Reducing Symmetry Increase in Equivariant Neural Networks

Equivariant Neural Networks (ENNs) have empowered numerous applications in scientific fields. Despite their remarkable capacity for representing geometric structures, ENNs suffer from degraded expressivity when processing symmetric inputs: the output representations are invariant to transformations that extend beyond the input's symmetries. The mathematical essence of this phenomenon is that a symmetric input, after being processed by an equivariant map, experiences an increase in symmetry. While prior research has documented symmetry increase in specific cases, a rigorous understanding of its underlying causes and general reduction strategies remains lacking. In this paper, we provide a detailed and in-depth characterization of symmetry increase together with a principled framework for its reduction: (i) For any given feature space and input symmetry group, we prove that the increased symmetry admits an infimum determined by the structure of the feature space; (ii) Building on this foundation, we develop a computable algorithm to derive this infimum, and propose practical guidelines for feature design to prevent harmful symmetry increases. (iii) Under standard regularity assumptions, we demonstrate that for most equivariant maps, our guidelines effectively reduce symmetry increase. To complement our theoretical findings, we provide visualizations and experiments on both synthetic datasets and the real-world QM9 dataset. The results validate our theoretical predictions.

MotifRole-Diff: Risk-Optimal Role-Aware Corruption for Masked Molecular Graph Diffusion

Masked discrete diffusion for molecular graph generation typically applies a uniform corruption schedule to all tokens in a lossless graph-to-sequence representation, implicitly treating structurally heterogeneous molecular components as equally difficult and equally important to reconstruct. However, different molecular graph token roles exhibit substantial variation in denoising difficulty and their influence on the decoded molecule, motivating role-specific corruption strategies. We introduce MotifRole-Diff, a role-aware corruption process that allocates masking rates according to empirically measured denoising difficulty and graph-level perturbation impact while preserving the model architecture, clean sequence space, and lossless molecular-graph decoder. We formulate schedule selection as the risk-optimal allocation of a fixed masking budget across token roles. Our theorem characterizes optimality for the modeled role-weighted residual risk, while downstream generation performance is evaluated empirically. Under matched architecture, training budget, and sampling compute, MotifRole-Diff improves validity on QM9 from 0.905 to 0.944 while reducing FCD from 1.701 to 1.609, and on MOSES improves validity from 0.920 to 0.938 while reducing FCD from 2.125 to 1.850. Role-wise diagnostics further show improved reconstruction across molecular graph token categories. Together, these matched-compute results indicate that structurally informed corruption is a more effective masking strategy than uniform schedules for serialized molecular graph diffusion.

Implementations of Quantum and Classical Topology-Aligned Architectures for Molecular Property Prediction

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.

Autoregressive latent diffusion for 3D molecule generation

Three-dimensional (3D) molecule generation has been dominated by diffusion models, which achieve strong generation quality but typically require the molecular size to be specified a priori. Recent autoregressive approaches have substantially narrowed the performance gap while naturally supporting variable-length generation and conditioning on partial molecular context. However, balancing unconditional and context-conditioned generation remains challenging. We introduce KRONOS, a latent autoregressive diffusion framework that generates molecules in the latent space of a pre-trained autoencoder, jointly modeling molecular graph topology and geometry, while retaining the flexibility of autoregressive generation. We further introduce a mixed training strategy inspired by Fill-in-the Middle (FIM) paradigm, enabling both unconditional and fragment-conditioned molecular generation within a single left-to-right autoregressive model. Experiments on QM9 and GEOM-Drugs demonstrate that KRONOS achieves leading unconditional generation performance among autoregressive methods, while remaining competitive with diffusion models. Moreover, fragment-conditioned generation is achieved with negligible impact on unconditional generation performance, demonstrating that both generation paradigms can be supported within a single architecture.

QUIVER: Quantum-Informed Views for Enhanced Representations in Large ML Models

Large machine learning models benefit substantially from multimodal inputs that provide a complementary view of the same example. We introduce QUIVER (QUantum-Informed Views for Enhanced Representations, a paradigm that enriches classical data-driven features with a quantum Fisher view: a geometrically motivated, basis-independent summary of higher-order correlations captured by a variational quantum circuit (VQC) trained to perform the same task. Unlike classical feature augmentation, the quantum Fisher information matrix encodes the intrinsic geometry of the learned quantum state manifold. While this feature map, motivated by quantum information theory, is ordinarily non-trivial to model classically, it can surface statistical structure that additional classical data or model capacity finds difficult to learn. This makes the quantum Fisher view a genuinely complementary modality rather than a redundant one. We demonstrate that QUIVER improves standard performance metrics on two benchmark datasets from very different fields: QM9 for predicting molecule properties, and JetClass for predicting jet flavor at the Large Hadron Collider (LHC). The core contribution, however, is domain-agnostic: the quantum Fisher view can be fused into a broad class of model architectures via targeted modifications to the base architecture, to incorporate information about the quantum geometry of the problem. These results demonstrate that quantum-geometric features, extracted from simulated variational circuits, can deliver measurable value for standard machine learning tasks, well before the advent of fault-tolerant quantum hardware.