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.

Identifying confounders in deep-learning-based model predictions using DeepRepViz

Deep Learning (DL) models are increasingly used to analyze neuroimaging data and uncover insights about the brain, brain pathologies, and psychological traits. However, extraneous `confounders' variables such as the age of the participants, sex, or imaging artifacts can bias model predictions, preventing the models from learning relevant brain-phenotype relationships. In this study, we provide a solution called the `DeepRepViz' framework that enables researchers to systematically detect confounders in their DL model predictions. The framework consists of (1) a metric that quantifies the effect of potential confounders and (2) a visualization tool that allows researchers to qualitatively inspect what the DL model is learning. By performing experiments on simulated and neuroimaging datasets, we demonstrate the benefits of using DeepRepViz in combination with DL models. For example, experiments on the neuroimaging datasets reveal that sex is a significant confounder in a DL model predicting chronic alcohol users (Con-score=0.35). Similarly, DeepRepViz identifies age as a confounder in a DL model predicting participants' performance on a cognitive task (Con-score=0.3). Overall, DeepRepViz enables researchers to systematically test for potential confounders and expose DL models that rely on extraneous information such as age, sex, or imaging artifacts.

Promises and pitfalls of deep neural networks in neuroimaging-based psychiatric research

By promising more accurate diagnostics and individual treatment recommendations, deep neural networks and in particular convolutional neural networks have advanced to a powerful tool in medical imaging. Here, we first give an introduction into methodological key concepts and resulting methodological promises including representation and transfer learning, as well as modelling domain-specific priors. After reviewing recent applications within neuroimaging-based psychiatric research, such as the diagnosis of psychiatric diseases, delineation of disease subtypes, normative modeling, and the development of neuroimaging biomarkers, we discuss current challenges. This includes for example the difficulty of training models on small, heterogeneous and biased data sets, the lack of validity of clinical labels, algorithmic bias, and the influence of confounding variables.