arXiv subjects

Junfeng Xia

Publications and source records attributed to Junfeng Xia.

12 recordsLinked to original sources

arXiv2026

BrainTaskonomy: Learning How to Pretrain and What to Transfer in fMRI Foundation Models

fMRI foundation models increasingly aggregate heterogeneous data across brain states, cohorts, and acquisition settings, yet pretraining domains are commonly treated as a flat mixture and downstream tasks are adapted independently. We study whether measured learning relations can organize both stages without modifying the backbone. During pretraining, a lightweight Brain-DiT proxy estimates difficulty and directed facilitation across ten fMRI domains, yielding a priority-guided cumulative domain curriculum combined with high-to-low-noise timestep scheduling and joint consolidation. During adaptation, controlled first- and higher-order transfer across fifteen tasks constructs a directed taskonomy, from which budgeted integer programming (BIP) selects directly supervised source tasks and target-specific routes. The joint priority-domain and high-to-low-timestep curriculum reduces v-NMSE, PSD-NMSE, and FC-MSE by 6.5%, 16.3%, and 10.5%, respectively, relative to uniform sampling over both dimensions, and shows strong downstream performance across six in- and out-of-domain tasks. The taskonomy reveals asymmetric, target-dependent transfer, while exploratory sealed-test evaluation shows larger descriptive gains for BIP policies when higher-order route spaces are available than for matched random controls. Together, these findings support organizing fMRI pretraining and adaptation by measured learning relations rather than treating domains and tasks as independent flat sets.

cs.CV↗

arXiv2026

Beyond Single-Source Cognitive Taskonomy:Multi-Source Task Relations through fMRI Transfer Learning

Cognitive tasks are organized by shared and specialized neural processes. Masked fMRI reconstruction provides a common self-supervised objective for quantifying transfer relations among task states, but existing reconstruction-based taskonomies mainly study one-to-one transfer from a single source task to a target. Here, we extend an fMRI cognitive taskonomy from single-source to multi-source transfer across 23 Human Connectome Project task states and use Boolean Integer Programming (BIP) to analyze budget-constrained task allocation. We train 1,127 task-specific and transfer models. Single-source transfer is directional and paradigm structured: motor states transfer well within the motor paradigm but provide limited support to most non-motor targets, consistent with a shared sensorimotor execution system and effector-specific representations. Multi-source transfer depends on the composition of the source set, suggesting that many-to-one task relations are not fully captured by pairwise taskonomy alone. Across supervision budgets, BIP repeatedly allocates direct supervision to several 0-back and 2-back working-memory states, although these states are not consistently the strongest individual sources. This pattern may reflect the integration of perceptual, attentional, and executive processes in working-memory tasks. Together, these findings reveal a cross-paradigm-limited motor cluster and working-memory states with high priority under the specified global allocation objective. Our study extends reconstruction-based fMRI taskonomy from one-to-one transfer to many-to-one task relations and budget-constrained task dependencies.

cs.CV↗

arXiv2026

BrainWorld: A Structural-Prior-Conditioned Generative Model for Whole-Brain 4D fMRI Dynamics

Whole-brain 4D fMRI generation is valuable for modeling functional brain dynamics, yet existing fMRI foundation models mainly target representation learning and downstream prediction rather than conditional predictive generation. We introduce BrainWorld, a structural-prior-conditioned generative model for whole-brain 4D fMRI dynamics. BrainWorld uses sMRI as subject-level anatomical context to guide future fMRI generation, integrating structural information into the denoising process rather than treating it as a parallel modality. Evaluated on 22 datasets spanning diverse cohorts and brain states, BrainWorld generates stable 4D fMRI trajectories up to 400 frames, improves downstream performance through generated-example augmentation, and learns transferable multimodal representations that outperform baselines. Together, these results establish BrainWorld as a condition-aware generative framework for long-horizon brain dynamics modeling and multimodal representation learning.

cs.CV↗

arXiv2026

FlexiBrain: Resolution-Agnostic Voxel-Level Encoding for Native fMRI

The success of large-scale deep learning models in neuroscience is fundamentally constrained by severe data heterogeneity. Native fMRI data aggregated from diverse sources exhibit substantial variation in both spatial and temporal resolutions. Consequently, most existing frameworks rely on lengthy, rigid preprocessing pipelines that enforce uniformity across datasets. This practice introduces two critical limitations: (1) potential degradation of subject-specific anatomical information; (2) significant computational overhead, often requiring hours of processing per subject. Here, we propose FlexiBrain, a resolution-agnostic voxel-level encoding framework for native fMRI based on Mamba-JEPA. FlexiBrain defines patch sizes in real-world physical units and employs a dynamic patch resizing, thereby bypassing destructive spatial standardization while enabling direct ingestion of data in native space. We instantiate the framework using an efficient Mamba-JEPA backbone to model high-dimensional 4D fMRI signals. Across five diverse downstream neuroscience tasks, FlexiBrain consistently outperforms recent state-of-the-art methods, achieving gains of up to 12 percentage points without external data augmentation. Importantly, FlexiBrain functions as a seamless plug-in module, substantially reducing preprocessing costs and accelerating the development of robust voxel-level fMRI foundation models. Code is available at https://github.com/OneMore1/FlexiBrain.

eess.IV↗

arXiv2026

Brain-DiT: A Universal Multi-state fMRI Foundation Model with Metadata-Conditioned Pretraining

Current fMRI foundation models primarily rely on a limited range of brain states and mismatched pretraining tasks, restricting their ability to learn generalized representations across diverse brain states. We present Brain-DiT, a universal multi-state fMRI foundation model pretrained on 349,898 sessions from 24 datasets spanning resting, task, naturalistic, disease, and sleep states. Unlike prior fMRI foundation models that rely on masked reconstruction in the raw-signal space or a latent space, Brain-DiT adopts metadata-conditioned diffusion pretraining with a Diffusion Transformer (DiT), enabling the model to learn multi-scale representations that capture both fine-grained functional structure and global semantics. Across extensive evaluations and ablations on 7 downstream tasks, we find consistent evidence that diffusion-based generative pretraining is a stronger proxy than reconstruction or alignment, with metadata-conditioned pretraining further improving downstream performance by disentangling intrinsic neural dynamics from population-level variability. We also observe that downstream tasks exhibit distinct preferences for representational scale: ADNI classification benefits more from global semantic representations, whereas age/sex prediction comparatively relies more on fine-grained local structure.

cs.CV↗

arXiv2026

Omni-fMRI: A Universal Atlas-Free fMRI Foundation Model

Self-supervised fMRI foundation models have shown promising transfer performance, yet most rely on predefined region-level parcellations that discard fine-grained voxel information and introduce atlas-dependent biases. We propose Omni-fMRI, an atlas-free foundation model that operates directly on voxel-level signals. To enable scalable pretraining on 49,497 fMRI sessions across nine datasets, Omni-fMRI introduces a dynamic patching mechanism that substantially reduces computational cost while preserving informative spatial structure. To support reproducibility and fair comparison, we establish a comprehensive benchmark suite spanning 11 datasets and a diverse set of resting-state and task-based fMRI tasks. Experimental results demonstrate that Omni-fMRI consistently outperforms existing foundation models, providing a scalable and reproducible framework for atlas-free brain representation learning. Code and logs are available.

cs.CE↗

arXiv2025

SLIM-Brain: A Data- and Training-Efficient Foundation Model for fMRI Data Analysis

Foundation models are emerging as a powerful paradigm for fMRI analysis, but current approaches face a dual bottleneck of data- and training-efficiency. Atlas-based methods aggregate voxel signals into fixed regions of interest, reducing data dimensionality but discarding fine-grained spatial details, and requiring extremely large cohorts to train effectively as general-purpose foundation models. Atlas-free methods, on the other hand, operate directly on voxel-level information - preserving spatial fidelity but are prohibitively memory- and compute-intensive, making large-scale pre-training infeasible. We introduce SLIM-Brain (Sample-efficient, Low-memory fMRI Foundation Model for Human Brain), a new atlas-free foundation model that simultaneously improves both data- and training-efficiency. SLIM-Brain adopts a two-stage adaptive design: (i) a lightweight temporal extractor captures global context across full sequences and ranks data windows by saliency, and (ii) a 4D hierarchical encoder (Hiera-JEPA) learns fine-grained voxel-level representations only from the top-$k$ selected windows, while deleting about 70% masked patches. Extensive experiments across seven public benchmarks show that SLIM-Brain establishes new state-of-the-art performance on diverse tasks, while requiring only 4 thousand pre-training sessions and approximately 30% of GPU memory comparing to traditional voxel-level methods.

cs.CV↗

arXiv2025

An Enhanced Pyramid Feature Network Based on Long-Range Dependencies for Multi-Organ Medical Image Segmentation

In the field of multi-organ medical image segmentation, recent methods frequently employ Transformers to capture long-range dependencies from image features. However, these methods overlook the high computational cost of Transformers and their deficiencies in extracting local detailed information. To address high computational costs and inadequate local detail information, we reassess the design of feature extraction modules and propose a new deep-learning network called LamFormer for fine-grained segmentation tasks across multiple organs. LamFormer is a novel U-shaped network that employs Linear Attention Mamba (LAM) in an enhanced pyramid encoder to capture multi-scale long-range dependencies. We construct the Parallel Hierarchical Feature Aggregation (PHFA) module to aggregate features from different layers of the encoder, narrowing the semantic gap among features while filtering information. Finally, we design the Reduced Transformer (RT), which utilizes a distinct computational approach to globally model up-sampled features. RRT enhances the extraction of detailed local information and improves the network's capability to capture long-range dependencies. LamFormer outperforms existing segmentation methods on seven complex and diverse datasets, demonstrating exceptional performance. Moreover, the proposed network achieves a balance between model performance and model complexity.

cs.CV↗

arXiv2024

DRExplainer: Quantifiable Interpretability in Drug Response Prediction with Directed Graph Convolutional Network

Predicting the response of a cancer cell line to a therapeutic drug is pivotal for personalized medicine. Despite numerous deep learning methods that have been developed for drug response prediction, integrating diverse information about biological entities and predicting the directional response remain major challenges. Here, we propose a novel interpretable predictive model, DRExplainer, which leverages a directed graph convolutional network to enhance the prediction in a directed bipartite network framework. DRExplainer constructs a directed bipartite network integrating multi-omics profiles of cell lines, the chemical structure of drugs and known drug response to achieve directed prediction. Then, DRExplainer identifies the most relevant subgraph to each prediction in this directed bipartite network by learning a mask, facilitating critical medical decision-making. Additionally, we introduce a quantifiable method for model interpretability that leverages a ground truth benchmark dataset curated from biological features. In computational experiments, DRExplainer outperforms state-of-the-art predictive methods and another graph-based explanation method under the same experimental setting. Finally, the case studies further validate the interpretability and the effectiveness of DRExplainer in predictive novel drug response. Our code is available at: https://github.com/vshy-dream/DRExplainer.

cs.LG↗

arXiv2024

Uncovering cognitive taskonomy through transfer learning in masked autoencoder-based fMRI reconstruction

Data reconstruction is a widely used pre-training task to learn the generalized features for many downstream tasks. Although reconstruction tasks have been applied to neural signal completion and denoising, neural signal reconstruction is less studied. Here, we employ the masked autoencoder (MAE) model to reconstruct functional magnetic resonance imaging (fMRI) data, and utilize a transfer learning framework to obtain the cognitive taskonomy, a matrix to quantify the similarity between cognitive tasks. Our experimental results demonstrate that the MAE model effectively captures the temporal dynamics patterns and interactions within the brain regions, enabling robust cross-subject fMRI signal reconstruction. The cognitive taskonomy derived from the transfer learning framework reveals the relationships among cognitive tasks, highlighting subtask correlations within motor tasks and similarities between emotion, social, and gambling tasks. Our study suggests that the fMRI reconstruction with MAE model can uncover the latent representation and the obtained taskonomy offers guidance for selecting source tasks in neural decoding tasks for improving the decoding performance on target tasks.

q-bio.NC↗

arXiv2023

Search for ER and/or NR-like dark matter signals with the especially low background liquid helium TPCs

In the Dark Matter (DM) direct detection community, the absence of convincing signals has become a "new normal" for decades. Among other possibilities, the "new normal" might indicate that DM-matter interactions could generate not only the hypothetical NR (Nuclear Recoil) events but also the ER (Electron Recoil) ones, which have often been tagged as backgrounds historically. Further, we argue that ER and NR-like DM signals could co-exist in a DM detector's same dataset. So in total, there would be three scenarios we can search for DM signals: (i) ER excess only, (ii) NR excess only, and (iii) ER and NR excesses combined. To effectively identify any possible DM signal under the three scenarios, a DM detector should (a) have the minimum ER and NR backgrounds and (b) be capable of discriminating ER events from NR ones. Accordingly, we introduce the newly established project, ALETHEIA, which implements liquid helium-filled TPCs (Time Projection Chambers) in hunting for DM. Thanks to the nearly single-digit number of ER and NR backgrounds on 1 ton*yr exposure, presumably, the ALETHEIA detectors could identify any form of DM-induced excess in its ROI (Research Of Interest). As far as we know, ALETHEIA is the first DM direct detection experiment claiming such an inclusive search; conventional detectors search DM mainly on the "ER excess only" and/or the "NR excess only" channel, not the "ER and NR excesses combined" channel.

astro-ph.IM↗

arXiv2023

Conceptual design and progress of transmitting $\sim$ MV DC HV into 4 K LHe detectors

A dual-phase TPC (Time Projection Chamber) is more advanced in characterizing an event than a single-phase one because it can, in principle, reconstruct the 3D (X-Y-Z) image of the event, while a single-phase detector can only show a 2D (X-Y) picture. As a result, more enriched physics is expected for a dual-phase detector than a single-phase one. However, to build such a detector, DC HV (High Voltage) must be delivered into the chamber (to have a static electric field), which is a challenging task, especially for an LHe detector due to the extremely low temperature, $\sim$ 4 K, and the very high voltage, $\sim$ MV (Million Volts). This article introduces a convincing design for transmitting $\sim$ MV DC into a 4 K LHe detector. We also report the progress of manufacturing a 100 kV DC feedthrough capable of working at 4 K. Surprisingly, we realized that the technology we developed here might be a valuable reference to the scientists and engineers aiming to build residential bases on the Moon or Mars.

physics.ins-det↗