arXiv subjects

Zimu Li

Publications and source records attributed to Zimu Li.

26 records · Page 2Linked to original sources

arXiv2024

Unifying O(3) Equivariant Neural Networks Design with Tensor-Network Formalism

Many learning tasks, including learning potential energy surfaces from ab initio calculations, involve global spatial symmetries and permutational symmetry between atoms or general particles. Equivariant graph neural networks are a standard approach to such problems, with one of the most successful methods employing tensor products between various tensors that transform under the spatial group. However, as the number of different tensors and the complexity of relationships between them increase, maintaining parsimony and equivariance becomes increasingly challenging. In this paper, we propose using fusion diagrams, a technique widely employed in simulating SU($2$)-symmetric quantum many-body problems, to design new equivariant components for equivariant neural networks. This results in a diagrammatic approach to constructing novel neural network architectures. When applied to particles within a given local neighborhood, the resulting components, which we term "fusion blocks," serve as universal approximators of any continuous equivariant function defined in the neighborhood. We incorporate a fusion block into pre-existing equivariant architectures (Cormorant and MACE), leading to improved performance with fewer parameters on a range of challenging chemical problems. Furthermore, we apply group-equivariant neural networks to study non-adiabatic molecular dynamics of stilbene cis-trans isomerization. Our approach, which combines tensor networks with equivariant neural networks, suggests a potentially fruitful direction for designing more expressive equivariant neural networks.

cs.LG↗

arXiv2024

Technical Report: The Graph Spectral Token -- Enhancing Graph Transformers with Spectral Information

Graph Transformers have emerged as a powerful alternative to Message-Passing Graph Neural Networks (MP-GNNs) to address limitations such as over-squashing of information exchange. However, incorporating graph inductive bias into transformer architectures remains a significant challenge. In this report, we propose the Graph Spectral Token, a novel approach to directly encode graph spectral information, which captures the global structure of the graph, into the transformer architecture. By parameterizing the auxiliary [CLS] token and leaving other tokens representing graph nodes, our method seamlessly integrates spectral information into the learning process. We benchmark the effectiveness of our approach by enhancing two existing graph transformers, GraphTrans and SubFormer. The improved GraphTrans, dubbed GraphTrans-Spec, achieves over 10% improvements on large graph benchmark datasets while maintaining efficiency comparable to MP-GNNs. SubFormer-Spec demonstrates strong performance across various datasets.

cs.LG↗

arXiv2023

Molecular tuning of DNA framework-programmed silicification by cationic silica cluster attachment

The organizational complexity of biominerals has long fascinated scientists seeking to understand biological programming and implement new developments in biomimetic materials chemistry. Nonclassical crystallization pathways have been observed and analyzed in typical crystalline biominerals, involving the controlled attachment and reconfiguration of nanoparticles and clusters on organic templates. However, the understanding of templated amorphous silica mineralization remains limited, hindering the rational design of complex silica-based materials. Here, we present a systematic study on the stabilization of self-capping cationic silica cluster (CSC) and their assembly dynamics using DNA nanostructures as programmable attachment templates. By tuning the composition and structure of CSC, we demonstrate high-fidelity silicification at single-cluster resolution, revealing a process of adaptive templating involving cooperative adjustments of both the DNA framework and cluster morphology. Our results provide a unified model of silicification by cluster attachment and pave the way towards the molecular tuning of pre- and post-nucleation stages of sol-gel reactions. Overall, our findings provide new insights for the design of silica-based materials with controlled organization and functionality, bridging the gap between biomineralization principles and the rational design of biomimetic material.

physics.chem-ph↗

arXiv2023

Transformers are efficient hierarchical chemical graph learners

Transformers, adapted from natural language processing, are emerging as a leading approach for graph representation learning. Contemporary graph transformers often treat nodes or edges as separate tokens. This approach leads to computational challenges for even moderately-sized graphs due to the quadratic scaling of self-attention complexity with token count. In this paper, we introduce SubFormer, a graph transformer that operates on subgraphs that aggregate information by a message-passing mechanism. This approach reduces the number of tokens and enhances learning long-range interactions. We demonstrate SubFormer on benchmarks for predicting molecular properties from chemical structures and show that it is competitive with state-of-the-art graph transformers at a fraction of the computational cost, with training times on the order of minutes on a consumer-grade graphics card. We interpret the attention weights in terms of chemical structures. We show that SubFormer exhibits limited over-smoothing and avoids over-squashing, which is prevalent in traditional graph neural networks.

cs.LG↗

arXiv2023

Speeding up Learning Quantum States through Group Equivariant Convolutional Quantum Ansätze

We develop a theoretical framework for $S_n$-equivariant convolutional quantum circuits with SU$(d)$-symmetry, building on and significantly generalizing Jordan's Permutational Quantum Computing (PQC) formalism based on Schur-Weyl duality connecting both SU$(d)$ and $S_n$ actions on qudits. In particular, we utilize the Okounkov-Vershik approach to prove Harrow's statement (Ph.D. Thesis 2005 p.160) on the equivalence between $\operatorname{SU}(d)$ and $S_n$ irrep bases and to establish the $S_n$-equivariant Convolutional Quantum Alternating Ansätze ($S_n$-CQA) using Young-Jucys-Murphy (YJM) elements. We prove that $S_n$-CQA is able to generate any unitary in any given $S_n$ irrep sector, which may serve as a universal model for a wide array of quantum machine learning problems with the presence of SU($d$) symmetry. Our method provides another way to prove the universality of Quantum Approximate Optimization Algorithm (QAOA) and verifies that 4-local SU($d$) symmetric unitaries are sufficient to build generic SU($d$) symmetric quantum circuits up to relative phase factors. We present numerical simulations to showcase the effectiveness of the ansätze to find the ground state energy of the $J_1$--$J_2$ antiferromagnetic Heisenberg model on the rectangular and Kagome lattices. Our work provides the first application of the celebrated Okounkov-Vershik's $S_n$ representation theory to quantum physics and machine learning, from which to propose quantum variational ansätze that strongly suggests to be classically intractable tailored towards a specific optimization problem.

quant-ph↗

arXiv2023

R-Mixup: Riemannian Mixup for Biological Networks

Biological networks are commonly used in biomedical and healthcare domains to effectively model the structure of complex biological systems with interactions linking biological entities. However, due to their characteristics of high dimensionality and low sample size, directly applying deep learning models on biological networks usually faces severe overfitting. In this work, we propose R-MIXUP, a Mixup-based data augmentation technique that suits the symmetric positive definite (SPD) property of adjacency matrices from biological networks with optimized training efficiency. The interpolation process in R-MIXUP leverages the log-Euclidean distance metrics from the Riemannian manifold, effectively addressing the swelling effect and arbitrarily incorrect label issues of vanilla Mixup. We demonstrate the effectiveness of R-MIXUP with five real-world biological network datasets on both regression and classification tasks. Besides, we derive a commonly ignored necessary condition for identifying the SPD matrices of biological networks and empirically study its influence on the model performance. The code implementation can be found in Appendix E.

cs.LG↗

arXiv2022

Towards a variational Jordan-Lee-Preskill quantum algorithm

Rapid developments of quantum information technology show promising opportunities for simulating quantum field theory in near-term quantum devices. In this work, we formulate the theory of (time-dependent) variational quantum simulation of the 1+1 dimensional $λϕ^4$ quantum field theory including encoding, state preparation, and time evolution, with several numerical simulation results. These algorithms could be understood as near-term variational quantum circuit (quantum neural network) analogs of the Jordan-Lee-Preskill algorithm, the basic algorithm for simulating quantum field theory using universal quantum devices. Besides, we highlight the advantages of encoding with harmonic oscillator basis based on the LSZ reduction formula and several computational efficiency such as when implementing a bosonic version of the unitary coupled cluster ansatz to prepare initial states. We also discuss how to circumvent the "spectral crowding" problem in the quantum field theory simulation and appraise our algorithm by both state and subspace fidelities.

quant-ph↗

arXiv2019

A Global Geometric Approach to Parallel Transport of Strings in Gauge Theory

This paper is motivated by recent developments of higher gauge theory. Different from its style of using higher category theory, we try to describe the concept of higher parallel transport within setting of classical principal bundle theory. From this perspective, we obtain a global geometric proof on a generalized 3-dimensional non-abelian Stokes' theorem related to parallel transport on surfaces. It can be naturally extended to four dimension when the underlying crossed module is replaced by crossed 2-module. This 4-dimensional Stokes' theorem yields a global formula for volume holonomy, and also guarantees its gauge invariance. In the process, we also find composition formulas for parallel transport on volumes which have been seen in the case of surfaces.

math.DG↗