Estimating the dimensionality of the latent representation needed for prediction-- the task-relevant dimension--is a difficult, largely unsolved problem with broad scientific applications. We cast it as an Information Bottleneck question: what embedding bottleneck dimension is sufficient to compress predictor and predicted views while preserving their mutual information (MI). We show that standard neural estimators with separable/bilinear critics systematically inflate the inferred dimension, and we address this by introducing a hybrid critic that retains an explicit dimensional bottleneck while allowing flexible nonlinear cross-view interactions, thereby preserving the latent geometry. We further propose a one-shot protocol that reads off the effective dimension from a single over-parameterized hybrid model, without sweeping over bottleneck sizes. We validate the approach on synthetic problems with known task-relevant dimension. We extend the approach to intrinsic dimensionality by constructing paired views of a single dataset, enabling comparison with classical geometric dimension estimators. In noisy regimes where those estimators degrade, our approach remains reliable. Finally, we demonstrate the utility of the method on multiple physics datasets. Before "low-dimensional latent embeddings" became a rallying cry of AI, they were already a basic aim of science: identify a low-dimensional state--a small set of degrees of freedom constructed from observations--that suffices to predict the quantities of interest. The long road from Aristotelian to Newtonian mechanics illustrates that determining the number of such state variables--the relevant latent dimensionality--can be hard, even before one argues about the right variables or the laws that relate them.

Aerosol-cloud--radiation interactions remain among the most uncertain components of the Earth's climate system, in partdue to the high dimensionality of aerosol state representations and the difficulty of obtaining complete \textit{in situ} measurements. Addressing these challenges requires methods that distill complex aerosol properties into compact yet physically meaningful forms. Generative autoencoder models provide such a pathway. We present a framework for learning deep variational autoencoder (VAE) models of speciated mass and number concentration distributions, which capture detailed aerosol size-composition characteristics. By compressing hundreds of original dimensions into ten latent variables, the approach enables efficient storage and processing while preserving the fidelity of key diagnostics, including cloud condensation nuclei (CCN) spectra, optical scattering and absorption coefficients, and ice nucleation properties. Results show that CCN spectra are easiest to reconstruct accurately, optical properties are moderately difficult, and ice nucleation properties are the most challenging. To improve performance, we introduce a preprocessing optimization strategy that avoids repeated retraining and yields latent representations resilient to high-magnitude Gaussian noise, boosting accuracy for CCN spectra, optical coefficients, and frozen fraction spectra. Finally, we propose a novel realism metric -- based on the sliced Wasserstein distance between generated samples and a held-out test set -- for optimizing the KL divergence weight in VAEs. Together, these contributions enable compact, robust, and physically meaningful representations of aerosol states for large-scale climate applications.

Biological neurons communicate through spike trains, discrete, irregular bursts of activity that exhibit variability far beyond the modeling capacity of conventional variational autoencoders (VAEs). Recent work, such as the Poisson-VAE, makes a biologically inspired move by modeling spike counts using the Poisson distribution. However, they impose a rigid constraint: equal mean and variance, which fails to reflect the true stochastic nature of neural activity. In this work, we challenge this constraint and introduce NegBio-VAE, a principled extension of the VAE framework that models spike counts using the negative binomial distribution. This shift grants explicit control over dispersion, unlocking a broader and more accurate family of neural representations. We further develop two ELBO optimization schemes and two differentiable reparameterization strategies tailored to the negative binomial setting. By introducing one additional dispersion parameter, NegBio-VAE generalizes the Poisson latent model to a negative binomial formulation. Empirical results demonstrate this minor yet impactful change leads to significant gains in reconstruction fidelity, highlighting the importance of explicitly modeling overdispersion in spike-like activations.

In many classification problems, the input is represented as a set of features, e.g., the bag-of-words (BoW) representation of documents. Support vector machines (SVMs) are widely used tools for such classification problems. The performance of the SVMs is generally determined by whether kernel values between data points can be defined properly. However, SVMs for BoW representations have a major weakness in that the co-occurrence of different but semantically similar words cannot be reflected in the kernel calculation. To overcome the weakness, we propose a kernel-based discriminative classifier for BoW data, which we call the latent support measure machine (latent SMM). With the latent SMM, a latent vector is associated with each vocabulary term, and each document is represented as a distribution of the latent vectors for words appearing in the document. To represent the distributions efficiently, we use the kernel embeddings of distributions that hold high order moment information about distributions. Then the latent SMM finds a separating hyperplane that maximizes the margins between distributions of different classes while estimating latent vectors for words to improve the classification performance. In the experiments, we show that the latent SMM achieves state-of-the-art accuracy for BoW text classification, is robust with respect to its own hyper-parameters, and is useful to visualize words.

Developments in neural recording technology are rapidly enabling the recording of populations of neurons in multiple brain areas simultaneously, as well as the identification of the types of neurons being recorded (e.g., excitatory vs. inhibitory). There is a growing need for statistical methods to study the interaction among multiple, labeled populations of neurons. Rather than attempting to identify direct interactions between neurons (where the number of interactions grows with the number of neurons squared), we propose to extract a smaller number of latent variables from each population and study how these latent variables interact. Specifically, we propose extensions to probabilistic canonical correlation analysis (pCCA) to capture the temporal structure of the latent variables, as well as to distinguish within-population dynamics from across-population interactions (termed Group Latent Auto-Regressive Analysis, gLARA). We then applied these methods to populations of neurons recorded simultaneously in visual areas V1 and V2, and found that gLARA provides a better description of the recordings than pCCA. This work provides a foundation for studying how multiple populations of neurons interact and how this interaction supports brain function.

In many classification problems, the input is represented as a set of features, e.g., the bag-of-words (BoW) representation of documents. Support vector machines (SVMs) are widely used tools for such classification problems. The performance of the SVMs is generally determined by whether kernel values between data points can be defined properly. However, SVMs for BoW representations have a major weakness in that the co-occurrence of different but semantically similar words cannot be reflected in the kernel calculation. To overcome the weakness, we propose a kernel-based discriminative classifier for BoW data, which we call the latent support measure machine (latent SMM). With the latent SMM, a latent vector is associated with each vocabulary term, and each document is represented as a distribution of the latent vectors for words appearing in the document. To represent the distributions efficiently, we use the kernel embeddings of distributions that hold high order moment information about distributions. Then the latent SMM finds a separating hyperplane that maximizes the margins between distributions of different classes while estimating latent vectors for words to improve the classification performance. In the experiments, we show that the latent SMM achieves state-of-the-art accuracy for BoW text classification, is robust with respect to its own hyper-parameters, and is useful to visualize words.

Developments in neural recording technology are rapidly enabling the recording of populations of neurons in multiple brain areas simultaneously, as well as the identification of the types of neurons being recorded (e.g., excitatory vs. inhibitory). There is a growing need for statistical methods to study the interaction among multiple, labeled populations of neurons. Rather than attempting to identify direct interactions between neurons (where the number of interactions grows with the number of neurons squared), we propose to extract a smaller number of latent variables from each population and study how these latent variables interact. Specifically, we propose extensions to probabilistic canonical correlation analysis (pCCA) to capture the temporal structure of the latent variables, as well as to distinguish within-population dynamics from across-population interactions (termed Group Latent Auto-Regressive Analysis, gLARA). We then applied these methods to populations of neurons recorded simultaneously in visual areas V1 and V2, and found that gLARA provides a better description of the recordings than pCCA. This work provides a foundation for studying how multiple populations of neurons interact and how this interaction supports brain function.

Variational Autoencoders (VAEs) are powerful generative models that have been widely used in various fields, including image and text generation. However, one of the known challenges in using VAEs is the model's sensitivity to its hyperparameters, such as the latent space size. This paper presents a simple extension of VAEs for automatically determining the optimal latent space size during the training process by gradually decreasing the latent size through neuron removal and observing the model performance. The proposed method is compared to traditional hyperparameter grid search and is shown to be significantly faster while still achieving the best optimal dimensionality on four image datasets. Furthermore, we show that the final performance of our method is comparable to training on the optimal latent size from scratch, and might thus serve as a convenient substitute.

Detection of artificial objects from underwater imagery gathered by Autonomous Underwater Vehicles (AUVs) is a key requirement for many subsea applications. Real-world AUV image datasets tend to be very large and unlabelled. Furthermore, such datasets are typically imbalanced, containing few instances of objects of interest, particularly when searching for unusual objects in a scene. It is therefore, difficult to fit models capable of reliably detecting these objects. Given these factors, we propose to treat artificial objects as anomalies and detect them through a semi-supervised framework based on Variational Autoencoders (VAEs). We develop a method which clusters image data in a learned low-dimensional latent space and extracts images that are likely to contain anomalous features. We also devise an anomaly score based on extracting poorly reconstructed regions of an image. We demonstrate that by applying both methods on large image datasets, human operators can be shown candidate anomalous samples with a low false positive rate to identify objects of interest. We apply our approach to real seafloor imagery gathered by an AUV and evaluate its sensitivity to the dimensionality of the latent representation used by the VAE. We evaluate the precision-recall tradeoff and demonstrate that by choosing an appropriate latent dimensionality and threshold, we are able to achieve an average precision of 0.64 on unlabelled datasets.

In this work, we provide a deterministic alternative to the stochastic variational training of generative autoencoders. We refer to these new generative autoencoders as AutoEncoders within Flows (AEF), since the encoder and decoder are defined as affine layers of an overall invertible architecture. This results in a deterministic encoding of the data, as opposed to the stochastic encoding of VAEs. The paper introduces two related families of AEFs. The first family relies on a partition of the ambient space and is trained by exact maximum-likelihood. The second family exploits a deterministic expansion of the ambient space and is trained by maximizing the log-probability in this extended space. This latter case leaves complete freedom in the choice of encoder, decoder and prior architectures, making it a drop-in replacement for the training of existing VAEs and VAE-style models. We show that these AEFs can have strikingly higher performance than architecturally identical VAEs in terms of log-likelihood and sample quality, especially for low dimensional latent spaces. Importantly, we show that AEF samples are substantially sharper than VAE samples.