QT-Net: Rethinking Evaluation of AI Models in Atomic Chemical Space

For low-data and resource-constrained regimes typical of quantum chemistry, parameter-efficient learning is a key objective. Here, we propose a topology-aligned inductive bias in which the model architecture mirrors the molecular bond graph: atoms map to a fixed register of computational units, and bonds determine which pairs interact through shared learnable parameters. This principle is instantiated in two architectures: a variational quantum circuit (Iso-QGNN), and a parameter-matched classical message-passing model (Iso-CGNN). The models are benchmarked on HOMO-LUMO and dipole moment binary classification tasks over the QM9 benchmark. With 64 trainable parameters, the implementations achieve test AUCs of approximately 0.88 (quantum) and 0.91 (classical) on the gap task, and close to 0.78 (both) on the dipole task. The models reach 90% of asymptotic performance within about 250 training molecules and gradient norms remain stable throughout training. These results indicate that the topology-aligned inductive bias is the active ingredient driving parameter efficiency at QM9 scale, with implications for matched-baseline benchmarking in quantum machine learning.

Advances in deep learning architectures and representations have enabled ML-driven chemical property prediction, but state-of-the-art (SOTA) models have remained largely confined to independent codebases and lack support for diverse chemical species. This work introduces ElemeNet, a unified, general-purpose software package for molecular machine learning. The ElemeNet software package enables the training of advanced ML models for diverse properties and datasets with an enlarged range of elemental compositions. We define molecular representations compatible with elements 1-100, supporting diverse organometallic and biological systems in addition to organic chemistry already well-served by the Chemprop ML toolkit. As well as more common atom-, bond-, and molecule-level predictions, we introduce moiety predictions. We also natively define optional conditioning on charge and spin states. Advanced E(3)-equivariant and transformer architectures are supported, as well as classical 2D models, with all classes including built-in uncertainty quantification through deterministic and statistical measures. We benchmark our protocols for ML model training against representative datasets from organic, inorganic, coordination, and biological chemistry, achieving competitive and SOTA performance relative to literature baselines and favorable scaling to millions of molecules. The entire workflow is exposed through a concise command-line interface, lowering the barrier to entry for non-expert users. We anticipate ElemeNet will empower non-computational researchers to leverage modern deep learning methods across the chemical and physical sciences.

We introduce a tensor-channel equivariant graph neural network for direct prediction of molecular polarizability tensors. Building on the efficient PaiNN architecture, we augment the hidden representation with explicit symmetric rank-2 tensor channels aligned with the decomposition of polarizability into isotropic and anisotropic components. In contrast to approaches that construct tensor outputs only at readout, our model propagates tensor structure throughout message passing using geometrically motivated tensor bases. This yields a target-aligned architecture for tensor-valued molecular prediction. On optimized QM7-X geometries, the proposed model achieves lower full-tensor and anisotropic error than both a PaiNN-style readout baseline and a dielectric MACE baseline under matched training conditions and at nearly identical parameter count. In this controlled setting, it also outperforms MACE while remaining substantially faster at inference. Ablation studies show that the gain does not arise from increased capacity alone, but from the combination of explicit tensor propagation and a traceless target parameterization matched to the anisotropic part of the polarizability tensor. Among the tensor bases considered, the strongest results are obtained from interactions between learned directional features, indicating that these are particularly effective for modeling molecular polarizability. Rotational equivariance tests further confirm that all compared models are numerically equivariant, so the observed improvements are attributable to better learning of the target tensor itself. Overall, our results show that for structured tensor-valued targets, propagating target-aligned tensor features can outperform both readout-only tensor construction and a more general higher-order equivariant model in the present training setting.