arXiv subjects

Liang Zhan

Publications and source records attributed to Liang Zhan.

At least 37 records · Page 2Linked to original sources

arXiv2024

Political-LLM: Large Language Models in Political Science

In recent years, large language models (LLMs) have been widely adopted in political science tasks such as election prediction, sentiment analysis, policy impact assessment, and misinformation detection. Meanwhile, the need to systematically understand how LLMs can further revolutionize the field also becomes urgent. In this work, we--a multidisciplinary team of researchers spanning computer science and political science--present the first principled framework termed Political-LLM to advance the comprehensive understanding of integrating LLMs into computational political science. Specifically, we first introduce a fundamental taxonomy classifying the existing explorations into two perspectives: political science and computational methodologies. In particular, from the political science perspective, we highlight the role of LLMs in automating predictive and generative tasks, simulating behavior dynamics, and improving causal inference through tools like counterfactual generation; from a computational perspective, we introduce advancements in data preparation, fine-tuning, and evaluation methods for LLMs that are tailored to political contexts. We identify key challenges and future directions, emphasizing the development of domain-specific datasets, addressing issues of bias and fairness, incorporating human expertise, and redefining evaluation criteria to align with the unique requirements of computational political science. Political-LLM seeks to serve as a guidebook for researchers to foster an informed, ethical, and impactful use of Artificial Intelligence in political science. Our online resource is available at: http://political-llm.org/.

cs.CL↗

arXiv2024

A Heterogeneous Graph Neural Network Fusing Functional and Structural Connectivity for MCI Diagnosis

Brain connectivity alternations associated with brain disorders have been widely reported in resting-state functional imaging (rs-fMRI) and diffusion tensor imaging (DTI). While many dual-modal fusion methods based on graph neural networks (GNNs) have been proposed, they generally follow homogenous fusion ways ignoring rich heterogeneity of dual-modal information. To address this issue, we propose a novel method that integrates functional and structural connectivity based on heterogeneous graph neural networks (HGNNs) to better leverage the rich heterogeneity in dual-modal images. We firstly use blood oxygen level dependency and whiter matter structure information provided by rs-fMRI and DTI to establish homo-meta-path, capturing node relationships within the same modality. At the same time, we propose to establish hetero-meta-path based on structure-function coupling and brain community searching to capture relations among cross-modal nodes. Secondly, we further introduce a heterogeneous graph pooling strategy that automatically balances homo- and hetero-meta-path, effectively leveraging heterogeneous information and preventing feature confusion after pooling. Thirdly, based on the flexibility of heterogeneous graphs, we propose a heterogeneous graph data augmentation approach that can conveniently address the sample imbalance issue commonly seen in clinical diagnosis. We evaluate our method on ADNI-3 dataset for mild cognitive impairment (MCI) diagnosis. Experimental results indicate the proposed method is effective and superior to other algorithms, with a mean classification accuracy of 93.3%.

cs.CV↗

arXiv2024

Distributed Harmonization: Federated Clustered Batch Effect Adjustment and Generalization

Independent and identically distributed (i.i.d.) data is essential to many data analysis and modeling techniques. In the medical domain, collecting data from multiple sites or institutions is a common strategy that guarantees sufficient clinical diversity, determined by the decentralized nature of medical data. However, data from various sites are easily biased by the local environment or facilities, thereby violating the i.i.d. rule. A common strategy is to harmonize the site bias while retaining important biological information. The ComBat is among the most popular harmonization approaches and has recently been extended to handle distributed sites. However, when faced with situations involving newly joined sites in training or evaluating data from unknown/unseen sites, ComBat lacks compatibility and requires retraining with data from all the sites. The retraining leads to significant computational and logistic overhead that is usually prohibitive. In this work, we develop a novel Cluster ComBat harmonization algorithm, which leverages cluster patterns of the data in different sites and greatly advances the usability of ComBat harmonization. We use extensive simulation and real medical imaging data from ADNI to demonstrate the superiority of the proposed approach. Our codes are provided in https://github.com/illidanlab/distributed-cluster-harmonization.

cs.LG↗

arXiv2024

SLIDE: A Framework Integrating Small and Large Language Models for Open-Domain Dialogues Evaluation

The long-standing one-to-many problem of gold standard responses in open-domain dialogue systems presents challenges for automatic evaluation metrics. Though prior works have demonstrated some success by applying powerful Large Language Models (LLMs), existing approaches still struggle with the one-to-many problem, and exhibit subpar performance in domain-specific scenarios. We assume the commonsense reasoning biases within LLMs may hinder their performance in domainspecific evaluations. To address both issues, we propose a novel framework SLIDE (Small and Large Integrated for Dialogue Evaluation), that leverages both a small, specialised model (SLM), and LLMs for the evaluation of open domain dialogues. Our approach introduces several techniques: (1) Contrastive learning to differentiate between robust and non-robust response embeddings; (2) A novel metric for semantic sensitivity that combines embedding cosine distances with similarity learned through neural networks, and (3) a strategy for incorporating the evaluation results from both the SLM and LLMs. Our empirical results demonstrate that our approach achieves state-of-the-art performance in both the classification and evaluation tasks, and additionally the SLIDE evaluator exhibits better correlation with human judgements. Our code is available at https:// github.com/hegehongcha/SLIDE-ACL2024.

cs.CL↗

arXiv2024

Interpretable Spatio-Temporal Embedding for Brain Structural-Effective Network with Ordinary Differential Equation

The MRI-derived brain network serves as a pivotal instrument in elucidating both the structural and functional aspects of the brain, encompassing the ramifications of diseases and developmental processes. However, prevailing methodologies, often focusing on synchronous BOLD signals from functional MRI (fMRI), may not capture directional influences among brain regions and rarely tackle temporal functional dynamics. In this study, we first construct the brain-effective network via the dynamic causal model. Subsequently, we introduce an interpretable graph learning framework termed Spatio-Temporal Embedding ODE (STE-ODE). This framework incorporates specifically designed directed node embedding layers, aiming at capturing the dynamic interplay between structural and effective networks via an ordinary differential equation (ODE) model, which characterizes spatial-temporal brain dynamics. Our framework is validated on several clinical phenotype prediction tasks using two independent publicly available datasets (HCP and OASIS). The experimental results clearly demonstrate the advantages of our model compared to several state-of-the-art methods.

cs.LG↗

arXiv2024

BrainODE: Dynamic Brain Signal Analysis via Graph-Aided Neural Ordinary Differential Equations

Brain network analysis is vital for understanding the neural interactions regarding brain structures and functions, and identifying potential biomarkers for clinical phenotypes. However, widely used brain signals such as Blood Oxygen Level Dependent (BOLD) time series generated from functional Magnetic Resonance Imaging (fMRI) often manifest three challenges: (1) missing values, (2) irregular samples, and (3) sampling misalignment, due to instrumental limitations, impacting downstream brain network analysis and clinical outcome predictions. In this work, we propose a novel model called BrainODE to achieve continuous modeling of dynamic brain signals using Ordinary Differential Equations (ODE). By learning latent initial values and neural ODE functions from irregular time series, BrainODE effectively reconstructs brain signals at any time point, mitigating the aforementioned three data challenges of brain signals altogether. Comprehensive experimental results on real-world neuroimaging datasets demonstrate the superior performance of BrainODE and its capability of addressing the three data challenges.

cs.LG↗

arXiv2024

Expected geoneutrino signal at JUNO using local integrated 3-D refined crustal model

Geoneutrinos serve as a potent tool for comprehending the radiogenic power and composition of Earth. Although geoneutrinos have been observed in prior experiments, the forthcoming generation of experiments,such as JUNO, will be necessary for fully harnessing their potential. Precise prediction of the crustal contribution is vital for interpreting particlephysics measurements in the context of geo-scientific inquiries. Nonetheless, existing models such as JULOC and GIGJ have limitations in accurately forecasting the crustal contribution. This paper introduces JULOCI, the novel 3-D integrated crustal model of JUNO, which employs seismic, gravity, rock sample, and heat flow data to precisely estimate the geoneutrino signal of the lithosphere. The model indicates elevated concentrations of uranium and thorium in southern China, resulting in unexpectedly strong geoneutrino signals.The accuracy of JULOC-I, coupled with a decade of experimental data, affords JUNO the opportunity to test multiple mantle models. Once operational, JUNO can validate the model predictions and enhance the precision of mantle measurements. All in all, the improved accuracy ofJULOC-I represents a substantial stride towards comprehending the geochemical distribution of the South China crust, offering a valuable tool for investigating the composition and evolution of the Earth through geoneutrinos.

physics.geo-ph↗

arXiv2024

Constrained Multiview Representation for Self-supervised Contrastive Learning

Representation learning constitutes a pivotal cornerstone in contemporary deep learning paradigms, offering a conduit to elucidate distinctive features within the latent space and interpret the deep models. Nevertheless, the inherent complexity of anatomical patterns and the random nature of lesion distribution in medical image segmentation pose significant challenges to the disentanglement of representations and the understanding of salient features. Methods guided by the maximization of mutual information, particularly within the framework of contrastive learning, have demonstrated remarkable success and superiority in decoupling densely intertwined representations. However, the effectiveness of contrastive learning highly depends on the quality of the positive and negative sample pairs, i.e. the unselected average mutual information among multi-views would obstruct the learning strategy so the selection of the views is vital. In this work, we introduce a novel approach predicated on representation distance-based mutual information (MI) maximization for measuring the significance of different views, aiming at conducting more efficient contrastive learning and representation disentanglement. Additionally, we introduce an MI re-ranking strategy for representation selection, benefiting both the continuous MI estimating and representation significance distance measuring. Specifically, we harness multi-view representations extracted from the frequency domain, re-evaluating their significance based on mutual information across varying frequencies, thereby facilitating a multifaceted contrastive learning approach to bolster semantic comprehension. The statistical results under the five metrics demonstrate that our proposed framework proficiently constrains the MI maximization-driven representation selection and steers the multi-view contrastive learning process.

cs.CV↗

arXiv2024

Uncertainty Regularized Evidential Regression

The Evidential Regression Network (ERN) represents a novel approach that integrates deep learning with Dempster-Shafer's theory to predict a target and quantify the associated uncertainty. Guided by the underlying theory, specific activation functions must be employed to enforce non-negative values, which is a constraint that compromises model performance by limiting its ability to learn from all samples. This paper provides a theoretical analysis of this limitation and introduces an improvement to overcome it. Initially, we define the region where the models can't effectively learn from the samples. Following this, we thoroughly analyze the ERN and investigate this constraint. Leveraging the insights from our analysis, we address the limitation by introducing a novel regularization term that empowers the ERN to learn from the whole training set. Our extensive experiments substantiate our theoretical findings and demonstrate the effectiveness of the proposed solution.

cs.LG↗

arXiv2023

Design optimization of JUNO-TAO plastic scintillator with WLS-fiber and SiPM readout

Plastic scintillators (PSs)embedded with wavelength-shifting fibers are widely used in high-energy particle physics, such as in muon taggers,as well as in medical physics and other applications. In this study,a simulation package was built to evaluate the effects of the diameter and layout of optical fibers on the light yield with different configurations. The optimal optical configuration was designed based on simulations and validated using two PS prototypes under certain experimental conditions. Atop veto tracker (TVT) for the JUNO-TAO experiment, comprising four layers of 160 strips of PS, was designed and evaluated. The threshold was evaluated when the muon tagging efficiency of a PS strip was >99%. The efficiency of three layer out of four layer of TVT is >99%,even with a tagging efficiency of a single strip as low as 97%, using a threshold of 10 photoelectrons and assuming a 40%silicon PM photon detection efficiency.

physics.ins-det↗

arXiv2023

Incomplete Multimodal Learning for Complex Brain Disorders Prediction

Recent advancements in the acquisition of various brain data sources have created new opportunities for integrating multimodal brain data to assist in early detection of complex brain disorders. However, current data integration approaches typically need a complete set of biomedical data modalities, which may not always be feasible, as some modalities are only available in large-scale research cohorts and are prohibitive to collect in routine clinical practice. Especially in studies of brain diseases, research cohorts may include both neuroimaging data and genetic data, but for practical clinical diagnosis, we often need to make disease predictions only based on neuroimages. As a result, it is desired to design machine learning models which can use all available data (different data could provide complementary information) during training but conduct inference using only the most common data modality. We propose a new incomplete multimodal data integration approach that employs transformers and generative adversarial networks to effectively exploit auxiliary modalities available during training in order to improve the performance of a unimodal model at inference. We apply our new method to predict cognitive degeneration and disease outcomes using the multimodal imaging genetic data from Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort. Experimental results demonstrate that our approach outperforms the related machine learning and deep learning methods by a significant margin.

eess.IV↗

arXiv2022

BrainGB: A Benchmark for Brain Network Analysis with Graph Neural Networks

Mapping the connectome of the human brain using structural or functional connectivity has become one of the most pervasive paradigms for neuroimaging analysis. Recently, Graph Neural Networks (GNNs) motivated from geometric deep learning have attracted broad interest due to their established power for modeling complex networked data. Despite their superior performance in many fields, there has not yet been a systematic study of how to design effective GNNs for brain network analysis. To bridge this gap, we present BrainGB, a benchmark for brain network analysis with GNNs. BrainGB standardizes the process by (1) summarizing brain network construction pipelines for both functional and structural neuroimaging modalities and (2) modularizing the implementation of GNN designs. We conduct extensive experiments on datasets across cohorts and modalities and recommend a set of general recipes for effective GNN designs on brain networks. To support open and reproducible research on GNN-based brain network analysis, we host the BrainGB website at https://braingb.us with models, tutorials, examples, as well as an out-of-box Python package. We hope that this work will provide useful empirical evidence and offer insights for future research in this novel and promising direction.

q-bio.NC↗

arXiv2022

Tensor-Based Multi-Modality Feature Selection and Regression for Alzheimer's Disease Diagnosis

The assessment of Alzheimer's Disease (AD) and Mild Cognitive Impairment (MCI) associated with brain changes remains a challenging task. Recent studies have demonstrated that combination of multi-modality imaging techniques can better reflect pathological characteristics and contribute to more accurate diagnosis of AD and MCI. In this paper, we propose a novel tensor-based multi-modality feature selection and regression method for diagnosis and biomarker identification of AD and MCI from normal controls. Specifically, we leverage the tensor structure to exploit high-level correlation information inherent in the multi-modality data, and investigate tensor-level sparsity in the multilinear regression model. We present the practical advantages of our method for the analysis of ADNI data using three imaging modalities (VBM- MRI, FDG-PET and AV45-PET) with clinical parameters of disease severity and cognitive scores. The experimental results demonstrate the superior performance of our proposed method against the state-of-the-art for the disease diagnosis and the identification of disease-specific regions and modality-related differences. The code for this work is publicly available at https://github.com/junfish/BIOS22.

cs.LG↗

arXiv2022

Ambient Neutron Measurement at Taishan Antineutrino Observatory

The Taishan Antineutrino Observatory (TAO) is a ton-level liquid scintillator detector to be placed at 30\,m from a core of the Taishan Nuclear Power Plant for precise reactor antineutrino spectrum measurements. One important background for TAO physics are the interactions of ambient neutrons that can penetrate its outer shieldings. The neutrons fluence and energy spectrum are measured with a Bonner sphere spectrometer. Data is unfolded with the iterative Maximum-Likelihood Expectation-Maximization (MLEM) method. A simulation based on Geant4 is performed to provide the initial input spectrum to the unfolding and to understand the unfolded result. The total neutron fluence rate is measured to be 36.1 $\pm$ 4.7 $Hz/m^2$, which is higher than the expectation. For neutrons with kinetic energy lower than 20\,MeV, the measured fluence rate and energy spectrum can be well reproduced by simulation. While for the region greater than 20\,MeV, a significant discrepancy is observed and shall be understood with further studies.

physics.ins-det↗

arXiv2022

Detector optimization to reduce the cosmogenic neutron backgrounds in the TAO experiment

Short-baseline reactor antineutrino experiments with shallow overburden usually have large cosmogenic neutron backgrounds. The Taishan Antineutrino Observatory (TAO) is a ton-level liquid scintillator detector located at about 30 m from a core of the Taishan Nuclear Power Plant. It will measure the reactor antineutrino spectrum with high precision and high energy resolution to provide a reference spectrum for JUNO and other reactor antineutrino experiments, and provide a benchmark measurement to test nuclear databases. Background is one of the critical concerns of TAO since the overburden is just 10 meter-water-equivalent. The cosmogenic neutron background was estimated to be ~10% of signals. With detailed Monte Carlo simulations, we propose several measures in this work to reduce the neutron backgrounds, including doping Gadolinium in the buffer liquid, adding a polyethylene layer above the bottom lead shield, and optimization of the veto strategy. With these improvements, the neutron background-to-signal ratio can be reduced to ~2%, and might be further suppressed with pulse shape discrimination.

physics.ins-det↗

arXiv2022

Unified Embeddings of Structural and Functional Connectome via a Function-Constrained Structural Graph Variational Auto-Encoder

Graph theoretical analyses have become standard tools in modeling functional and anatomical connectivity in the brain. With the advent of connectomics, the primary graphs or networks of interest are structural connectome (derived from DTI tractography) and functional connectome (derived from resting-state fMRI). However, most published connectome studies have focused on either structural or functional connectome, yet complementary information between them, when available in the same dataset, can be jointly leveraged to improve our understanding of the brain. To this end, we propose a function-constrained structural graph variational autoencoder (FCS-GVAE) capable of incorporating information from both functional and structural connectome in an unsupervised fashion. This leads to a joint low-dimensional embedding that establishes a unified spatial coordinate system for comparing across different subjects. We evaluate our approach using the publicly available OASIS-3 Alzheimer's disease (AD) dataset and show that a variational formulation is necessary to optimally encode functional brain dynamics. Further, the proposed joint embedding approach can more accurately distinguish different patient sub-populations than approaches that do not use complementary connectome information.

q-bio.NC↗

arXiv2022

Calibration Strategy of the JUNO-TAO Experiment

The Taishan Antineutrino Observatory (JUNO-TAO, or TAO) is a satellite detector for the Jiangmen Underground Neutrino Observatory (JUNO). Located near the Taishan reactor, TAO independently measures the reactor's antineutrino energy spectrum with unprecedented energy resolution. To achieve this goal, energy response must be well calibrated. Using the Automated Calibration Unit (ACU) and the Cable Loop System (CLS) of TAO, multiple radioactive sources are deployed to various positions in the detector to perform a precise calibration of energy response. The non-linear energy response can be controlled within 0.6% with different energy points of these radioactive sources. It can be further improved by using $^{12}\rm B$ decay signals produced by cosmic muons. Through the energy non-uniformity calibration, residual non-uniformity is less than 0.2%. The energy resolution degradation and energy bias caused by the residual non-uniformity can be controlled within 0.05% and 0.3%, respectively. In addition, the stability of other detector parameters, such as the gain of each silicon photo-multiplier, can be monitored with a special ultraviolet LED calibration system.

physics.ins-det↗

arXiv2022

Functional2Structural: Cross-Modality Brain Networks Representation Learning

MRI-based modeling of brain networks has been widely used to understand functional and structural interactions and connections among brain regions, and factors that affect them, such as brain development and disease. Graph mining on brain networks may facilitate the discovery of novel biomarkers for clinical phenotypes and neurodegenerative diseases. Since brain networks derived from functional and structural MRI describe the brain topology from different perspectives, exploring a representation that combines these cross-modality brain networks is non-trivial. Most current studies aim to extract a fused representation of the two types of brain network by projecting the structural network to the functional counterpart. Since the functional network is dynamic and the structural network is static, mapping a static object to a dynamic object is suboptimal. However, mapping in the opposite direction is not feasible due to the non-negativity requirement of current graph learning techniques. Here, we propose a novel graph learning framework, known as Deep Signed Brain Networks (DSBN), with a signed graph encoder that, from an opposite perspective, learns the cross-modality representations by projecting the functional network to the structural counterpart. We validate our framework on clinical phenotype and neurodegenerative disease prediction tasks using two independent, publicly available datasets (HCP and OASIS). The experimental results clearly demonstrate the advantages of our model compared to several state-of-the-art methods.

cs.LG↗