arXiv subjects

Sam Gijsen

Publications and source records attributed to Sam Gijsen.

6 recordsLinked to original sources

arXiv2026

Motor, Cognitive, or Corpus? What Survives Cross-Lingual Transfer in Speech-Based Parkinsons Disease Detection

Self-supervised learning (SSL) speech representations achieve strong performance for Parkinson's disease (PD) detection within individual corpora. However, it remains unclear whether these models capture disease-related characteristics or exploit dataset-specific confounds, particularly since most SSL backbones are pretrained exclusively on healthy speech. To investigate this question, we perform a layer-wise analysis of nine SSL speech backbones using a low-capacity logistic regression probe across three languages. We structure the evaluation as multiple scenarios that progressively introduce distribution shifts in participant identity, recording conditions, language, and pathology. Our results reveal two key findings. First, layer selection is highly corpus-dependent: the optimal representation layer is determined primarily by the source dataset rather than by the SSL architecture itself. Second, the transferred discriminative signal lacks pathological specificity: classifiers trained to detect PD assign similarly high probabilities to both PD and dementia speech in the target corpus. These results highlight critical limitations that must be addressed before speech-based pathology recognition models can be reliably deployed in clinical settings.

cs.CL↗

arXiv2026

Flow Matching with In-Context Priors for Out-of-Distribution Brain Dynamics

Flow matching and diffusion models enable conditional generation across domains ranging from images to proteins, with recent extensions to out-of-distribution contexts. Yet generative models of neural time series have largely remained restricted to categorical conditioning, precluding compositional and zero-shot generalization. In this work, we propose a per-timestep conditioned diffusion transformer for generating realistic fMRI brain dynamics during unseen cognitive tasks by injecting both compositional language and optional spatial priors in-context. Such zero-shot generation could enable counterfactual neuroscience by supporting in-silico design and evaluation of novel cognitive experiments before empirical validation. Leveraging this model, we evaluate across hundreds of held-out task conditions and characterize predictive performance in relation to the training manifold. From language alone, the model recovers region-specific recruitment across tasks and held-out spatial activation patterns. Spatial priors, when available, complement the text pathway by anchoring generation in regions of task space where language alone degrades, while retaining the compositional structure needed for counterfactual task specification. To our knowledge this is the first generative model of whole-cortex fMRI dynamics for unseen cognitive tasks, advancing counterfactual neuroscience and data-driven experimental design.

cs.LG↗

arXiv2026

Beyond Binary: Speech Representations Across the Cognitive Score Hierarchy

This study examines the relationship between speech representations and the hierarchical structure of cognitive assessment in mild cognitive impairment. Utilizing 5,754 German neuropsychological assessment recordings, we evaluate six cognitive tasks across three score levels: task, domain, and global levels. We compare hand-crafted acoustic features with self-supervised learning (SSL) embeddings. Results show that although SSL representations generally outperform hand-crafted features at lower levels, this trend reverses for MCI classification. Furthermore, task-specific constraints influence performance: tasks with greater response freedom exhibit performance dilution as hierarchical levels increase, suggesting ``specialist'' representations, whereas the performance of highly structured tasks increases toward higher levels, suggesting ``generalist'' representations. These findings show links between task constraints and assessment hierarchy in automated clinical speech analysis.

cs.CL↗

arXiv2025

Brain-Semantoks: Learning Semantic Tokens of Brain Dynamics with a Self-Distilled Foundation Model

The development of foundation models for functional magnetic resonance imaging (fMRI) time series holds significant promise for predicting phenotypes related to disease and cognition. Current models, however, are often trained using a mask-and-reconstruct objective on small brain regions. This focus on low-level information leads to representations that are sensitive to noise and temporal fluctuations, necessitating extensive fine-tuning for downstream tasks. We introduce Brain-Semantoks, a self-supervised framework designed specifically to learn abstract representations of brain dynamics. Its architecture is built on two core innovations: a semantic tokenizer that aggregates noisy regional signals into robust tokens representing functional networks, and a self-distillation objective that enforces representational stability across time. We show that this objective is stabilized through a novel training curriculum, ensuring the model robustly learns meaningful features from low signal-to-noise time series. We demonstrate that learned representations enable strong performance on a variety of downstream tasks even when only using a linear probe. Furthermore, we provide comprehensive scaling analyses indicating more unlabeled data reliably results in out-of-distribution performance gains without domain adaptation.

cs.LG↗

arXiv2025

Scaling Vision Transformers for Functional MRI with Flat Maps

We study the problem of training self-supervised foundation models for functional MRI. Our main contributions are: (1) we introduce a new model family (CortexMAE) trained using the masked autoencoder framework on 2.1K hours of open fMRI data, and (2) we release the first open evaluation suite (Brainmarks) for fMRI foundation models. Our core innovation is simple: we adapt the Vision Transformer to fMRI by first converting each 3D fMRI volume to a 2D map using a cortical flat map projection. We directly compare flat maps to both parcellation and volume-based representations. While each has its advantages, flat maps generally perform best. We perform the first systematic scaling analysis for fMRI and observe strict power law scaling, albeit with limits. Finally, we use Brainmarks to do controlled benchmark comparisons. On subject-level trait prediction, we report a challenging null result: no single model achieves clear state-of-the-art performance. Moreover, all models struggle to outperform a simple functional connectivity baseline. On cognitive state decoding, we observe more robust performance, and in this setting our CortexMAE family outperforms prior models by a large margin. Code, models, and datasets are available at https://github.com/MedARC-AI/CortexMAE and https://github.com/MedARC-AI/Brainmarks.

cs.CV↗

arXiv2024

EEG-Language Pretraining for Highly Label-Efficient Clinical Phenotyping

Multimodal language modeling has enabled breakthroughs for representation learning, yet remains unexplored in the realm of functional brain data for clinical phenotyping. This paper pioneers EEG-language models (ELMs) trained on clinical reports and 15000 EEGs. We propose to combine multimodal alignment in this novel domain with timeseries cropping and text segmentation, enabling an extension based on multiple instance learning to alleviate misalignment between irrelevant EEG or text segments. Our multimodal models significantly improve over EEG-only models across four clinical evaluations and for the first time enable zero-shot classification as well as retrieval of both neural signals and reports. In sum, these results highlight the potential of ELMs, representing significant progress for clinical applications.

eess.SP↗