arXiv subjects

Fanqi Shen

Publications and source records attributed to Fanqi Shen.

5 recordsLinked to original sources

arXiv2026

Brain4FMs: A Benchmark of Foundation Models for Electrical Brain Signal

Brain foundation models (BFMs) are advancing neurotechnology by learning transferable representations from neural signals, with broad potential in clinical diagnosis and neuroscience research. Their development relies on large-scale pretraining corpora of electrical brain signals, including scalp electroencephalography (EEG) and intracranial EEG (iEEG). However, existing BFM benchmarks primarily focus on EEG, cover only a limited subset of models, and provide limited analysis beyond downstream performance. We introduce Brain4FMs, the first unified benchmark, to our knowledge, for jointly evaluating BFMs on EEG and iEEG. It integrates 17 representative models and 21 public datasets across clinical diagnosis, sleep staging, communication, and affective computing. Brain4FMs is open and plug-and-play, with dataset-aware preprocessing, cross-subject evaluation, heterogeneous multichannel handling, and standardized downstream adaptation workflows. The benchmark reveals performance variation across tasks, signal modalities, and adaptation protocols, with no single BFM consistently dominating all evaluation scenarios. % To better understand these heterogeneous transfer behaviors, we further conduct exploratory analyses of model-specific properties. To better understand these behaviors, we further conduct exploratory analyses of model-specific properties of spatial, spectral, and discrete representations. The code is available at https://github.com/wajtsq/Brain4FMs.

cs.LG↗

arXiv2026

Assembling the Mind's Mosaic: Towards EEG Semantic Intent Decoding

Enabling natural communication through brain-computer interfaces (BCIs) remains one of the most profound challenges in neuroscience and neurotechnology. While existing frameworks offer partial solutions, they are constrained by oversimplified semantic representations and a lack of interpretability. To overcome these limitations, we introduce Semantic Intent Decoding (SID), a novel framework that translates neural activity into natural language by modeling meaning as a flexible set of compositional semantic units. SID is built on three core principles: semantic compositionality, continuity and expandability of semantic space, and fidelity in reconstruction. We present BrainMosaic, a deep learning architecture implementing SID. BrainMosaic decodes multiple semantic units from EEG/SEEG signals using set matching and then reconstructs coherent sentences through semantic-guided reconstruction. This approach moves beyond traditional pipelines that rely on fixed-class classification or unconstrained generation, enabling a more interpretable and expressive communication paradigm. Extensive experiments on multilingual EEG and clinical SEEG datasets demonstrate that SID and BrainMosaic offer substantial advantages over existing frameworks, paving the way for natural and effective BCI-mediated communication.

q-bio.NC↗

arXiv2025

Versatile and Risk-Sensitive Cardiac Diagnosis via Graph-Based ECG Signal Representation

Despite the rapid advancements of electrocardiogram (ECG) signal diagnosis and analysis methods through deep learning, two major hurdles still limit their clinical adoption: the lack of versatility in processing ECG signals with diverse configurations, and the inadequate detection of risk signals due to sample imbalances. Addressing these challenges, we introduce VersAtile and Risk-Sensitive cardiac diagnosis (VARS), an innovative approach that employs a graph-based representation to uniformly model heterogeneous ECG signals. VARS stands out by transforming ECG signals into versatile graph structures that capture critical diagnostic features, irrespective of signal diversity in the lead count, sampling frequency, and duration. This graph-centric formulation also enhances diagnostic sensitivity, enabling precise localization and identification of abnormal ECG patterns that often elude standard analysis methods. To facilitate representation transformation, our approach integrates denoising reconstruction with contrastive learning to preserve raw ECG information while highlighting pathognomonic patterns. We rigorously evaluate the efficacy of VARS on three distinct ECG datasets, encompassing a range of structural variations. The results demonstrate that VARS not only consistently surpasses existing state-of-the-art models across all these datasets but also exhibits substantial improvement in identifying risk signals. Additionally, VARS offers interpretability by pinpointing the exact waveforms that lead to specific model outputs, thereby assisting clinicians in making informed decisions. These findings suggest that our VARS will likely emerge as an invaluable tool for comprehensive cardiac health assessment.

cs.AI↗

arXiv2025

Deep Learning-Powered Electrical Brain Signals Analysis: Advancing Neurological Diagnostics

Neurological disorders pose major global health challenges, driving advances in brain signal analysis. Scalp electroencephalography (EEG) and intracranial EEG (iEEG) are widely used for diagnosis and monitoring. However, dataset heterogeneity and task variations hinder the development of robust deep learning solutions. This review systematically examines recent advances in deep learning approaches for EEG/iEEG-based neurological diagnostics, focusing on applications across 7 neurological conditions using 46 datasets. For each condition, we review representative methods and their quantitative results, integrating performance comparisons with analyses of data usage, model design, and task-specific adaptations, while highlighting the role of pre-trained multi-task models in achieving scalable, generalizable solutions. Finally, we propose a standardized benchmark to evaluate models across diverse datasets and improve reproducibility, emphasizing how recent innovations are transforming neurological diagnostics toward intelligent, adaptable healthcare systems.

q-bio.NC↗

arXiv2024

BrainWave: A Brain Signal Foundation Model for Clinical Applications

Neural electrical activity is fundamental to brain function, underlying a range of cognitive and behavioral processes, including movement, perception, decision-making, and consciousness. Abnormal patterns of neural signaling often indicate the presence of underlying brain diseases. The variability among individuals, the diverse array of clinical symptoms from various brain disorders, and the limited availability of diagnostic classifications, have posed significant barriers to formulating reliable model of neural signals for diverse application contexts. Here, we present BrainWave, the first foundation model for both invasive and non-invasive neural recordings, pretrained on more than 40,000 hours of electrical brain recordings (13.79 TB of data) from approximately 16,000 individuals. Our analysis show that BrainWave outperforms all other competing models and consistently achieves state-of-the-art performance in the diagnosis and identification of neurological disorders. We also demonstrate robust capabilities of BrainWave in enabling zero-shot transfer learning across varying recording conditions and brain diseases, as well as few-shot classification without fine-tuning, suggesting that BrainWave learns highly generalizable representations of neural signals. We hence believe that open-sourcing BrainWave will facilitate a wide range of clinical applications in medicine, paving the way for AI-driven approaches to investigate brain disorders and advance neuroscience research.

q-bio.NC↗