Software

Natural Language Processing

  • NILE
    Fast natural language processing for electronic health records
  • EXTEND [ GitHub ]
    Extraction of numerical data from electronic medical records
  • CHANL [ GitHub ]
    Chart review tool powered by natural language processing

Electronic Health Records

  • PheCAP [ GitHub | CRAN ]
    High-throughput phenotyping using a common semi-supervised approach
  • PheNorm [ GitHub | CRAN ]
    Phenotyping algorithm that does not require expert-labeled samples for training
  • MAP [ GitHub | CRAN ]
    High-throughput multimodal automated phenotyping
  • sureLDA [ GitHub | CRAN ]
    Multidisease automated phenotyping method for the electronic health records
  • KESER [ GitHub ]
    Clinical knowledge extraction via sparse embedding regression
  • SCORNET [ GitHub | CRAN ]
    Semi-supervised calibration of risk with noisy event times
  • SAMGEP [ GitHub | CRAN ]
    Semi-supervised adaptive Markov Gaussian embedding process
  • MASTA [ GitHub ]
    Multi-modal automated survival time annotation

High Dimensional Inference

  • StructureMC [ GitHub | CRAN ]
    Structured matrix completion with applications to genomic data integration
  • solid [ GitHub ]
    Divide-and-conquer method for sparse risk prediction and evaluation
  • dcalasso [ GitHub ]
    Fast divide-and-conquer sparse Cox regression
  • SRAT [ GitHub ]
    Sequence robust association test for familial data

Survival Analysis

Surrogate Marker