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Liang Zhan

Publications and source records attributed to Liang Zhan.

At least 19 recordsLinked to original sources
arXiv2026

Binary Hypothesis Testing: A Robust Framework Against the Look Elsewhere Effect

In particle physics, discovery claims conventionally require an observed significance exceeding $5\sigma$. However, the interpretation of a $5\sigma$ result depends critically on the testing procedure, namely whether the hypothesis is tested at a single pre-specified point in parameter space or by scanning over a range of possible signal locations. This distinction gives rise to the look-elsewhere effect, a concept that is widely used but often interpreted as a simple penalty for scanning. In this work, we reinterpret the look-elsewhere effect as a correction for procedural inconsistency arising when the null distribution is generated under one procedure while the test statistic is evaluated under another. Within the framework of hypothesis testing, we examine its implications and clarify the distinct roles of the look-elsewhere effect in binary and peak-search scenarios. In particular, we show that binary test is robust against the look-elsewhere effect, whereas peak searches require an explicit correction for the search over signal locations. Using a moderate trial factor of approximately 26, calibrated from the ATLAS Higgs search, we show that a $3\sigma$ global significance of peak search can correspond to approximately $4\sigma$ significance of the binary test for the same value of the observed test statistic. This reformulation provides a clearer statistical interpretation of the look-elsewhere effect and offers a more coherent framework for understanding significance claims in particle physics.

hep-ex↗
arXiv2026

Longitudinal Bayesian Learning of Continuous Disease Position across the Alzheimer's Disease Continuum

Alzheimer's disease (AD) progresses as a continuous biological process, whereas most existing neuroimaging-based artificial intelligence methods remain limited to discrete diagnosis or clinical score prediction from cross-sectional imaging. In this work, we propose Disease Continuum Positioning (DCP), a longitudinal Bayesian Learning framework that continuously estimates disease severity from longitudinal diffusion tensor imaging (DTI). Specifically, DCP models disease severity as a low-dimensional probabilistic latent variable by jointly integrating longitudinal observations with weak clinical supervision, from which the proposed Disease Continuum Score (DCS) is derived to quantify an individual's position along the Alzheimer's disease continuum together with its associated uncertainty. Extensive experiments on the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort demonstrate that DCP consistently outperforms representative disease progression methods. More importantly, comprehensive validation analyses show that DCS accurately characterizes disease severity, exhibits strong clinical relevance, preserves longitudinal disease evolution, and predicts future disease conversion. These results suggest that DCS provides a quantitative imaging-derived representation for continuous assessment of Alzheimer's disease progression beyond conventional diagnostic labels and clinical scores.

cs.LG↗
arXiv2026

Artemis: Anatomy-Resolved inTervention for Eliminating Multimodal NeuroImage confounderS

Multimodal neuroimaging, integrating functional connectivity from fMRI and structural connectivity from DTI, enables non-invasive analysis of brain networks using graph neural networks. However, demographic factors such as age and sex systematically confound the relationship between brain connectivity and clinical outcomes, causing GNNs to exploit spurious shortcuts rather than learning causally invariant representations. While recent causal GNN methods introduce causality at the graph-modeling level, their causal mechanisms remain domain-agnostic without accounting for the real-world confounders inherent in clinical neuroimaging data. Moreover, brain networks are constructed from atlas-based parcellations where each region exhibits distinct sensitivity to demographic factors, necessitating region-aware adjustment. We propose Artemis, a region-level causal framework that bridges this gap with causal intervention at each brain region independently by learning region-specific confounder representations with lightweight parameters. Our adjustment comprehensively utilized the multimodal functional and structural features for graph reasoning as a plug-in module compatible with arbitrary GNN backbones. Experiments on three benchmarks, ADNI for disease diagnosis, OASIS for dementia staging, and HCP for sex classification, demonstrate consistent improvements over representative GNN-based baselines. Multiple supporting experiments further demonstrate statistical significance and neuroscientific interpretability.

cs.LG↗
arXiv2026

OralAgent: Integrating Reasoning, Tools, and Knowledge for Interactive Dental Image Analysis

Dental image analysis plays a pivotal role in supporting accurate diagnosis and treatment planning in oral healthcare. Although recent advances have produced dental AI models for specific tasks and individual imaging modalities, their isolated designs limit practical use in real-world clinical workflows. In this paper, we present OralAgent, the first dental-specialized AI agent that unifies multimodal reasoning, tool-based decision-making, and knowledge-grounded retrieval within an end-to-end automated framework. It integrates 22 visual analysis tools and 368 widely-used classical dental textbooks, enabling autonomous reasoning, planning, tool use, knowledge retrieval, and multi-step workflow execution. Furthermore, we introduce OralCorpus, a large-scale, high-quality bilingual textual resource containing 134.8M tokens curated for dental retrieval-augmented generation (RAG). To evaluate models' multidisciplinary dental knowledge, we construct OralQA-ZH, a Chinese multiple-choice question benchmark consisting of 798 items across eleven oral subspecialties. Extensive experiments demonstrate that OralAgent achieves state-of-the-art performance on the MMOral-Uni, MMOral-OPG, and OralQA-ZH benchmarks, highlighting its effectiveness, interpretability, and adaptability in real-world clinical settings. The code and models are publicly available at https://github.com/isjinghao/OralAgent.

cs.CL↗
arXiv2026

Deep Models, Shallow Alignment: Uncovering the Granularity Mismatch in Neural Decoding

Neural visual decoding is a central problem in brain-computer interface research, aiming to reconstruct human visual perception and to elucidate the structure of neural representations. Recent contrastive neural visual decoding methods commonly align neural signals with the final embeddings of pretrained vision encoders. However, such representations are optimized for high-level semantic invariance, whereas EEG/MEG signals contain information spanning multiple levels of visual abstraction, potentially creating a representational granularity mismatch. Motivated by prior evidence that brain representations correspond to multiple levels of the DNN hierarchy, we propose Shallow Alignment, a granularity-calibration framework that systematically explores intermediate visual representations as alignment targets for neural decoding. Extensive experiments across multiple benchmarks demonstrate that Shallow Alignment significantly outperforms standard final-layer alignment, with performance gains ranging from 22% to 58% across diverse vision backbones. Notably, our approach reveals a positive scaling trend in neural visual decoding, enabling decoding performance to improve consistently with the capacity of pre-trained vision backbones. We further conduct systematic empirical analyses to shed light on the mechanisms underlying the observed performance gains. Code is available at https://github.com/yangdu-neuroai/shallow-alignment.

cs.CV↗
arXiv2026

HERO: Hierarchical Evidential Reasoning Optimization for Radiology Report Generation via Reason-then-Summarize

Multimodal Large Language Models (MLLMs) have substantially advanced Radiology Report Generation (RRG), yet aligning them through reinforcement learning (RL) remains challenging due to heterogeneous medical supervision. Vanilla Group Relative Policy Optimization (GRPO) assigns uniform credit across the entire generation, leading to segment interference, token dilution, and evidence--diagnosis decoupling, which exacerbates clinical hallucinations. We propose HERO (Hierarchical Evidential Reasoning Optimization), a factorized policy optimization framework that aligns heterogeneous supervision with three optimization granularities. HERO separately optimizes reasoning, diagnosis, and evidence grounding through complementary segment-, token-, and completion-level optimization with a heterogeneous reward formulation covering diagnostic accuracy, reasoning quality, and think--answer consistency. Experiments on MIMIC-CXR and IU-Xray show that HERO outperforms strong supervised and reinforcement learning baselines, achieving state-of-the-art clinical efficacy while producing more evidence-grounded and think--answer-consistent reports, thereby substantially mitigating clinical hallucinations.

cs.LG↗
arXiv2025

R-GenIMA: Integrating Neuroimaging and Genetics with Interpretable Multimodal AI for Alzheimer's Disease Progression

Early detection of Alzheimer's disease (AD) requires models capable of integrating macro-scale neuroanatomical alterations with micro-scale genetic susceptibility, yet existing multimodal approaches struggle to align these heterogeneous signals. We introduce R-GenIMA, an interpretable multimodal large language model that couples a novel ROI-wise vision transformer with genetic prompting to jointly model structural MRI and single nucleotide polymorphisms (SNPs) variations. By representing each anatomically parcellated brain region as a visual token and encoding SNP profiles as structured text, the framework enables cross-modal attention that links regional atrophy patterns to underlying genetic factors. Applied to the ADNI cohort, R-GenIMA achieves state-of-the-art performance in four-way classification across normal cognition (NC), subjective memory concerns (SMC), mild cognitive impairment (MCI), and AD. Beyond predictive accuracy, the model yields biologically meaningful explanations by identifying stage-specific brain regions and gene signatures, as well as coherent ROI-Gene association patterns across the disease continuum. Attention-based attribution revealed genes consistently enriched for established GWAS-supported AD risk loci, including APOE, BIN1, CLU, and RBFOX1. Stage-resolved neuroanatomical signatures identified shared vulnerability hubs across disease stages alongside stage-specific patterns: striatal involvement in subjective decline, frontotemporal engagement during prodromal impairment, and consolidated multimodal network disruption in AD. These results demonstrate that interpretable multimodal AI can synthesize imaging and genetics to reveal mechanistic insights, providing a foundation for clinically deployable tools that enable earlier risk stratification and inform precision therapeutic strategies in Alzheimer's disease.

cs.LG↗
arXiv2025

Why Text Prevails: Vision May Undermine Multimodal Medical Decision Making

With the rapid progress of large language models (LLMs), advanced multimodal large language models (MLLMs) have demonstrated impressive zero-shot capabilities on vision-language tasks. In the biomedical domain, however, even state-of-the-art MLLMs struggle with basic Medical Decision Making (MDM) tasks. We investigate this limitation using two challenging datasets: (1) three-stage Alzheimer's disease (AD) classification (normal, mild cognitive impairment, dementia), where category differences are visually subtle, and (2) MIMIC-CXR chest radiograph classification with 14 non-mutually exclusive conditions. Our empirical study shows that text-only reasoning consistently outperforms vision-only or vision-text settings, with multimodal inputs often performing worse than text alone. To mitigate this, we explore three strategies: (1) in-context learning with reason-annotated exemplars, (2) vision captioning followed by text-only inference, and (3) few-shot fine-tuning of the vision tower with classification supervision. These findings reveal that current MLLMs lack grounded visual understanding and point to promising directions for improving multimodal decision making in healthcare.

cs.CV↗
arXiv2025

Conditional Neural ODE for Longitudinal Parkinson's Disease Progression Forecasting

Parkinson's disease (PD) shows heterogeneous, evolving brain-morphometry patterns. Modeling these longitudinal trajectories enables mechanistic insight, treatment development, and individualized 'digital-twin' forecasting. However, existing methods usually adopt recurrent neural networks and transformer architectures, which rely on discrete, regularly sampled data while struggling to handle irregular and sparse magnetic resonance imaging (MRI) in PD cohorts. Moreover, these methods have difficulty capturing individual heterogeneity including variations in disease onset, progression rate, and symptom severity, which is a hallmark of PD. To address these challenges, we propose CNODE (Conditional Neural ODE), a novel framework for continuous, individualized PD progression forecasting. The core of CNODE is to model morphological brain changes as continuous temporal processes using a neural ODE model. In addition, we jointly learn patient-specific initial time and progress speed to align individual trajectories into a shared progression trajectory. We validate CNODE on the Parkinson's Progression Markers Initiative (PPMI) dataset. Experimental results show that our method outperforms state-of-the-art baselines in forecasting longitudinal PD progression.

cs.LG↗
arXiv2025

Modeling Causal Interactions Across Brain Functional Subnetworks for Population-specific Disease Analysis

Current neuroimaging studies on neurodegenerative diseases and psychological risk factors have been developed predominantly in non Hispanic White cohorts, with other populations markedly underrepresented. In this work, we construct directed hyper connectomes among large scale functional brain systems based on causal influences between brain regions, and examine their links to Alzheimer Disease progression and worry levels across racial groups. By using Health and Aging Brain Study Health Disparities (HABS HD) dataset, our experimental results suggest that neglecting racial variation in brain network architecture may reduce predictive performance in both cognitive and affective phenotypes. Important shared and population-specific hyper-connectome patterns related to both AD progression and worry levels were identified. We further observed distinct closed loop directed circuits across groups, suggesting that different populations may rely on distinct feedback based network regulation strategies when supporting cognition or managing emotional states. Together, these results indicate a common backbone of network vulnerability with population-dependent variations in regulatory coordination, underscoring the importance of population-aware neuroimaging models.

q-bio.NC↗
arXiv2025

DRE: An Effective Dual-Refined Method for Integrating Small and Large Language Models in Open-Domain Dialogue Evaluation

Large Language Models (LLMs) excel at many tasks but struggle with ambiguous scenarios where multiple valid responses exist, often yielding unreliable results. Conversely, Small Language Models (SLMs) demonstrate robustness in such scenarios but are susceptible to misleading or adversarial inputs. We observed that LLMs handle negative examples effectively, while SLMs excel with positive examples. To leverage their complementary strengths, we introduce SLIDE (Small and Large Integrated for Dialogue Evaluation), a method integrating SLMs and LLMs via adaptive weighting. Building on SLIDE, we further propose a Dual-Refinement Evaluation (DRE) method to enhance SLM-LLM integration: (1) SLM-generated insights guide the LLM to produce initial evaluations; (2) SLM-derived adjustments refine the LLM's scores for improved accuracy. Experiments demonstrate that DRE outperforms existing methods, showing stronger alignment with human judgment across diverse benchmarks. This work illustrates how combining small and large models can yield more reliable evaluation tools, particularly for open-ended tasks such as dialogue evaluation.

cs.CL↗
arXiv2025

Zeus: Zero-shot LLM Instruction for Union Segmentation in Multimodal Medical Imaging

Medical image segmentation has achieved remarkable success through the continuous advancement of UNet-based and Transformer-based foundation backbones. However, clinical diagnosis in the real world often requires integrating domain knowledge, especially textual information. Conducting multimodal learning involves visual and text modalities shown as a solution, but collecting paired vision-language datasets is expensive and time-consuming, posing significant challenges. Inspired by the superior ability in numerous cross-modal tasks for Large Language Models (LLMs), we proposed a novel Vision-LLM union framework to address the issues. Specifically, we introduce frozen LLMs for zero-shot instruction generation based on corresponding medical images, imitating the radiology scanning and report generation process. {To better approximate real-world diagnostic processes}, we generate more precise text instruction from multimodal radiology images (e.g., T1-w or T2-w MRI and CT). Based on the impressive ability of semantic understanding and rich knowledge of LLMs. This process emphasizes extracting special features from different modalities and reunion the information for the ultimate clinical diagnostic. With generated text instruction, our proposed union segmentation framework can handle multimodal segmentation without prior collected vision-language datasets. To evaluate our proposed method, we conduct comprehensive experiments with influential baselines, the statistical results and the visualized case study demonstrate the superiority of our novel method.}

cs.CV↗
arXiv2025

End-to-End Deep Learning for Structural Brain Imaging: A Unified Framework

Brain imaging analysis is fundamental in neuroscience, providing valuable insights into brain structure and function. Traditional workflows follow a sequential pipeline-brain extraction, registration, segmentation, parcellation, network generation, and classification-treating each step as an independent task. These methods rely heavily on task-specific training data and expert intervention to correct intermediate errors, making them particularly burdensome for high-dimensional neuroimaging data, where annotations and quality control are costly and time-consuming. We introduce UniBrain, a unified end-to-end framework that integrates all processing steps into a single optimization process, allowing tasks to interact and refine each other. Unlike traditional approaches that require extensive task-specific annotations, UniBrain operates with minimal supervision, leveraging only low-cost labels (i.e., classification and extraction) and a single labeled atlas. By jointly optimizing extraction, registration, segmentation, parcellation, network generation, and classification, UniBrain enhances both accuracy and computational efficiency while significantly reducing annotation effort. Experimental results demonstrate its superiority over existing methods across multiple tasks, offering a more scalable and reliable solution for neuroimaging analysis. Our code and data can be found at https://github.com/Anonymous7852/UniBrain

eess.IV↗
arXiv2025

Rethinking Functional Brain Connectome Analysis: Do Graph Deep Learning Models Help

Graph deep learning models, a class of AI-driven approaches employing a message aggregation mechanism, have gained popularity for analyzing the functional brain connectome in neuroimaging. However, their actual effectiveness remains unclear. In this study, we re-examine graph deep learning versus classical machine learning models based on four large-scale neuroimaging studies. Surprisingly, we find that the message aggregation mechanism, a hallmark of graph deep learning models, does not help with predictive performance as typically assumed, but rather consistently degrades it. To address this issue, we propose a hybrid model combining a linear model with a graph attention network through dual pathways, achieving robust predictions and enhanced interpretability by revealing both localized and global neural connectivity patterns. Our findings urge caution in adopting complex deep learning models for functional brain connectome analysis, emphasizing the need for rigorous experimental designs to establish tangible performance gains and perhaps more importantly, to pursue improvements in model interpretability.

cs.NE↗
arXiv2024

A Self-guided Multimodal Approach to Enhancing Graph Representation Learning for Alzheimer's Diseases

Graph neural networks (GNNs) are powerful machine learning models designed to handle irregularly structured data. However, their generic design often proves inadequate for analyzing brain connectomes in Alzheimer's Disease (AD), highlighting the need to incorporate domain knowledge for optimal performance. Infusing AD-related knowledge into GNNs is a complicated task. Existing methods typically rely on collaboration between computer scientists and domain experts, which can be both time-intensive and resource-demanding. To address these limitations, this paper presents a novel self-guided, knowledge-infused multimodal GNN that autonomously incorporates domain knowledge into the model development process. Our approach conceptualizes domain knowledge as natural language and introduces a specialized multimodal GNN capable of leveraging this uncurated knowledge to guide the learning process of the GNN, such that it can improve the model performance and strengthen the interpretability of the predictions. To evaluate our framework, we curated a comprehensive dataset of recent peer-reviewed papers on AD and integrated it with multiple real-world AD datasets. Experimental results demonstrate the ability of our method to extract relevant domain knowledge, provide graph-based explanations for AD diagnosis, and improve the overall performance of the GNN. This approach provides a more scalable and efficient alternative to inject domain knowledge for AD compared with the manual design from the domain expert, advancing both prediction accuracy and interpretability in AD diagnosis.

cs.LG↗
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

X-ray Made Simple: Lay Radiology Report Generation and Robust Evaluation

Radiology Report Generation (RRG) has advanced considerably with the development of multimodal generative models. Despite the progress, the field still faces significant challenges in evaluation, as existing metrics lack robustness and fairness. We reveal that, RRG with high performance on existing lexical-based metrics (e.g. BLEU) might be more of a mirage - a model can get a high BLEU only by learning the template of reports. This has become a pressing issue for RRG due to the highly patternized nature of these reports. In addition, standard radiology reports are often highly technical. Helping patients understand these reports is crucial from a patient's perspective, yet this has been largely overlooked in previous work. In this work, we un-intuitively approach these problems by proposing the Layman's RRG framework that can systematically improve RRG with day-to-day language. Specifically, our framework first contributes a translated Layman's terms dataset. Building upon the dataset, we then propose a semantics-based evaluation method, which is effective in mitigating the inflated numbers of BLEU and provides more robust evaluation. We show that training on the layman's terms dataset encourages models to focus on the semantics of the reports, as opposed to overfitting to learning the report templates. Last, we reveal a promising scaling law between the number of training examples and semantics gain provided by our dataset, compared to the inverse pattern brought by the original formats.

cs.CL↗