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At least 325 records · Page 18

Experimental Observations of the Topology of Convolutional Neural Network Activations

Topological data analysis (TDA) is a branch of computational mathematics, bridging algebraic topology and data science, that provides compact, noise-robust representations of complex structures. Deep neural networks (DNNs) learn millions of parameters associated with a series of transformations defined by the model architecture resulting in high-dimensional, difficult to interpret internal representations of input data. As DNNs become more ubiquitous across multiple sectors of our society, there is increasing recognition that mathematical methods are needed to aid analysts, researchers, and practitioners in understanding and interpreting how these models' internal representations relate to the final classification. In this paper we apply cutting edge techniques from TDA with the goal of gaining insight towards interpretability of convolutional neural networks used for image classification. We use two common TDA approaches to explore several methods for modeling hidden layer activations as high-dimensional point clouds, and provide experimental evidence that these point clouds capture valuable structural information about the model's process. First, we demonstrate that a distance metric based on persistent homology can be used to quantify meaningful differences between layers and discuss these distances in the broader context of existing representational similarity metrics for neural network interpretability. Second, we show that a mapper graph can provide semantic insight as to how these models organize hierarchical class knowledge at each layer. These observations demonstrate that TDA is a useful tool to help deep learning practitioners unlock the hidden structures of their models.

topological data analysis, deep learning↗

AMORE-Isoprene v1.0: a new reduced mechanism for gas-phase isoprene oxidation

Abstract. Gas-phase oxidation of isoprene by ozone (O3) and the hydroxyl (OH) and nitrate (NO3) radicals significantly impacts tropospheric oxidant levels and secondary organic aerosol formation. The most comprehensive and up-to-date chemical mechanism for isoprene oxidation consists of several hundred species and over 800 reactions. Therefore, the computational expense of including the entire mechanism in large-scale atmospheric chemical transport models is usually prohibitive, and most models employ reduced isoprene mechanisms ranging in size from ∼ 10 to ∼ 200 species. We have developed a new reduced isoprene oxidation mechanism using a directed-graph path-based automated model reduction approach, with minimal manual adjustment of the output mechanism. The approach takes as inputs a full isoprene oxidation mechanism, the environmental parameter space, and a list of priority species which are protected from elimination during the reduction process. Our reduced mechanism, AMORE-Isoprene (where AMORE stands for Automated Model Reduction), consists of 12 species which are unique to the isoprene mechanism as well as 22 reactions. We demonstrate its performance in a box model in comparison with experimental data from the literature and other current isoprene oxidation mechanisms. AMORE-Isoprene's performance with respect to predicting the time evolution of isoprene oxidation products, including isoprene epoxydiols (IEPOX) and formaldehyde, is favorable compared with other similarly sized mechanisms. When AMORE-Isoprene is included in the Community Regional Atmospheric Chemistry Multiphase Mechanism 1.0 (CRACMM1AMORE) in the Community Multiscale Air Quality Model (CMAQ, v5.3.3), O3 and formaldehyde agreement with Environmental Protection Agency (EPA) Air Quality System observations is improved. O3 bias is reduced by 3.4 ppb under daytime conditions for O3 concentrations over 50 ppb. Formaldehyde bias is reduced by 0.26 ppb on average for all formaldehyde measurements compared with the base CRACMM1. There was no significant change in computation time between CRACMM1AMORE and the base CRACMM. AMORE-Isoprene shows a 35 % improvement in agreement between simulated IEPOX concentrations and chamber data over the base CRACMM1 mechanism when compared in the Framework for 0-D Atmospheric Modeling (F0AM) box model framework. This work demonstrates a new highly reduced isoprene mechanism and shows the potential value of automated model reduction for complex reaction systems.

58 GEOSCIENCES↗

Accelerating Scientific Computing in the Post-Moore’s Era

Novel uses of graphical processing units for accelerated computation revolutionized the field of high-performance scientific computing by providing specialized workflows tailored to algorithmic requirements. As the era of Moore’s law draws to a close, many new non–von Neumann processors are emerging as potential computational accelerators, including those based on the principles of neuromorphic computing, tensor algebra, and quantum information. While development of these new processors is continuing to mature, the potential impact on accelerated computing is anticipated to be profound. We discuss how different processing models can advance computing in key scientific paradigms: machine learning and constraint satisfaction. Significantly, each of these new processor types utilizes a fundamentally different model of computation, and this raises questions about how to best use such processors in the design and implementation of applications. While many processors are being developed with a specific domain target, the ubiquity of spin-glass models and neural networks provides an avenue for multi-functional applications. Furthermore, this also hints at the infrastructure needed to integrate next-generation processing units into future high-performance computing systems.

97 MATHEMATICS AND COMPUTING↗

Real-Time event reconstruction for Nuclear Physics Experiments using Artificial Intelligence

Charged track reconstruction is a critical task in nuclear physics experiments, enabling the identification and analysis of particles produced in high-energy collisions. Machine learning (ML) has emerged as a powerful tool for this purpose, addressing the challenges posed by complex detector geometries, high event multiplicities, and noisy data. Traditional methods rely on pattern recognition algorithms like the Kalman filter, but ML techniques, such as neural networks, graph neural networks (GNNs), and recurrent neural networks (RNNs), offer improved accuracy and scalability. By learning from simulated and real detector data, ML models can identify and classify tracks, predict trajectories, and handle ambiguities caused by overlapping or missing hits. Moreover, ML-based approaches can process data in near-real-time, enhancing the efficiency of experiments at large-scale facilities like the Large Hadron Collider (LHC) and Jefferson Lab (JLAB). As detector technologies and computational resources evolve, ML-driven charged track reconstruction continues to push the boundaries of precision and discovery in nuclear physics. In these proceedings, we highlight advancements in charged track identification leveraging Artificial Intelligence within the CLAS12 detector, achieving a notable enhancement in experimental statistics compared to traditional methods. Additionally, we showcase real-time event reconstruction capabilities, including the inference of charged particle properties, such as momentum, direction, and species identification, at speeds matching data acquisition rates. These innovations enable the extraction of physics observables directly from the experiment in real-time.

Gavalian, Gagik (ORCID:0000000267385457)↗

EvoDiffMol: evolutionary diffusion framework for 3D molecular design with optimized properties

Designing molecules with specific target properties remains a fundamental challenge in computational chemistry. While existing approaches show promise, most rely on simplified representations like SMILES strings or 2D graphs that lack essential three-dimensional geometric information. We present EvoDiffMol, a computational framework that integrates evolutionary algorithms with three-dimensional diffusion models for property-driven molecular generation. The method operates through adaptive evolutionary optimization, where population-based selection guides the generation process toward desired property landscapes. EvoDiffMol supports both unconstrained molecular design and scaffold-constrained generation that preserves fixed substructures while optimizing complementary regions. Comprehensive evaluation demonstrates exceptional performance, achieving the highest drug-likeness score (0.94) among all compared state-of-the-art methods while maintaining excellent validity, uniqueness, and novelty. Beyond single property optimization, the framework demonstrates flexible multi-property optimization capabilities, simultaneously controlling multiple molecular descriptors including synthetic accessibility, lipophilicity, topological polar surface area, and clinically relevant ADMET properties such as cardiotoxicity (hERG) and intestinal permeability (Caco-2). This adaptability spans from simple descriptors to practical pharmaceutical endpoints without requiring complete model retraining. The framework achieves precise control over target property values, generating molecules with properties closely matching specified targets for both single and multiple descriptors. Scaffold-constrained experiments preserve fixed molecular cores while maintaining effective property optimization. The three-dimensional representation offers advantages in maintaining structural validity during iterative optimization, with potential for geometry-aware applications in materials science and drug discovery.

3D molecular generation↗

Benders Decomposition Using Graph Modeling and Multi-Parametric Programming

Benders decomposition is a widely used method for solving large and structured optimization problems, but its performance is affected by the repeated solution of subproblems. We propose a flexible and modular algorithmic framework for accelerating Benders decomposition. Specifically, we express the problem structure by using a graph-theoretic modeling abstraction in which nodes represent optimization subproblems and edges represent connectivity between subproblems. A key innovation of our approach is that we embed multiparametric programming (mp) surrogates for node subproblems, which maps the exact analytical map of the subproblem solution space. The use of mp surrogates allows us to replace subproblem solves with fast look-ups and function evaluations for primal and dual variables during the iterative Benders process. We formally show the equivalence between classical Benders cuts and those derived from the mp solution. We implement our framework in the open-source PlasmoBenders.jl software package. To demonstrate the capabilities of the proposed framework, we apply it to a two-stage stochastic programming problem, which aims to make optimal capacity expansion decisions under market uncertainty. We evaluate both single-cut and multicut variants of Benders decomposition and show that the use of mp surrogates achieves substantial speedups in subproblem solve time, while preserving the convergence guarantees of Benders decomposition. We highlight advantages in solution analysis and interpretability that is enabled by mp critical region tracking; specifically, we show that these reveal how decisions evolve geometrically across the Benders search. Our results aim to demonstrate that combining surrogate modeling with graph modeling offers a promising and extensible foundation for structure-exploiting decomposition. In addition, by decomposing the problem into more tractable subproblems, the proposed approach also aims to overcome scalability issues of mp. Finally, the use of mp surrogates provides a unifying and modular optimization framework that enables the representation of heterogeneous node subproblems as modeling objects with a homogeneous structure.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Adaptive continuity-preserving simplification of street networks

Street network data is widely used to study human-based activities and urban structure. Often, these data are geared towards transportation applications, which require highly granular, directed graphs that capture the complex relationships of potential traffic patterns. While this level of network detail is critical for certain fine-grained mobility models, it represents a hindrance for studies concerned with the morphology of the street network. For the latter case, street network simplification — the process of converting a highly granular input network into its most simple morphological form — is a necessary, but highly tedious preprocessing step, especially when conducted manually. In this manuscript, we develop and present a novel adaptive algorithm for simplifying street networks that is both fully automated and able to mimic results obtained through a manual simplification routine. The algorithm — available in the neatnet Python package — outperforms current state-of-the-art procedures when comparing those methods to manually, human-simplified data, while preserving network continuity.

Python↗

Comparing three generations of D-Wave quantum annealers for minor embedded combinatorial optimization problems

Abstract Quantum annealing (QA) is a novel type of analog computation that aims to use quantum mechanical fluctuations to search for optimal solutions of Ising problems. QA in the transverse Ising model, implemented on D-Wave quantum processing units, are available as cloud computing resources. In this study we report concise benchmarks across three generations of D-Wave quantum annealers, consisting of four different devices, for the NP-hard discrete combinatorial optimization problems unweighted maximum clique and unweighted maximum cut on random graphs. The Ising, or equivalently quadratic unconstrained binary optimization, formulation of these problems do not require auxiliary variables for order reduction, and their overall structure and weights are not highly variable, which makes these problems simple test cases to understand the sampling capability of current D-Wave quantum annealers. All-to-all minor embeddings of size 52, with relatively uniform chain lengths, are used for a direct comparison across the Chimera, Pegasus, and Zephyr device topologies. A grid-search over annealing times and the minor embedding chain strengths is performed in order to determine the level of reasonable performance for each device and problem type. Experiment metrics that are reported are approximation ratios for non-broken chain samples, chain break proportions, and time-to-solution for the maximum clique problem instances. How fairly the quantum annealers sample optimal maximum cliques, for instances which contain multiple maximum cliques, is quantified using entropy of the measured ground state distributions. The newest generation of quantum annealing hardware, which has a Zephyr hardware connectivity, performed the best overall with respect to approximation ratios and chain break frequencies.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Harnessing distributed GPU computing for generalizable graph convolutional networks in power grid reliability assessments

Although machine learning (ML) has emerged as a powerful tool for rapidly assessing grid contingencies, prior studies have largely considered a static grid topology in their analyses. This limits their application, since they need to be re-trained for every new topology. Here, this paper explores the development of generalizable graph convolutional network (GCN) models by pre-training them across a range of grid topologies and contingency types. We found that a GCN model with auto-regressive moving average (ARMA) layers with a line graph representation of the grid offered the best predictive performance in predicting voltage magnitudes (VM) and voltage angles (VA). We introduced the concept of phantom nodes to consider disparate grid topologies with a varying number of nodes and lines. For pre-training the GCN ARMA model across a variety of topologies, distributed graphics processing unit (GPU) computing afforded us significant training scalability. The predictive performance of this model on grid topologies that were part of the training data is substantially better than the direct current (DC) approximation. Although direct application of the pre-trained model to topologies that are not part of the grid is not particularly satisfactory, fine-tuning with small amounts of data from a specific topology of interest significantly improves predictive performance. In general, this paper highlights the feasibility of training large-scale GNN models to assess the reliability of power grids by considering a wide variety of grid topologies and contingency types. With the advent of foundational models in ML and the exponential increase in GPU computing clusters, generalizable ML models will significantly enhance how utilities manage power systems and make decisions in real-time or near-real-time.

24 - POWER TRANSMISSION AND DISTRIBUTION↗

Ensuring thermodynamic consistency with invertible coarse-graining

Coarse-grained models are a core computational tool in theoretical chemistry and biophysics. A judicious choice of a coarse-grained model can yield physical insights by isolating the essential degrees of freedom that dictate the thermodynamic properties of a complex, condensed-phase system. The reduced complexity of the model typically leads to lower computational costs and more efficient sampling compared with atomistic models. Designing “good” coarse-grained models is an art. Generally, the mapping from fine-grained configurations to coarse-grained configurations itself is not optimized in any way; instead, the energy function associated with the mapped configurations is. In this work, we explore the consequences of optimizing the coarse-grained representation alongside its potential energy function. We use a graph machine learning framework to embed atomic configurations into a low-dimensional space to produce efficient representations of the original molecular system. Because the representation we obtain is no longer directly interpretable as a real-space representation of the atomic coordinates, we also introduce an inversion process and an associated thermodynamic consistency relation that allows us to rigorously sample fine-grained configurations conditioned on the coarse-grained sampling. We illustrate that this technique is robust, recovering the first two moments of the distribution of several observables in proteins such as chignolin and alanine dipeptide.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

An Intelligent Garbage Sorting System Based on Edge Computing and Visual Understanding of Social Internet of Vehicles

In order to enable Social Internet of Vehicles devices to achieve the purpose of intelligent and autonomous garbage classification in a public environment, while avoiding network congestion caused by a large amount of data accessing the cloud at the same time, it is therefore considered to combine mobile edge computing with Social Internet of Vehicles to give full play to mobile edge computing features of high bandwidth and low latency. At the same time, based on cutting-edge technologies such as deep learning, knowledge graph, and 5G transmission, the paper builds an intelligent garbage sorting system based on edge computing and visual understanding of Social Internet of Vehicles. First of all, for the massive multisource heterogeneous Social Internet of Vehicles big data in the public environment, different item modal data adopts different processing methods, aiming to obtain a visual understanding model. Secondly, using the 5G network, the model is deployed on the edge device and the cloud for cloud-side collaborative management, aiming to avoid the waste of edge node resources, while ensuring the data privacy of the edge node. Finally, the Social Internet of Vehicles devices is used to make intelligent decision-making on the big data of the items. First, the items are judged as garbage, and then the category is judged, and finally the task of grabbing and sorting is realized. The experimental results show that the system proposed in this paper can efficiently process the big data of Social Internet of Vehicles and make valuable intelligent decisions. At the same time, it also has a certain role in promoting the promotion of Social Internet of Vehicles devices.

Shen, Xuehao↗

A Data Processing Pipeline for Socio-Technical Network Analysis [Slides]

With the rapid adoption of emerging technologies, there is a need to catalog and model sociotechnical interdependencies that have been historically used to influence the operation of Critical Infrastructure networks including the impacts of mergers and acquisitions, hostile takeovers, and foreign investment. Our research intends to address this need with two primary contributions. First, we have developed a data curation and processing pipeline to generate sociotechnical networks extracted from a variety of data sources including SEC filings and infrastructure asset databases. The pipeline, implemented in Apache Airflow, extracts and normalizes the representation of entities and relations, specified within ontologies. Second, networks produced by our pipeline enable the development of graph-theoretic metrics that consider the properties of network components in addition to its topology. Measures of network complexity, such as degree distribution, reachability analyses, temporal analysis, and community detection may be adapted to indicate adversarial organizational influence. Our intent is to provide an extensible, machine-actionable approach to quickly communicate such models, reproduce previous results, and adapt them to new, unanticipated situations.

97 MATHEMATICS AND COMPUTING↗

Leveraging Structured Biological Knowledge for Counterfactual Inference: A Case Study of Viral Pathogenesis

Counterfactual inference is a useful tool for comparing outcomes of interventions on complex systems. It requires us to represent the system in form of a structural causal model, complete with a causal diagram, probabilistic assumptions on exogenous variables, and functional assignments. Specifying such models can be extremely difficult in practice. The process requires substantial domain expertise, and does not scale easily to large systems, multiple systems, or novel system modifications. At the same time, many application domains, such as molecular biology, are rich in structured causal knowledge that is qualitative in nature. This manuscript proposes a general approach for querying a causal knowledge graph with a causal question and converting the qualitative result into a quantitative structural causal model that can learn from data to answer the question. Here, we demonstrate the feasibility, accuracy and versatility of this approach using two case studies in systems biology. The first demonstrates the appropriateness of the underlying assumptions and the accuracy of the results. The second demonstrates the versatility of the approach by querying a knowledge base for the molecular determinants of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-induced cytokine storm and performing counterfactual inference to predict the causal effect of medical countermeasures for severely ill COVID-19 patients.

60 APPLIED LIFE SCIENCES↗

Generative Design for Resilience of Interdependent Network Systems

Abstract Interconnected complex systems usually undergo disruptions due to internal uncertainties and external negative impacts such as those caused by harsh operating environments or regional natural disaster events. To maintain the operation of interconnected network systems under both internal and external challenges, design for resilience research has been conducted from both enhancing the reliability of the system through better designs and improving the failure recovery capabilities. As for enhancing the designs, challenges have arisen for designing a robust system due to the increasing scale of modern systems and the complicated underlying physical constraints. To tackle these challenges and design a resilient system efficiently, this study presents a generative design method that utilizes graph learning algorithms. The generative design framework contains a performance estimator and a candidate design generator. The generator can intelligently mine good properties from existing systems and output new designs that meet predefined performance criteria while the estimator can efficiently predict the performance of the generated design for a fast iterative learning process. Case studies results based on synthetic supply chain networks and power systems from the IEEE dataset have illustrated the applicability of the developed method for designing resilient interdependent network systems.

Engineering↗

Application of Modified Meshgraphnets for Subsurface Prediction during CO2 Sequestration

In the face of the increasingly dire consequences of anthropogenic climate change, capturing and storing carbon dioxide is paramount. However, several impediments exist to the safe and effective subsurface storage of CO2, such as cost of transport, identification of suitable sites for subsurface storage, and assessment of long-term risk from storage in subsurface aquifers. Accurate subsurface modeling is necessary to ensure that CO2 storage is both safe and effective. Still, such modeling has traditionally required either substantial time and computational power (numerical simulation) or a substantial amount of pre-existing data for training (machine learning models). Additionally, these models lack flexibility in dealing with both changes in discretization of the input data and generalizability beyond the data on which they are trained. In order to address these issues, this research applies graph neural networks (GNNs) to predict subsurface saturation and pressure during CO₂ injection in a model of the Illinois Basin-Decatur Project (IBDP). GNNs provide a flexible, intuitive method for representing and manipulating complex unstructured data, which is often found in many practical domain problems such as fluid flow and subsurface characterization. These unstructured grids are easily represented in GNNs by representing spatially-localized features such as permeability, porosity, saturation, and pressure as nodes in a graph and relationships between these properties as edges connecting these nodes. This research applies a specific GNN model called MeshGraphNets (MGN) to model the change in CO2 saturation and pressure over a 50-month time period (36 months of injection, 14 months post-injection). The MGN model leverages a message passing process that allows the network to learn both the spatial and temporal dynamics of this system simultaneously. Additionally, training on a limited dataset (64 realizations, 20 time points each) resulted in a high degree of accuracy in saturation prediction both within the same timeframe as the training (20 months, 0.039 average RMSE) and when projecting out to the end of injection (36 months, 0.053 average RMSE). Temporal predictions such as those generated by MGNs and other similar models are prone to accumulated error over time; in order to address this, a multi-step rollout (MSR) training process was applied to calculate training loss. This method mimics the forward prediction during inference by “rolling out” multiple time points in a single training step using the previous prediction as input to the MGN model. By calculating the loss several time steps forward from the current prediction, the model is forced to find a more stable state over time. Application of MSR to the MGN model resulted in an average 15% reduction in inference error over time during forward prediction. This study showcases the immense potential of GNNs as a game-changing methodology for predicting pressure and saturation evolution in CCS projects, ultimately paving the way for more sustainable and effective carbon storage solutions. Presentation prepared for the 2024 AiChE Annual Meeting, October 27 to November 1 2024, San Diego, CA.

Holcomb, Paul↗

On the integration of molecular dynamics, data science, and experiments for studying solvent effects on catalysis

Computational workflows that combine molecular dynamics (MD) simulations and emerging data-centric (DC) methods can accelerate the screening and analysis of solvent systems experimentally and computationally. Here, MD simulations provide atomic positions and velocities of reactant, solvent, and catalyst materials that can be manipulated into data representations that in turn can be used by DC techniques to conduct predictive modeling, feature extraction, and experimental design. For liquid-phase catalytic applications, emerging DC techniques such as Convolutional and Graph Neural Networks (CNN/GNN), Topological Data Analysis (TDA), and Active Learning (AL) can leverage MD and experimental data to quickly predict solvent effects on reaction outcomes. For instance, in recent studies, 3D solvent environments obtained with MD have been exploited by CNNs to predict experimental reaction rates for homogeneous acid-catalyzed lignocellulosic processes. In this perspective, we discuss basic principles of DC methods and how these can be combined with MD to enable high-throughput screening of solvent selection for diverse catalysis applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Adsorbate chemical environment-based machine learning framework for heterogeneous catalysis

Abstract Heterogeneous catalytic reactions are influenced by a subtle interplay of atomic-scale factors, ranging from the catalysts’ local morphology to the presence of high adsorbate coverages. Describing such phenomena via computational models requires generation and analysis of a large space of atomic configurations. To address this challenge, we present Adsorbate Chemical Environment-based Graph Convolution Neural Network (ACE-GCN), a screening workflow that accounts for atomistic configurations comprising diverse adsorbates, binding locations, coordination environments, and substrate morphologies. Using this workflow, we develop catalyst surface models for two illustrative systems: (i) NO adsorbed on a Pt 3 Sn(111) alloy surface, of interest for nitrate electroreduction processes, where high adsorbate coverages combined with low symmetry of the alloy substrate produce a large configurational space, and (ii) OH* adsorbed on a stepped Pt(221) facet, of relevance to the Oxygen Reduction Reaction, where configurational complexity results from the presence of irregular crystal surfaces, high adsorbate coverages, and directionally-dependent adsorbate-adsorbate interactions. In both cases, the ACE-GCN model, trained on a fraction (~10%) of the total DFT-relaxed configurations, successfully describes trends in the relative stabilities of unrelaxed atomic configurations sampled from a large configurational space. This approach is expected to accelerate development of rigorous descriptions of catalyst surfaces under in-situ conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

cuTS: Scaling Subgraph Isomorphism on Distributed Multi-GPUSystems Using Trie Based Data Structure

Subgraph isomorphism is a pattern-matching algorithm widely used in many domains such as chem-informatics, bioinformatics, databases, and social network analysis. It is computationally expensive and is a proven NP-hard problem. The massive parallelism offered by the GPU hardware is well suited for solving the subgraph isomorphism. However, current GPU implementations are far from the achievable performance. Moreover, the enormous memory requirement of current approaches limits the problem size that can be handled. This work analyzes the fundamental challenges associated with processing the subgraph isomorphism on GPUs and develops an efficient GPU hardware-aware implementation. We also develop a new GPU-friendly trie-based data structure to drastically reduce the intermediate storage space requirement. Hence, our approach runs larger benchmarks than the competitors. We also develop the first distributed sub-graph isomorphism algorithm for GPUs. Our experimental evaluation section demonstrates the efficacy of our approach by comparing the execution time and number of cases that we can handle against the state-of-the-art GPU implementations.

Xiang, Lizhi↗