Explanipedia

Using stochastic block models for community detection Open

The-Anh Vu-Le, Minhyuk Park, I Chen, Tandy Warnow · 2025

A recent study reported by Park et al. (Improved community detection using stochastic block models, Springer, Heidelberg, 2025) in Complex Networks and their Applications 2024 showed that clusterings from three Stochastic Block Models (SBM…

FastEnsemble: Scalable ensemble clustering on large networks Open

Yasamin Tabatabaee, Eleanor Wedell, Minhyuk Park, Tandy Warnow · 2025

Many community detection algorithms are inherently stochastic, leading to variations in their output depending on input parameters and random seeds. This variability makes the results of a single run of these algorithms less reliable. More…

The Earth BioGenome Project Phase II: illuminating the eukaryotic tree of life Open

Mark Blaxter, Harris A. Lewin, Federica Di-Palma, Richard Challis, Manuela da Silva , et al. · 2025

The Earth BioGenome Project (EBP) aims to “sequence life for the future of life” by generating high-quality reference genome sequences for all recognized eukaryotic species, thereby building a rich knowledge base to inform conservation, in…

TIPP-SD: A New Method for Species Detection in Microbiomes Open

Chengze Shen, Eleanor Wedell, Mihai Pop, Tandy Warnow · 2025

In this study, we present TIPP-SD (i.e., TIPP for Species Detection), a new technique for species detection in a microbiome sample. TIPP-SD uses a modified version of TIPP3, which is a recently developed abundance profiling tool based on m…

Dense Subgraph Clustering and a New Cluster Ensemble Method Open

The-Anh Vu-Le, João Alfredo Cardoso Lamy, George Chacko, Tandy Warnow · 2025

We propose DSC-Flow-Iter, a new community detection algorithm that is based on iterative extraction of dense subgraphs. Although DSC-Flow-Iter leaves many nodes unclustered, it is competitive with leading methods and has high-precision and…

EC-SBM synthetic network generator Open

The-Anh Vu-Le, Lahari Anne, George Chacko, Tandy Warnow · 2025

Generating high-quality synthetic networks with realistic community structure is vital to effectively evaluate community detection algorithms. In this study, we propose a new synthetic network generator called the Edge-Connected Stochastic…

BSCAMPP: Batch-Scaled Phylogenetic Placement on Large Trees Open

Eleanor Wedell, Chengze Shen, Tandy Warnow · 2025

Phylogenetic placement is the problem of placing sequences into a given phylogenetic tree, called a "backbone tree". EPA-ng and pplacer are the two most accurate phylogenetic placement methods, but both can fail to complete when the backbo…

TIPP3 and TIPP3-fast: Improved abundance profiling in metagenomics Open

Chengze Shen, Eleanor Wedell, Mihai Pop, Tandy Warnow · 2025

We present TIPP3 and TIPP3-fast, new tools for abundance profiling in metagenomic datasets. Like its predecessor, TIPP2, the TIPP3 pipeline uses a maximum likelihood approach to place reads into labeled taxonomies using marker genes, but i…

EC-SBM Synthetic Network Generator Open

The-Anh Vu-Le, Lahari Anne, George Chacko, Tandy Warnow · 2025

Generating high-quality synthetic networks with realistic community structure is vital to effectively evaluate community detection algorithms. In this study, we propose a new synthetic network generator called the Edge-Connected Stochastic…

RECCS: Realistic Cluster Connectivity Simulator for Synthetic Network Generation Open

Lahari Anne, The-Anh Vu-Le, Minhyuk Park, Tandy Warnow, George Chacko · 2025

The limited availability of useful ground-truth communities in real-world networks presents a challenge to evaluating and selecting a "best" community detection method for a given network or family of networks. The use of synthetic network…

Improved Community Detection using Stochastic Block Models Open

Minhyuk Park, Daniel Wang Feng, Siya Digra, The-Anh Vue-Le, Lahari Anne , et al. · 2025

Identifying edge-dense communities that are also well-connected is an important aspect of understanding community structure. Prior work has shown that community detection methods can produce poorly connected communities, and some can even …

Biological databases in the age of generative artificial intelligence Open

Mihai Pop, Teresa K. Attwood, Judith A. Blake, Philip E. Bourne, Ana Conesa , et al. · 2024

Summary Modern biological research critically depends on public databases. The introduction and propagation of errors within and across databases can lead to wasted resources as scientists are led astray by bad data or have to conduct expe…

Well-connectedness and community detection Open

Minhyuk Park, Yasamin Tabatabaee, Vikram Ramavarapu, Baqiao Liu, Vidya Kamath Pailodi , et al. · 2024

Community detection methods help reveal the meso-scale structure of complex networks. Integral to detecting communities is the expectation that communities in a network are edge-dense and “well-connected”. Surprisingly, we find that five d…

TIPP3 and TIPP3-fast: Improved Abundance Profiling in Metagenomics Open

Chengze Shen, Eleanor Wedell, Mihai Pop, Tandy Warnow · 2024

We present TIPP3 and TIPP3-fast, new tools for abundance profiling in metagenomic datasets. Like its predecessor, TIPP2, the TIPP3 pipeline uses a maximum likelihood approach to place reads into labeled taxonomies using marker genes, but i…

Axioms for clustering simple unweighted graphs: No impossibility result Open

James K. V. Willson, Tandy Warnow · 2024

In 2002, Kleinberg proposed three axioms for distance-based clustering, and proved that it was impossible for a clustering method to satisfy all three. While there has been much subsequent work examining and modifying these axioms for dist…

FastEnsemble: scalable ensemble clustering on large networks Open

Yasamin Tabatabaee, Eleanor Wedell, Minhyuk Park, Tandy Warnow · 2024

Many community detection algorithms are inherently stochastic, leading to variations in their output depending on input parameters and random seeds. This variability makes the results of a single run of these algorithms less reliable. More…

Synthetic Networks That Preserve Edge Connectivity Open

Lahari Anne, The-Anh Vu-Le, Minhyuk Park, Tandy Warnow, George Chacko · 2024

Since true communities within real-world networks are rarely known, synthetic networks with planted ground truths are valuable for evaluating the performance of community detection methods. Of the synthetic network generation tools availab…

Improved Community Detection using Stochastic Block Models Open

Minhyuk Park, Daniel Wang Feng, Siya Digra, The-Anh Vu-Le, George Chacko , et al. · 2024

Community detection approaches resolve complex networks into smaller groups (communities) that are expected to be relatively edge-dense and well-connected. The stochastic block model (SBM) is one of several approaches used to uncover commu…

Addressing Polymorphism in Linguistic Phylogenetics Open

Marc E. Canby, Steven N. Evans, Donald A. Ringe, Tandy Warnow · 2024

Understanding how languages change is important not only for the reconstruction of protolanguages and for estimating diversification dates (i.e. the dates when languages split), but also for the inference of evolutionary trees (or phylogen…

Complexity of avian evolution revealed by family-level genomes Open

Josefin Stiller, Shaohong Feng, Al-Aabid Chowdhury, Iker Rivas-González, David A. Duchêne , et al. · 2024

CM++ - A Meta-method for Well-Connected CommunityDetection Open

Vikram Ramavarapu, Fábio J. Ayres, Minhyuk Park, Vidya Kamath Pailodi, João Alfredo Cardoso Lamy , et al. · 2024

EMMA: a new method for computing multiple sequence alignments given a constraint subset alignment Open

Chengze Shen, Baqiao Liu, Kelly P. Williams, Tandy Warnow · 2023

Axioms for Distanceless Graph Partitioning Open

James K. V. Willson, Tandy Warnow · 2023

In 2002, Kleinberg proposed three axioms for distance-based clustering, and proved that it was impossible for a clustering method to satisfy all three. While there has been much subsequent work examining and modifying these axioms for dist…

Weighted ASTRID: fast and accurate species trees from weighted internode distances Open

Baqiao Liu, Tandy Warnow · 2023

Background Species tree estimation is a basic step in many biological research projects, but is complicated by the fact that gene trees can differ from the species tree due to processes such as incomplete lineage sorting (ILS), gene duplic…

EMMA: A New Method for Computing Multiple Sequence Alignments given a Constraint Subset Alignment Open

Chengze Shen, Baqiao Liu, Kelly P. Williams, Tandy Warnow · 2023

Background Adding sequences into an existing (possibly user-provided) alignment has multiple applications, including updating a large alignment with new data, adding sequences into a constraint alignment constructed using biological knowle…

Progress on Constructing Phylogenetic Networks for Languages Open

Tandy Warnow, Steven N. Evans, Luay Nakhleh · 2023

In 2006, Warnow, Evans, Ringe, and Nakhleh proposed a stochastic model (hereafter, the WERN 2006 model) of multi-state linguistic character evolution that allowed for homoplasy and borrowing. They proved that if there is no borrowing betwe…

Phylogenomic branch length estimation using quartets Open

Yasamin Tabatabaee, Chao Zhang, Tandy Warnow, Siavash Mirarab · 2023

Motivation Branch lengths and topology of a species tree are essential in most downstream analyses, including estimation of diversification dates, characterization of selection, understanding adaptation, and comparative genomics. Modern ph…

Well-Connected Communities in Real-World and Synthetic Networks Open

Minhyuk Park, Yasamin Tabatabaee, Baqiao Liu, Vidya Kamath Pailodi, Vikram Ramavarapu , et al. · 2023

Integral to the problem of detecting communities through graph clustering is the expectation that they are "well connected". In this respect, we examine five different community detection approaches optimizing different criteria: the Leide…

DISCO+QR: Rooting Species Trees in the Presence of GDL and ILS Open

James K. V. Willson, Yasamin Tabatabaee, Baqiao Liu, Tandy Warnow · 2023

A bstract Genes evolve under processes such as gene duplication and loss (GDL), so that gene family trees are multi-copy, as well as incomplete lineage sorting (ILS); both processes produce gene trees that differ from the species tree. The…

DISCO+QR: rooting species trees in the presence of GDL and ILS Open

James K. V. Willson, Yasamin Tabatabaee, Baqiao Liu, Tandy Warnow · 2023

Motivation Genes evolve under processes such as gene duplication and loss (GDL), so that gene family trees are multi-copy, as well as incomplete lineage sorting (ILS); both processes produce gene trees that differ from the species tree. Th…

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