Paolo Pellizzoni

Simone Moretti, Paolo Pellizzoni, Andrea Pietracaprina et al.

The $k$-center problem is a fundamental clustering variant with applications in learning systems and data summarization. In several real-world scenarios, the dataset to be clustered is not static, but evolves over time, as new data points arrive and old ones become stale. To account for dynamicity, the $k$-center problem has been mainly studied under the sliding window setting, where only the $N$ most recent points are considered non-stale, or the fully dynamic setting, where arbitrary sequences of point arrivals and deletions without prior notice may occur. In this paper, we introduce the dynamic setting with lifetimes, which bridges the two aforementioned classical settings by still allowing arbitrary arrivals and deletions, but making the deletion time of each point known upon its arrival. Under this new setting, we devise a deterministic $(2+\varepsilon)$-approximation algorithm with $\tilde{O}(k/\varepsilon)$ amortized update time and memory usage linear in the number of currently active points. Moreover, we develop a deterministic $(6+\varepsilon)$-approximation algorithm that, under tame update sequences, has $\tilde{O}(k/\varepsilon)$ worst-case update time and heavily sublinear working memory.

Simone Moretti, Paolo Pellizzoni, Francesco Silvestri

The weighted Euclidean norm $\|x\|_w$ of a vector $x\in \mathbb{R}^d$ with weights $w\in \mathbb{R}^d$ is the Euclidean norm where the contribution of each dimension is scaled by a given weight. Approaches to dimensionality reduction that satisfy the Johnson-Lindenstrauss (JL) lemma can be easily adapted to the weighted Euclidean distance if weights are known and fixed: it suffices to scale each dimension of the input vectors according to the weights, and then apply any standard approach. However, this is not the case when weights are unknown during the dimensionality reduction or might dynamically change. In this paper, we address this issue by providing a linear function that maps vectors into a smaller complex vector space and allows to retrieve a JL-like estimate for the weighted Euclidean distance once weights are revealed. Our results are based on the decomposition of the complex dimensionality reduction into several Rademacher chaos random variables, which are studied using novel concentration inequalities for sums of independent Rademacher chaoses.

Dexiong Chen, Philip Hartout, Paolo Pellizzoni et al.

Understanding the relationships between protein sequence, structure and function is a long-standing biological challenge with manifold implications from drug design to our understanding of evolution. Recently, protein language models have emerged as the preferred method for this challenge, thanks to their ability to harness large sequence databases. Yet, their reliance on expansive sequence data and parameter sets limits their flexibility and practicality in real-world scenarios. Concurrently, the recent surge in computationally predicted protein structures unlocks new opportunities in protein representation learning. While promising, the computational burden carried by such complex data still hinders widely-adopted practical applications. To address these limitations, we introduce a novel framework that enhances protein language models by integrating protein structural data. Drawing from recent advances in graph transformers, our approach refines the self-attention mechanisms of pretrained language transformers by integrating structural information with structure extractor modules. This refined model, termed Protein Structure Transformer (PST), is further pretrained on a small protein structure database, using the same masked language modeling objective as traditional protein language models. Empirical evaluations of PST demonstrate its superior parameter efficiency relative to protein language models, despite being pretrained on a dataset comprising only 542K structures. Notably, PST consistently outperforms the state-of-the-art foundation model for protein sequences, ESM-2, setting a new benchmark in protein function prediction. Our findings underscore the potential of integrating structural information into protein language models, paving the way for more effective and efficient protein modeling Code and pretrained models are available at https://github.com/BorgwardtLab/PST.

Dexiong Chen, Paolo Pellizzoni, Karsten Borgwardt

Attention-based graph neural networks (GNNs), such as graph attention networks (GATs), have become popular neural architectures for processing graph-structured data and learning node embeddings. Despite their empirical success, these models rely on labeled data and the theoretical properties of these models have yet to be fully understood. In this work, we propose a novel attention-based node embedding framework for graphs. Our framework builds upon a hierarchical kernel for multisets of subgraphs around nodes (e.g. neighborhoods) and each kernel leverages the geometry of a smooth statistical manifold to compare pairs of multisets, by "projecting" the multisets onto the manifold. By explicitly computing node embeddings with a manifold of Gaussian mixtures, our method leads to a new attention mechanism for neighborhood aggregation. We provide theoretical insights into generalizability and expressivity of our embeddings, contributing to a deeper understanding of attention-based GNNs. We propose both efficient unsupervised and supervised methods for learning the embeddings. Through experiments on several node classification benchmarks, we demonstrate that our proposed method outperforms existing attention-based graph models like GATs. Our code is available at https://github.com/BorgwardtLab/fisher_information_embedding.

Florian Graf, Paolo Pellizzoni, Martin Uray et al.

We consider the problem of computing persistent homology (PH) for large-scale Euclidean point cloud data, aimed at downstream machine learning tasks, where the exponential growth of the most widely-used Vietoris-Rips complex imposes serious computational limitations. Although more scalable alternatives such as the Alpha complex or sparse Rips approximations exist, they often still result in a prohibitively large number of simplices. This poses challenges in the complex construction and in the subsequent PH computation, prohibiting their use on large-scale point clouds. To mitigate these issues, we introduce the Flood complex, inspired by the advantages of the Alpha and Witness complex constructions. Informally, at a given filtration value $r\geq 0$, the Flood complex contains all simplices from a Delaunay triangulation of a small subset of the point cloud $X$ that are fully covered by balls of radius $r$ emanating from $X$, a process we call flooding. Our construction allows for efficient PH computation, possesses several desirable theoretical properties, and is amenable to GPU parallelization. Scaling experiments on 3D point cloud data show that we can compute PH of up to dimension 2 on several millions of points. Importantly, when evaluating object classification performance on real-world and synthetic data, we provide evidence that this scaling capability is needed, especially if objects are geometrically or topologically complex, yielding performance superior to other PH-based methods and neural networks for point cloud data.

Paolo Pellizzoni, Andrea Pietracaprina, Geppino Pucci

Metric $k$-center clustering is a fundamental unsupervised learning primitive. Although widely used, this primitive is heavily affected by noise in the data, so that a more sensible variant seeks for the best solution that disregards a given number $z$ of points of the dataset, called outliers. We provide efficient algorithms for this important variant in the streaming model under the sliding window setting, where, at each time step, the dataset to be clustered is the window $W$ of the most recent data items. Our algorithms achieve $O(1)$ approximation and, remarkably, require a working memory linear in $k+z$ and only logarithmic in $|W|$. As a by-product, we show how to estimate the effective diameter of the window $W$, which is a measure of the spread of the window points, disregarding a given fraction of noisy distances. We also provide experimental evidence of the practical viability of our theoretical results.