arXiv subjects
Publications and source records attributed to Quan Long.
We introduce the notion of 'centre' for pomonoid-graded strong monads which generalizes some previous work that describes the centre of (not graded) strong monads. We show that, whenever the centre exists, this determines a pomonoid-graded commutative submonad of the original one. We also discuss how this relates to duoidally-graded strong monads.
Plasmon-driven ultrafast nonlinearities hold promise for advanced photonics but remain challenging to harness in two-dimensional materials at telecommunication wavelengths. Here, we demonstrate few-layer V2C MXene as a high-performance saturable absorber by leveraging its tailored surface plasmon resonance. Combining transient absorption spectroscopy and first-principles calculations, we unveil a plasmon-driven relaxation mechanism dominated by interfacial high-energy hot electron generation (~100 fs), enabling giant ultrafast nonlinearities. Crucially, at the communication band (1550 nm), V2C exhibits a high saturable absorption coefficient of -1.35 cm/GW. Integrating this into an erbium-doped fiber laser, we generate mode-locked pulses with a duration of 486 fs at 1569 nm, a 39.51 MHz repetition rate, and exceptional stability (92 dB SNR). This work establishes plasmonic MXenes as a paradigm for tailored ultrafast photonic devices.
The construction of entangling gates with individual addressing capability represents a crucial approach for implementing quantum computation in trapped ion crystals. Conventional entangling gate schemes typically rely on laser beam wave vectors to couple the ions' spin and motional degrees of freedom. Here, we experimentally demonstrate an alternative method that employs a polarization gradient field generated by a tightly focused laser beam, previously proposed as a Magnus-type quantum logic gate. Using this technique, we perform Raman operations on nuclear spin qubits encoded in 171Yb+ ions, generating spin-dependent forces along axial motional modes in a linear trap. By utilizing an acousto-optic deflector to create arbitrary spot pairs for individual ion addressing in two-ion (four-ion) chains, we achieve MS gates with fidelities exceeding 98.5% (97.2%). Further improvements in numerical aperture and laser power could reduce gate durations while enhancing fidelity. This method is compatible with, and can significantly simplify, optical tweezer gate proposals, where motional mode engineering enables scalable trapped-ion quantum computation. The technique can be extended to two-dimensional ion crystals, representing a key step toward large-scale trapped-ion quantum processors.
Brain aging trajectories differ between males and females, yet the genetic factors underlying these differences remain underexplored. Using structural MRI and genotyping data from 40,940 UK Biobank participants (aged 45-83), we computed Brain Age Gap Estimates (BrainAGE) for total brain, hippocampal, and ventricular volumes. We conducted sex-stratified genome-wide association studies (GWAS) and Post-GWAS analyses to identify genetic variants associated with accelerated brain aging. Distinct gene sets emerged by sex: in females, neurotransmitter transport and mitochondrial stress response genes were implicated; in males, immune and inflammation-related genes dominated. Shared genes, including GMNC and OSTN, were consistently linked to brain volumes across sexes, suggesting core roles in neurostructural maintenance. Tissue expression analyses revealed sex-specific enrichment in pathways tied to neurodegeneration. These findings highlight the importance of sex-stratified approaches in aging research and suggest genetic targets for personalized interventions against age-related cognitive decline.
To address the issue of interpretability in multilayer perceptrons (MLPs), Kolmogorov-Arnold Networks (KANs) are introduced in 2024. However, optimizing KAN structures is labor-intensive, typically requiring manual intervention and parameter tuning. This paper proposes GA-KAN, a genetic algorithm-based approach that automates the optimization of KANs, requiring no human intervention in the design process. To the best of our knowledge, this is the first time that evolutionary computation is explored to optimize KANs automatically. Furthermore, inspired by the use of sparse connectivity in MLPs in effectively reducing the number of parameters, GA-KAN further explores sparse connectivity to tackle the challenge of extensive parameter spaces in KANs. GA-KAN is validated on two toy datasets, achieving optimal results without the manual tuning required by the original KAN. Additionally, GA-KAN demonstrates superior performance across five classification datasets, outperforming traditional methods on all datasets and providing interpretable symbolic formulae for the Wine and Iris datasets, thereby enhancing model transparency. Furthermore, GA-KAN significantly reduces the number of parameters over the standard KAN across all the five datasets. The core contributions of GA-KAN include automated optimization, a new encoding strategy, and a new decoding process, which together improve the accuracy and interpretability, and reduce the number of parameters.
Most methods in explainable AI (XAI) focus on providing reasons for the prediction of a given set of features. However, we solve an inverse explanation problem, i.e., given the deviation of a label, find the reasons of this deviation. We use a Bayesian framework to recover the ``true'' features, conditioned on the observed label value. We efficiently explain the deviation of a label value from the mode, by identifying and ranking the influential features using the ``distances'' in the ANOVA functional decomposition. We show that the new method is more human-intuitive and robust than methods based on mean values, e.g., SHapley Additive exPlanations (SHAP values). The extra costs of solving a Bayesian inverse problem are dimension-independent.
Polaronic effects involving stabilization of localized charge character by structural deformations and polarizations have attracted considerable investigations in soft lattice lead halide perovskites. However, the concept of polaron assisted nonlinear photonics remains largely unexplored, which has a wide range of applications from optoelectronics to telecommunications and quantum technologies. Here, we report the first observation of the polaronic state assisted saturable absorption through subbandgap excitation with a redshift exceeding 60 meV. By combining photoluminescence, transient absorption measurements and density functional theory calculations, we explicate that the anomalous nonlinear saturable absorption is caused by the transient picosecond timescale polaronic state formed by strong carrier exciton phonon coupling effect. The bandgap fluctuation can be further tuned through exciton phonon coupling of perovskites with different Young's modulus. This suggests that we can design targeted soft lattice lead halide perovskite with a specific structure to effectively manipulate exciton phonon coupling and exciton polaron formation. These findings profoundly expand our understanding of exciton polaronic nonlinear optics physics and provide an ideal platform for developing actively tunable nonlinear photonics applications.
We introduce a novel method to simultaneously perform variable selection and estimation in the joint frailty model of recurrent and terminal events using the Broken Adaptive Ridge Regression penalty. The BAR penalty can be summarized as an iteratively reweighted squared $L_2$-penalized regression, which approximates the $L_0$-regularization method. Our method allows for the number of covariates to diverge with the sample size. Under certain regularity conditions, we prove that the BAR estimator implemented under the model framework is consistent and asymptotically normally distributed, which are known as the oracle properties in the variable selection literature. In our simulation studies, we compare our proposed method to the Minimum Information Criterion (MIC) method. We apply our method on the Medical Information Mart for Intensive Care (MIMIC-III) database, with the aim of investigating which variables affect the risks of repeated ICU admissions and death during ICU stay.
Motivated by the CATHGEN data, we develop a new statistical learning method for simultaneous variable selection and parameter estimation under the context of generalized partly linear models for data with high-dimensional covariates. The method is referred to as the broken adaptive ridge (BAR) estimator, which is an approximation of the $L_0$-penalized regression by iteratively performing reweighted squared $L_2$-penalized regression. The generalized partly linear model extends the generalized linear model by including a non-parametric component to construct a flexible model for modeling various types of covariate effects. We employ the Bernstein polynomials as the sieve space to approximate the non-parametric functions so that our method can be implemented easily using the existing R packages. Extensive simulation studies suggest that the proposed method performs better than other commonly used penalty-based variable selection methods. We apply the method to the CATHGEN data with a binary response from a coronary artery disease study, which motivated our research, and obtained new findings in both high-dimensional genetic and low-dimensional non-genetic covariates.
One of the well-known challenges in optimal experimental design is how to efficiently estimate the nested integrations of the expected information gain. The Gaussian approximation and associated importance sampling have been shown to be effective at reducing the numerical costs. However, they may fail due to the non-negligible biases and the numerical instabilities. A new approach is developed to compute the expected information gain, when the posterior distribution is multimodal - a situation previously ignored by the methods aiming at accelerating the nested numerical integrations. Specifically, the posterior distribution is approximated using a mixture distribution constructed by multiple runs of global search for the modes and weighted local Laplace approximations. Under any given probability of capturing all the modes, we provide an estimation of the number of runs of searches, which is dimension independent. It is shown that the novel global-local multimodal approach can be significantly more accurate and more efficient than the other existing approaches, especially when the number of modes is large. The methods can be applied to the designs of experiments with both calibrated and uncalibrated observation noises.
In this paper, we present a joint multi-task learning framework for semantic segmentation and boundary detection. The critical component in the framework is the iterative pyramid context module (PCM), which couples two tasks and stores the shared latent semantics to interact between the two tasks. For semantic boundary detection, we propose the novel spatial gradient fusion to suppress nonsemantic edges. As semantic boundary detection is the dual task of semantic segmentation, we introduce a loss function with boundary consistency constraint to improve the boundary pixel accuracy for semantic segmentation. Our extensive experiments demonstrate superior performance over state-of-the-art works, not only in semantic segmentation but also in semantic boundary detection. In particular, a mean IoU score of 81:8% on Cityscapes test set is achieved without using coarse data or any external data for semantic segmentation. For semantic boundary detection, we improve over previous state-of-the-art works by 9.9% in terms of AP and 6:8% in terms of MF(ODS).
Uncertainty propagation of large scale discrete supply chains can be prohibitive when a large number of events occur during the simulated period and discrete event simulations (DES) are costly. We present a time bucket method to approximate and accelerate the DES of supply chains. Its stochastic version, which we call the L(logistic)-leap method, can be viewed as an extension of the leap methods, e.g., tau-leap, D-leap, developed in the chemical engineering community for the acceleration of stochastic DES of chemical reactions. The L-leap method instantaneously updates the system state vector at discrete time points and the production rates and policies of a supply chain are assumed to be stationary during each time bucket. We propose to use Multilevel Monte Carlo (MLMC) to efficiently propagate the uncertainties in a supply chain network, where the levels are naturally defined by the sizes of the time buckets of the simulations. We demonstrate the efficiency and accuracy of our methods using four numerical examples derived from a real world manufacturing material flow. In these examples, our multilevel L-leap approach can be faster than the standard Monte Carlo (MC) method by one or two orders of magnitudes without compromising the accuracy.
In calculating expected information gain in optimal Bayesian experimental design, the computation of the inner loop in the classical double-loop Monte Carlo requires a large number of samples and suffers from underflow if the number of samples is small. These drawbacks can be avoided by using an importance sampling approach. We present a computationally efficient method for optimal Bayesian experimental design that introduces importance sampling based on the Laplace method to the inner loop. We derive the optimal values for the method parameters in which the average computational cost is minimized according to the desired error tolerance. We use three numerical examples to demonstrate the computational efficiency of our method compared with the classical double-loop Monte Carlo, and a more recent single-loop Monte Carlo method that uses the Laplace method as an approximation of the return value of the inner loop. The first example is a scalar problem that is linear in the uncertain parameter. The second example is a nonlinear scalar problem. The third example deals with the optimal sensor placement for an electrical impedance tomography experiment to recover the fiber orientation in laminate composites.
We develop a fast method for optimally designing experiments in the context of statistical seismic source inversion. In particular, we efficiently compute the optimal number and locations of the receivers or seismographs. The seismic source is modeled by a point moment tensor multiplied by a time-dependent function. The parameters include the source location, moment tensor components, and start time and frequency in the time function. The forward problem is modeled by elastodynamic wave equations. We show that the Hessian of the cost functional, which is usually defined as the square of the weighted L2 norm of the difference between the experimental data and the simulated data, is proportional to the measurement time and the number of receivers. Consequently, the posterior distribution of the parameters, in a Bayesian setting, concentrates around the "true" parameters, and we can employ Laplace approximation and speed up the estimation of the expected Kullback-Leibler divergence (expected information gain), the optimality criterion in the experimental design procedure. Since the source parameters span several magnitudes, we use a scaling matrix for efficient control of the condition number of the original Hessian matrix. We use a second-order accurate finite difference method to compute the Hessian matrix and either sparse quadrature or Monte Carlo sampling to carry out numerical integration. We demonstrate the efficiency, accuracy, and applicability of our method on a two-dimensional seismic source inversion problem.
Epigenome modulation in response to the environment potentially provides a mechanism for organisms to adapt, both within and between generations. However, neither the extent to which this occurs, nor the molecular mechanisms involved are known. Here we investigate DNA methylation variation in Swedish Arabidopsis thaliana accessions grown at two different temperatures. Environmental effects on DNA methylation were limited to transposons, where CHH methylation was found to increase with temperature. Genome-wide association mapping revealed that the extensive CHH methylation variation was strongly associated with genetic variants in both cis and trans, including a major trans-association close to the DNA methyltransferase CMT2. Unlike CHH methylation, CpG gene body methylation (GBM) on the coding region of genes was not affected by growth temperature, but was instead strongly correlated with the latitude of origin. Accessions from colder regions had higher levels of GBM for a significant fraction of the genome, and this was correlated with elevated transcription levels for the genes affected. Genome-wide association mapping revealed that this effect was largely due to trans-acting loci, a significant fraction of which showed evidence of local adaptation. These findings constitute the first direct link between DNA methylation and adaptation to the environment, and provide a basis for further dissecting how environmentally driven and genetically determined epigenetic variation interact and influence organismal fitness.
Arabidopsis thaliana is an important model organism for understanding the genetics and molecular biology of plants. Its highly selfing nature, together with other important features, such as small size, short generation time, small genome size, and wide geographic distribution, make it an ideal model organism for understanding natural variation. Genome-wide association studies (GWAS) have proven a useful technique for identifying genetic loci responsible for natural variation in A. thaliana. Previously genotyped accessions (natural inbred lines) can be grown in replicate under different conditions, and phenotyped for different traits. These important features greatly simplify association mapping of traits and allow for systematic dissection of the genetics of natural variation by the entire Arabidopsis community. To facilitate this, we present GWAPP, an interactive web-based application for conducting GWAS in A. thaliana. Using an efficient Python implementation of a linear mixed model, traits measured for a subset of 1386 publicly available ecotypes can be uploaded and mapped with an efficient mixed model and other methods in just a couple of minutes. GWAPP features an extensive, interactive, and a user-friendly interface that includes interactive manhattan plots and interactive local and genome-wide LD plots. It facilitates exploratory data analysis by implementing features such as the inclusion of candidate SNPs in the model as cofactors.
We present up to 24-photon Bragg diffraction as a beam splitter in light-pulse atom interferometers to achieve the largest splitting in momentum space so far. Relative to the 2-photon processes used in the most sensitive present interferometers, these large momentum transfer beam splitters increase the phase shift 12-fold for Mach-Zehnder (MZ-) and 144-fold for Ramsey-Borde (RB-) geometries. We achieve a high visibility of the interference fringes (up to 52% for MZ or 36% for RB) and long pulse separation times that are possible only in atomic fountain setups. As the atom's internal state is not changed, important systematic effects can cancel.
We present a painless, almost-free upgrade to present extended cavity diode lasers (ECDLs), which improves the long term mode-hop free performance by stabilizing the resonance of the internal cavity to the external cavity. This stabilization is based on the observation that the frequency or amplitude noise of the ECDL is lowest at the optimum laser diode temperature or injection current. Thus, keeping the diode current at the level where the noise is lowest ensures mode-hop free operation within one of the stable regions of the mode chart, even if these should drift due to external influences. This method can be applied directly to existing laser systems without modifying the optical setup. We demonstrate the method in two ECDLs stabilized to vapor cells at 852 nm and 895 nm wavelength. We achieve long term mode-hop free operation and low noise at low power consumption, even with an inexpensive non-antireflection coated diode.