• ANFIS

  • Referenced in 285 articles [sw08730]
  • ANFIS: adaptive-network-based fuzzy inference system. The architecture and learning procedure underlying ANFIS (adaptive ... network-based fuzzy inference system) is presented, which is a fuzzy inference system implemented...
  • bnlearn

  • Referenced in 78 articles [sw08265]
  • network structure learning, parameter learning and inference. Bayesian network structure learning, parameter learning and inference ... learning algorithms for both discrete and Gaussian networks, along with many score functions and conditional ... parameter estimation (maximum likelihood and Bayesian) and inference, conditional probability queries and cross-validation. Development...
  • REVEAL

  • Referenced in 29 articles [sw36999]
  • general reverse engineering algorithm for inference of genetic network architectures. Given the immanent gene expression ... seek computational methods to maximize functional inference from such large data sets ... possible, in principle, to completely infer a complex regulatory network architecture from input/output patterns ... infer the sets of input elements controlling each element or gene in the network. This...
  • Cytoscape

  • Referenced in 81 articles [sw09080]
  • other molecular states; and to link the network to databases of functional annotations. The Core ... recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium...
  • GeneNetWeaver

  • Referenced in 13 articles [sw22862]
  • benchmark generation and performance profiling of network inference methods. We are using in vivo microarray ... data to assess the performance of network inference methods in the DREAM challenge...
  • ARACNE

  • Referenced in 38 articles [sw17200]
  • enough to address a wider range of network deconvolution problems. This method uses an information ... interactions inferred by co-expression methods. Results: We prove that ARACNE reconstructs the network exactly ... genetic networks in human B cells demonstrates ARACNE’s ability to infer validated transcriptional targets ... effects of misestimation of mutual information on network reconstruction, and show that algorithms based...
  • Tuffy

  • Referenced in 13 articles [sw28901]
  • open-source Markov Logic Network inference engine, and part of Felix. Markov Logic Networks (MLNs ... data management techniques, Tuffy is an MLN inference engine that achieves scalability and orders...
  • NETWORKINFERENCE

  • Referenced in 8 articles [sw06744]
  • approach for testing the accuracy of network inference algorithms by applying them to biologically realistic ... influence the ability of our Bayesian network inference algorithm, NETWORKINFERENCE, to recover gene regulatory networks ... elucidate the possibilities and limitations of network inference based on biological data...
  • minet

  • Referenced in 8 articles [sw08432]
  • minet: A R/Bioconductor Package for Inferring Large Transcriptional Networks Using Mutual Information. Results: This paper ... functions to infer mutual information networks from a dataset. Once fed with a microarray dataset ... curves in order to compare the inferred network with a reference one. Conclusion: The package ... provides a series of tools for inferring transcriptional networks from microarray data. It is freely...
  • epinet

  • Referenced in 14 articles [sw24733]
  • diseases through contact networks. Performs Bayesian inference on network and epidemic parameters, given epidemic data...
  • PyHawkes

  • Referenced in 13 articles [sw26587]
  • variety of Bayesian inference algorithms for discovering latent network structure given point process observations. Suppose ... connected to one another. You might infer that there is an unobserved connection from ... Hawkes processes) with random network models and performing Bayesian inference to discover the latent network...
  • TIGRESS

  • Referenced in 9 articles [sw23826]
  • using Stability Selection. BACKGROUND: Inferring the structure of gene regulatory networks (GRN) from a collection ... RESULTS: In this paper, we formulate GRN inference as a sparse regression problem and investigate ... inference methods in the DREAM5 gene network inference challenge. In particular, TIGRESS was evaluated ... cerevisiae) networks. This study confirms the potential of feature selection techniques for GRN inference. Code...
  • SIRENE

  • Referenced in 7 articles [sw17419]
  • SIRENE: Supervised inference of regulatory networks. Motivation: Living cells are the product of gene expression ... methods have been proposed to infer gene regulatory networks from gene expression data, a recent ... Results: We propose SIRENE (Supervised Inference of Regulatory Networks), a new method for the inference ... decomposes the problem of gene regulatory network inference into a large number of local binary...
  • WEBWEAVR-III

  • Referenced in 8 articles [sw05619]
  • that supports the construction of Bayesian networks, inference in standard and dynamic Bayesian networks ... verification of multiply sectioned Bayesian networks (MSBNs), inference in multi-agent MSBNs, and learning decomposable...
  • GeneNet

  • Referenced in 9 articles [sw07992]
  • GeneNet: Modeling and Inferring Gene Networks. GeneNet is a package for analyzing gene expression (time ... data with focus on the inference of gene networks. In particular, GeneNet implements the methods...
  • Gazelle

  • Referenced in 5 articles [sw38099]
  • Latency Framework for Secure Neural Network Inference. The growing popularity of cloud-based machine learning ... classify private images using a convolutional neural network (CNN) trained by a server. Our goal ... latency system for secure neural network inference, using an intricate combination of homomorphic encryption ... enable implementation of complete neural network inference. We evaluate our protocols on benchmark neural networks...
  • catnet

  • Referenced in 6 articles [sw08170]
  • package catnet: Categorical Bayesian Network Inference. A package that handles discrete Bayesian network models...
  • DREAM4

  • Referenced in 5 articles [sw36908]
  • DREAM4 100-gene in-silico network inference challenge. We demonstrate complementarity between this method ... performance of multiple methods for network inference suggests avenues for future methods development and provides...
  • NetKit

  • Referenced in 27 articles [sw22730]
  • case-study of its application to networked data used in prior machine learning research. NetKit ... sifier, a relational classifier, and a collective inference procedure...
  • NARROMI

  • Referenced in 6 articles [sw24066]
  • technique improves accuracy of gene regulatory network inference. MOTIVATION: Reconstruction of gene regulatory networks (GRNs ... NARROMI, to improve the accuracy of GRN inference by combining ordinary differential equation-based recursive...