Search Results for "bipartite"
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Showing 9 open source projects for "bipartite"
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MultilayerGraphs.jl
Julia package for the creation and analysis of multilayer graphs
MultilayerGraphs.jl is a Julia package for the creation, manipulation and analysis of the structure, dynamics and functions of multilayer graphs. A multilayer graph is a graph consisting of multiple standard subgraphs called layers which can be interconnected through bipartite graphs called interlayers composed of the vertex sets of two different layers and the edges between them. The vertices in each layer represent a single set of nodes, although not all nodes have to be represented in every layer. -
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GANformer
Generative Adversarial Transformers
This is an implementation of the GANformer model, a novel and efficient type of transformer, explored for the task of image generation. The network employs a bipartite structure that enables long-range interactions across the image, while maintaining computation of linearly efficiency, that can readily scale to high-resolution synthesis. The model iteratively propagates information from a set of latent variables to the evolving visual features and vice versa, to support the refinement of each in light of the other and encourage the emergence of compositional representations of objects and scenes. ... -
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DETR
End-to-end object detection with transformers
...Unlike traditional computer vision techniques, DETR approaches object detection as a direct set prediction problem. It consists of a set-based global loss, which forces unique predictions via bipartite matching, and a Transformer encoder-decoder architecture. Given a fixed small set of learned object queries, DETR reasons about the relations of the objects and the global image context to directly output the final set of predictions in parallel. Due to this parallel nature, DETR is very fast and efficient. -
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AccNET
AccNET: Accessory Genome Constellation Network.
AccNET is a Perl application that presents a new way to study the accessory genome of a given set of organisms. Using the proteomes of these organisms, AccNET create a bipartite network compatible with common network analysis platforms. AccNET collects phylogenetic and functional information in a network improving the analysis capability. Networks offer a new perspective of organism organization through elements acquired by horizontal gene transfers and not constricted by hierarchical structures. AccNET has moved to GitHub Repository: https://github.com/valflanza/accnet -
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Satsuma .NET Graph Library
a delicious .NET graph library
Satsuma is a graph library for .NET, written in C#. Satsuma is an easy-to-use and flexible library, which implements all the necessary graph structures, and the fastest possible graph algorithms. DOCUMENTATION: http://satsumagraph.sourceforge.net/ Satsuma is not a charting library. 'Graph' is used in the mathematical sense here (e.g. nodes connected with arcs). Satsuma is released under the zlib license. This license is very permissive and allows you to use Satsuma for both personal... -
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program.MODULAR
MODULAR: Autonomous Computation of Modularity
MODULAR is a software developed to perform rapid and automatic calculation of modularity in sets of networks. MODULAR reads a set of text files with bipartite or adjacency binary matrices representing networks. The software can identify and define modules by two different modularity metrics widely used in studies with different types of networks such as social, ecological and biochemical networks. In order to find the network partition that maximizes modularity, the software offers five optimization methods to the user: simulated annealing, fast greedy, spectral partitioning, a hybrid of fast greedy and simulated annealing, and a hybrid of spectral partitioning and simulated annealing. ... -
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RT-alignment
Graph-based time alignment algorithms for multiple LC-MS datasets
Liquid chromatography coupled to mass spectrometry (LC-MS) is the dominant technological platform for proteomics. An LC-MS analysis of a complex biological sample can be visualized as a “map” of which the positional coordinates are the mass-to-charge ratio (m/z) and chromatographic retention time (RT) of the chemical species profiled. Label-free quantitative-proteomics requires the alignment and comparison of multiple LC-MS maps to ascertain the reproducibility of experiments or reveal... -
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AlertWheel
AlertWheel is a visualization-based analysis tool for Snort IDS logs
...It is based on a novel radial visualization capable of simultaneously displaying several thousand alerts, emphasizing the most important alerts or patterns in the dataset. Among other things, AlertWheel offers a new technique for representing bipartite graphs (where links exist between two distinct node groups). Using this approach, links are positioned in a way to reduce occlusion in the visualization. AlertWheel simultaneously combines three link bundling techniques in a novel way to reduce cluttering on the interface. Our solution also incorporates filtering options, annotation, logging and details-on-demand, to support analysis processes as described by specialists in this field. ... -
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AMBIENT
Find active modules in metabolic networks using high-throughput data
...If you wish to use the version used in the paper it is v0.6.3, however I recommend using the latest version which works in the same way but with additional options and has stability and performance improvements. Thanks for your interest! AMBIENT (Active Modules for Bipartite Networks) is a Python module that uses simulated annealing to find areas of a metabolic network (modules) that have some consistent characteristic. AMBIENT does not require predefined pathways and gives highly specific predictions of affected areas of metabolism. For example, scores for reactions based on transcriptional data of their annotated encoding genes can be used in the network and modules of coordinated expression changes can be found. ... -
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