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Jian Kang

Publications and source records attributed to Jian Kang.

At least 109 records · Page 6Linked to original sources
arXiv2023

Penalized Deep Partially Linear Cox Models with Application to CT Scans of Lung Cancer Patients

Lung cancer is a leading cause of cancer mortality globally, highlighting the importance of understanding its mortality risks to design effective patient-centered therapies. The National Lung Screening Trial (NLST) employed computed tomography texture analysis, which provides objective measurements of texture patterns on CT scans, to quantify the mortality risks of lung cancer patients. Partially linear Cox models have gained popularity for survival analysis by dissecting the hazard function into parametric and nonparametric components, allowing for the effective incorporation of both well-established risk factors (such as age and clinical variables) and emerging risk factors (e.g., image features) within a unified framework. However, when the dimension of parametric components exceeds the sample size, the task of model fitting becomes formidable, while nonparametric modeling grapples with the curse of dimensionality. We propose a novel Penalized Deep Partially Linear Cox Model (Penalized DPLC), which incorporates the SCAD penalty to select important texture features and employs a deep neural network to estimate the nonparametric component of the model. We prove the convergence and asymptotic properties of the estimator and compare it to other methods through extensive simulation studies, evaluating its performance in risk prediction and feature selection. The proposed method is applied to the NLST study dataset to uncover the effects of key clinical and imaging risk factors on patients' survival. Our findings provide valuable insights into the relationship between these factors and survival outcomes.

stat.ML↗
arXiv2023

Joint Prediction of Audio Event and Annoyance Rating in an Urban Soundscape by Hierarchical Graph Representation Learning

Sound events in daily life carry rich information about the objective world. The composition of these sounds affects the mood of people in a soundscape. Most previous approaches only focus on classifying and detecting audio events and scenes, but may ignore their perceptual quality that may impact humans' listening mood for the environment, e.g. annoyance. To this end, this paper proposes a novel hierarchical graph representation learning (HGRL) approach which links objective audio events (AE) with subjective annoyance ratings (AR) of the soundscape perceived by humans. The hierarchical graph consists of fine-grained event (fAE) embeddings with single-class event semantics, coarse-grained event (cAE) embeddings with multi-class event semantics, and AR embeddings. Experiments show the proposed HGRL successfully integrates AE with AR for AEC and ARP tasks, while coordinating the relations between cAE and fAE and further aligning the two different grains of AE information with the AR.

eess.AS↗
arXiv2023

Topological Phases in Magnonics

Magnonics or magnon spintronics is an emerging field focusing on generating, detecting, and manipulating magnons. As charge-neutral quasi-particles, magnons are promising information carriers because of their low energy dissipation and long coherence length. In the past decade, topological phases in magnonics have attracted intensive attention due to their fundamental importance in condensed-matter physics and potential applications of spintronic devices. In this review, we mainly focus on recent progress in topological magnonics, such as the Hall effect of magnons, magnon Chern insulators, topological magnon semimetals, etc. In addition, the evidence supporting topological phases in magnonics and candidate materials are also discussed and summarized. The aim of this review is to provide readers with a comprehensive and systematic understanding of the recent developments in topological magnonics.

cond-mat.mes-hall↗
arXiv2023

Latent Subgroup Identification in Image-on-scalar Regression

Image-on-scalar regression has been a popular approach to modeling the association between brain activities and scalar characteristics in neuroimaging research. The associations could be heterogeneous across individuals in the population, as indicated by recent large-scale neuroimaging studies, e.g., the Adolescent Brain Cognitive Development (ABCD) study. The ABCD data can inform our understanding of heterogeneous associations and how to leverage the heterogeneity and tailor interventions to increase the number of youths who benefit. It is of great interest to identify subgroups of individuals from the population such that: 1) within each subgroup the brain activities have homogeneous associations with the clinical measures; 2) across subgroups the associations are heterogeneous; and 3) the group allocation depends on individual characteristics. Existing image-on-scalar regression methods and clustering methods cannot directly achieve this goal. We propose a latent subgroup image-on-scalar regression model (LASIR) to analyze large-scale, multi-site neuroimaging data with diverse sociodemographics. LASIR introduces the latent subgroup for each individual and group-specific, spatially varying effects, with an efficient stochastic expectation maximization algorithm for inferences. We demonstrate that LASIR outperforms existing alternatives for subgroup identification of brain activation patterns with functional magnetic resonance imaging data via comprehensive simulations and applications to the ABCD study. We have released our reproducible codes for public use with the software package available on Github: https://github.com/zikaiLin/lasir.

stat.ME↗
arXiv2023

Mediation with External Summary Statistic Information (MESSI)

Environmental health studies are increasingly measuring endogenous omics data ($\boldsymbol{M}$) to study intermediary biological pathways by which an exogenous exposure ($\boldsymbol{A}$) affects a health outcome ($\boldsymbol{Y}$), given confounders ($\boldsymbol{C}$). Mediation analysis is frequently carried out to understand such mechanisms. If intermediary pathways are of interest, then there is likely literature establishing statistical and biological significance of the total effect, defined as the effect of $\boldsymbol{A}$ on $\boldsymbol{Y}$ given $\boldsymbol{C}$. For mediation models with continuous outcomes and mediators, we show that leveraging external summary-level information on the total effect improves estimation efficiency of the natural direct and indirect effects. Moreover, the efficiency gain depends on the asymptotic partial $R^2$ between the outcome ($\boldsymbol{Y}\mid\boldsymbol{M},\boldsymbol{A},\boldsymbol{C}$) and total effect ($\boldsymbol{Y}\mid\boldsymbol{A},\boldsymbol{C}$) models, with smaller (larger) values benefiting direct (indirect) effect estimation. We robustify our estimation procedure to incongenial external information by assuming the total effect follows a random distribution. This framework allows shrinkage towards the external information if the total effects in the internal and external populations agree. We illustrate our methodology using data from the Puerto Rico Testsite for Exploring Contamination Threats, where Cytochrome p450 metabolites are hypothesized to mediate the effect of phthalate exposure on gestational age at delivery. External information on the total effect comes from a recently published pooled analysis of 16 studies. The proposed framework blends mediation analysis with emerging data integration techniques.

stat.ME↗
arXiv2023

Bayesian Inference for Brain Activity from Functional Magnetic Resonance Imaging Collected at Two Spatial Resolutions

Neuroradiologists and neurosurgeons increasingly opt to use functional magnetic resonance imaging (fMRI) to map functionally relevant brain regions for noninvasive presurgical planning and intraoperative neuronavigation. This application requires a high degree of spatial accuracy, but the fMRI signal-to-noise ratio (SNR) decreases as spatial resolution increases. In practice, fMRI scans can be collected at multiple spatial resolutions, and it is of interest to make more accurate inference on brain activity by combining data with different resolutions. To this end, we develop a new Bayesian model to leverage both better anatomical precision in high resolution fMRI and higher SNR in standard resolution fMRI. We assign a Gaussian process prior to the mean intensity function and develop an efficient, scalable posterior computation algorithm to integrate both sources of data. We draw posterior samples using an algorithm analogous to Riemann manifold Hamiltonian Monte Carlo in an expanded parameter space. We illustrate our method in analysis of presurgical fMRI data, and show in simulation that it infers the mean intensity more accurately than alternatives that use either the high or standard resolution fMRI data alone.

stat.ME↗
arXiv2023

Sequential Best-Arm Identification with Application to Brain-Computer Interface

A brain-computer interface (BCI) is a technology that enables direct communication between the brain and an external device or computer system. It allows individuals to interact with the device using only their thoughts, and holds immense potential for a wide range of applications in medicine, rehabilitation, and human augmentation. An electroencephalogram (EEG) and event-related potential (ERP)-based speller system is a type of BCI that allows users to spell words without using a physical keyboard, but instead by recording and interpreting brain signals under different stimulus presentation paradigms. Conventional non-adaptive paradigms treat each word selection independently, leading to a lengthy learning process. To improve the sampling efficiency, we cast the problem as a sequence of best-arm identification tasks in multi-armed bandits. Leveraging pre-trained large language models (LLMs), we utilize the prior knowledge learned from previous tasks to inform and facilitate subsequent tasks. To do so in a coherent way, we propose a sequential top-two Thompson sampling (STTS) algorithm under the fixed-confidence setting and the fixed-budget setting. We study the theoretical property of the proposed algorithm, and demonstrate its substantial empirical improvement through both synthetic data analysis as well as a P300 BCI speller simulator example.

cs.HC↗
arXiv2023

CVGG-Net: Ship Recognition for SAR Images Based on Complex-Valued Convolutional Neural Network

Ship target recognition is a vital task in synthetic aperture radar (SAR) imaging applications. Although convolutional neural networks have been successfully employed for SAR image target recognition, surpassing traditional algorithms, most existing research concentrates on the amplitude domain and neglects the essential phase information. Furthermore, several complex-valued neural networks utilize average pooling to achieve full complex values, resulting in suboptimal performance. To address these concerns, this paper introduces a Complex-valued Convolutional Neural Network (CVGG-Net) specifically designed for SAR image ship recognition. CVGG-Net effectively leverages both the amplitude and phase information in complex-valued SAR data. Additionally, this study examines the impact of various widely-used complex activation functions on network performance and presents a novel complex max-pooling method, called Complex Area Max-Pooling. Experimental results from two measured SAR datasets demonstrate that the proposed algorithm outperforms conventional real-valued convolutional neural networks. The proposed framework is validated on several SAR datasets.

eess.SP↗
arXiv2023

Statistical inferences for complex dependence of multimodal imaging data

Statistical analysis of multimodal imaging data is a challenging task, since the data involves high-dimensionality, strong spatial correlations and complex data structures. In this paper, we propose rigorous statistical testing procedures for making inferences on the complex dependence of multimodal imaging data. Motivated by the analysis of multi-task fMRI data in the Human Connectome Project (HCP) study, we particularly address three hypothesis testing problems: (a) testing independence among imaging modalities over brain regions, (b) testing independence between brain regions within imaging modalities, and (c) testing independence between brain regions across different modalities. Considering a general form for all the three tests, we develop a global testing procedure and a multiple testing procedure controlling the false discovery rate. We study theoretical properties of the proposed tests and develop a computationally efficient distributed algorithm. The proposed methods and theory are general and relevant for many statistical problems of testing independence structure among the components of high-dimensional random vectors with arbitrary dependence structures. We also illustrate our proposed methods via extensive simulations and analysis of five task fMRI contrast maps in the HCP study.

stat.ME↗
arXiv2023

Phase diagram of twisted bilayer graphene at filling factor $ν=\pm3$

We study the correlated insulating phases of twisted bilayer graphene (TBG) in the absence of lattice strain at integer filling $ν=\pm3$. Using the self-consistent Hartree-Fock method on a particle-hole symmetric model and allowing translation symmetry breaking terms, we obtain the phase diagram with respect to the ratio of $AA$ interlayer hopping $(w_0)$ and $AB$ interlayer hopping $(w_1)$. When the interlayer hopping ratio is close to the chiral limit ($w_0/w_1 \lesssim 0.5$), a quantum anomalous Hall state with Chern number $ν_c = \pm 1$ can be observed consistent with previous studies. Around the realistic value $w_0/w_1 \approx 0.8$, we find a spin and valley polarized, translation symmetry breaking, state with $C_{2z}T$ symmetry, a charge gap and a doubling of the moiré unit cell, dubbed the $C_{2z}T$ stripe phase. The real space total charge distribution of this $C_{2z}T$ stripe phase in the flat band limit does not have modulation between different moiré unit cells, although the charge density in each layer is modulated, and the translation symmetry is strongly broken. Other symmetries, including $C_{2z}$, $C_{2x}$ and particle-hole symmetry $P$, and the topology of the $C_{2z}T$ stripe phase are also discussed in detail. We observed braiding and annihilation of the Dirac nodes by continuously turning on the order parameter to its fully self-consistent value, and provide a detailed explanation of the mechanism for the charge gap opening despite preserving $C_{2z}T$ and valley $U(1)$ symmetries. In the transition region between the quantum anomalous Hall phase and the $C_{2z}T$ stripe phase, we find an additional competing state with comparable energy corresponding to a phase with a tripling of the moiré unit cell.

cond-mat.str-el↗
arXiv2023

IMBENS: Ensemble Class-imbalanced Learning in Python

imbalanced-ensemble, abbreviated as imbens, is an open-source Python toolbox for leveraging the power of ensemble learning to address the class imbalance problem. It provides standard implementations of popular ensemble imbalanced learning (EIL) methods with extended features and utility functions. These ensemble methods include resampling-based, e.g., under/over-sampling, and reweighting-based, e.g., cost-sensitive learning. Beyond the implementation, we empower EIL algorithms with new functionalities like customizable resampling scheduler and verbose logging, thus enabling more flexible training and evaluating strategies. The package was developed under a simple, well-documented API design that follows scikit-learn for increased ease of use. imbens is released under the MIT open-source license and can be installed from Python Package Index (PyPI) or https://github.com/ZhiningLiu1998/imbalanced-ensemble.

cs.LG↗
arXiv2023

Do We Really Need Complicated Model Architectures For Temporal Networks?

Recurrent neural network (RNN) and self-attention mechanism (SAM) are the de facto methods to extract spatial-temporal information for temporal graph learning. Interestingly, we found that although both RNN and SAM could lead to a good performance, in practice neither of them is always necessary. In this paper, we propose GraphMixer, a conceptually and technically simple architecture that consists of three components: (1) a link-encoder that is only based on multi-layer perceptrons (MLP) to summarize the information from temporal links, (2) a node-encoder that is only based on neighbor mean-pooling to summarize node information, and (3) an MLP-based link classifier that performs link prediction based on the outputs of the encoders. Despite its simplicity, GraphMixer attains an outstanding performance on temporal link prediction benchmarks with faster convergence and better generalization performance. These results motivate us to rethink the importance of simpler model architecture.

cs.LG↗
arXiv2023

Pseudo-magnetic fields, particle-hole asymmetry, and microscopic effective continuum Hamitonians of twisted bilayer graphene

Using the method developed in the companion paper, we construct the effective continuum theories for two different microscopic tight binding models of the twisted bilayer graphene at the twist angle of $1.05^\circ$, one Slater-Koster based and the other ab-initio Wannier based. The energy spectra obtained from the continuum theory -- either for rigid twist or including lattice relaxation -- are found to be in nearly perfect agreement with the spectra from the tight binding models when the gradient expansion is carried out to second order, demonstrating the validity of the method. We also analyze the properties of the Bloch states of the resulting narrow bands, finding non-negligible particle-hole symmetry breaking near the $Γ$ point in our continuum theory constructed for the ab-initio based microscopic model due to a term in the continuum theory that was previously overlooked. This reveals the difference with all existing continuum models where the particle-hole symmetry of the narrow band Hilbert space is nearly perfect.

cond-mat.str-el↗
arXiv2023

Continuum effective Hamiltonian for graphene bilayers for an arbitrary smooth lattice deformation from microscopic theories

We provide a systematic real space derivation of the continuum Hamiltonian for a graphene bilayer starting from a microscopic lattice theory, allowing for an arbitrary inhomogeneous smooth lattice deformation, including a twist. Two different microscopic models are analyzed: first, a Slater-Koster like model and second, ab-initio derived model. We envision that our effective Hamiltonian can be used in conjunction with an experimentally determined atomic lattice deformation in twisted bilayer graphene in a specific device to predict and compare the electronic spectra with scanning tunneling spectroscopy measurements. As a byproduct, our approach provides electron-phonon couplings in the continuum Hamiltonian from microscopic models for any bilayer stacking. In the companion paper we analyze in detail the continuum models for relaxed atomic configurations of magic angle twisted bilayer graphene.

cond-mat.str-el↗
arXiv2023

InfoFair: Information-Theoretic Intersectional Fairness

Algorithmic fairness is becoming increasingly important in data mining and machine learning. Among others, a foundational notation is group fairness. The vast majority of the existing works on group fairness, with a few exceptions, primarily focus on debiasing with respect to a single sensitive attribute, despite the fact that the co-existence of multiple sensitive attributes (e.g., gender, race, marital status, etc.) in the real-world is commonplace. As such, methods that can ensure a fair learning outcome with respect to all sensitive attributes of concern simultaneously need to be developed. In this paper, we study the problem of information-theoretic intersectional fairness (InfoFair), where statistical parity, a representative group fairness measure, is guaranteed among demographic groups formed by multiple sensitive attributes of interest. We formulate it as a mutual information minimization problem and propose a generic end-to-end algorithmic framework to solve it. The key idea is to leverage a variational representation of mutual information, which considers the variational distribution between learning outcomes and sensitive attributes, as well as the density ratio between the variational and the original distributions. Our proposed framework is generalizable to many different settings, including other statistical notions of fairness, and could handle any type of learning task equipped with a gradient-based optimizer. Empirical evaluations in the fair classification task on three real-world datasets demonstrate that our proposed framework can effectively debias the classification results with minimal impact to the classification accuracy.

cs.LG↗
arXiv2022

Bregman Divergence-Based Data Integration with Application to Polygenic Risk Score (PRS) Heterogeneity Adjustment

Polygenic risk scores (PRS) have recently received much attention for genetics risk prediction. While successful for the Caucasian population, the PRS based on the minority population suffer from small sample sizes, high dimensionality and low signal-to-noise ratios, exacerbating already severe health disparities. Due to population heterogeneity, direct trans-ethnic prediction by utilizing the Caucasian model for the minority population also has limited performance. In addition, due to data privacy, the individual genotype data is not accessible for either the Caucasian population or the minority population. To address these challenges, we propose a Bregman divergence-based estimation procedure to measure and optimally balance the information from different populations. The proposed method only requires the use of encrypted summary statistics and improves the PRS performance for ethnic minority groups by incorporating additional information. We provide the asymptotic consistency and weak oracle property for the proposed method. Simulations and real data analyses also show its advantages in prediction and variable selection.

stat.ME↗
arXiv2022

JuryGCN: Quantifying Jackknife Uncertainty on Graph Convolutional Networks

Graph Convolutional Network (GCN) has exhibited strong empirical performance in many real-world applications. The vast majority of existing works on GCN primarily focus on the accuracy while ignoring how confident or uncertain a GCN is with respect to its predictions. Despite being a cornerstone of trustworthy graph mining, uncertainty quantification on GCN has not been well studied and the scarce existing efforts either fail to provide deterministic quantification or have to change the training procedure of GCN by introducing additional parameters or architectures. In this paper, we propose the first frequentist-based approach named JuryGCN in quantifying the uncertainty of GCN, where the key idea is to quantify the uncertainty of a node as the width of confidence interval by a jackknife estimator. Moreover, we leverage the influence functions to estimate the change in GCN parameters without re-training to scale up the computation. The proposed JuryGCN is capable of quantifying uncertainty deterministically without modifying the GCN architecture or introducing additional parameters. We perform extensive experimental evaluation on real-world datasets in the tasks of both active learning and semi-supervised node classification, which demonstrate the efficacy of the proposed method.

cs.LG↗
arXiv2022

Understanding the dynamic impact of COVID-19 through competing risk modeling with bivariate varying coefficients

The coronavirus disease 2019 (COVID-19) pandemic has exerted a profound impact on patients with end-stage renal disease relying on kidney dialysis to sustain their lives. Motivated by a request by the U.S. Centers for Medicare & Medicaid Services, our analysis of their postdischarge hospital readmissions and deaths in 2020 revealed that the COVID-19 effect has varied significantly with postdischarge time and time since the onset of the pandemic. However, the complex dynamics of the COVID-19 effect trajectories cannot be characterized by existing varying coefficient models. To address this issue, we propose a bivariate varying coefficient model for competing risks within a cause-specific hazard framework, where tensor-product B-splines are used to estimate the surface of the COVID-19 effect. An efficient proximal Newton algorithm is developed to facilitate the fitting of the new model to the massive Medicare data for dialysis patients. Difference-based anisotropic penalization is introduced to mitigate model overfitting and the wiggliness of the estimated trajectories; various cross-validation methods are considered in the determination of optimal tuning parameters. Hypothesis testing procedures are designed to examine whether the COVID-19 effect varies significantly with postdischarge time and the time since pandemic onset, either jointly or separately. Simulation experiments are conducted to evaluate the estimation accuracy, type I error rate, statistical power, and model selection procedures. Applications to Medicare dialysis patients demonstrate the real-world performance of the proposed methods.

stat.ME↗