Search Results for "hierarchical clustering"
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Showing 27 open source projects for "hierarchical clustering"
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HDBSCAN
A high performance implementation of HDBSCAN clustering
HDBSCAN - Hierarchical Density-Based Spatial Clustering of Applications with Noise. Performs DBSCAN over varying epsilon values and integrates the result to find a clustering that gives the best stability over epsilon. This allows HDBSCAN to find clusters of varying densities (unlike DBSCAN), and be more robust to parameter selection. In practice this means that HDBSCAN returns a good clustering straight away with little or no parameter tuning -- and the primary parameter, minimum cluster size, is intuitive and easy to select. ... -
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RAPTOR
The official implementation of RAPTOR
RAPTOR is a retrieval architecture designed to improve retrieval-augmented generation systems by organizing documents into hierarchical structures that enable more effective context retrieval. Traditional RAG systems typically retrieve small text chunks independently, which can limit a model’s ability to understand broader document context. RAPTOR addresses this limitation by recursively embedding, clustering, and summarizing documents to create a tree-structured hierarchy of information. ... -
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DBreeze Database
C# .NET NOSQL ( key value store embedded ) ACID database
DBreeze Database is a professional, open-source, multi-paradigm (embedded Key-Value store, objects, NoSql, text search, multi-parameter search, embedding vector database, vector similarity search/clustering, etc.), multi-threaded, transactional and ACID-compliant data management system for .NET5> / .NET Framework 3.5> / Xamarin MONO Android iOS / .NET Core 1.0> / .NET Standard 1.6> / Universal Windows Platform / .NET Portable / UNITY / CoreRT. -
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Orange Data Mining
Orange: Interactive data analysis
...Perform simple data analysis with clever data visualization. Explore statistical distributions, box plots and scatter plots, or dive deeper with decision trees, hierarchical clustering, heatmaps, MDS and linear projections. Even your multidimensional data can become sensible in 2D, especially with clever attribute ranking and selections. Interactive data exploration for rapid qualitative analysis with clean visualizations. Graphic user interface allows you to focus on exploratory data analysis instead of coding, while clever defaults make fast prototyping of a data analysis workflow extremely easy. ... -
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vis-network
Display dynamic, automatically organised, customizable network views
Network is a visualization to display networks and networks consisting of nodes and edges. The visualization is easy to use and supports custom shapes, styles, colors, sizes, images, and more. The network visualization works smooth on any modern browser for up to a few thousand nodes and edges. To handle a larger amount of nodes, Network has clustering support. Network uses HTML canvas for rendering. As of 4.0, the network consists of individual modules which handle specific parts of the... -
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MooseFS
Fault tolerant, POSIX-compliant, Net Distributed Storage / File System
MooseFS (MFS) is a fault tolerant, highly performing, scaling-out, network distributed file system. It spreads data over several physical servers which are visible to the user as one resource. For standard file operations MooseFS mounted with FUSE acts as other Unix-alike file systems: * A hierarchical structure (directory tree) * Stores POSIX file attributes (permissions, last access and modification times) Supports special files (block and character devices, pipes and sockets) *... -
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HA Cluster Manager
Multi Node Cluster Manager
Build high availability Linux server clusters to manage system resources with automatic fail over and fail back. -
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TransMCL
a noval Transcriptome optimization tool
To improve the quality of transcriptome assembly, we introduce TransMCL, a novel transcriptome optimization tool, to reconstruct full-length coding sequences while eliminating redundancy from assembled transcriptomes. TransMCL employs homologs from closely related species to guide the assembly, clustering raw transcripts from transcriptome data and genes from annotated genomes into hierarchical ortholog groups (HOGs). -
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Hierarchical DP
Source code of DC-HDP
This Matlab code is used for demonstration of the clustering results of DP, LC-DP and DC-HDP. Written by Ye Zhu, Deakin University, May 2021, version 1.0. This software is under GNU General Public License version 3.0 (GPLv3) This code is a demo of method described by the following publication: Zhu, Y., Ting, K.M., Jin, Y. and Angelova, M., 2021, August. Hierarchical clustering that takes advantage of both density-peak and density-connectivity. -
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Texthero
Text preprocessing, representation and visualization from zero to hero
Texthero is a python package to work with text data efficiently. It empowers NLP developers with a tool to quickly understand any text-based dataset and it provides a solid pipeline to clean and represent text data, from zero to hero. -
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End-to-End Negotiator
Deal or No Deal? End-to-End Learning for Negotiation Dialogues
End-to-End Negotiator is a PyTorch-based research framework developed by Facebook AI Research to train neural agents capable of conducting strategic negotiations in natural language. The project implements the models presented in two key papers: “Deal or No Deal? End-to-End Learning for Negotiation Dialogues” and “Hierarchical Text Generation and Planning for Strategic Dialogue”. It enables agents to plan, reason, and communicate effectively to maximize outcomes in multi-turn negotiations... -
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NOVA
Analysis and visualization of complexome profiling data.
NOVA is a program designed to analysis complexome profiling data (Heide et al., 2012). A graphical user interface (GUI) provides various visualization tools, such as heat maps and 2D plots. Several hierarchical clustering algorithms (e.g., single linkage, average linkage, Wards linkage), different distance measures (e.g., Euclidean distance, Manhattan distance, Pearson distance), and various normalization techniques are implemented. Many additional functions like zooming, searching for proteins, image export, and automatic file format recognition support intuitive handling for biologists. ... -
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GSMLBook
Recipes for basic machine learning algorithms using sklearn in jupyter
...Topics include linear, multilinear, polynomial, stepwise, lasso, ridge, and logistic regression; ROC curves and measures of binary classification; nonlinear regression (including an introduction to gradient descent); classification and regression trees; random forests; neural networks; probabilistic methods (KNN, naive Bayes', QDA, LDA); dimensionality reduction with PCA; support vector machines; and clustering with K-Means, hierarchical, and DBScan. Appendices provide a review of probability and linear algebra. While some mathematical foundation is provided, it is not essential for understanding the implementations. The target audience is advanced community college and university students. -
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Zika-RNAseq-Pipeline
An open RNA-Seq data analysis pipeline tutorial
...The pipeline uses state-of-the-art tools and can run on various platforms with minimal configuration overhead. The pipeline enables the extraction of knowledge from typical RNA-seq studies by generating interactive principal component analysis (PCA) and hierarchical clustering (HC) plots, performing enrichment analyses against over 90 gene set libraries, and obtaining lists of small molecules that are predicted to either mimic or reverse the observed changes in mRNA expression. -
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Ganglia
Scalable, distributed monitoring system for high-performance computing
Ganglia is a scalable distributed monitoring system for high-performance computing systems such as clusters and Grids. It is based on a hierarchical design targeted at federations of clusters. Supports clusters up to 2000 nodes in size. -
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CPAG
Cross-Phenotype Analysis of GWAS
CPAG (Cross-Phenotype Analysis of GWAS) can estimate disease and trait similarity, identify informative disease clusters, and carry out pathway enrichment analysis. It also provides visualization of these results in the form of hierarchical clustering trees, heatmaps, and networks. -
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HClust
Hierarchical clustering package
A simple java package to create clusters (in a tree form) of multi-dimensional data points based on euclidean distances. -
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JClassifier
Java data mining library and application
Java data mining library for multi-class one nearest neighbor classification and vector quantization by optimized dimension-wise hierarchical clustering to reduce data. The application can process LibSVM files. -
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DEC routing protocol for WSN
A Deterministic Energy-efficient Clustering protocol for WSN
...It is worthy of note that our approach approximates an ideal solution for balanced energy consumption in hierarchical wireless sensor networks. -
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Efficient analysis of complex networks using hierarchical clustering. If you use Jerarca, please cite: Aldecoa R, Marín I (2010) Jerarca: Efficient analysis of complex networks using hierarchical clustering PLoS ONE 5(7): e11585
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Visualization of Mappings between the Gene Ontology and Cluster Trees
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The final build of this software now is distributed in R, embedded in "RedeR': an R/Bioconductor package for hierarchical and nested network analysis... more about RedeR: http://bioconductor.org/packages/2.9/bioc/html/RedeR.html
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Probabilistic biclustering method for protein complex identification using quantitative AP-MS data. Implementation of plain and hierarchical form of Dirichlet process priors for two-stage clustering.
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brCluster is a class library, written in java, that implements generic clustering algorithms carefully designed to allow its aplication in any kind of data. The algorithms implemented are K-means and Hierarchical Clustering (Simple and Complete Link).
