Prof. Yanjun Qi, PhD @ UVA (email: yanjun at virginia.edu)   

Group GitHub Code Repos / Tool Sharing / Webservices

Tool Sharing through paper supplement websites

Name (+Description) Site
GaKCo-SVM:
GaKCo: a Fast Gapped k-mer string Kernel using Counting
(Site)
FeatureSqueezing:
A novel TensorFlow toolbox for Detecting Adversarial Examples in Deep Neural Networks
(Site)
SIMULE R:
A novel R toolbox for a constrained L1 minimization approach for estimating multiple Sparse Gaussian or Nonparanormal Graphical Models
(Site)
FASJEM R:
A novel R toolbox for A Fast and Scalable Joint Estimator for Learning Multiple Related Sparse Gaussian Graphical Models by AISTAT 2017
(Site)
DeepChrome:
Deep-learning for predicting gene expression from histone modifications .
(Site)
DeepMotif:
Deep Motif Dashboard (PSB17): Visualizing Genomic Sequence Classifications.
(Site)
MUST-CNN :
DeepLearning4BioSeqText : A novel CNN toolbox - MUST-CNN: A Multilayer Shift-and-Stitch Deep Convolutional Architecture for Sequence-based Tagging
(Site)
DeepMultiProtein:
DeepLearning4BioSeqText : Multitask Deep Learning based Toolbox for Large-scale protein local structure labeling
(Download)
(GIT)
(bibTex)
EvadeML:
Automatically Evading Classifiers using Genetic Algorithm
(Site)
(GitSite)
MetricCancer:
Metric Learning for Cancer Diagnosis using High-Dimensional Molecular Profiling Data
(Site)
GGMFactors:
DataFusion4NetBio : Learning the Dependency Structure (sparse Gaussian Graphical model) among Latent Factors
(Site)
(bibTex)
SupervisedComplex:
DataFusion4NetBio : Code for Detecting Protein Complex (i.e. Group) Detection from Protein Interaction Graph
(Download)
(Site)
SupervisedPPI:
DataFusion4NetBio : Standalone toolbox for Human Protein-Protein Interaction (PPI) Prediction
(Download)
(Site)
YeastPPI:
DataFusion4NetBio : Feature Generation Package for Yeast Protein-Protein Interaction Prediction based on Information Fusion
(Download)
(site)
SupervisedHIVPPI:
DataFusion4NetBio : Data Integration Tool Package for HIV-1 vs. Human Protein-Protein Interaction Prediction based on Information Fusion
(Download)
(Site)
Random Forest Tool:
Perl Wrapper for Random Forest Fortune based Implementation
(Site)
((bibTex))
SparseLSI:
RepresentationLearning4Text : Sparse latent semenatic indexing
(Site)
((bibTex))

Webservices we provide

Name Site
DeepChrome (Site)
EvadeMachineLearning (Site)

Archived Group GitHub Repositories /
(URLMain)(OurGitBlog)

Name Site
Repos related to DataFusion-for-Network UVA DataFusion4NetBio
Repos related to RepresentationLearning-for-SequenceText UVA DeepLearning4BioSeqText
Repos related to secure machine learning UVA SecureMachineLearning
Repos related to general papers + capstone projects UVA MLBD CapstoneRepos

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