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PerfMeas - Performance Measures for Ranking and Classification Tasks

Implementation of different performance measures for classification and ranking tasks including Area Under the Receiving Characteristic Curve (AUROC) and Area Under the Precision Recall Curve (AUPRC), precision at a given recall, F-score for single and multiple classes.

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2.19 score 1 dependents 26 scripts 307 downloads

RANKS - Ranking of Nodes with Kernelized Score Functions

Implementation of Kernelized score functions and other semi-supervised learning algorithms for node label ranking to analyze biomolecular networks. RANKS can be easily applied to a large set of different relevant problems in computational biology, ranging from automatic protein function prediction, to gene disease prioritization and drug repositioning, and more in general to any bioinformatics problem that can be formalized as a node label ranking problem in a graph. The modular nature of the implementation allows to experiment with different score functions and kernels and to easily compare the results with baseline network-based methods such as label propagation and random walk algorithms, as well as to enlarge the algorithmic scheme by adding novel user-defined score functions and kernels.

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1.90 score 7 scripts 231 downloads

bionetdata - Biological and Chemical Data Networks

Data Package that includes several examples of chemical and biological data networks, i.e. data graph structured.

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1.76 score 58 scripts 254 downloads

NetPreProc - Network Pre-Processing and Normalization

Network Pre-Processing and normalization. Methods for normalizing graphs, including Chua normalization, Laplacian normalization, Binary magnification, min-max normalization and others. Methods to sparsify adjacency matrices. Methods for graph pre-processing and for filtering edges of the graph.

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1.48 score 1 dependents 2 scripts 192 downloads