arXiv subjects

Juan Helen Zhou

Publications and source records attributed to Juan Helen Zhou.

15 recordsLinked to original sources

arXiv2026

Bringing analytic rigor to agentic AI for science: The Brain Researcher platform for neuroimaging data analysis

AI agents can execute scientific analyses, but an analytic output becomes a defensible claim only after alternatives are weighed and the claim is limited to what the evidence supports. Agents may reproduce failures including selective analysis, premature declarations of success and optimization of imperfect criteria. We present Brain Researcher, an agentic research harness operating in a neuroimaging researcher's computational environment under rules for admissible analyses, required checks and claim scope. In benchmarks, Brain Researcher increased first-choice tool-selection accuracy across seven models by 70.2 percentage points (23.3% without it versus 93.6% with it) and verifiable grounding from 4.6% to 22.0%. In collaborator-led and self-evolving studies, multiverse analyses exposed analytic-choice sensitivity, and scientific review classified claims as accepted, qualified, revised, blocked, rejected or deferred. By linking decisions to evidence and provenance, Brain Researcher embeds methodological judgment within the workflow, not after it.

cs.AI↗

arXiv2026

NeuroWorld: A Latent Brain World Model for Stimulus-Conditioned Human Brain Dynamics

Forecasting human brain activity during naturalistic experience requires modeling how endogenous neural states evolve causally under continuous sensory drive. Existing brain encoding models instead frame this as stimulus-to-response regression without strict temporal constraints, allowing future stimuli to leak into current predictions. We introduce NeuroWorld, to our knowledge the first brain world model, which casts naturalistic brain functional dynamics prediction as stimulus-conditioned evolution in a learned latent brain-state space, separating endogenous states (measured via fMRI) from exogenous multimodal stimuli across two stages. Latent Dynamics Learning (LDL) jointly learns a transition-sufficient representation and causal dynamics through next-latent prediction, without reconstructing the observed fMRI signal. Latent Rollout Decoding (LRD) freezes LDL, autoregressively rolls latent states forward from an observed fMRI prefix, and decodes them into subject-specific whole-brain responses. Across three naturalistic movie-fMRI benchmarks spanning 30 participants, including our newly collected Singapore Multimodal Imaging & Naturalistic Dataset (SG-MIND; 20 participants, 8,519 paired stimulus-response clips, 140.7 person-hours of viewing), NeuroWorld achieves state-of-the-art multi-step rollout performance under strictly causal stimulus access, with greater robustness to long-horizon autoregressive drift, supporting reliable simulation of extended brain-state trajectories. Extensive interpretability analyses characterize the functional organization of the learned dynamics, establishing latent-space world modeling as a principled framework for causal forecasting of human brain activity.

q-bio.NC↗

arXiv2026

BrainFIBRE: A Foundation Model via Information Decomposition for Brain Microstructure

Diffusion MRI probes brain microstructure with particular sensitivity to early cerebrovascular and neurodegenerative changes. Neurite Orientation Dispersion and Density Imaging (NODDI) decomposes the diffusion signal into three biophysically interpretable maps: neurite density index (NDI), orientation dispersion index (ODI), and free water fraction (FWF), capturing neurite packing, fiber coherence, and extracellular fluid. These 3D maps offer a rich substrate for transferable microstructural representations, yet integrating them is challenging: standard representation learning struggles to disentangle the unique information in each map from their shared and synergistic interactions. We present BrainFIBRE, the first foundation model for brain microstructure, pretrained on NODDI-derived maps from 55,592 UK Biobank participants. We propose Self-supervised Partial Information Decomposition (SPID), which extends PID-guided multimodal learning to the self-supervised regime for the first time. A novel Counterfactual Candidate Construction (CCC) paradigm perturbs inter-modality alignment through modality dropping and swapping, providing the contrastive signal for a Mixture-of-Experts architecture to disentangle unique, synergistic, and redundant information without any downstream label. On both Caucasian and Asian cohorts, BrainFIBRE achieves state-of-the-art performance across diverse tasks predicting age, sex, cerebrovascular and neurodegenerative markers, and cognition, while yielding neurobiologically interpretable representations that reveal task- and cohort-specific interaction patterns. BrainFIBRE establishes a versatile foundation for neuroimaging analysis at the microstructural level.

cs.CV↗

arXiv2025

Standardized Evaluation of Automatic Methods for Perivascular Spaces Segmentation in MRI -- MICCAI 2024 Challenge Results

Perivascular spaces (PVS), when abnormally enlarged and visible in magnetic resonance imaging (MRI) structural sequences, are important imaging markers of cerebral small vessel disease and potential indicators of neurodegenerative conditions. Despite their clinical significance, automatic enlarged PVS (EPVS) segmentation remains challenging due to their small size, variable morphology, similarity with other pathological features, and limited annotated datasets. This paper presents the EPVS Challenge organized at MICCAI 2024, which aims to advance the development of automated algorithms for EPVS segmentation across multi-site data. We provided a diverse dataset comprising 100 training, 50 validation, and 50 testing scans collected from multiple international sites (UK, Singapore, and China) with varying MRI protocols and demographics. All annotations followed the STRIVE protocol to ensure standardized ground truth and covered the full brain parenchyma. Seven teams completed the full challenge, implementing various deep learning approaches primarily based on U-Net architectures with innovations in multi-modal processing, ensemble strategies, and transformer-based components. Performance was evaluated using dice similarity coefficient, absolute volume difference, recall, and precision metrics. The winning method employed MedNeXt architecture with a dual 2D/3D strategy for handling varying slice thicknesses. The top solutions showed relatively good performance on test data from seen datasets, but significant degradation of performance was observed on the previously unseen Shanghai cohort, highlighting cross-site generalization challenges due to domain shift. This challenge establishes an important benchmark for EPVS segmentation methods and underscores the need for the continued development of robust algorithms that can generalize in diverse clinical settings.

q-bio.QM↗

arXiv2025

Brain Harmony: A Multimodal Foundation Model Unifying Morphology and Function into 1D Tokens

We present Brain Harmony (BrainHarmonix), the first multimodal brain foundation model that unifies structural morphology and functional dynamics into compact 1D token representations. The model was pretrained on two of the largest neuroimaging datasets to date, encompassing 64,594 T1-weighted structural MRI 3D volumes (~ 14 million images) and 70,933 functional MRI (fMRI) time series. BrainHarmonix is grounded in two foundational neuroscience principles: structure complements function - structural and functional modalities offer distinct yet synergistic insights into brain organization; function follows structure - brain functional dynamics are shaped by cortical morphology. The modular pretraining process involves single-modality training with geometric pre-alignment followed by modality fusion through shared brain hub tokens. Notably, our dynamics encoder uniquely handles fMRI time series with heterogeneous repetition times (TRs), addressing a major limitation in existing models. BrainHarmonix is also the first to deeply compress high-dimensional neuroimaging signals into unified, continuous 1D tokens, forming a compact latent space of the human brain. BrainHarmonix achieves strong generalization across diverse downstream tasks, including neurodevelopmental and neurodegenerative disorder classification and cognition prediction - consistently outperforming previous approaches. Our models - pretrained on 8 H100 GPUs - aim to catalyze a new era of AI-driven neuroscience powered by large-scale multimodal neuroimaging.

q-bio.NC↗

arXiv2025

Is an Ultra Large Natural Image-Based Foundation Model Superior to a Retina-Specific Model for Detecting Ocular and Systemic Diseases?

The advent of foundation models (FMs) is transforming medical domain. In ophthalmology, RETFound, a retina-specific FM pre-trained sequentially on 1.4 million natural images and 1.6 million retinal images, has demonstrated high adaptability across clinical applications. Conversely, DINOv2, a general-purpose vision FM pre-trained on 142 million natural images, has shown promise in non-medical domains. However, its applicability to clinical tasks remains underexplored. To address this, we conducted head-to-head evaluations by fine-tuning RETFound and three DINOv2 models (large, base, small) for ocular disease detection and systemic disease prediction tasks, across eight standardized open-source ocular datasets, as well as the Moorfields AlzEye and the UK Biobank datasets. DINOv2-large model outperformed RETFound in detecting diabetic retinopathy (AUROC=0.850-0.952 vs 0.823-0.944, across three datasets, all P<=0.007) and multi-class eye diseases (AUROC=0.892 vs. 0.846, P<0.001). In glaucoma, DINOv2-base model outperformed RETFound (AUROC=0.958 vs 0.940, P<0.001). Conversely, RETFound achieved superior performance over all DINOv2 models in predicting heart failure, myocardial infarction, and ischaemic stroke (AUROC=0.732-0.796 vs 0.663-0.771, all P<0.001). These trends persisted even with 10% of the fine-tuning data. These findings showcase the distinct scenarios where general-purpose and domain-specific FMs excel, highlighting the importance of aligning FM selection with task-specific requirements to optimise clinical performance.

eess.IV↗

arXiv2025

SupReMix: Supervised Contrastive Learning for Medical Imaging Regression with Mixup

In medical image analysis, regression plays a critical role in computer-aided diagnosis. It enables quantitative measurements such as age prediction from structural imaging, cardiac function quantification, and molecular measurement from PET scans. While deep learning has shown promise for these tasks, most approaches focus solely on optimizing regression loss or model architecture, neglecting the quality of learned feature representations which are crucial for robust clinical predictions. Directly applying representation learning techniques designed for classification to regression often results in fragmented representations in the latent space, yielding sub-optimal performance. In this paper, we argue that the potential of contrastive learning for medical image regression has been overshadowed due to the neglect of two crucial aspects: ordinality-awareness and hardness. To address these challenges, we propose Supervised Contrastive Learning for Medical Imaging Regression with Mixup (SupReMix). It takes anchor-inclusive mixtures (mixup of the anchor and a distinct negative sample) as hard negative pairs and anchor-exclusive mixtures (mixup of two distinct negative samples) as hard positive pairs at the embedding level. This strategy formulates harder contrastive pairs by integrating richer ordinal information. Through theoretical analysis and extensive experiments on six datasets spanning MRI, X-ray, ultrasound, and PET modalities, we demonstrate that SupReMix fosters continuous ordered representations, significantly improving regression performance.

cs.LG↗

arXiv2025

Improve Representation for Imbalanced Regression through Geometric Constraints

In representation learning, uniformity refers to the uniform feature distribution in the latent space (i.e., unit hypersphere). Previous work has shown that improving uniformity contributes to the learning of under-represented classes. However, most of the previous work focused on classification; the representation space of imbalanced regression remains unexplored. Classification-based methods are not suitable for regression tasks because they cluster features into distinct groups without considering the continuous and ordered nature essential for regression. In a geometric aspect, we uniquely focus on ensuring uniformity in the latent space for imbalanced regression through two key losses: enveloping and homogeneity. The enveloping loss encourages the induced trace to uniformly occupy the surface of a hypersphere, while the homogeneity loss ensures smoothness, with representations evenly spaced at consistent intervals. Our method integrates these geometric principles into the data representations via a Surrogate-driven Representation Learning (SRL) framework. Experiments with real-world regression and operator learning tasks highlight the importance of uniformity in imbalanced regression and validate the efficacy of our geometry-based loss functions.

cs.LG↗

arXiv2024

Brain-JEPA: Brain Dynamics Foundation Model with Gradient Positioning and Spatiotemporal Masking

We introduce Brain-JEPA, a brain dynamics foundation model with the Joint-Embedding Predictive Architecture (JEPA). This pioneering model achieves state-of-the-art performance in demographic prediction, disease diagnosis/prognosis, and trait prediction through fine-tuning. Furthermore, it excels in off-the-shelf evaluations (e.g., linear probing) and demonstrates superior generalizability across different ethnic groups, surpassing the previous large model for brain activity significantly. Brain-JEPA incorporates two innovative techniques: Brain Gradient Positioning and Spatiotemporal Masking. Brain Gradient Positioning introduces a functional coordinate system for brain functional parcellation, enhancing the positional encoding of different Regions of Interest (ROIs). Spatiotemporal Masking, tailored to the unique characteristics of fMRI data, addresses the challenge of heterogeneous time-series patches. These methodologies enhance model performance and advance our understanding of the neural circuits underlying cognition. Overall, Brain-JEPA is paving the way to address pivotal questions of building brain functional coordinate system and masking brain activity at the AI-neuroscience interface, and setting a potentially new paradigm in brain activity analysis through downstream adaptation.

q-bio.NC↗

arXiv2024

Prompt Your Brain: Scaffold Prompt Tuning for Efficient Adaptation of fMRI Pre-trained Model

We introduce Scaffold Prompt Tuning (ScaPT), a novel prompt-based framework for adapting large-scale functional magnetic resonance imaging (fMRI) pre-trained models to downstream tasks, with high parameter efficiency and improved performance compared to fine-tuning and baselines for prompt tuning. The full fine-tuning updates all pre-trained parameters, which may distort the learned feature space and lead to overfitting with limited training data which is common in fMRI fields. In contrast, we design a hierarchical prompt structure that transfers the knowledge learned from high-resource tasks to low-resource ones. This structure, equipped with a Deeply-conditioned Input-Prompt (DIP) mapping module, allows for efficient adaptation by updating only 2% of the trainable parameters. The framework enhances semantic interpretability through attention mechanisms between inputs and prompts, and it clusters prompts in the latent space in alignment with prior knowledge. Experiments on public resting state fMRI datasets reveal ScaPT outperforms fine-tuning and multitask-based prompt tuning in neurodegenerative diseases diagnosis/prognosis and personality trait prediction, even with fewer than 20 participants. It highlights ScaPT's efficiency in adapting pre-trained fMRI models to low-resource tasks.

q-bio.NC↗

arXiv2023

Beyond the Snapshot: Brain Tokenized Graph Transformer for Longitudinal Brain Functional Connectome Embedding

Under the framework of network-based neurodegeneration, brain functional connectome (FC)-based Graph Neural Networks (GNN) have emerged as a valuable tool for the diagnosis and prognosis of neurodegenerative diseases such as Alzheimer's disease (AD). However, these models are tailored for brain FC at a single time point instead of characterizing FC trajectory. Discerning how FC evolves with disease progression, particularly at the predementia stages such as cognitively normal individuals with amyloid deposition or individuals with mild cognitive impairment (MCI), is crucial for delineating disease spreading patterns and developing effective strategies to slow down or even halt disease advancement. In this work, we proposed the first interpretable framework for brain FC trajectory embedding with application to neurodegenerative disease diagnosis and prognosis, namely Brain Tokenized Graph Transformer (Brain TokenGT). It consists of two modules: 1) Graph Invariant and Variant Embedding (GIVE) for generation of node and spatio-temporal edge embeddings, which were tokenized for downstream processing; 2) Brain Informed Graph Transformer Readout (BIGTR) which augments previous tokens with trainable type identifiers and non-trainable node identifiers and feeds them into a standard transformer encoder to readout. We conducted extensive experiments on two public longitudinal fMRI datasets of the AD continuum for three tasks, including differentiating MCI from controls, predicting dementia conversion in MCI, and classification of amyloid positive or negative cognitively normal individuals. Based on brain FC trajectory, the proposed Brain TokenGT approach outperformed all the other benchmark models and at the same time provided excellent interpretability. The code is available at https://github.com/ZijianD/Brain-TokenGT.git

q-bio.NC↗

arXiv2023

Cinematic Mindscapes: High-quality Video Reconstruction from Brain Activity

Reconstructing human vision from brain activities has been an appealing task that helps to understand our cognitive process. Even though recent research has seen great success in reconstructing static images from non-invasive brain recordings, work on recovering continuous visual experiences in the form of videos is limited. In this work, we propose Mind-Video that learns spatiotemporal information from continuous fMRI data of the cerebral cortex progressively through masked brain modeling, multimodal contrastive learning with spatiotemporal attention, and co-training with an augmented Stable Diffusion model that incorporates network temporal inflation. We show that high-quality videos of arbitrary frame rates can be reconstructed with Mind-Video using adversarial guidance. The recovered videos were evaluated with various semantic and pixel-level metrics. We achieved an average accuracy of 85% in semantic classification tasks and 0.19 in structural similarity index (SSIM), outperforming the previous state-of-the-art by 45%. We also show that our model is biologically plausible and interpretable, reflecting established physiological processes.

cs.CV↗

arXiv2023

Seeing Beyond the Brain: Conditional Diffusion Model with Sparse Masked Modeling for Vision Decoding

Decoding visual stimuli from brain recordings aims to deepen our understanding of the human visual system and build a solid foundation for bridging human and computer vision through the Brain-Computer Interface. However, reconstructing high-quality images with correct semantics from brain recordings is a challenging problem due to the complex underlying representations of brain signals and the scarcity of data annotations. In this work, we present MinD-Vis: Sparse Masked Brain Modeling with Double-Conditioned Latent Diffusion Model for Human Vision Decoding. Firstly, we learn an effective self-supervised representation of fMRI data using mask modeling in a large latent space inspired by the sparse coding of information in the primary visual cortex. Then by augmenting a latent diffusion model with double-conditioning, we show that MinD-Vis can reconstruct highly plausible images with semantically matching details from brain recordings using very few paired annotations. We benchmarked our model qualitatively and quantitatively; the experimental results indicate that our method outperformed state-of-the-art in both semantic mapping (100-way semantic classification) and generation quality (FID) by 66% and 41% respectively. An exhaustive ablation study was also conducted to analyze our framework.

cs.CV↗

arXiv2022

Decomposing 3D Neuroimaging into 2+1D Processing for Schizophrenia Recognition

Deep learning has been successfully applied to recognizing both natural images and medical images. However, there remains a gap in recognizing 3D neuroimaging data, especially for psychiatric diseases such as schizophrenia and depression that have no visible alteration in specific slices. In this study, we propose to process the 3D data by a 2+1D framework so that we can exploit the powerful deep 2D Convolutional Neural Network (CNN) networks pre-trained on the huge ImageNet dataset for 3D neuroimaging recognition. Specifically, 3D volumes of Magnetic Resonance Imaging (MRI) metrics (grey matter, white matter, and cerebrospinal fluid) are decomposed to 2D slices according to neighboring voxel positions and inputted to 2D CNN models pre-trained on the ImageNet to extract feature maps from three views (axial, coronal, and sagittal). Global pooling is applied to remove redundant information as the activation patterns are sparsely distributed over feature maps. Channel-wise and slice-wise convolutions are proposed to aggregate the contextual information in the third view dimension unprocessed by the 2D CNN model. Multi-metric and multi-view information are fused for final prediction. Our approach outperforms handcrafted feature-based machine learning, deep feature approach with a support vector machine (SVM) classifier and 3D CNN models trained from scratch with better cross-validation results on publicly available Northwestern University Schizophrenia Dataset and the results are replicated on another independent dataset.

eess.IV↗

arXiv2020

Brain MRI-based 3D Convolutional Neural Networks for Classification of Schizophrenia and Controls

Convolutional Neural Network (CNN) has been successfully applied on classification of both natural images and medical images but not yet been applied to differentiating patients with schizophrenia from healthy controls. Given the subtle, mixed, and sparsely distributed brain atrophy patterns of schizophrenia, the capability of automatic feature learning makes CNN a powerful tool for classifying schizophrenia from controls as it removes the subjectivity in selecting relevant spatial features. To examine the feasibility of applying CNN to classification of schizophrenia and controls based on structural Magnetic Resonance Imaging (MRI), we built 3D CNN models with different architectures and compared their performance with a handcrafted feature-based machine learning approach. Support vector machine (SVM) was used as classifier and Voxel-based Morphometry (VBM) was used as feature for handcrafted feature-based machine learning. 3D CNN models with sequential architecture, inception module and residual module were trained from scratch. CNN models achieved higher cross-validation accuracy than handcrafted feature-based machine learning. Moreover, testing on an independent dataset, 3D CNN models greatly outperformed handcrafted feature-based machine learning. This study underscored the potential of CNN for identifying patients with schizophrenia using 3D brain MR images and paved the way for imaging-based individual-level diagnosis and prognosis in psychiatric disorders.

cs.CV↗