RANKS: Ranking of Nodes with Kernelized Score Functions
Implementation of Kernelized score functions and other semi-supervised learning algorithms for node label ranking in 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.
- Giorgio Valentini -- AnacletoLab, Dipartimento di Informatica, Universita' degli Studi di Milano
- Date of publication
- 2015-12-10 10:04:15
- Giorgio Valentini <email@example.com>
- GPL (>= 2)
- GBA cross-validation experiments with multiple classes
- RANKS leave-one-out experiments with multiple classes
- RANKS cross-validation experiments with multiple classes
- Random walk cross-validation experiments with multiple...
- Random walk with restart cross-validation experiments with...
- Function to find the optimal RANKS score thereshold
- Guilt By Association (GBA) using the maximum rule
- Guilt By Association (GBA) using the sum rule
- Kernel functions
- Multiple cross-validation with RANKS for classification
- RANKS held-out procedure for a single class
- RANKS cross-validation for a single class
- Label propagation
- RANKS multiple cross-validation for a single class
- Function for RANKS multiple cross-validation and optimal...
- Random walk, GBA and labelprop multiple cross-validation for...
- Random walk on a graph
- Random walk, GBA and labelprop cross-validation for a single...
- Random walk kernel
- Random walk with Restart on a graph
- Multiple vertex score functions
- Single vertex score functions
- Utility functions
Files in this package