainstream PINNs lies in their handling of discontinuous input data, leading to inaccuracies in predictions. This study addresses these challenges by incorporating the discretized forms of the governing equations into the PINN framework. We propose to combine the power of neural networks with the dynamics imposed by the discretized differential equations. By discretizing the governing equations, the PINN learns to account for the discontinuities and accurately capture the underlying relationships between inputs and outputs, improving the accuracy compared to traditional interpolation techniques. Moreover, by leveraging the power of neural networks, the computational cost associated with numerical simulations is substantially reduced. We evaluate our model on a large-scale dataset for the prediction of pressure and saturation fields demonstrating high accuracies compared to non-physically aware models.

cs.LG↗

arXiv2022

W-Transformers : A Wavelet-based Transformer Framework for Univariate Time Series Forecasting

Deep learning utilizing transformers has recently achieved a lot of success in many vital areas such as natural language processing, computer vision, anomaly detection, and recommendation systems, among many others. Among several merits of transformers, the ability to capture long-range temporal dependencies and interactions is desirable for time series forecasting, leading to its progress in various time series applications. In this paper, we build a transformer model for non-stationary time series. The problem is challenging yet crucially important. We present a novel framework for univariate time series representation learning based on the wavelet-based transformer encoder architecture and call it W-Transformer. The proposed W-Transformers utilize a maximal overlap discrete wavelet transformation (MODWT) to the time series data and build local transformers on the decomposed datasets to vividly capture the nonstationarity and long-range nonlinear dependencies in the time series. Evaluating our framework on several publicly available benchmark time series datasets from various domains and with diverse characteristics, we demonstrate that it performs, on average, significantly better than the baseline forecasters for short-term and long-term forecasting, even for datasets that consist of only a few hundred training samples.

cs.LG↗