arXiv subjects

Xiaoran Li

Publications and source records attributed to Xiaoran Li.

At least 19 recordsLinked to original sources

arXiv2026

OntologyAligner: Ontology-Aligned Retrieval and Hierarchy-Guided Large Language Model Reranking for Biomedical Ontology Normalization

Biomedical ontology normalization maps free-text expressions to standardized concepts, enabling consistent integration and analysis of biomedical data. This task remains challenging because lexical variation and subtle distinctions among hierarchically related concepts can obscure concept boundaries. We present OntologyAligner, a three-stage framework that combines ontology-aligned retrieval, large language model candidate reranking, and selective hierarchy-guided refinement. We also construct PhenoNormBench, a unified benchmark comprising 13,390 samples from seven Human Phenotype Ontology datasets. OntologyAligner achieved state-of-the-art performance on HPO normalization, with 88.78% Macro Top-1 Accuracy and 86.75% Micro Top-1 Accuracy, exceeding the strongest baseline by 4.85 and 5.07 percentage points, respectively. Ablation analyses showed complementary contributions from all three stages, and sensitivity analyses demonstrated stability across candidate-set sizes and model backbones. Applications to MONDO, MEDIC, and NCBITaxon further established portability to other ontologies. OntologyAligner offers a generalizable framework for accurate mapping of biomedical text to structured ontology concepts. PhenoNormBench and the code are publicly available at https://github.com/zhelishisongjie/OntologyAligner.

cs.AI↗

arXiv2026

Breaking the Curse of Dimensionality in Quantum PDE Solvers via Gevrey Regularity

We connect different degrees of smoothness of real-valued periodic functions to the number of qubits required for their high-precision Fourier-basis amplitude encodings as quantum states. Our resulting central observation is that the Gevrey hierarchy, which stratifies the space between smooth and analytic functions, provides a natural class for high-precision quantum algorithms. We then specialize to solving general linear partial differential equations (PDEs) with periodic boundary conditions, showing how our Fourier methods do so efficiently at varying target precisions on a quantum computer. This also demonstrates how our framework enables passage from query-complexity results to explicit elementary gate counts. As an application, we introduce a hierarchy of many-body quantum simulation pipelines that harness these high-precision algorithms to probe the linear response of atomistic systems in first quantization. Each level of the hierarchy unlocks a further polynomial-degree quantum speedup, yielding a gradual improvement in simulation efficiency as quantum computers scale.

quant-ph↗

arXiv2025

Thermodynamic formalism for correspondences

In this article, we investigate the Variational Principle and develop thermodynamic formalism for correspondences. We define the measure-theoretic entropy for transition probability kernels and topological pressure for correspondences. Based on these two notions, we establish the following results: The Variational Principle holds and equilibrium states exist for continuous potential functions, provided that the correspondence satisfies some expansion property called forward expansiveness. If, in addition, the correspondence satisfies the specification property and the potential function is Bowen summable, then the equilibrium state is unique. On the other hand, for a distance-expanding, open, strongly transitive correspondence and a Hölder continuous potential function, there exists a unique equilibrium state, and the backward orbits are equidistributed. Furthermore, we investigate the Variational Principle for general correspondences. In complex dynamics, we establish the Variational Principle for the Lee-Lyubich-Markorov-Mukherjee anti-holomorphic correspondences, which are matings of some anti-ho\-lo\-mor\-phic rational maps with anti-Hecke groups and are not forward expansive. We also show a Ruelle-Perron-Frobenius theorem for a family of hyperbolic holomorphic correspondences of the form $\boldsymbol{f}_c (z)= z^{q/p}+c$.

math.DS↗

arXiv2025

Benchmarking the Impact of Active Space Selection on the VQE Pipeline for Quantum Drug Discovery

Quantum computers promise scalable treatments of electronic structure, yet applying variational quantum eigensolvers (VQE) on realistic drug-like molecules remains constrained by the performance limitations of near-term quantum hardwares. A key strategy for addressing this challenge which effectively leverages current Noisy Intermediate-Scale Quantum (NISQ) hardwares yet remains under-benchmarked is active space selection. We introduce a benchmark that heuristically proposes criteria based on chemically grounded metrics to classify the suitability of a molecule for using quantum computing and then quantifies the impact of active space choices across the VQE pipeline for quantum drug discovery. The suite covers several representative drug-like molecules (e.g., lovastatin, oseltamivir, morphine) and uses chemically motivated active spaces. Our VQE evaluations employ both simulation and quantum processing unit (QPU) execution using unitary coupled-cluster with singles and doubles (UCCSD) and hardware-efficient ansatz (HEA). We adopt a more comprehensive evaluation, including chemistry metrics and architecture-centric metrics. For accuracy, we compare them with classical quantum chemistry methods. This work establishes the first systematic benchmark for active space driven VQE and lays the groundwork for future hardware-algorithm co-design studies in quantum drug discovery.

physics.chem-ph↗

arXiv2025

Investigation of Inverse Bremsstrahlung Heating Driven by Broadband Lasers

Broadband lasers have become a key strategy for mitigating laser plasma instabilities in inertial confinement fusion, yet their impact on collisional inverse bremsstrahlung (IB) heating remains unclear. Using one-dimensional collisional particle-in-cell simulations, we systematically examine the effect of bandwidth-induced temporal incoherence on IB absorption in Au plasmas. The simulations are first benchmarked against classical absorption theory, verifying that the implemented Coulomb collision model accurately reproduces the theoretical IB heating rate. A direct comparison of the electron temperature evolution in the broadband and monochromatic cases shows that, although spectral broadening introduces transient picosecond-scale oscillations in the heating rate driven by stochastic intensity fluctuations, the long-term averaged heating and net IB absorption remain essentially unchanged.

physics.plasm-ph↗

arXiv2025

Investigation of Stimulated Brillouin Scattering Driven by Broadband Lasers in High-Z Plasmas

The evolution of stimulated Brillouin scattering (SBS) driven by broadband lasers in high-Z plasmas is investigated using one-dimensional collisional particle-in-cell simulations. The temporal incoherence of broadband lasers modulates the pump intensity, generating stochastic intensity pulses that intermittently drive SBS. The shortened coherence time weakens the three-wave coupling and continuously reduces the temporal growth rate, while the saturated reflectivity remains nearly unchanged until the bandwidth exceeds a critical threshold. Simulations with varying laser intensities and bandwidths reveal a consistent scaling behavior, indicating that effective suppression occurs only when the laser bandwidth exceeds the temporal growth rate of SBS by several tens of times. Comparative simulations in Au and AuB plasmas exhibit similar suppression trends, with AuB showing reduced SBS growth rate and reflectivity, and the onset of suppression occurring at a lower bandwidth. These findings elucidate the coupled dependence of SBS mitigation on bandwidth and laser intensity in high-Z plasmas, offering useful guidance for optimizing broadband laser designs in inertial confinement fusion.

physics.plasm-ph↗

arXiv2025

SMILES-Inspired Transfer Learning for Quantum Operators in Generative Quantum Eigensolver

Given the inherent limitations of traditional Variational Quantum Eigensolver(VQE) algorithms, the integration of deep generative models into hybrid quantum-classical frameworks, specifically the Generative Quantum Eigensolver(GQE), represents a promising innovative approach. However, taking the Unitary Coupled Cluster with Singles and Doubles(UCCSD) ansatz which is widely used in quantum chemistry as an example, different molecular systems require constructions of distinct quantum operators. Considering the similarity of different molecules, the construction of quantum operators utilizing the similarity can reduce the computational cost significantly. Inspired by the SMILES representation method in computational chemistry, we developed a text-based representation approach for UCCSD quantum operators by leveraging the inherent representational similarities between different molecular systems. This framework explores text pattern similarities in quantum operators and employs text similarity metrics to establish a transfer learning framework. Our approach with a naive baseline setting demonstrates knowledge transfer between different molecular systems for ground-state energy calculations within the GQE paradigm. This discovery offers significant benefits for hybrid quantum-classical computation of molecular ground-state energies, substantially reducing computational resource requirements.

physics.chem-ph↗

arXiv2025

Ergodic Optimization for Open Expanding Multi-valued Topological Dynamical Systems

We study the optimization of ergodic averages for multi-valued dynamical systems, i.e. where points may have multiple different forward orbits. Under upper semi-continuity assumptions, we show that the maximum space average with respect to invariant probability measures for such systems can be characterised in terms of maximum time averages on an auxiliary shift space. For all multi-valued expanding systems that are open mappings, we show that every Hölder continuous real-valued function can be modified by a coboundary, of the same Hölder exponent, such that the resulting function is dominated by its maximum ergodic average.

math.DS↗

arXiv2025

Typical Uniqueness in Ergodic Optimization

For ergodic optimization on any topological dynamical system, with real-valued potential function $f$ belonging to any separable Banach space $B$ of continuous functions, we show that the $f$-maximizing measure is typically unique, in the strong sense that a countable collection of hypersurfaces contains the exceptional set of those $f\in B$ with non-unique maximizing measure. This strengthens previous results asserting that the uniqueness set is both residual and prevalent.

math.DS↗

arXiv2025

Investigation of Plasma Mixing Processes in the Context of Indirect Drive Inertial Confinement Fusion

In inertial confinement fusion (ICF), the dynamics of plasma mixing in hohlraums critically influence laser-plasma instabilities (LPI) and implosion performance. This study investigates the mixing of hohlraum ablated Au plasmas and filling C$_5$H$_{12}$ plasmas using one-dimensional particle-in-cell (PIC) simulations. We find that ion-ion collisions slow the diffusion of ions, rendering Au ions sub-diffusive, while C and H ions remain super-diffusive. Due to their lower collisionality, H ions diffuse faster into Au regions than C ions, leading to a distinct separation between C and H ions at the interface. Although an electrostatic shock is still generated at the plasma interface in the presence of collisions, its electric field strength and propagation speed are notably reduced. To systematically explore plasma mixing in hohlraum environments, we evaluate the individual effects of incident laser irradiation, plasma flow, and inhomogeneous density profiles on ion mixing. We find that laser irradiation and plasma flow have a minor impact on ion mixing compared to diffusion-driven processes, while the inhomogeneous density profile restricts diffusion from low-density to high-density regions. By incorporating realistic hohlraum plasma conditions derived from radiation hydrodynamic models into the PIC simulations, we demonstrate that the diffusion of C and H ions continues to dominate ion mixing. Simple phenomenological fits are derived to describe the evolution of the mixing width in a hohlraum condition. Further theoretical calculations indicate that the penetration of H and C into Au plasmas suppresses stimulated Brillouin scattering (SBS) within the mixing layer. This finding underscores the importance of integrating ion mixing effects into LPI codes for more accurate modeling of ICF hohlraum dynamics.

physics.plasm-ph↗

arXiv2025

Conformal measures of (anti)holomorphic correspondences

In this paper, we study the existence and properties of conformal measures on limit sets of (anti)holomorphic correspondences. We show that if the critical exponent satisfies $1\leq δ_{\operatorname{crit}}(x) <+\infty,$ the correspondence $F$ is (relatively) hyperbolic on the limit set $Λ_+(x)$, and $Λ_+(x)$ is minimal, then $Λ_+(x)$ admits a non-atomic conformal measure for $F$ and the Hausdorff dimension of $Λ_+(x)$ is strictly less than 2. As a special case, this shows that for a parameter $a$ in the interior of a hyperbolic component of the modular Mandelbrot set, the limit set of the Bullett--Penrose correspondence $F_a$ has a non-atomic conformal measure and its Hausdorff dimension is strictly less than 2. The same results hold for the LLMM correspondences, under some extra assumptions on its defining function $f$.

math.DS↗

arXiv2024

Investigation of positive streamers in CO$_2$: experiments and 3D particle-in-cell simulations

We investigate the propagation of positive streamers in CO$_2$ through 3D particle-in-cell simulations, which are qualitatively compared against experimental results at 50 mbar. The experiments show that CO$_2$ streamers are much more stochastic than air streamers at the same applied voltage, indicating that few electrons are available in front of the streamer head. In the simulations, we include a photoionization model for CO$_2$. The computational results show that even a small amount of photoionization can sustain positive streamer propagation, but this requires a background electric field close to the critical field. When we compare streamers in CO$_2$ and in air at the same applied voltage, the electric field at the streamer head and the electron density in the streamer channel are higher in CO$_2$. We discuss the uncertainties in CO$_2$ photoionization and provide an estimate for the quenching pressure, which is based on the radiative lifetime of emitting states and the collision frequency of the gas. Furthermore, a criterion for self-sustained streamer growth in CO$_2$ is presented and compared against simulation results.

physics.plasm-ph↗

arXiv2024

A Hybrid Quantum Computing Pipeline for Real World Drug Discovery

Quantum computing, with its superior computational capabilities compared to classical approaches, holds the potential to revolutionize numerous scientific domains, including pharmaceuticals. However, the application of quantum computing for drug discovery has primarily been limited to proof-of-concept studies, which often fail to capture the intricacies of real-world drug development challenges. In this study, we diverge from conventional investigations by developing \rev{a hybrid} quantum computing pipeline tailored to address genuine drug design problems. Our approach underscores the application of quantum computation in drug discovery and propels it towards more scalable system. We specifically construct our versatile quantum computing pipeline to address two critical tasks in drug discovery: the precise determination of Gibbs free energy profiles for prodrug activation involving covalent bond cleavage, and the accurate simulation of covalent bond interactions. This work serves as a pioneering effort in benchmarking quantum computing against veritable scenarios encountered in drug design, especially the covalent bonding issue present in both of the case studies, thereby transitioning from theoretical models to tangible applications. Our results demonstrate the potential of a quantum computing pipeline for integration into real world drug design workflows.

physics.chem-ph↗

arXiv2023

A computational study of accelerating, steady and fading negative streamers in ambient air

We study negative streamers in ambient air using a 2D axisymmetric fluid model. Depending on the background electric field, we observe accelerating, steady and fading negative streamers. Fading occurs in low background fields, when negative streamers lose their field enhancement and when their velocities become comparable to their maximal electron drift velocities. Our focus is on the steady propagation mode, during which streamer properties like radius and velocity hardly change. However, this mode is unstable, in the sense that a small change in conditions leads to acceleration or deceleration. We observe steady negative streamers in background fields ranging from 9.19 kV/cm to 15.75 kV/cm, indicating that there is no unique steady propagation field (or stability field). Another finding is that steady negative streamers are able to keep propagating over tens of centimeters, with only a finite conductive length behind their heads, similar to steady positive streamers. Approximately linear relationships are observed between the optical diameter and properties like the streamer velocity and the streamer head potential. From these linear relations, we obtain rough lower bounds of about 0.27 mm to 0.35 mm for the minimal optical diameter of steady negative streamers. The lowest background field in which a steady negative streamer could be obtained is 9.19 kV/cm. In contrast, steady positive streamers have recently been obtained in a background field as low as 4.05 kV/cm. We find that the properties of steady negative and positive streamers differ significantly. For example, for steady negative streamers the ratio between streamer velocity and maximal electron drift velocity ranges from about 2 to 4.5, whereas for steady positive streamers this ratio ranges from about 0.05 to 0.26.

physics.plasm-ph↗

arXiv2022

The Analysis about Building Cross-lingual Sememe Knowledge Base Based on Deep Clustering Network

A sememe is defined as the minimum semantic unit of human languages. Sememe knowledge bases (KBs), which contain words annotated with sememes, have been successfully applied to many NLP tasks, and we believe that by learning the smallest unit of meaning, computers can more easily understand human language. However, Existing sememe KBs are built on only manual annotation, human annotations have personal understanding biases, and the meaning of vocabulary will be constantly updated and changed with the times, and artificial methods are not always practical. To address the issue, we propose an unsupervised method based on a deep clustering network (DCN) to build a sememe KB, and you can use any language to build a KB through this method. We first learn the distributed representation of multilingual words, use MUSE to align them in a single vector space, learn the multi-layer meaning of each word through the self-attention mechanism, and use a DNC to cluster sememe features. Finally, we completed the prediction using only the 10-dimensional sememe space in English. We found that the low-dimensional space can still retain the main feature of the sememes.

cs.CL↗

arXiv2022

A computational study of steady and stagnating positive streamers in N2-O2 mixtures

In this paper, we address two main topics: steady propagation fields for positive streamers in air and streamer deceleration in fields below the steady propagation field. We generate constant-velocity positive streamers in air with an axisymmetric fluid model, by initially adjusting the applied voltage based on the streamer velocity. After an initial transient, we observe steady propagation for velocities of $3\times10^4$ m/s to $1.2\times10^5$ m/s, during which streamer properties and the background field do not change. This propagation mode is not fully stable, in the sense that a small change in streamer properties or background field eventually leads to acceleration or deceleration. An important finding is that faster streamers are able to propagate in significantly lower background fields than slower ones, indicating that there is no unique stability field. We relate the streamer radius, velocity, maximal electric field and background electric field to a characteristic time scale for the loss of conductivity. This relation is qualitatively confirmed by studying streamers in N2-O2 mixtures with less oxygen than air. In such mixtures, steady streamers require lower background fields, due to a reduction in the attachment and recombination rates. We also study the deceleration of streamers, which is important to predict how far they can propagate in a low field. Stagnating streamers are simulated by applying a constant applied voltage. We show how the properties of these streamers relate to the steady cases, and present a phenomenological model with fitted coefficients that describes the evolution of the velocity and radius. Finally, we compare the lengths of the stagnated streamers with predictions based on the conventional stability field.

physics.plasm-ph↗

arXiv2021

Comparing simulations and experiments of positive streamers in air: steps toward model validation

We compare simulations and experiments of single positive streamer discharges in air at 100 mbar, aiming towards model validation. Experimentally, streamers are generated in a plate-plate geometry with a protruding needle. We are able to capture the complete time evolution of reproducible single-filament streamers with a ns gate-time camera. A 2D axisymmetric drift-diffusion-reaction fluid model is used to simulate streamers under conditions closely matching those of the experiments. Streamer velocities, radii and light emission profiles are compared between model and experiment. Good qualitative agreement is observed between the experimental and simulated optical emission profiles, and for the streamer velocity and radius during the entire evolution. Quantitatively, the simulated streamer velocity is about 20% to 30% lower at the same streamer length, and the simulated radius is about 1 mm (20% to 30%) smaller. The effect of various parameters on the agreement between model and experiment is studied, such as the used transport data, the background ionization level, the photoionization rate, the gas temperature, the voltage rise time and the voltage boundary conditions. An increase in gas temperature due to the 50 Hz experimental repetition frequency could probably account for some of the observed discrepancies.

physics.plasm-ph↗

arXiv2020

A computational study of positive streamers interacting with dielectrics

We use numerical simulations to study the dynamics of surface discharges, which are common in high-voltage engineering. We simulate positive streamer discharges that propagate towards a dielectric surface, attach to it, and then propagate over the surface. The simulations are performed in air with a two-dimensional plasma fluid model, in which a flat dielectric is placed between two plate electrodes. Electrostatic attraction is the main mechanism that causes streamers to grow towards the dielectric. Due to the net charge in the streamer head, the dielectric gets polarized, and the electric field between the streamer and the dielectric is increased. Compared to streamers in bulk gas, surface streamers have a smaller radius, a higher electric field, a higher electron density, and higher propagation velocity. A higher applied voltage leads to faster inception and faster propagation of the surface discharge. A higher dielectric permittivity leads to more rapid attachment of the streamer to the surface and a thinner surface streamer. Secondary emission coefficients are shown to play a modest role, which is due to relatively strong photoionization in air. In the simulations, a high electric field is present between the positive streamers and the dielectric surface. We show that the magnitude and decay of this field are affected by the positive ion mobility.

physics.plasm-ph↗