Paper proposes MLPCD for protein community detection in large PPI networks.
problem Identifying reliable protein communities from large-scale PPI networks.
method Integrates Gene Expression Data and uses Multi-source Learning with cloud computing.
result Demonstrates superior performance compared to existing methods.
New estimator for overlapping community detection in graphs.
problem Reconstructing community relations in graphs with overlapping memberships.
method Proposes a new estimator for Mixed-Membership Stochastic Block Model (MMSB) under diverging spiked eigenvalues condition.
result New estimator matches theoretical minimax lower bound on estimation error.
The paper tests for association between latent community memberships in multi-view network data.
problem Evaluating the independence of latent community memberships in multi-view network data.
method Extended stochastic block model for two-view network data, developed a new hypothesis test.
result Evidence of weak association between latent community memberships in binary interaction and co-complex association data.
New method detects and compares folding pathways of knotted proteins.
problem Understanding the function of knots in protein folding.
method Topological analysis of protein knotoid distributions and entanglement.
result Reveals unique folding pathway for shallow knotted Carbonic Anhydrases.
Community recovery is a central problem that arises in a wide variety of applications such as network clustering, motion segmentation, face clustering and protein complex detection. The objective of the problem is to cluster data points into distinct communities based on a set of measurements, each of which is associat…
A new model explains protein interactions via electron delocalization.
problem Understanding how protein interactions affect each other.
method Quantized discrete differential geometry of n-simplices.
result Allosteric regulation follows from the model of interactions.
The backbone of most proteins forms an open curve. To study their entanglement, a common strategy consists in searching for the presence of knots in their backbones using topological invariants. However, this approach requires to close the curve into a loop, which alters the geometry of curve. Knoto-ID allows evaluatin…
When searching for gene pathways leading to specific disease outcomes, additional information on gene characteristics is often available that may facilitate to differentiate genes related to the disease from irrelevant background when connections involving both types of genes are observed and their relationships to the…
TAPE benchmarks protein learning tasks, finds self-supervised pretraining boosts performance.
problem Fragmented datasets and lack of standardized evaluation in protein modeling.
method TAPE introduces five semi-supervised learning tasks, curates splits, benchmarks models.
result Self-supervised pretraining more than doubles performance in some cases.
Persistent homology can recognize knotting in curves.
problem Recognizing knotting in curves
method Compute one-dimensional persistent homology, extract cycle representatives, and assign a hypergraph curvature-based score.
result Systematic differences between knotted and unknotted structures are revealed.
Nuclear magnetic resonance (NMR) spectroscopy is one of the leading techniques for protein studies. The method features a number of properties, allowing to explain macromolecular interactions mechanistically and resolve structures with atomic resolution. However, due to laborious data analysis, a full potential of NMR …
ProteinNet provides a standardized data set for protein structure prediction.
problem Lack of standardized data sets for protein structure prediction.
method Created high-quality sequence alignments, multiple data splits, and validation sets.
result Facilitates fair assessment of machine learning models for protein structure.
KCUSUM detects abrupt changes in real-time data streams efficiently.
problem Detecting abrupt changes in high-volume scientific data streams.
method Kernel-based Cumulative Sum (KCUSUM) algorithm using Maximum Mean Discrepancy (MMD).
result KCUSUM outperforms traditional CUSUM in online change point detection.
New method maps protein sequences to embeddings encoding structural information.
problem Inferring structural properties from amino acid sequences when structures are unknown.
method Representation learning using bidirectional LSTM models with structural similarity and residue contact maps.
result Trained embeddings improve structural similarity prediction and transfer to other tasks.
Statistical estimates can often be improved by fusion of data from several different sources. One example is so-called ensemble methods which have been successfully applied in areas such as machine learning for classification and clustering. In this paper, we present an ensemble method to improve community detection by…
Community detection improves stock market portfolio optimization.
problem Improving portfolio optimization in financial markets.
method Community detection in correlation-based networks of worldwide stock markets.
result Portfolios constructed using community detection outperform traditional methods.
Study exact community detection in k-community Gaussian mixtures with different intensities.
problem Community detection in k-community Gaussian mixtures with varying intensities.
method Explicitly find the threshold for exact recovery of maximum likelihood estimation.
result Threshold for exact recovery of maximum likelihood estimation is identified.
New GNN model detects overlapping communities better than existing methods.
problem Detecting overlapping communities in graphs.
method Graph Neural Network (GNN) for overlapping community detection.
result The proposed GNN model outperforms existing baselines significantly.
Graph energy helps detect communities in networks better than traditional methods.
problem Detecting communities in sparse networks where traditional methods fail.
method Using graph energy based on the full spectrum of adjacency matrices.
result The difference in graph energy between a planted partition model and an Erdős--Rényi network has a distinct transition at the detectability threshold.
Real-world networks usually have community structure, that is, nodes are grouped into densely connected communities. Community detection is one of the most popular and best-studied research topics in network science and has attracted attention in many different fields, including computer science, statistics, social sci…
Detection of protein-protein interactions (PPIs) plays a vital role in molecular biology. Particularly, infections are caused by the interactions of host and pathogen proteins. It is important to identify host-pathogen interactions (HPIs) to discover new drugs to counter infectious diseases. Conventional wet lab PPI pr…
Spectral clustering with edge counting detects communities in sparse models.
problem Detecting communities in sparse latent space models.
method Spectral clustering followed by edge counting.
result Algorithm achieves consistency and optimality for a broad class of models.
Study compares community detection methods in various networks.
problem Determine which community detection method is best for specific network types.
method Comprehensive empirical analysis of multiple methods on diverse network categories.
result Identifies different types of communities produced by various methods.
Enhances Infomap algorithm to prioritize metadata in community detection.
problem Balancing metadata importance in community detection.
method Introduces a tuning parameter to the Infomap algorithm.
result Improves mutual information with metadata at the cost of structural detectability.
Paper introduces a hyperbolic approach for community detection on graphs.
problem Detecting communities on graphs efficiently and effectively.
method Combines hyperbolic embeddings with Riemannian K-means or mixture models.
result Demonstrates effectiveness through experiments on real-world social networks.
Community detection is a central problem of network data analysis. Given a network, the goal of community detection is to partition the network nodes into a small number of clusters, which could often help reveal interesting structures. The present paper studies community detection in Degree-Corrected Block Models (DCB…
Efficient method for vertex embedding and community detection.
problem Vertex embedding and community detection.
method Normalized one-hot graph encoder and rank-based cluster size measure.
result Excellent numerical performance of graph encoder ensemble algorithm.
A new probabilistic model detects communities in networks using both structure and node features.
problem Detecting communities in networks with node features for more accurate results.
method Generative probabilistic model considering network structure and node features.
result The model accurately detects communities and determines feature strength.
Local network community detection aims to find a single community in a large network, while inspecting only a small part of that network around a given seed node. This is much cheaper than finding all communities in a network. Most methods for local community detection are formulated as ad-hoc optimization problems. In…
Paper shows how to hide individuals in graphs to fool community detection models.
problem Adversarial attack on community detection models by hiding individuals.
method Iterative learning framework that updates a graph generator and a community detection model.
result Adversarial graphs generated by the method can fool multiple community detection models.
Paper uses EXIT analysis for community detection with side information.
problem Community detection in the presence of side information.
method Imported EXIT method from iterative decoding of error control codes.
result Predicts asymptotic phase transition and residual errors for community detection.
A new model detects complex network communities using node attributes.
problem Lack of methods integrating node attributes for community detection in attributed networks.
method BCSBM model that integrates betweenness centrality and clustering coefficient of nodes.
result BCSBM model outperforms other methods in detecting various network structures.
In this paper, we study the sensitivity of the spectral clustering based community detection algorithm subject to a Erdos-Renyi type random noise model. We prove phase transitions in community detectability as a function of the external edge connection probability and the noisy edge presence probability under a general…
Multiplex networks, a special type of multilayer networks, are increasingly applied in many domains ranging from social media analytics to biology. A common task in these applications concerns the detection of community structures. Many existing algorithms for community detection in multiplexes attempt to detect commun…
A new SBM for bipartite networks improves community detection in noisy data.
problem Community detection in bipartite networks with stochastic blockmodels.
method Bayesian nonparametric formulation of SBM for bipartite networks, algorithm to find communities efficiently.
result Improves community detection results over general SBMs, especially in noisy data.
New method compares community detection algorithms without ground truth.
problem Comparing community detection algorithms without ground truth.
method Integrates any objective with its implicit generative model.
result More expressive methods consistently outperform others.
We introduce a new paradigm that is important for community detection in the realm of network analysis. Networks contain a set of strong, dominant communities, which interfere with the detection of weak, natural community structure. When most of the members of the weak communities also belong to stronger communities, t…
This paper improves hierarchical community detection efficiency using local structural properties.
problem Efficiency of hierarchical community detection methods in large networks.
method Use of local structural network properties as proxies to improve efficiency.
result Achieves competitive results in modularity with improved efficiency.
This study compares community detection algorithms for delineating health service areas.
problem Delineating health service areas to improve health care services.
method Comparative analysis of community detection algorithms on hospital-patient discharge networks.
result Infomap algorithm produced the best delineation of health service areas.
A new modularity density measure improves community detection in heterogeneous networks.
problem Detecting meaningful communities in heterogeneous networks.
method Formulated a novel metric, modularity density, for undirected, weighted networks.
result Maximization of modularity density is free from bias and better at detecting weakly-separated communities.
The paper introduces a method for detecting principal communities and embedding vertices.
problem Detecting and embedding vertices in graphs with community structure.
method Principal graph encoder embedding method that detects principal communities and produces vertex embeddings.
result The method successfully detects principal communities and produces accurate vertex embeddings.
Analyzes methods for detecting communities in networks.
problem Detecting communities in networks.
method Examined graph theory, reviewed community detection methods, classified them, and evaluated community quality.
result Developed a classification of community detection methods and evaluated their strengths and weaknesses.
New method quantifies network cycles to enhance community detection.
problem Challenges in detecting communities in networks, especially in sparse graphs.
method Renewal non-backtracking random walks (RNBRW) to quantify cyclic structure.
result RNBRW improves community detection algorithms, especially in sparse graphs.
vGraph learns community membership and node representation jointly.
problem Independent study of community detection and node representation learning limits graph analysis.
method vGraph is a probabilistic generative model that learns community membership and node representation collaboratively.
result vGraph outperforms many baselines in both community detection and node representation learning.
Many methods have been proposed for community detection in networks, but most of them do not take into account additional information on the nodes that is often available in practice. In this paper, we propose a new joint community detection criterion that uses both the network edge information and the node features to…
The motivation for this paper is to apply Bayesian structure learning using Model Averaging in large-scale networks. Currently, Bayesian model averaging algorithm is applicable to networks with only tens of variables, restrained by its super-exponential complexity. We present a novel framework, called LSBN(Large-Scale …
Improved spectral clustering for community detection in networks.
problem Community detection in networks.
method Improved spectral clustering (ISC) based on k-means clustering on weighted eigenvectors of a regularized Laplacian matrix.
result ISC yields stable consistent community detection under mild conditions and outperforms classical methods.
Across many scientific domains, there is a common need to automatically extract a simplified view or coarse-graining of how a complex system's components interact. This general task is called community detection in networks and is analogous to searching for clusters in independent vector data. It is common to evaluate …