Acquisition differences across sites, scanners, and protocols in dMRI introduce variability that complicates structural connectome analysis. This motivates deep learning models that can represent high-dimensional connectomes in a low-dimensional space while explicitly separating acquisition-related effects from biological variation. Conventional dimensionality reduction methods model all variance as continuous, so acquisition effects often get absorbed into a continuous latent space. Recent hybrid latent-space models combine discrete and continuous components to address this, but typically require manual capacity tuning to ensure the discrete component captures the intended variability. We introduce an unsupervised framework that removes this manual tuning by architecturally annealing encoder outputs before decoding, allowing the model to adaptively balance discrete and continuous latent variables during training. To evaluate it, we curated a dataset of N=7,416 structural connectomes derived from dMRI, spanning ages 2 to 102 and 13 studies with 25 unique acquisition-parameter combinations. Of these, 5,900 are cognitively unimpaired, 877 have mild cognitive impairment (MCI), and 639 have Alzheimer's disease (AD). We compare against a standard VAE, PCA with k-means clustering, and hybrid models that anneal only through the loss function. Our architectural annealing produces stronger site learning (ARI=0.53, p<0.05) than these baselines. Results show that a hybrid continuous-discrete latent space, with architectural rather than loss-based annealing, provides a useful unsupervised mechanism for capturing acquisition variability in dMRI: by jointly modeling smooth and categorical structure, the Joint-VAE recovers clusters aligned with scanner and protocol differences.

There has been remarkable progress over the past decade in establishing finite-sample, non-asymptotic bounds on recovering unknown system parameters from observed system behavior. Surprisingly, however, we show that the current state-of-the-art bounds do not accurately capture the statistical complexity of system identification, even in the most fundamental setting of estimating a discrete-time linear dynamical system (LDS) via ordinary least-squares regression (OLS). Specifically, we utilize asymptotic normality to identify classes of problem instances for which current bounds overstate the squared parameter error, in both spectral and Frobenius norm, by a factor of the state-dimension of the system. Informed by this discrepancy, we then sharpen the OLS parameter error bounds via a novel second-order decomposition of the parameter error, where crucially the lower-order term is a matrix-valued martingale that we show correctly captures the CLT scaling. From our analysis we obtain finite-sample bounds for both (i) stable systems and (ii) the many-trajectories setting that match the instance-specific optimal rates up to constant factors in Frobenius norm, and polylogarithmic state-dimension factors in spectral norm.

As deep neural networks are deployed in safety-critical domains such as autonomous driving and medical diagnosis, stakeholders need explanations that are interpretable but also trustworthy with formal guarantees. Existing XAI methods fall short: heuristic attribution techniques (e.g., LIME, Integrated Gradients) highlight influential features but offer no mathematical guarantees about decision boundaries, while formal methods verify robustness yet remain untargeted, analyzing the nearest boundary regardless of whether it represents a critical risk. In safety-critical systems, not all misclassifications carry equal consequences; confusing a "Stop" sign for a "60 kph" sign is far more dangerous than confusing it with a "No Passing" sign. We introduce ViTaX (Verified and Targeted Explanations), a formal XAI framework that generates targeted semifactual explanations with mathematical guarantees. For a given input (class y) and a user-specified critical alternative (class t), ViTaX: (1) identifies the minimal feature subset most sensitive to the y->t transition, and (2) applies formal reachability analysis to guarantee that perturbing these features by epsilon cannot flip the classification to t. We formalize this through Targeted epsilon-Robustness, certifying whether a feature subset remains robust under perturbation toward a specific target class. ViTaX is the first method to provide formally guaranteed explanations of a model's resilience against user-identified alternatives. Evaluations on MNIST, GTSRB, EMNIST, and TaxiNet demonstrate over 30% fidelity improvement with minimal explanation cardinality.

Foundation models for biology and physics optimize predictive accuracy, but their internal representations systematically fail to preserve the continuous geometry of the systems they model. We identify the root cause: the Geometric Alignment Tax, an intrinsic cost of forcing continuous manifolds through discrete categorical bottlenecks. Controlled ablations on synthetic dynamical systems demonstrate that replacing cross-entropy with a continuous head on an identical encoder reduces geometric distortion by up to 8.5x, while learned codebooks exhibit a non-monotonic double bind where finer quantization worsens geometry despite improving reconstruction. Under continuous objectives, three architectures differ by 1.3x; under discrete tokenization, they diverge by 3,000x. Evaluating 14 biological foundation models with rate-distortion theory and MINE, we identify three failure regimes: Local-Global Decoupling, Representational Compression, and Geometric Vacuity. A controlled experiment confirms that Evo 2's reverse-complement robustness on real DNA reflects conserved sequence composition, not learned symmetry. No model achieves simultaneously low distortion, high mutual information, and global coherence.

Early and accurate detection of anomalous events on the freeway, such as accidents, can improve emergency response and clearance. However, existing delays and mistakes from manual crash reporting records make it a difficult problem to solve. Current large-scale freeway traffic datasets are not designed for anomaly detection and ignore these challenges. In this paper, we introduce the first large-scale lane-level freeway traffic dataset for anomaly detection. Our dataset consists of a month of weekday radar detection sensor data collected in 4 lanes along an 18-mile stretch of Interstate 24 heading toward Nashville, TN, comprising over 3.7 million sensor measurements.

In many scenarios, this failure can be attributed to obscuring the crucial interplay between the training algorithm and the underlying data distribution.