arXiv subjects

Shangdi Yu

Publications and source records attributed to Shangdi Yu.

17 recordsLinked to original sources

arXiv2025

DynHAC: Fully Dynamic Approximate Hierarchical Agglomerative Clustering

We consider the problem of maintaining a hierarchical agglomerative clustering (HAC) in the dynamic setting, when the input is subject to point insertions and deletions. We introduce DynHAC - the first dynamic HAC algorithm for the popular average-linkage version of the problem which can maintain a 1+\epsilon approximate solution. Our approach leverages recent structural results on (1+\epsilon)-approximate HAC to carefully identify the part of the clustering dendrogram that needs to be updated in order to produce a solution that is consistent with what a full recomputation from scratch would have output. We evaluate DynHAC on a number of real-world graphs. We show that DynHAC can handle each update up to 423x faster than what it would take to recompute the clustering from scratch. At the same time it achieves up to 0.21 higher NMI score than the state-of-the-art dynamic hierarchical clustering algorithms, which do not provably approximate HAC.

cs.DS↗

arXiv2024

The ParClusterers Benchmark Suite (PCBS): A Fine-Grained Analysis of Scalable Graph Clustering

We introduce the ParClusterers Benchmark Suite (PCBS) -- a collection of highly scalable parallel graph clustering algorithms and benchmarking tools that streamline comparing different graph clustering algorithms and implementations. The benchmark includes clustering algorithms that target a wide range of modern clustering use cases, including community detection, classification, and dense subgraph mining. The benchmark toolkit makes it easy to run and evaluate multiple instances of different clustering algorithms, which can be useful for fine-tuning the performance of clustering on a given task, and for comparing different clustering algorithms based on different metrics of interest, including clustering quality and running time. Using PCBS, we evaluate a broad collection of real-world graph clustering datasets. Somewhat surprisingly, we find that the best quality results are obtained by algorithms that not included in many popular graph clustering toolkits. The PCBS provides a standardized way to evaluate and judge the quality-performance tradeoffs of the active research area of scalable graph clustering algorithms. We believe it will help enable fair, accurate, and nuanced evaluation of graph clustering algorithms in the future.

cs.DC↗

arXiv2024

Approximate Nearest Neighbor Search with Window Filters

We define and investigate the problem of $\textit{c-approximate window search}$: approximate nearest neighbor search where each point in the dataset has a numeric label, and the goal is to find nearest neighbors to queries within arbitrary label ranges. Many semantic search problems, such as image and document search with timestamp filters, or product search with cost filters, are natural examples of this problem. We propose and theoretically analyze a modular tree-based framework for transforming an index that solves the traditional c-approximate nearest neighbor problem into a data structure that solves window search. On standard nearest neighbor benchmark datasets equipped with random label values, adversarially constructed embeddings, and image search embeddings with real timestamps, we obtain up to a $75\times$ speedup over existing solutions at the same level of recall.

cs.DS↗

arXiv2023

PECANN: Parallel Efficient Clustering with Graph-Based Approximate Nearest Neighbor Search

This paper studies density-based clustering of point sets. These methods use dense regions of points to detect clusters of arbitrary shapes. In particular, we study variants of density peaks clustering, a popular type of algorithm that has been shown to work well in practice. Our goal is to cluster large high-dimensional datasets, which are prevalent in practice. Prior solutions are either sequential, and cannot scale to large data, or are specialized for low-dimensional data. This paper unifies the different variants of density peaks clustering into a single framework, PECANN, by abstracting out several key steps common to this class of algorithms. One such key step is to find nearest neighbors that satisfy a predicate function, and one of the main contributions of this paper is an efficient way to do this predicate search using graph-based approximate nearest neighbor search (ANNS). To provide ample parallelism, we propose a doubling search technique that enables points to find an approximate nearest neighbor satisfying the predicate in a small number of rounds. Our technique can be applied to many existing graph-based ANNS algorithms, which can all be plugged into PECANN. We implement five clustering algorithms with PECANN and evaluate them on synthetic and real-world datasets with up to 1.28 million points and up to 1024 dimensions on a 30-core machine with two-way hyper-threading. Compared to the state-of-the-art FASTDP algorithm for high-dimensional density peaks clustering, which is sequential, our best algorithm is 45x-734x faster while achieving competitive ARI scores. Compared to the state-of-the-art parallel DPC-based algorithm, which is optimized for low dimensions, we show that PECANN is two orders of magnitude faster. As far as we know, our work is the first to evaluate DPC variants on large high-dimensional real-world image and text embedding datasets.

cs.DS↗

arXiv2023

AuthentiGPT: Detecting Machine-Generated Text via Black-Box Language Models Denoising

Large language models (LLMs) have opened up enormous opportunities while simultaneously posing ethical dilemmas. One of the major concerns is their ability to create text that closely mimics human writing, which can lead to potential misuse, such as academic misconduct, disinformation, and fraud. To address this problem, we present AuthentiGPT, an efficient classifier that distinguishes between machine-generated and human-written texts. Under the assumption that human-written text resides outside the distribution of machine-generated text, AuthentiGPT leverages a black-box LLM to denoise input text with artificially added noise, and then semantically compares the denoised text with the original to determine if the content is machine-generated. With only one trainable parameter, AuthentiGPT eliminates the need for a large training dataset, watermarking the LLM's output, or computing the log-likelihood. Importantly, the detection capability of AuthentiGPT can be easily adapted to any generative language model. With a 0.918 AUROC score on a domain-specific dataset, AuthentiGPT demonstrates its effectiveness over other commercial algorithms, highlighting its potential for detecting machine-generated text in academic settings.

cs.CL↗

arXiv2023

Faster Parallel Exact Density Peaks Clustering

Clustering multidimensional points is a fundamental data mining task, with applications in many fields, such as astronomy, neuroscience, bioinformatics, and computer vision. The goal of clustering algorithms is to group similar objects together. Density-based clustering is a clustering approach that defines clusters as dense regions of points. It has the advantage of being able to detect clusters of arbitrary shapes, rendering it useful in many applications. In this paper, we propose fast parallel algorithms for Density Peaks Clustering (DPC), a popular version of density-based clustering. Existing exact DPC algorithms suffer from low parallelism both in theory and in practice, which limits their application to large-scale data sets. Our most performant algorithm, which is based on priority search kd-trees, achieves $O(\log n\log\log n)$ span (parallel time complexity) for a data set of $n$ points. Our algorithm is also work-efficient, achieving a work complexity matching the best existing sequential exact DPC algorithm. In addition, we present another DPC algorithm based on a Fenwick tree that makes fewer assumptions for its average-case complexity to hold. We provide optimized implementations of our algorithms and evaluate their performance via extensive experiments. On a 30-core machine with two-way hyperthreading, we find that our best algorithm achieves a 10.8--13169x speedup over the previous best parallel exact DPC algorithm. Compared to the state-of-the-art parallel approximate DPC algorithm, our best algorithm achieves a 1.5--4206x speedup, while being exact.

cs.DC↗

arXiv2023

Improving Small Language Models on PubMedQA via Generative Data Augmentation

Large Language Models (LLMs) have made remarkable advancements in the field of natural language processing. However, their increasing size poses challenges in terms of computational cost. On the other hand, Small Language Models (SLMs) are known for their efficiency, but they often struggle with limited capacity and training data, especially in specific domains. In this paper, we introduce a novel method aimed at improving SLMs in the medical domain using LLM-based generative data augmentation. The objective of our approach is to develop more efficient and capable models that are specifically tailored for specialized applications. Through experiments conducted on the PubMedQA dataset, we demonstrate the effectiveness of LLMs in refining and diversifying existing question-answer pairs. This refinement process leads to improved performance in a significantly smaller model after fine-tuning. Notably, our best SLM, with under 1.6 billion parameters, outperforms the few-shot GPT-4 on the PubMedQA dataset. Our code and generated data are publicly available to facilitate further explorations.

cs.CL↗

arXiv2023

Parallel Filtered Graphs for Hierarchical Clustering

Given all pairwise weights (distances) among a set of objects, filtered graphs provide a sparse representation by only keeping an important subset of weights. Such graphs can be passed to graph clustering algorithms to generate hierarchical clusters. In particular, the directed bubble hierarchical tree (DBHT) algorithm on filtered graphs has been shown to produce good hierarchical clusters for time series data. We propose a new parallel algorithm for constructing triangulated maximally filtered graphs (TMFG), which produces valid inputs for DBHT, and a scalable parallel algorithm for generating DBHTs that is optimized for TMFG inputs. In addition to parallelizing the original TMFG construction, which has limited parallelism, we also design a new algorithm that inserts multiple vertices on each round to enable more parallelism. We show that the graphs generated by our new algorithm have similar quality compared to the original TMFGs, while being much faster to generate. Our new parallel algorithms for TMFGs and DBHTs are 136--2483x faster than state-of-the-art implementations, while achieving up to 41.56x self-relative speedup on 48 cores with hyper-threading, and achieve better clustering results compared to the standard average-linkage and complete-linkage hierarchical clustering algorithms. We show that on a stock data set, our algorithms produce clusters that align well with human experts' classification.

cs.DC↗

arXiv2022

Differential Privacy from Locally Adjustable Graph Algorithms: $k$-Core Decomposition, Low Out-Degree Ordering, and Densest Subgraphs

Differentially private algorithms allow large-scale data analytics while preserving user privacy. Designing such algorithms for graph data is gaining importance with the growth of large networks that model various (sensitive) relationships between individuals. While there exists a rich history of important literature in this space, to the best of our knowledge, no results formalize a relationship between certain parallel and distributed graph algorithms and differentially private graph analysis. In this paper, we define \emph{locally adjustable} graph algorithms and show that algorithms of this type can be transformed into differentially private algorithms. Our formalization is motivated by a set of results that we present in the central and local models of differential privacy for a number of problems, including $k$-core decomposition, low out-degree ordering, and densest subgraphs. First, we design an $\varepsilon$-edge differentially private (DP) algorithm that returns a subset of nodes that induce a subgraph of density at least $\frac{D^*}{1+\eta} - O\left(\text{poly}(\log n)/\varepsilon\right),$ where $D^*$ is the density of the densest subgraph in the input graph (for any constant $\eta > 0$). This algorithm achieves a two-fold improvement on the multiplicative approximation factor of the previously best-known private densest subgraph algorithms while maintaining a near-linear runtime. Then, we present an $\varepsilon$-locally edge differentially private (LEDP) algorithm for $k$-core decompositions. Our LEDP algorithm provides approximates the core numbers (for any constant $\eta > 0$) with $(2+\eta)$ multiplicative and $O\left(\text{poly}\left(\log n\right)/\varepsilon\right)$ additive error. This is the first differentially private algorithm that outputs private $k$-core decomposition statistics.

cs.DS↗

arXiv2022

ParGeo: A Library for Parallel Computational Geometry

This paper presents ParGeo, a multicore library for computational geometry. ParGeo contains modules for fundamental tasks including $k$d-tree based spatial search, spatial graph generation, and algorithms in computational geometry. We focus on three new algorithmic contributions provided in the library. First, we present a new parallel convex hull algorithm based on a reservation technique to enable parallel modifications to the hull. We also provide the first parallel implementations of the randomized incremental convex hull algorithm as well as a divide-and-conquer convex hull algorithm in $\mathbb{R}^3$. Second, for the smallest enclosing ball problem, we propose a new sampling-based algorithm to quickly reduce the size of the data set. We also provide the first parallel implementation of Welzl's classic algorithm for smallest enclosing ball. Third, we present the BDL-tree, a parallel batch-dynamic $k$d-tree that allows for efficient parallel updates and $k$-NN queries over dynamically changing point sets. BDL-trees consist of a log-structured set of $k$d-trees which can be used to efficiently insert, delete, and query batches of points in parallel. On 36 cores with two-way hyper-threading, our fastest convex hull algorithm achieves up to 44.7x self-relative parallel speedup and up to 559x speedup against the best existing sequential implementation. Our smallest enclosing ball algorithm using our sampling-based algorithm achieves up to 27.1x self-relative parallel speedup and up to 178x speedup against the best existing sequential implementation. Our implementation of the BDL-tree achieves self-relative parallel speedup of up to 46.1x. Across all of the algorithms in ParGeo, we achieve self-relative parallel speedup of 8.1--46.61x.

cs.CG↗

arXiv2021

ParChain: A Framework for Parallel Hierarchical Agglomerative Clustering using Nearest-Neighbor Chain

This paper studies the hierarchical clustering problem, where the goal is to produce a dendrogram that represents clusters at varying scales of a data set. We propose the ParChain framework for designing parallel hierarchical agglomerative clustering (HAC) algorithms, and using the framework we obtain novel parallel algorithms for the complete linkage, average linkage, and Ward's linkage criteria. Compared to most previous parallel HAC algorithms, which require quadratic memory, our new algorithms require only linear memory, and are scalable to large data sets. ParChain is based on our parallelization of the nearest-neighbor chain algorithm, and enables multiple clusters to be merged on every round. We introduce two key optimizations that are critical for efficiency: a range query optimization that reduces the number of distance computations required when finding nearest neighbors of clusters, and a caching optimization that stores a subset of previously computed distances, which are likely to be reused. Experimentally, we show that our highly-optimized implementations using 48 cores with two-way hyper-threading achieve 5.8--110.1x speedup over state-of-the-art parallel HAC algorithms and achieve 13.75--54.23x self-relative speedup. Compared to state-of-the-art algorithms, our algorithms require up to 237.3x less space. Our algorithms are able to scale to data set sizes with tens of millions of points, which existing algorithms are not able to handle.

cs.DS↗

arXiv2021

Parallel Batch-Dynamic Algorithms for $k$-Core Decomposition and Related Graph Problems

Maintaining a $k$-core decomposition quickly in a dynamic graph has important applications in network analysis. The main challenge for designing efficient exact algorithms is that a single update to the graph can cause significant global changes. Our paper focuses on \emph{approximation} algorithms with small approximation factors that are much more efficient than what exact algorithms can obtain. We present the first parallel, batch-dynamic algorithm for approximate $k$-core decomposition that is efficient in both theory and practice. Our algorithm is based on our novel parallel level data structure, inspired by the sequential level data structures of Bhattacharya et al [STOC '15] and Henzinger et al [2020]. Given a graph with $n$ vertices and a batch of updates $\mathcal{B}$, our algorithm provably maintains a $(2 + \varepsilon)$-approximation of the coreness values of all vertices (for any constant $\varepsilon > 0$) in $O(|\mathcal{B}|\log^2 n)$ amortized work and $O(\log^2 n \log\log n)$ depth (parallel time) with high probability. As a by-product, our $k$-core decomposition algorithm also gives a batch-dynamic algorithm for maintaining an $O(\alpha)$ out-degree orientation, where $\alpha$ is the current arboricity of the graph. We demonstrate the usefulness of our low out-degree orientation algorithm by presenting a new framework to formally study batch-dynamic algorithms in bounded-arboricity graphs. Our framework obtains new provably-efficient parallel batch-dynamic algorithms for maximal matching, clique counting, and vertex coloring. We implemented and experimentally evaluated our $k$-core decomposition algorithm on a 30-core machine with two-way hyper-threading on $11$ graphs of varying densities and sizes. [...]

cs.DS↗

arXiv2021

Fast Parallel Algorithms for Euclidean Minimum Spanning Tree and Hierarchical Spatial Clustering

This paper presents new parallel algorithms for generating Euclidean minimum spanning trees and spatial clustering hierarchies (known as HDBSCAN$^*$). Our approach is based on generating a well-separated pair decomposition followed by using Kruskal's minimum spanning tree algorithm and bichromatic closest pair computations. We introduce a new notion of well-separation to reduce the work and space of our algorithm for HDBSCAN$^*$. We also present a parallel approximate algorithm for OPTICS based on a recent sequential algorithm by Gan and Tao. Finally, we give a new parallel divide-and-conquer algorithm for computing the dendrogram and reachability plots, which are used in visualizing clusters of different scale that arise for both EMST and HDBSCAN$^*$. We show that our algorithms are theoretically efficient: they have work (number of operations) matching their sequential counterparts, and polylogarithmic depth (parallel time). We implement our algorithms and propose a memory optimization that requires only a subset of well-separated pairs to be computed and materialized, leading to savings in both space (up to 10x) and time (up to 8x). Our experiments on large real-world and synthetic data sets using a 48-core machine show that our fastest algorithms outperform the best serial algorithms for the problems by 11.13--55.89x, and existing parallel algorithms by at least an order of magnitude.

cs.DS↗

arXiv2020

A Parallel Batch-Dynamic Data Structure for the Closest Pair Problem

We propose a theoretically-efficient and practical parallel batch-dynamic data structure for the closest pair problem. Our solution is based on a serial dynamic closest pair data structure by Golin et al., and supports batches of insertions and deletions in parallel. For a data set of size $n$, our data structure supports a batch of insertions or deletions of size $m$ in $O(m(1+\log ((n+m)/m)))$ expected work and $O(\log (n+m)\log^*(n+m))$ depth with high probability, and takes linear space. The key techniques for achieving these bounds are a new work-efficient parallel batch-dynamic binary heap, and careful management of the computation across sets of points to minimize work and depth. We provide an optimized multicore implementation of our data structure using dynamic hash tables, parallel heaps, and dynamic $k$-d trees. Our experiments on a variety of synthetic and real-world data sets show that it achieves a parallel speedup of up to 38.57x (15.10x on average) on 48 cores with hyper-threading. In addition, we also implement and compare four parallel algorithms for static closest pair problem, for which we are not aware of any existing practical implementations. On 48 cores with hyper-threading, the static algorithms achieve up to 51.45x (29.42x on average) speedup, and Rabin's algorithm performs the best on average. Comparing our dynamic algorithm to the fastest static algorithm, we find that it is advantageous to use the dynamic algorithm for batch sizes of up to 20\% of the data set. As far as we know, our work is the first to experimentally evaluate parallel closest pair algorithms, in both the static and the dynamic settings.

cs.DS↗

arXiv2020

Parallel Batch-Dynamic $k$-Clique Counting

In this paper, we study new batch-dynamic algorithms for the $k$-clique counting problem, which are dynamic algorithms where the updates are batches of edge insertions and deletions. We study this problem in the parallel setting, where the goal is to obtain algorithms with low (polylogarithmic) depth. Our first result is a new parallel batch-dynamic triangle counting algorithm with $O(\Delta\sqrt{\Delta+m})$ amortized work and $O(\log^* (\Delta+m))$ depth with high probability, and $O(\Delta+m)$ space for a batch of $\Delta$ edge insertions or deletions. Our second result is an algebraic algorithm based on parallel fast matrix multiplication. Assuming that a parallel fast matrix multiplication algorithm exists with parallel matrix multiplication constant $\omega_p$, the same algorithm solves dynamic $k$-clique counting with $O\left(\min\left(\Delta m^{\frac{(2k - 1)\omega_p}{3(\omega_p + 1)}}, (\Delta+m)^{\frac{2(k + 1)\omega_p}{3(\omega_p + 1)}}\right)\right)$ amortized work and $O(\log (\Delta+m))$ depth with high probability, and $O\left((\Delta+m)^{\frac{2(k + 1)\omega_p}{3(\omega_p + 1)}}\right)$ space. Using a recently developed parallel $k$-clique counting algorithm, we also obtain a simple batch-dynamic algorithm for $k$-clique counting on graphs with arboricity $\alpha$ running in $O(\Delta(m+\Delta)\alpha^{k-4})$ expected work and $O(\log^{k-2} n)$ depth with high probability, and $O(m + \Delta)$ space. Finally, we present a multicore CPU implementation of our parallel batch-dynamic triangle counting algorithm. On a 72-core machine with two-way hyper-threading, our implementation achieves 36.54--74.73x parallel speedup, and in certain cases achieves significant speedups over existing parallel algorithms for the problem, which are not theoretically-efficient.

cs.DS↗

arXiv2019

Analyzing the Spotify Top 200 Through a Point Process Lens

Every generation throws a hero up the pop charts. For the current generation, one of the most relevant pop charts is the Spotify Top 200. Spotify is the world's largest music streaming service and the Top 200 is a daily list of the platform's 200 most streamed songs. In this paper, we analyze a data set collected from over 20 months of these rankings. Via exploratory data analysis, we investigate the popularity, rarity, and longevity of songs on the Top 200 and we construct a stochastic process model for the daily streaming counts that draws upon ideas from stochastic intensity point processes and marked point processes. Using the parameters of this model as estimated from the Top 200 data, we apply a clustering algorithm to identify songs with similar features and performance.

cs.SI↗

arXiv2019

Modeling and Analysis of Tagging Networks in Stack Exchange Communities

Large Question-and-Answer (Q&A) platforms support diverse knowledge curation on the Web. While researchers have studied user behavior on the platforms in a variety of contexts, there is relatively little insight into important by-products of user behavior that also encode knowledge. Here, we analyze and model the macroscopic structure of tags applied by users to annotate and catalog questions, using a collection of 168 Stack Exchange websites. We find striking similarity in tagging structure across these Stack Exchange communities, even though each community evolves independently (albeit under similar guidelines). Using our empirical findings, we develop a simple generative model that creates random bipartite graphs of tags and questions. Our model accounts for the tag frequency distribution but does not explicitly account for co-tagging correlations. Even under these constraints, we demonstrate empirically and theoretically that our model can reproduce a number of statistical properties of the co-tagging graph that links tags appearing in the same post.

cs.SI↗