A trainable clustering algorithm based on shortest paths from density peaks

Optimization of Density Peak Clustering Algorithm Based on Improved Black Widow Algorithm

Clustering is an unsupervised learning method. Density Peak Clustering (DPC), a density-based algorithm, intuitively determines the number of clusters and identifies clusters of arbitrary shapes. However, it cannot function effectively without the correct parameter, referred to as the cutoff distance (dc). The traditional DPC algorithm exhibits noticeable shortcomings in the initial setting of dc when confronted with different datasets, necessitating manual readjustment. To solve this defect, we propose a new algorithm where we integrate DPC with the Black Widow Optimization Algorithm (BWOA), named Black Widow Density Peaks Clustering (BWDPC), to automatically optimize dc for maximizing accuracy, achieving automatic determination of dc. In the experiment, BWDPC is used to compare with three other algorithms on six synthetic data and six University of California Irvine (UCI) datasets. The results demonstrate that the proposed BWDPC algorithm more accurately identifies density peak points (cluster centers). Moreover, BWDPC achieves superior clustering results. Therefore, BWDPC represents an effective improvement over DPC.

SMMP: A Stable-Membership-Based Auto-Tuning Multi-Peak Clustering Algorithm

Since most existing single-prototype clustering algorithms are unsuitable for complex-shaped clusters, many multi-prototype clustering algorithms have been proposed. Nevertheless, the automatic estimation of the number of clusters and the detection of complex shapes are still challenging, and to solve such problems usually relies on user-specified parameters and may be prohibitively time-consuming. Herein, a stable-membership-based auto-tuning multi-peak clustering algorithm (SMMP) is proposed, which can achieve fast, automatic, and effective multi-prototype clustering without iteration. A dynamic association-transfer method is designed to learn the representativeness of points to sub-cluster centers during the generation of sub-clusters by applying the density peak clustering technique. According to the learned representativeness, a border-link-based connectivity measure is used to achieve high-fidelity similarity evaluation of sub-clusters. Meanwhile, based on the assumption that a reasonable clustering should have a relatively stable membership state upon the change of clustering thresholds, SMMP can automatically identify the number of sub-clusters and clusters, respectively. Also, SMMP is designed for large datasets. Experimental results on both synthetic and real datasets demonstrated the effectiveness of SMMP.

Multiphoton intravital microscopy of rodents

Tissues are heterogeneous with respect to cellular and non-cellular components and in the dynamic interactions between these elements. To study the behaviour and fate of individual cells in these complex tissues, intravital microscopy (IVM) techniques such as multiphoton microscopy have been developed to visualize intact and live tissues at cellular and subcellular resolution. IVM experiments have revealed unique insights into the dynamic interplay between different cell types and their local environment, and how this drives morphogenesis and homeostasis of tissues, inflammation and immune responses, and the development of various diseases. This Primer introduces researchers to IVM technologies, with a focus on multiphoton microscopy of rodents, and discusses challenges, solutions and practical tips on how to perform IVM. To illustrate the unique potential of IVM, several examples of results are highlighted. Finally, we discuss data reproducibility and how to handle big imaging data sets.

Clustering by measuring local direction centrality for data with heterogeneous density and weak connectivity

Clustering is a powerful machine learning method for discovering similar patterns according to the proximity of elements in feature space. It is widely used in computer science, bioscience, geoscience, and economics. Although the state-of-the-art partition-based and connectivity-based clustering methods have been developed, weak connectivity and heterogeneous density in data impede their effectiveness. In this work, we propose a boundary-seeking Clustering algorithm using the local Direction Centrality (CDC). It adopts a density-independent metric based on the distribution of K-nearest neighbors (KNNs) to distinguish between internal and boundary points. The boundary points generate enclosed cages to bind the connections of internal points, thereby preventing cross-cluster connections and separating weakly-connected clusters. We demonstrate the validity of CDC by detecting complex structured clusters in challenging synthetic datasets, identifying cell types from single-cell RNA sequencing (scRNA-seq) and mass cytometry (CyTOF) data, recognizing speakers on voice corpuses, and testifying on various types of real-world benchmarks.

Clustering is a powerful machine learning method for discovering similar patterns according to the proximity of elements in feature space. Here the authors propose a local direction centrality clustering algorithm that copes with heterogeneous density and weak connectivity issues.

CANCOL, a Computer-Assisted Annotation Tool to Facilitate Colocalization and Tracking of Immune Cells in Intravital Microscopy

Two-photon intravital microscopy (2P-IVM) has become a widely used technique to study cell-to-cell interactions in living organisms. Four-dimensional imaging data obtained via 2P-IVM are classically analyzed by performing automated cell tracking, a procedure that computes the trajectories followed by each cell. However, technical artifacts, such as brightness shifts, the presence of autofluorescent objects, and channel crosstalking, affect the specificity of imaging channels for the cells of interest, thus hampering cell detection. Recently, machine learning has been applied to overcome a variety of obstacles in biomedical imaging. However, existing methods are not tailored for the specific problems of intravital imaging of immune cells. Moreover, results are highly dependent on the quality of the annotations provided by the user. In this study, we developed CANCOL, a tool that facilitates the application of machine learning for automated tracking of immune cells in 2P-IVM. CANCOL guides the user during the annotation of specific objects that are problematic for cell tracking when not properly annotated. Then, it computes a virtual colocalization channel that is specific for the cells of interest. We validated the use of CANCOL on challenging 2P-IVM videos from murine organs, obtaining a significant improvement in the accuracy of automated tracking while reducing the time required for manual track curation.

Characterization of the Dynamic Behavior of Neutrophils Following Influenza Vaccination

Neutrophils are amongst the first cells to respond to inflammation and infection. Although they play a key role in limiting the dissemination of pathogens, the study of their dynamic behavior in immune organs remains elusive. In this work, we characterized in vivo the dynamic behavior of neutrophils in the mouse popliteal lymph node (PLN) after influenza vaccination with UV-inactivated virus. To achieve this, we used an image-based systems biology approach to detect the motility patterns of neutrophils and to associate them to distinct actions. We described a prominent and rapid recruitment of neutrophils to the PLN following vaccination, which was dependent on the secretion of the chemokine CXCL1 and the alarmin molecule IL-1α. In addition, we observed that the initial recruitment occurred mainly via high endothelial venules located in the paracortical and interfollicular regions of the PLN. The analysis of the spatial-temporal patterns of neutrophil migration demonstrated that, in the initial stage, the majority of neutrophils displayed a patrolling behavior, followed by the formation of swarms in the subcapsular sinus of the PLN, which were associated with macrophages in this compartment. Finally, we observed using multiple imaging techniques, that neutrophils phagocytize and transport influenza virus particles. These processes might have important implications in the capacity of these cells to present viral antigens.