Amey P. Pasarkar

Amey P. Pasarkar, Adji Bousso Dieng

Measuring diversity accurately is important for many scientific fields, including machine learning (ML), ecology, and chemistry. The Vendi Score was introduced as a generic similarity-based diversity metric that extends the Hill number of order q=1 by leveraging ideas from quantum statistical mechanics. Contrary to many diversity metrics in ecology, the Vendi Score accounts for similarity and does not require knowledge of the prevalence of the categories in the collection to be evaluated for diversity. However, the Vendi Score treats each item in a given collection with a level of sensitivity proportional to the item's prevalence. This is undesirable in settings where there is a significant imbalance in item prevalence. In this paper, we extend the other Hill numbers using similarity to provide flexibility in allocating sensitivity to rare or common items. This leads to a family of diversity metrics -- Vendi scores with different levels of sensitivity -- that can be used in a variety of applications. We study the properties of the scores in a synthetic controlled setting where the ground truth diversity is known. We then test their utility in improving molecular simulations via Vendi Sampling. Finally, we use the Vendi scores to better understand the behavior of image generative models in terms of memorization, duplication, diversity, and sample quality.

Amey P. Pasarkar, Adji Bousso Dieng

Out-of-distribution (OOD) detection is critical for the safe deployment of machine learning systems. Existing post-hoc detectors typically rely on model confidence scores or likelihood estimates in feature space, often under restrictive distributional assumptions. In this work, we introduce a third paradigm and formulate OOD detection from a diversity perspective. We propose the Vendi Novelty Score (VNS), an OOD detector based on the Vendi Scores (VS), a family of similarity-based diversity metrics. VNS quantifies how much a test sample increases the VS of the in-distribution feature set, providing a principled notion of novelty that does not require density modeling. VNS is linear-time, non-parametric, and naturally combines class-conditional (local) and dataset-level (global) novelty signals. Across multiple image classification benchmarks and network architectures, VNS achieves state-of-the-art OOD detection performance. Remarkably, VNS retains this performance when computed using only 1% of the training data, enabling deployment in memory- or access-constrained settings.

Amey P. Pasarkar, Adji Bousso Dieng

The evolution of microscopy, beginning with its invention in the late 16th century, has continuously enhanced our ability to explore and understand the microscopic world, enabling increasingly detailed observations of structures and phenomena. In parallel, the rise of data-driven science has underscored the need for sophisticated methods to explore and understand the composition of complex data collections. This paper introduces the Vendiscope, the first algorithmic microscope designed to extend traditional microscopy to computational analysis. The Vendiscope leverages the Vendi scores -- a family of differentiable diversity metrics rooted in ecology and quantum mechanics -- and assigns weights to data points based on their contribution to the overall diversity of the collection. These weights enable high-resolution data analysis at scale. We demonstrate this across biology, materials science, and machine learning (ML). We analyzed the $250$ million protein sequences in the protein universe, discovering that over $200$ million are near-duplicates and that AlphaFold fails on proteins with Gene Ontology (GO) functions that contribute most to diversity. Applying the Vendiscope to the Materials Project database led to similar findings: more than $85\%$ of the crystals with formation energy data are near-duplicates and ML models perform poorly on materials that enhance diversity. Additionally, the Vendiscope can be used to study phenomena such as memorization in generative models. We used the Vendiscope to identify memorized training samples from $13$ different generative models and found that the best-performing ones often memorize the training samples that contribute least to diversity. Our findings demonstrate that the Vendiscope can serve as a powerful tool for data-driven science.