Hannah Choi

Amir Sadikov, Xinlei Pan, Hannah Choi et al.

Diffusion MRI is a non-invasive, in-vivo biomedical imaging method for mapping tissue microstructure. Applications include structural connectivity imaging of the human brain and detecting microstructural neural changes. However, acquiring high signal-to-noise ratio dMRI datasets with high angular and spatial resolution requires prohibitively long scan times, limiting usage in many important clinical settings, especially for children, the elderly, and in acute neurological disorders that may require conscious sedation or general anesthesia. We employ a Swin UNEt Transformers model, trained on augmented Human Connectome Project data and conditioned on registered T1 scans, to perform generalized denoising of dMRI. We also qualitatively demonstrate super-resolution with artificially downsampled HCP data in normal adult volunteers. Remarkably, Swin UNETR can be fine-tuned for an out-of-domain dataset with a single example scan, as we demonstrate on dMRI of children with neurodevelopmental disorders and of adults with acute evolving traumatic brain injury, each cohort scanned on different models of scanners with different imaging protocols at different sites. We exceed current state-of-the-art denoising methods in accuracy and test-retest reliability of rapid diffusion tensor imaging requiring only 90 seconds of scan time. Applied to tissue microstructural modeling of dMRI, Swin UNETR denoising achieves dramatic improvements over the state-of-the-art for test-retest reliability of intracellular volume fraction and free water fraction measurements and can remove heavy-tail noise, improving biophysical modeling fidelity. Swin UNeTR enables rapid diffusion MRI with unprecedented accuracy and reliability, especially for probing biological tissues for scientific and clinical applications. The code and model are publicly available at https://github.com/ucsfncl/dmri-swin.

Kseniia Shilova, Abdelrahman Sharafeldin, Advay Balakrishnan et al.

Active sensing links behavior and learning through an action-perception loop: actions determine the observations used to update internal predictive models of perception, which subsequently guide the next actions. Predictive-coding frameworks provide a natural way to model this process, since internal representations are continuously updated to predict future observations. Here, we ask how exploratory and exploitative behavioral strategies shape these internal predictive representations. We build an online learning agent in a tree-like maze with a controllable parameter regulating the balance between exploratory and exploitative regimes. The agent updates a predictive-coding-based perception model from experience generated by its own behavior. The model predicts both future maze states and reward probability, allowing the agent to select actions either by expected information gain during exploration or by predicted reward during exploitation. We show that the resulting internal predictive representations depend strongly on the agent's behavioral regime. Exploratory agents develop representations that are more spatially organized and better preserve the structure of maze transitions in latent space. In contrast, exploitative agents learn less organized representations. We then train this predictive model on natural trajectories of water-deprived mice navigating the same maze and compare the resulting representations with those learned from agent trajectories. More exploratory mice show representational geometries that closely match those of exploratory agents, whereas mice with more restricted visitation patterns resemble reward-driven, exploitative agents. Together, these findings suggest that exploration enables predictive models to form generalized internal representations by organizing latent space around both spatial location and transition context in artificial agents and animals.

Abdelrahman Sharafeldin, Nabil Imam, Hannah Choi

We present an end-to-end procedure for embodied exploration inspired by two biological computations: predictive coding and uncertainty minimization. The procedure can be applied to exploration settings in a task-independent and intrinsically driven manner. We first demonstrate our approach in a maze navigation task and show that it can discover the underlying transition distributions and spatial features of the environment. Second, we apply our model to a more complex active vision task, where an agent actively samples its visual environment to gather information. We show that our model builds unsupervised representations through exploration that allow it to efficiently categorize visual scenes. We further show that using these representations for downstream classification leads to superior data efficiency and learning speed compared to other baselines while maintaining lower parameter complexity. Finally, the modularity of our model allows us to probe its internal mechanisms and analyze the interaction between perception and action during exploration.

Chengrui Li, Soon Ho Kim, Chris Rodgers et al.

Exposing meaningful and interpretable neural interactions is critical to understanding neural circuits. Inferred neural interactions from neural signals primarily reflect functional interactions. In a long experiment, subject animals may experience different stages defined by the experiment, stimuli, or behavioral states, and hence functional interactions can change over time. To model dynamically changing functional interactions, prior work employs state-switching generalized linear models with hidden Markov models (i.e., HMM-GLMs). However, we argue they lack biological plausibility, as functional interactions are shaped and confined by the underlying anatomical connectome. Here, we propose a novel prior-informed state-switching GLM. We introduce both a Gaussian prior and a one-hot prior over the GLM in each state. The priors are learnable. We will show that the learned prior should capture the state-constant interaction, shedding light on the underlying anatomical connectome and revealing more likely physical neuron interactions. The state-dependent interaction modeled by each GLM offers traceability to capture functional variations across multiple brain states. Our methods effectively recover true interaction structures in simulated data, achieve the highest predictive likelihood with real neural datasets, and render interaction structures and hidden states more interpretable when applied to real neural data.

Aram Ansary Ogholbake, Hannah Choi, Spencer Brandenburg et al.

We propose AttentionMixer, a unified deep learning framework for multimodal detection of brain edema that combines structural head CT (HCT) with routine clinical metadata. While HCT provides rich spatial information, clinical variables such as age, laboratory values, and scan timing capture complementary context that might be ignored or naively concatenated. AttentionMixer is designed to fuse these heterogeneous sources in a principled and efficient manner. HCT volumes are first encoded using a self-supervised Vision Transformer Autoencoder (ViT-AE++), without requiring large labeled datasets. Clinical metadata are mapped into the same feature space and used as keys and values in a cross-attention module, where HCT-derived feature vector serves as queries. This cross-attention fusion allows the network to dynamically modulate imaging features based on patient-specific context and provides an interpretable mechanism for multimodal integration. A lightweight MLP-Mixer then refines the fused representation before final classification, enabling global dependency modeling with substantially reduced parameter overhead. Missing or incomplete metadata are handled via a learnable embedding, promoting robustness to real-world clinical data quality. We evaluate AttentionMixer on a curated brain HCT cohort with expert edema annotations using five-fold cross-validation. Compared with strong HCT-only, metadata-only, and prior multimodal baselines, AttentionMixer achieves superior performance (accuracy 87.32%, precision 92.10%, F1-score 85.37%, AUC 94.14%). Ablation studies confirm the benefit of both cross-attention and MLP-Mixer refinement, and permutation-based metadata importance analysis highlights clinically meaningful variables driving predictions. These results demonstrate that structured, interpretable multimodal fusion can substantially improve edema detection in clinical practice.