Hierarchical clustering with maximum density paths and mixture models

Hierarchical clustering is an effective and interpretable technique for analyzing structure in data, offering a nuanced understanding by revealing insights at multiple scales and resolutions. It is particularly helpful in settings where the exact number of clusters is unknown, and provides a robust framework for exploring complex datasets. Additionally, hierarchical clustering can uncover inner structures within clusters, capturing subtle relationships and nested patterns that may be obscured by traditional flat clustering methods. However, existing hierarchical clustering methods struggle with high-dimensional data, especially when there are no clear density gaps between modes. Our method addresses this limitation by leveraging a two-stage approach, first employing a Gaussian or Student's t mixture model to overcluster the data, and then hierarchically merging clusters based on the induced density landscape. This approach yields state-of-the-art clustering performance while also providing a meaningful hierarchy, making it a valuable tool for exploratory data analysis. Code is available at https://github.com/ecker-lab/tneb clustering.

Modeling dynamic neural activity by combining naturalistic video stimuli and stimulus-independent latent factors

Understanding how the brain processes dynamic natural stimuli remains a fundamental challenge in neuroscience. Current dynamic neural encoding models either take stimuli as input but ignore shared variability in neural responses, or they model this variability by deriving latent embeddings from neural responses or behavior while ignoring the visual input. To address this gap, we propose a probabilistic model that incorporates video inputs along with stimulus-independent latent factors to capture variability in neuronal responses, predicting a joint distribution for the entire population. After training and testing our model on mouse V1 neuronal responses, we found that it outperforms video-only models in terms of log-likelihood and achieves further improvements when conditioned on responses from other neurons. Furthermore, we find that the learned latent factors strongly correlate with mouse behavior, although the model was trained without behavior data.

MNIST-Nd: a set of naturalistic datasets to benchmark clustering across dimensions

Driven by advances in recording technology, large-scale high-dimensional datasets have emerged across many scientific disciplines. Especially in biology, clustering is often used to gain insights into the structure of such datasets, for instance to understand the organization of different cell types. However, clustering is known to scale poorly to high dimensions, even though the exact impact of dimensionality is unclear as current benchmark datasets are mostly two-dimensional. Here we propose MNIST-Nd, a set of synthetic datasets that share a key property of real-world datasets, namely that individual samples are noisy and clusters do not perfectly separate. MNIST-Nd is obtained by training mixture variational autoencoders with 2 to 64 latent dimensions on MNIST, resulting in six datasets with comparable structure but varying dimensionality. It thus offers the chance to disentangle the impact of dimensionality on clustering. Preliminary common clustering algorithm benchmarks on MNIST-Nd suggest that Leiden is the most robust for growing dimensions.

Bootstrap Your Own Variance

Understanding model uncertainty is important for many applications. We propose Bootstrap Your Own Variance (BYOV), combining Bootstrap Your Own Latent (BYOL), a negative-free Self-Supervised Learning (SSL) algorithm, with Bayes by Backprop (BBB), a Bayesian method for estimating model posteriors. We find that the learned predictive std of BYOV vs. a supervised BBB model is well captured by a Gaussian distribution, providing preliminary evidence that the learned parameter posterior is useful for label free uncertainty estimation. BYOV improves upon the deterministic BYOL baseline (+2.83% test ECE, +1.03% test Brier) and presents better calibration and reliability when tested with various augmentations (eg: +2.4% test ECE, +1.2% test Brier for Salt & Pepper noise).