arXiv subjects

Junhao Wen

Publications and source records attributed to Junhao Wen.

At least 19 recordsLinked to original sources

arXiv2026

GenFAR: A generalized representation of brain structure, derived from 49,246 multi-cohort MRIs via deep learning

Deep learning models for neuroimaging have largely been developed for individual tasks, limiting knowledge transfer across applications. Here we introduce GenFAR, a modular deep learning framework that learns general, clinically informed features from brain MRIs. We trained this modular architecture on 49,246 individuals across 11 cohorts, using 17 diverse classification and regression tasks spanning cognition, clinical, diagnosis, demographics, and biomarkers. This yields aggregated, focused feature sets that capture rich, clinically- and biologically-relevant brain representations. We developed a sequential learning approach where tasks progressively build on previously learned representations. Through an analysis of 5,000 task sequences, we identified an optimal sequence length of six tasks and introduced a Donor Score metric to quantify each task's contribution to downstream performance. This analysis revealed five consistently strong donor tasks (Age, AD/MCI, MMSE, Hypertension, Hyperlipidemia) that formed the base of our sequential model. We demonstrated the utility of our learned representation, in various tasks beyond those included in the training set, to serve as the foundation for specialized secondary predictors. We further showed that using the learned feature representation can substantially increase the sample efficiency of secondary deep learning training tasks and models, as well as improve their accuracy.

cs.CV↗

arXiv2026

Pan-FM: A Pan-Organ Foundation Model with Saliency-Guided Masking for Missing Robustness

Foundation models (FMs) have shown great promise in medical imaging, but most FMs are trained on unimodal data within isolated domains, such as brain MRI alone. Human aging and disease arise through coordinated biological processes across organs, therefore motivating multimodal FMs that learn whole-body representations. A key challenge, however, is that real-world multimodal biomedical data are often missing not at random, which can reduce power, limit generalizability, and introduce bias. We propose Pan-FM, a pan-organ foundation model pre-trained on imaging from seven organs (Brain, Heart, Adipose, Liver, Kidney, Spleen, and Pancreas) under realistic missing-organ scenarios. Pan-FM uses a unified backbone that handles organ missingness during both training and inference, and is pre-trained with masking-based self-distillation. We find that naive multimodal pre-training leads to dominant-organ shortcut learning bias, with the model over-relying on dominant organs such as adipose and heart. To address this, we introduce Saliency-Guided Masking (SGM), which uses the model attention distribution to adaptively mask dominant organs during pre-training, thus encouraging more balanced cross-organ, whole-body learning. Notably, SGM introduces negligible computational overhead and can be seamlessly integrated into existing self-supervised learning frameworks to improve multi-organ representation learning. On the UK Biobank, Pan-FM achieves stronger prediction across 13 disease categories and 14 single disease entities than single-organ and multi-organ baselines, with improved robustness under missing-organ settings. Pan-FM serves as a scalable solution to realistic modality-missingness in multimodal learning in system neuroscience and as a step toward more generalizable whole-body FMs.

cs.CV↗

arXiv2026

Group of Skills: Group-Structured Skill Retrieval for Agent Skill Libraries

Skill-augmented agents increasingly rely on large reusable skill libraries, but retrieving relevant skills is not the same as presenting usable context. Existing methods typically return atomic skills or dependency-aware bundles whose internal roles remain implicit, leaving the agent to infer the execution entry point, support skills, visible requirements, and failure-avoidance guidance. We introduce Group of Skills (GoSkills), an inference-time group-structured retrieval method that changes the agent-facing retrieval object from a flat skill list to a compact, role-labeled execution context. GoSkills builds anchor-centered skill groups from a typed skill graph, expands support groups through a group graph, bottlenecks the selected group plan into a bounded set of atomic skill payloads, and renders a fixed execution contract with Start, Support, Check, and Avoid fields, without changing the downstream agent, skill payloads, or execution environment. Experiments on SkillsBench and ALFWorld show that GoSkills preserves visible-requirement coverage under a small skill budget, improves over flat skill-access baselines, and often improves reward and agent-only runtime relative to structural retrieval references.

cs.CL↗

arXiv2026

Can LLMs Help Decentralized Dispute Arbitration? A Case Study of UMA-Resolved Markets on Polymarket

Web3 prediction markets, exemplified by Polymarket, have gained prominence for leveraging collective intelligence to forecast a wide range of social, political, and sports events. However, among the thousands of prediction market events, consensus disputes still arise due to imperfections in market mechanisms. On Polymarket alone, the trading volume involving disputed events has reached $972,370,804.71, underscoring the critical need for objective and efficient dispute resolution. In this study, we introduce large language models (LLMs) to: (1) evaluate whether web-enabled LLMs can reproduce the decision quality of UMA's on-chain voting process once a dispute has been raised, and (2) predict, based on event rules, which market events are likely to face future disputes before they occur. Our findings show that LLMs are unable to reliably predict which events will become disputed in advance; however, once a dispute is initiated, web-enabled LLMs achieve 89.58% agreement with UMA's final resolutions and demonstrate strong stability.

cs.CY↗

arXiv2025

Gated Rotary-Enhanced Linear Attention with Rank Modulation for Long-term Sequential Recommendation

In Sequential Recommendation Systems (SRSs), Transformer models have demonstrated remarkable performance but face computational and memory cost challenges, especially when modeling long-term user behavior sequences. Due to its quadratic complexity, the dot-product attention mechanism in Transformers becomes expensive for processing long sequences. By approximating the dot-product attention using elaborate mapping functions, linear attention provides a more efficient option with linear complexity. However, existing linear attention methods face three limitations: 1) they often use learnable position encodings, which incur extra computational costs in long-term sequence scenarios, 2) limited by the low-rank deficiency, they may not sufficiently account for user's fine-grained local preferences (short-lived burst of interest), and 3) they try to capture some temporary activities, but often confuse these with stable and long-term interests. This can result in unclear or less effective recommendations. To remedy these drawbacks, we propose a long-term sequential Recommendation model with Gated Rotary Enhanced Linear Attention (RecGRELA). Specifically, we first propose a Rotary-Enhanced Linear Attention (RELA) module to efficiently model long-range dependency within the user's historical information using rotary position encodings. Then, to address the low-rank deficiency of linear attention, we introduce an Adaptive Rank Modulator. It incorporates a rank augmentation branch to explicitly inject local token mixing and a Gated Rank Selector to dynamically balance stable long-term preferences and transient short-term interests. Experimental results on four public benchmark datasets show that our RecGRELA achieves state-of-the-art performance compared with existing SRSs based on Recurrent Neural Networks, Transformer, and Mamba while keeping low memory overhead.

cs.IR↗

arXiv2025

Distance-aware Self-adaptive Graph Convolution for Fine-grained Hierarchical Recommendation

Graph Convolutional Networks (GCNs) are widely used to improve recommendation accuracy and performance by effectively learning the representations of user and item nodes. However, two major challenges remain: (1) the lack of further optimization in the graph representation structure and (2) insufficient attention given to the varying contributions of different convolutional layers.This paper proposes SAGCN, a distance-based adaptive hierarchical aggregation method that refines the aggregation process through differentiated representation metrics. SAGCN introduces a detailed approach to multilayer information aggregation and representation space optimization, enabling the model to learn hierarchical embedding weights based on the distance between hierarchical representations. This innovation allows for more precise cross-layer information aggregation, improves the model's ability to capture hierarchical embeddings, and optimizes the representation space structure. Additionally, the objective loss function is refined to better align with recommendation tasks.Extensive experiments conducted on four real-world datasets demonstrate significant improvements, including over a 5% increase on Yelp and a 5.58% increase in Recall@10 on the ML_1M dataset.

cs.IR↗

arXiv2025

Breaking the Clusters: Uniformity-Optimization for Text-Based Sequential Recommendation

Traditional sequential recommendation (SR) methods heavily rely on explicit item IDs to capture user preferences over time. This reliance introduces critical limitations in cold-start scenarios and domain transfer tasks, where unseen items and new contexts often lack established ID mappings. To overcome these limitations, recent studies have shifted towards leveraging text-only information for recommendation, thereby improving model generalization and adaptability across domains. Although promising, text-based SR faces unique difficulties: items' text descriptions often share semantic similarities that lead to clustered item representations, compromising their uniformity, a property essential for promoting diversity and enhancing generalization in recommendation systems. In this paper, we explore a novel framework to improve the uniformity of item representations in text-based SR. Our analysis reveals that items within a sequence exhibit marked semantic similarity, meaning they are closer in representation than items overall, and that this effect is more pronounced for less popular items, which form tighter clusters compared to their more popular counterparts. Based on these findings, we propose UniT, a framework that employs three pairwise item sampling strategies: Unified General Sampling Strategy, Sequence-Driven Sampling Strategy, and Popularity-Driven Sampling Strategy. Each strategy applies varying degrees of repulsion to selectively adjust the distances between item pairs, thereby refining representation uniformity while considering both sequence context and item popularity. Extensive experiments on multiple real-world datasets demonstrate that our proposed approach outperforms state-of-the-art models, validating the effectiveness of UniT in enhancing both representation uniformity and recommendation accuracy.The source code is available at https://github.com/ccwwhhh/Model-Rec.

cs.IR↗

arXiv2024

Multi-view Intent Learning and Alignment with Large Language Models for Session-based Recommendation

Session-based recommendation (SBR) methods often rely on user behavior data, which can struggle with the sparsity of session data, limiting performance. Researchers have identified that beyond behavioral signals, rich semantic information in item descriptions is crucial for capturing hidden user intent. While large language models (LLMs) offer new ways to leverage this semantic data, the challenges of session anonymity, short-sequence nature, and high LLM training costs have hindered the development of a lightweight, efficient LLM framework for SBR. To address the above challenges, we propose an LLM-enhanced SBR framework that integrates semantic and behavioral signals from multiple views. This two-stage framework leverages the strengths of both LLMs and traditional SBR models while minimizing training costs. In the first stage, we use multi-view prompts to infer latent user intentions at the session semantic level, supported by an intent localization module to alleviate LLM hallucinations. In the second stage, we align and unify these semantic inferences with behavioral representations, effectively merging insights from both large and small models. Extensive experiments on two real datasets demonstrate that the LLM4SBR framework can effectively improve model performance. We release our codes along with the baselines at https://github.com/tsinghua-fib-lab/LLM4SBR.

cs.IR↗

arXiv2024

Dimensional Neuroimaging Endophenotypes: Neurobiological Representations of Disease Heterogeneity Through Machine Learning

Machine learning has been increasingly used to obtain individualized neuroimaging signatures for disease diagnosis, prognosis, and response to treatment in neuropsychiatric and neurodegenerative disorders. Therefore, it has contributed to a better understanding of disease heterogeneity by identifying disease subtypes that present significant differences in various brain phenotypic measures. In this review, we first present a systematic literature overview of studies using machine learning and multimodal MRI to unravel disease heterogeneity in various neuropsychiatric and neurodegenerative disorders, including Alzheimer disease, schizophrenia, major depressive disorder, autism spectrum disorder, multiple sclerosis, as well as their potential in transdiagnostic settings. Subsequently, we summarize relevant machine learning methodologies and discuss an emerging paradigm which we call dimensional neuroimaging endophenotype (DNE). DNE dissects the neurobiological heterogeneity of neuropsychiatric and neurodegenerative disorders into a low dimensional yet informative, quantitative brain phenotypic representation, serving as a robust intermediate phenotype (i.e., endophenotype) largely reflecting underlying genetics and etiology. Finally, we discuss the potential clinical implications of the current findings and envision future research avenues.

cs.LG↗

arXiv2023

Inverse Measurements in Active Nematics

We present a framework to take new measurements in nematic systems that contain active elements such as molecular motors. Spatio-temporal fields of stress, traction, velocity, pressure, and forces are estimated jointly from microscopy images alone. Our inverse-problem approach ensures that these fields comply with physical laws and are accurate at system boundaries. Our novel measurements in active biological materials provide new insight for the design of boundary-aware nematic systems. The shear stress at the wall unveils a correlation with the nucleation of topological defects. The pressure gradients and the velocity characterize how boundary effects drive system-wide dynamics. And the forces link the underlying fluid with the nematic tensor to reveal the time scales of the system. More broadly, our work establishes a generalizable approach to quantitatively study experimental systems that are inaccessible to measuring probes.

cond-mat.soft↗

arXiv2023

Applications of Generative Adversarial Networks in Neuroimaging and Clinical Neuroscience

Generative adversarial networks (GANs) are one powerful type of deep learning models that have been successfully utilized in numerous fields. They belong to a broader family called generative methods, which generate new data with a probabilistic model by learning sample distribution from real examples. In the clinical context, GANs have shown enhanced capabilities in capturing spatially complex, nonlinear, and potentially subtle disease effects compared to traditional generative methods. This review appraises the existing literature on the applications of GANs in imaging studies of various neurological conditions, including Alzheimer's disease, brain tumors, brain aging, and multiple sclerosis. We provide an intuitive explanation of various GAN methods for each application and further discuss the main challenges, open questions, and promising future directions of leveraging GANs in neuroimaging. We aim to bridge the gap between advanced deep learning methods and neurology research by highlighting how GANs can be leveraged to support clinical decision making and contribute to a better understanding of the structural and functional patterns of brain diseases.

cs.LG↗

arXiv2023

Gene-SGAN: a method for discovering disease subtypes with imaging and genetic signatures via multi-view weakly-supervised deep clustering

Disease heterogeneity has been a critical challenge for precision diagnosis and treatment, especially in neurologic and neuropsychiatric diseases. Many diseases can display multiple distinct brain phenotypes across individuals, potentially reflecting disease subtypes that can be captured using MRI and machine learning methods. However, biological interpretability and treatment relevance are limited if the derived subtypes are not associated with genetic drivers or susceptibility factors. Herein, we describe Gene-SGAN - a multi-view, weakly-supervised deep clustering method - which dissects disease heterogeneity by jointly considering phenotypic and genetic data, thereby conferring genetic correlations to the disease subtypes and associated endophenotypic signatures. We first validate the generalizability, interpretability, and robustness of Gene-SGAN in semi-synthetic experiments. We then demonstrate its application to real multi-site datasets from 28,858 individuals, deriving subtypes of Alzheimer's disease and brain endophenotypes associated with hypertension, from MRI and SNP data. Derived brain phenotypes displayed significant differences in neuroanatomical patterns, genetic determinants, biological and clinical biomarkers, indicating potentially distinct underlying neuropathologic processes, genetic drivers, and susceptibility factors. Overall, Gene-SGAN is broadly applicable to disease subtyping and endophenotype discovery, and is herein tested on disease-related, genetically-driven neuroimaging phenotypes.

q-bio.QM↗

arXiv2022

The Best of Both Worlds: Combining Learned Embeddings with Engineered Features for Accurate Prediction of Correct Patches

A large body of the literature on automated program repair develops approaches where patches are automatically generated to be validated against an oracle (e.g., a test suite). Because such an oracle can be imperfect, the generated patches, although validated by the oracle, may actually be incorrect. Our empirical work investigates different representation learning approaches for code changes to derive embeddings that are amenable to similarity computations of patch correctness identification, and assess the possibility of accurate classification of correct patch by combining learned embeddings with engineered features. Experimental results demonstrate the potential of learned embeddings to empower Leopard (a patch correctness predicting framework implemented in this work) with learning algorithms in reasoning about patch correctness: a machine learning predictor with BERT transformer-based learned embeddings associated with XGBoost achieves an AUC value of about 0.803 in the prediction of patch correctness on a new dataset of 2,147 labeled patches that we collected for the experiments. Our investigations show that deep learned embeddings can lead to complementary/better performance when comparing against the state-of-the-art, PATCH-SIM, which relies on dynamic information. By combining deep learned embeddings and engineered features, Panther (the upgraded version of Leopard implemented in this work) outperforms Leopard with higher scores in terms of AUC, +Recall and -Recall, and can accurately identify more (in)correct patches that cannot be predicted by the classifiers only with learned embeddings or engineered features. Finally, we use an explainable ML technique, SHAP, to empirically interpret how the learned embeddings and engineered features are contributed to the patch correctness prediction.

cs.SE↗

arXiv2022

Surreal-GAN:Semi-Supervised Representation Learning via GAN for uncovering heterogeneous disease-related imaging patterns

A plethora of machine learning methods have been applied to imaging data, enabling the construction of clinically relevant imaging signatures of neurological and neuropsychiatric diseases. Oftentimes, such methods don't explicitly model the heterogeneity of disease effects, or approach it via nonlinear models that are not interpretable. Moreover, unsupervised methods may parse heterogeneity that is driven by nuisance confounding factors that affect brain structure or function, rather than heterogeneity relevant to a pathology of interest. On the other hand, semi-supervised clustering methods seek to derive a dichotomous subtype membership, ignoring the truth that disease heterogeneity spatially and temporally extends along a continuum. To address the aforementioned limitations, herein, we propose a novel method, termed Surreal-GAN (Semi-SUpeRvised ReprEsentAtion Learning via GAN). Using cross-sectional imaging data, Surreal-GAN dissects underlying disease-related heterogeneity under the principle of semi-supervised clustering (cluster mappings from normal control to patient), proposes a continuously dimensional representation, and infers the disease severity of patients at individual level along each dimension. The model first learns a transformation function from normal control (CN) domain to the patient (PT) domain with latent variables controlling transformation directions. An inverse mapping function together with regularization on function continuity, pattern orthogonality and monotonicity was also imposed to make sure that the transformation function captures necessarily meaningful imaging patterns with clinical significance. We first validated the model through extensive semi-synthetic experiments, and then demonstrate its potential in capturing biologically plausible imaging patterns in Alzheimer's disease (AD).

cs.LG↗

arXiv2022

Subtyping brain diseases from imaging data

The imaging community has increasingly adopted machine learning (ML) methods to provide individualized imaging signatures related to disease diagnosis, prognosis, and response to treatment. Clinical neuroscience and cancer imaging have been two areas in which ML has offered particular promise. However, many neurologic and neuropsychiatric diseases, as well as cancer, are often heterogeneous in terms of their clinical manifestations, neuroanatomical patterns or genetic underpinnings. Therefore, in such cases, seeking a single disease signature might be ineffectual in delivering individualized precision diagnostics. The current chapter focuses on ML methods, especially semi-supervised clustering, that seek disease subtypes using imaging data. Work from Alzheimer Disease and its prodromal stages, psychosis, depression, autism, and brain cancer are discussed. Our goal is to provide the readers with a broad overview in terms of methodology and clinical applications.

cs.LG↗

arXiv2021

Multidimensional representations in late-life depression: convergence in neuroimaging, cognition, clinical symptomatology and genetics

Late-life depression (LLD) is characterized by considerable heterogeneity in clinical manifestation. Unraveling such heterogeneity would aid in elucidating etiological mechanisms and pave the road to precision and individualized medicine. We sought to delineate, cross-sectionally and longitudinally, disease-related heterogeneity in LLD linked to neuroanatomy, cognitive functioning, clinical symptomatology, and genetic profiles. Multimodal data from a multicentre sample (N=996) were analyzed. A semi-supervised clustering method (HYDRA) was applied to regional grey matter (GM) brain volumes to derive dimensional representations. Two dimensions were identified, which accounted for the LLD-related heterogeneity in voxel-wise GM maps, white matter (WM) fractional anisotropy (FA), neurocognitive functioning, clinical phenotype, and genetics. Dimension one (Dim1) demonstrated relatively preserved brain anatomy without WM disruptions relative to healthy controls. In contrast, dimension two (Dim2) showed widespread brain atrophy and WM integrity disruptions, along with cognitive impairment and higher depression severity. Moreover, one de novo independent genetic variant (rs13120336) was significantly associated with Dim 1 but not with Dim 2. Notably, the two dimensions demonstrated significant SNP-based heritability of 18-27% within the general population (N=12,518 in UKBB). Lastly, in a subset of individuals having longitudinal measurements, Dim2 demonstrated a more rapid longitudinal decrease in GM and brain age, and was more likely to progress to Alzheimers disease, compared to Dim1 (N=1,413 participants and 7,225 scans from ADNI, BLSA, and BIOCARD datasets).

q-bio.NC↗

arXiv2021

Clinica: an open source software platform for reproducible clinical neuroscience studies

We present Clinica (www.clinica.run), an open-source software platform designed to make clinical neuroscience studies easier and more reproducible. Clinica aims for researchers to i) spend less time on data management and processing, ii) perform reproducible evaluations of their methods, and iii) easily share data and results within their institution and with external collaborators. The core of Clinica is a set of automatic pipelines for processing and analysis of multimodal neuroimaging data (currently, T1-weighted MRI, diffusion MRI and PET data), as well as tools for statistics, machine learning and deep learning. It relies on the brain imaging data structure (BIDS) for the organization of raw neuroimaging datasets and on established tools written by the community to build its pipelines. It also provides converters of public neuroimaging datasets to BIDS (currently ADNI, AIBL, OASIS and NIFD). Processed data include image-valued scalar fields (e.g. tissue probability maps), meshes, surface-based scalar fields (e.g. cortical thickness maps) or scalar outputs (e.g. regional averages). These data follow the ClinicA Processed Structure (CAPS) format which shares the same philosophy as BIDS. Consistent organization of raw and processed neuroimaging files facilitates the execution of single pipelines and of sequences of pipelines, as well as the integration of processed data into statistics or machine learning frameworks. The target audience of Clinica is neuroscientists or clinicians conducting clinical neuroscience studies involving multimodal imaging, and researchers developing advanced machine learning algorithms applied to neuroimaging data.

q-bio.QM↗

arXiv2021

Disentangling brain heterogeneity via semi-supervised deep-learning and MRI: dimensional representations of Alzheimer's Disease

Heterogeneity of brain diseases is a challenge for precision diagnosis/prognosis. We describe and validate Smile-GAN (SeMI-supervised cLustEring-Generative Adversarial Network), a novel semi-supervised deep-clustering method, which dissects neuroanatomical heterogeneity, enabling identification of disease subtypes via their imaging signatures relative to controls. When applied to MRIs (2 studies; 2,832 participants; 8,146 scans) including cognitively normal individuals and those with cognitive impairment and dementia, Smile-GAN identified 4 neurodegenerative patterns/axes: P1, normal anatomy and highest cognitive performance; P2, mild/diffuse atrophy and more prominent executive dysfunction; P3, focal medial temporal atrophy and relatively greater memory impairment; P4, advanced neurodegeneration. Further application to longitudinal data revealed two distinct progression pathways: P1$\rightarrow$P2$\rightarrow$P4 and P1$\rightarrow$P3$\rightarrow$P4. Baseline expression of these patterns predicted the pathway and rate of future neurodegeneration. Pattern expression offered better yet complementary performance in predicting clinical progression, compared to amyloid/tau. These deep-learning derived biomarkers offer promise for precision diagnostics and targeted clinical trial recruitment.

cs.LG↗