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.
We introduce a framework of the equivariant convolutional quantum algorithms which is tailored for a number of machine-learning tasks on physical systems with arbitrary SU$(d)$ symmetries. It allows us to enhance a natural model of quantum computation -- permutational quantum computing (PQC) -- and define a more powerful model: PQC+. While PQC was shown to be efficiently classically simulatable, we exhibit a problem which can be efficiently solved on PQC+ machine, whereas no classical polynomial time algorithm is known; thus providing evidence against PQC+ being classically simulatable. We further discuss practical quantum machine learning algorithms which can be carried out in the paradigm of PQC+.
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.
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.
Sparse-view 3D reconstruction is increasingly addressed with feed-forward splatting networks that predict explicit primitives directly from images. Yet most existing methods remain centered on Gaussian primitives and expose surfaces only indirectly: extracting a usable mesh for downstream simulation, physics reasoning, or embodied interaction still requires expensive post-hoc steps that break the feed-forward promise. This limitation is especially pronounced in pose-free settings, where scene structure and camera parameters must be estimated jointly from sparse observations. We present TriSplat, a feed-forward reconstruction network that represents scenes with oriented triangle primitives and directly exports simulation-ready mesh scenes from a single forward pass. Given input images, the network predicts local 3D point maps, triangle attributes, camera poses, and optional intrinsics. Rather than regressing triangle orientation as an unconstrained latent variable, our approach constructs geometry normals from the predicted point maps, refines them with an image-conditioned normal head, and converts them into stable local frames for triangle parameterization. A mono-normal bootstrap schedule further stabilizes early training, while opacity and blur scheduling progressively sharpens the learned surface representation for direct mesh extraction. Experiments on RealEstate10K and DL3DV show that this representation produces more geometry-faithful reconstructions than Gaussian feed-forward baselines while maintaining competitive novel-view rendering quality. Because the rendering primitives are themselves surface triangles, the output can be directly ingested by physics engines, collision detectors, and standard rendering pipelines without any conversion, making it a practical simulation-ready solution for feed-forward 3D scene reconstruction.
As semiconductor technology nodes scale, computational lithography is essential for ensuring yield and performance. However, lithography is a continuous physical process involving mask optimization, optical imaging, resist exposure, and development, which existing models fail to capture. To overcome this limitation, we present LithoDreamer, the first physics-informed World Model (WM) framework for computational lithography, which formulates the ``Layout-Mask-Resist Image-After Development Image (ADI)'' pipeline as a decision-driven multi-step evolution system. LithoDreamer captures feature changes between adjacent states to model stage-specific physics-informed latent spaces, in which it controls process intervention exploration and drives subsequent state transitions. To achieve interpretable intervention optimization without continuous supervision, we propose a contrastive variational optimization paradigm that contrasts the latent differences between intervention paths with variational evolution constraints, guiding the model to generate evolutions consistent with real lithography physics. Experiments show LithoDreamer achieves state-of-the-art performance in forward evolution and inverse planning. Our lithography dataset is publicly available at GitHub (https://github.com/7jiangyq/lithodreamer.git).
Monocular 3D lane detection is challenging due to the difficulty in capturing depth information from single-camera images. A common strategy involves transforming front-view (FV) images into bird's-eye-view (BEV) space through inverse perspective mapping (IPM), facilitating lane detection using BEV features. However, IPM's flat-ground assumption and loss of contextual information lead to inaccuracies in reconstructing 3D information, especially height. In this paper, we introduce a BEV-based framework to address these limitations and improve 3D lane detection accuracy. Our approach incorporates a Hierarchical Depth-Aware Head that provides multi-scale depth features, mitigating the flat-ground assumption by enhancing spatial awareness across varying depths. Additionally, we leverage Depth Prior Distillation to transfer semantic depth knowledge from a teacher model, capturing richer structural and contextual information for complex lane structures. To further refine lane continuity and ensure smooth lane reconstruction, we introduce a Conditional Random Field module that enforces spatial coherence in lane predictions. Extensive experiments validate that our method achieves state-of-the-art performance in terms of z-axis error and outperforms other methods in the field in overall performance. The code is released at: https://anonymous.4open.science/r/Depth3DLane-DCDD.
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.
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.
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.