arXiv subjects

Zehao Dong

Publications and source records attributed to Zehao Dong.

At least 19 recordsLinked to original sources

arXiv2025

Atomic-Scale Roughness of Freestanding Oxide Membranes Revealed by Electron Ptychography

Freestanding oxide films offer significant potential for integrating exotic quantum functionalities with semiconductor technologies. However, their performance is critically limited by surface roughness and interfacial imperfection caused by dangling bonds, which disrupt coherent interactions and suppress quantum phenomena at heterointerfaces. To address the challenge of structural characterization of surfaces and interfaces, we develop a metrological approach achieving atomic-scale precision in mapping the topography of both free surfaces and buried interfaces within ultrathin oxide heterostructures leveraging three-dimensional structures reconstructed from multislice electron ptychography. This method also allows for counting the number of atoms, even including light elements such as oxygen, along the electron trajectory in electron microscopy, leading to the identification of surface termination in oxide films. The planar-view of measurement geometry, allowing for large field-of-view imaging, provides remarkably rich information and high statistics about the atomic-scale structural inhomogeneities in freestanding membranes. This quantitative analysis provides unprecedented capabilities for correlating structural imperfection with quantum device performance, offering critical insights for engineering robust heterointerfaces in next-generation oxide electronics.

cond-mat.mtrl-sci↗

arXiv2025

Distinct orbital contributions to electronic and magnetic structures in La$_{4}$Ni$_{3}$O$_{10}$

High-T$_c$ superconductivity has recently been discovered in Ruddlesden-Popper phase nickelates under pressure, where the low-energy electronic structure is dominated by Ni $d_{x^2 - y^2}$ and $d_{z^2}$ orbitals. However, the respective roles of these orbitals in superconductivity remain unclear. Here, by combining X-ray absorption, electron energy loss spectroscopy, and density functional theory calculations on La$_{4}$Ni$_{3}$O$_{10}$ single crystals, we identify ligand holes in the $p_{x,y}$ orbitals of planar oxygen and the $p_z$ orbitals of apical oxygen, which hybridize with the Ni $d_{x^2-y^2}$ and $d_{z^2}$ orbitals, respectively. These ligand holes enable orbital-selective O K-edge resonant inelastic X-ray scattering (RIXS) study, which reveals that $d_{x^2-y^2}$ states dominate the low-energy charge excitations and are more itinerant. We also observe a $\sim$0.1 eV bimagnon through RIXS and Raman spectroscopy, which leads to an interlayer superexchange interaction J$_z$ of $\sim$50 meV. Our results reveal distinct contributions of Ni $d_{x^2-y^2}$ and $d_{z^2}$ orbitals to the electronic and magnetic structure and provide direct experimental insights to understand the RP-phase nickelate superconductors.

cond-mat.supr-con↗

arXiv2025

Interstitial oxygen order and its competition with superconductivity in La$_2$PrNi$_2$O$_{7+δ}$

High-temperature superconductivity in bilayer nickelate La$_3$Ni$_2$O$_7$ under pressure has attracted significant interest in condensed matter physics. While early samples exhibited limited superconducting volume fractions, Pr substitution for La enabled bulk superconductivity in polycrystals under pressure and enhanced transition temperatures in thin films at ambient pressure. Beyond rare-earth doping, moderate oxygen or ozone annealing improves superconductivity by mitigating oxygen vacancies, whereas high-pressure oxygen annealing leads to a trivial, non-superconducting metallic state across all pressure regimes. These findings highlight the need to elucidate both the individual and combined effects of Pr doping and oxygen stoichiometry in modulating superconductivity in bilayer nickelates. Here, using multislice electron ptychography and electron energy-loss spectroscopy, we investigate the structural and electronic properties of as-grown La$_2$PrNi$_2$O$_7$ and high-pressure-oxygen-annealed La$_2$PrNi$_2$O$_{7+δ}$ polycrystals. We find that Pr dopants preferentially occupy outer La sites, effectively eliminating inner-apical oxygen vacancies and ensuring near-stoichiometry in as-grown La$_2$PrNi$_2$O$_7$ that is bulk-superconducting under pressure. In contrast, high-pressure oxygen annealing induces a striped interstitial oxygen order, introducing quasi-1D lattice potentials and excess hole carriers into p-d hybridized orbitals, ultimately suppressing superconductivity. This behavior starkly contrasts with cuprate superconductors, where similar interstitial oxygen ordering enhances superconductivity instead. Our findings reveal a competition between striped interstitial oxygen order and superconductivity in bilayer nickelates, offering key insights into their distinct pairing mechanisms and providing a roadmap for designing more robust superconducting phases.

cond-mat.supr-con↗

arXiv2025

Atomic-Scale Heterogeneity of Hydrogen in Metal Hydrides Revealed by Electron Ptychography

Hydrogen plays critical roles in materials science, particularly for advancing technologies in hydrogen storage and phase manipulation, while also posing challenges like hydrogen embrittlement. Understanding its behavior, vital for improving material properties, requires precise determination of atomic-scale distribution-a persistent challenge due to hydrogen's weak electron scattering and high mobility, as well as the limitations of conventional transmission electron microscopy. We demonstrate that multislice electron ptychography (MEP) overcomes these constraints through three key advances: exceptional sensitivity for hydrogen occupancy, three-dimensional quantification, and picometer-level precision in atomic positioning. Experimentally, MEP resolves heterogeneous hydrogen distributions and quantifies hydrogen-induced lattice displacements with picometer precision in multi-principal-element alloy hydrides. This work demonstrates MEP as a transformative method for directly probing hydrogen atoms in solids, unlocking fundamental understanding of hydrogen's impact on material properties.

cond-mat.mtrl-sci↗

arXiv2024

Sub-nanometer depth resolution and single dopant visualization achieved by tilt-coupled multislice electron ptychography

Real-space imaging of three-dimensional atomic structures is a critical yet challenging task in materials science. Although scanning transmission electron microscopy has achieved sub-angstrom lateral resolution through techniques like electron ptychography1,2, depth resolution remains limited to only 2 to 3 nanometers with a single projection setup3,4. Attaining better depth resolution typically necessitates large sample tilt angles and many projections, as seen in atomic electron tomography5,6. Here, we develop a new algorithm based on multislice electron ptychography which couples only a few projections at small tilt angles, but is sufficient to improve the depth resolution by more than threefold to the sub-nanometer scale, and potentially to the atomic level. This technique maintains high resolving power for both light and heavy atoms, and significantly improves the visibility of single dopants. We are thus able to experimentally detect dilute substitutional praseodymium dopants in a brownmillerite oxide, Ca2Co2O5, in three dimensions and observe the accompanying lattice distortion. This technique requires only a moderate level of data acquisition or processing, and can be seamlessly integrated into electron microscopes equipped with conventional components.

cond-mat.mtrl-sci↗

arXiv2024

Antiferromagnetic Quantum Anomalous Hall Effect Modulated by Spin Flips and Flops

The interplay between nontrivial band topology and layered antiferromagnetism in MnBi2Te4 has opened up a new avenue for exploring topological phases of matter. Representative examples include the quantum anomalous Hall effect and axion insulator state observed in odd and even number layers of MnBi2Te4, when the top and bottom surfaces have parallel and antiparallel spin alignments respectively. The rich and complex spin dynamics associated with the van der Waals antiferromagnetic order is expected to generate novel topological phases and phase transitions that are unique to MnBi2Te4. Here we fabricate a device of 7-septuple-layer MnBi2Te4 covered with AlOx capping layer, which enables the investigation of antiferromagnetic quantum anomalous Hall effect over wide parameter spaces. By tuning the gate voltage and perpendicular magnetic field, we uncover a cascade of quantum phase transitions that can be attributed to the influence of spin configurations on charge transport. Furthermore, we find that an in-plane magnetic field enhances both the coercive field and exchange gap of the surface state, in sharp contrast to that in ferromagnetic quantum anomalous Hall state. We propose that these peculiar features arise from the spin flip and flop transitions inherent to van der Waals antiferromagnet. The versatile tunability of the quantum anomalous Hall effect in MnBi2Te4 paves the way for potential applications in topological antiferromagnetic spintronics.

cond-mat.mtrl-sci↗

arXiv2024

SPGNN: Recognizing Salient Subgraph Patterns via Enhanced Graph Convolution and Pooling

Graph neural networks (GNNs) have revolutionized the field of machine learning on non-Euclidean data such as graphs and networks. GNNs effectively implement node representation learning through neighborhood aggregation and achieve impressive results in many graph-related tasks. However, most neighborhood aggregation approaches are summation-based, which can be problematic as they may not be sufficiently expressive to encode informative graph structures. Furthermore, though the graph pooling module is also of vital importance for graph learning, especially for the task of graph classification, research on graph down-sampling mechanisms is rather limited. To address the above challenges, we propose a concatenation-based graph convolution mechanism that injectively updates node representations to maximize the discriminative power in distinguishing non-isomorphic subgraphs. In addition, we design a novel graph pooling module, called WL-SortPool, to learn important subgraph patterns in a deep-learning manner. WL-SortPool layer-wise sorts node representations (i.e. continuous WL colors) to separately learn the relative importance of subtrees with different depths for the purpose of classification, thus better characterizing the complex graph topology and rich information encoded in the graph. We propose a novel Subgraph Pattern GNN (SPGNN) architecture that incorporates these enhancements. We test the proposed SPGNN architecture on many graph classification benchmarks. Experimental results show that our method can achieve highly competitive results with state-of-the-art graph kernels and other GNN approaches.

cs.LG↗

arXiv2024

Large-Language-Model Empowered Dose Volume Histogram Prediction for Intensity Modulated Radiotherapy

Treatment planning is currently a patient specific, time-consuming, and resource demanding task in radiotherapy. Dose-volume histogram (DVH) prediction plays a critical role in automating this process. The geometric relationship between DVHs in radiotherapy plans and organs-at-risk (OAR) and planning target volume (PTV) has been well established. This study explores the potential of deep learning models for predicting DVHs using images and subsequent human intervention facilitated by a large-language model (LLM) to enhance the planning quality. We propose a pipeline to convert unstructured images to a structured graph consisting of image-patch nodes and dose nodes. A novel Dose Graph Neural Network (DoseGNN) model is developed for predicting DVHs from the structured graph. The proposed DoseGNN is enhanced with the LLM to encode massive knowledge from prescriptions and interactive instructions from clinicians. In this study, we introduced an online human-AI collaboration (OHAC) system as a practical implementation of the concept proposed for the automation of intensity-modulated radiotherapy (IMRT) planning. In comparison to the widely-employed DL models used in radiotherapy, DoseGNN achieved mean square errors that were 80$\%$, 76$\%$ and 41.0$\%$ of those predicted by Swin U-Net Transformer, 3D U-Net CNN and vanilla MLP, respectively. Moreover, the LLM-empowered DoseGNN model facilitates seamless adjustment to treatment plans through interaction with clinicians using natural language.

cs.AI↗

arXiv2024

Highly Accurate Disease Diagnosis and Highly Reproducible Biomarker Identification with PathFormer

Biomarker identification is critical for precise disease diagnosis and understanding disease pathogenesis in omics data analysis, like using fold change and regression analysis. Graph neural networks (GNNs) have been the dominant deep learning model for analyzing graph-structured data. However, we found two major limitations of existing GNNs in omics data analysis, i.e., limited-prediction (diagnosis) accuracy and limited-reproducible biomarker identification capacity across multiple datasets. The root of the challenges is the unique graph structure of biological signaling pathways, which consists of a large number of targets and intensive and complex signaling interactions among these targets. To resolve these two challenges, in this study, we presented a novel GNN model architecture, named PathFormer, which systematically integrate signaling network, priori knowledge and omics data to rank biomarkers and predict disease diagnosis. In the comparison results, PathFormer outperformed existing GNN models significantly in terms of highly accurate prediction capability ( 30% accuracy improvement in disease diagnosis compared with existing GNN models) and high reproducibility of biomarker ranking across different datasets. The improvement was confirmed using two independent Alzheimer's Disease (AD) and cancer transcriptomic datasets. The PathFormer model can be directly applied to other omics data analysis studies.

q-bio.GN↗

arXiv2024

CktGNN: Circuit Graph Neural Network for Electronic Design Automation

The electronic design automation of analog circuits has been a longstanding challenge in the integrated circuit field due to the huge design space and complex design trade-offs among circuit specifications. In the past decades, intensive research efforts have mostly been paid to automate the transistor sizing with a given circuit topology. By recognizing the graph nature of circuits, this paper presents a Circuit Graph Neural Network (CktGNN) that simultaneously automates the circuit topology generation and device sizing based on the encoder-dependent optimization subroutines. Particularly, CktGNN encodes circuit graphs using a two-level GNN framework (of nested GNN) where circuits are represented as combinations of subgraphs in a known subgraph basis. In this way, it significantly improves design efficiency by reducing the number of subgraphs to perform message passing. Nonetheless, another critical roadblock to advancing learning-assisted circuit design automation is a lack of public benchmarks to perform canonical assessment and reproducible research. To tackle the challenge, we introduce Open Circuit Benchmark (OCB), an open-sourced dataset that contains $10$K distinct operational amplifiers with carefully-extracted circuit specifications. OCB is also equipped with communicative circuit generation and evaluation capabilities such that it can help to generalize CktGNN to design various analog circuits by producing corresponding datasets. Experiments on OCB show the extraordinary advantages of CktGNN through representation-based optimization frameworks over other recent powerful GNN baselines and human experts' manual designs. Our work paves the way toward a learning-based open-sourced design automation for analog circuits. Our source code is available at \url{https://github.com/zehao-dong/CktGNN}.

cs.LG↗

arXiv2024

Rethinking the Power of Graph Canonization in Graph Representation Learning with Stability

The expressivity of Graph Neural Networks (GNNs) has been studied broadly in recent years to reveal the design principles for more powerful GNNs. Graph canonization is known as a typical approach to distinguish non-isomorphic graphs, yet rarely adopted when developing expressive GNNs. This paper proposes to maximize the expressivity of GNNs by graph canonization, then the power of such GNNs is studies from the perspective of model stability. A stable GNN will map similar graphs to close graph representations in the vectorial space, and the stability of GNNs is critical to generalize their performance to unseen graphs. We theoretically reveal the trade-off of expressivity and stability in graph-canonization-enhanced GNNs. Then we introduce a notion of universal graph canonization as the general solution to address the trade-off and characterize a widely applicable sufficient condition to solve the universal graph canonization. A comprehensive set of experiments demonstrates the effectiveness of the proposed method. In many popular graph benchmark datasets, graph canonization successfully enhances GNNs and provides highly competitive performance, indicating the capability and great potential of proposed method in general graph representation learning. In graph datasets where the sufficient condition holds, GNNs enhanced by universal graph canonization consistently outperform GNN baselines and successfully improve the SOTA performance up to $31\%$, providing the optimal solution to numerous challenging real-world graph analytical tasks like gene network representation learning in bioinformatics.

cs.LG↗

arXiv2024

DoseGNN: Improving the Performance of Deep Learning Models in Adaptive Dose-Volume Histogram Prediction through Graph Neural Networks

Dose-Volume Histogram (DVH) prediction is fundamental in radiation therapy that facilitate treatment planning, dose evaluation, plan comparison and etc. It helps to increase the ability to deliver precise and effective radiation treatments while managing potential toxicities to healthy tissues as needed to reduce the risk of complications. This paper extends recently disclosed research findings presented on AAPM (AAPM 65th Annual Meeting $\&$ Exhibition) and includes necessary technique details. The objective is to design efficient deep learning models for DVH prediction on general radiotherapy platform equipped with high performance CBCT system, where input CT images and target dose images to predict may have different origins, spacing and sizes. Deep learning models widely-adopted in DVH prediction task are evaluated on the novel radiotherapy platform, and graph neural networks (GNNs) are shown to be the ideal architecture to construct a plug-and-play framework to improve predictive performance of base deep learning models in the adaptive setting.

cs.LG↗

arXiv2023

Visualization of Oxygen Vacancies and Self-doped Ligand Holes in La3Ni2O7-δ

The recent discovery of superconductivity in La3Ni2O7-δ under high pressure with a transition temperature around 80 K has sparked extensive experimental and theoretical efforts. Several key questions regarding the pairing mechanism remain to be answered, such as the most relevant atomic orbitals and the role of atomic deficiencies. Here, we develop a new energy-filtered multislice electron ptychography technique, assisted with electron energy loss spectroscopy, to address these critical issues. Oxygen vacancies are directly visualized and are found to primarily occupy the inner apical sites, which have been proposed to be crucial to superconductivity. We precisely determine the nanoscale stoichiometry and its correlation to the oxygen K edge spectra, which reveals a significant inhomogeneity in the oxygen content and electronic structure within the sample. The spectroscopic results also unveil that stoichiometric La3Ni2O7 is in the charge-transfer regime, with holes that are self-doped from Ni sites into O sites. The outer apical oxygen is found to be less relevant to the low-energy physics and can be safely disregarded in theoretical models. These observations will assist in further development and understanding of superconducting nickelate materials. Our imaging technique for quantifying atomic deficiencies can also be widely applied in materials science and condensed matter physics.

cond-mat.supr-con↗

arXiv2023

GNNHLS: Evaluating Graph Neural Network Inference via High-Level Synthesis

With the ever-growing popularity of Graph Neural Networks (GNNs), efficient GNN inference is gaining tremendous attention. Field-Programming Gate Arrays (FPGAs) are a promising execution platform due to their fine-grained parallelism, low-power consumption, reconfigurability, and concurrent execution. Even better, High-Level Synthesis (HLS) tools bridge the gap between the non-trivial FPGA development efforts and rapid emergence of new GNN models. In this paper, we propose GNNHLS, an open-source framework to comprehensively evaluate GNN inference acceleration on FPGAs via HLS, containing a software stack for data generation and baseline deployment, and FPGA implementations of 6 well-tuned GNN HLS kernels. We evaluate GNNHLS on 4 graph datasets with distinct topologies and scales. The results show that GNNHLS achieves up to 50.8x speedup and 423x energy reduction relative to the CPU baselines. Compared with the GPU baselines, GNNHLS achieves up to 5.16x speedup and 74.5x energy reduction.

cs.LG↗

arXiv2023

Visualizing the Zhang-Rice singlet, molecular orbitals and pair formation in cuprate

The parent compound of cuprates is a charge-transfer-type Mott insulator with strong hybridization between the Cu $3d_{\mathrm x^2-y^2}$ and O $2p$ orbitals. A key question concerning the pairing mechanism is the behavior of doped holes in the antiferromagnetic (AF) Mott insulator background, which is a prototypical quantum many-body problem. It was proposed that doped hole on the O site tends to form a singlet, known as Zhang-Rice singlet (ZRS), with the unpaired Cu spin. But experimentally little is known about the properties of a single hole and the interplay between them that leads to superconductivity. Here we use scanning tunneling microscopy to visualize the electronic states in hole-doped $\mathrm{Ca_2CuO_2Cl_2}$, aiming to establish the atomic-scale local basis for pair formation. A single doped hole is shown to have an in-gap state and a clover-shaped spatial distribution that can be attributed to a localized ZRS. When the dopants are close enough, they develop delocalized molecular orbitals with characteristic stripe- and ladder-shaped patterns, accompanied by the opening of a small gap around the Fermi level ($E_{\mathrm F}$). With increasing doping, the molecular orbitals proliferate in space and gradually form densely packed plaquettes, but the stripe and ladder patterns remain nearly the same. The low-energy electronic states of the molecular orbitals are intimately related to the local pairing properties, thus play a vitally important role in the emergence of superconductivity. We propose that the Cooper pair is formed by two holes occupying the stripe-like molecular orbital, while the attractive interaction is mediated by the AF spin background.

cond-mat.supr-con↗

arXiv2023

Interpreting the Mechanism of Synergism for Drug Combinations Using Attention-Based Hierarchical Graph Pooling

Synergistic drug combinations provide huge potentials to enhance therapeutic efficacy and to reduce adverse reactions. However, effective and synergistic drug combination prediction remains an open question because of the unknown causal disease signaling pathways. Though various deep learning (AI) models have been proposed to quantitatively predict the synergism of drug combinations, the major limitation of existing deep learning methods is that they are inherently not interpretable, which makes the conclusions of AI models untransparent to human experts, henceforth limiting the robustness of the model conclusion and the implementation ability of these models in real-world human--AI healthcare. In this paper, we develop an interpretable graph neural network (GNN) that reveals the underlying essential therapeutic targets and the mechanism of the synergy (MoS) by mining the sub-molecular network of great importance. The key point of the interpretable GNN prediction model is a novel graph pooling layer, a self-attention-based node and edge pool (henceforth SANEpool), that can compute the attention score (importance) of genes and connections based on the genomic features and topology. As such, the proposed GNN model provides a systematic way to predict and interpret the drug combination synergism based on the detected crucial sub-molecular network. Experiments on various well-adopted drug-synergy-prediction datasets demonstrate that (1) the SANEpool model has superior predictive ability to generate accurate synergy score prediction, and (2) the sub-molecular networks detected by the SANEpool are self-explainable and salient for identifying synergistic drug combinations.

q-bio.QM↗

arXiv2023

The emergence of global phase coherence from local pairing in underdoped cuprates

In conventional metal superconductors such as aluminum, the large number of weakly bounded Cooper pairs become phase coherent as soon as they start to form. The cuprate high critical temperature ($T_c$) superconductors, in contrast, belong to a distinctively different category. To account for the high $T_c$, the attractive pairing interaction is expected to be strong and the coherence length is short. Being doped Mott insulators, the cuprates are known to have low superfluid density, thus are susceptible to phase fluctuations. It has been proposed that pairing and phase coherence may occur separately in cuprates, and $T_c$ corresponds to the phase coherence temperature controlled by the superfluid density. To elucidate the microscopic processes of pairing and phase ordering in cuprates, here we use scanning tunneling microscopy to image the evolution of electronic states in underdoped $\rm Bi_2La_xSr_{2-x}CuO_{6+δ}$. Even in the insulating sample, we observe a smooth crossover from the Mott insulator to superconductor-type spectra on small islands with chequerboard order and emerging quasiparticle interference patterns following the octet model. Each chequerboard plaquette contains approximately two holes, and exhibits a stripy internal structure that has strong influence on the superconducting features. Across the insulator to superconductor boundary, the local spectra remain qualitatively the same while the quasiparticle interferences become long-ranged. These results suggest that the chequerboard plaquette with internal stripes plays a crucial role on local pairing in cuprates, and the global phase coherence is established once its spatial occupation exceeds a threshold.

cond-mat.supr-con↗

arXiv2023

Time Associated Meta Learning for Clinical Prediction

Rich Electronic Health Records (EHR), have created opportunities to improve clinical processes using machine learning methods. Prediction of the same patient events at different time horizons can have very different applications and interpretations; however, limited number of events in each potential time window hurts the effectiveness of conventional machine learning algorithms. We propose a novel time associated meta learning (TAML) method to make effective predictions at multiple future time points. We view time-associated disease prediction as classification tasks at multiple time points. Such closely-related classification tasks are an excellent candidate for model-based meta learning. To address the sparsity problem after task splitting, TAML employs a temporal information sharing strategy to augment the number of positive samples and include the prediction of related phenotypes or events in the meta-training phase. We demonstrate the effectiveness of TAML on multiple clinical datasets, where it consistently outperforms a range of strong baselines. We also develop a MetaEHR package for implementing both time-associated and time-independent few-shot prediction on EHR data.

cs.LG↗