Sontag Lab

structuredinference

Structured Inference Networks for Nonlinear State Space Models

embeddings

Code for AMIA CRI 2016 paper "Learning Low-Dimensional Representations of Medical Concepts"

dmm

Deep Markov Models

deepDiagnosis

A torch package for learning diagnosis models from temporal patient data.

HealthKnowledgeGraph

Health knowledge graph for 157 diseases and 491 symptoms, learned from >270,000 patients' data

gumbel-max-scm

Code for "Counterfactual Off-Policy Evaluation with Gumbel-Max Structural Causal Models" (ICML 2019)

ML-tools

Miscellaneous tools for clinical ML

anchorExplorer

trajectory-inspection

Code for "Trajectory Inspection: A Method for Iterative Clinician-Driven Design of Reinforcement Learning Studies"

dgm

Deep Generative Model (Torch)

amr-uti-stm

Code for "A decision algorithm to promote outpatient antimicrobial stewardship for uncomplicated urinary tract infection"

dgc_predict

Applies and evaluates a variety of methods to complete a partially-observed data tensor, e.g. comprising gene expression profiles corresponding to various drugs, applied in various cellular contexts.

mimic-language-model

A conditional language model for MIMIC-III.

ckd_progression

overparam

amr-uti-kdd

Treatment Policy Learning in Multiobjective Settings with Fully Observed Outcomes (KDD 2020)

mimicnotes

Concept extraction from MIMIC3 notes

CommonDataModel

Definition and DDLs for the OMOP Common Data Model (CDM)

mimic_annotations

surprising-sepsis

clinical-anchors

fully-observed-policy-learning

Code for "Treatment Policy Learning in Multiobjective Settings with Fully Observed Outcomes" (KDD 2020)

theanomodels

A lightweight wrapper around theano for rapid-prototyping of models

fw-inference

Barrier Frank-Wolfe for Marginal Inference

oncology_rationale_extraction

Functionality from "Automated NLP extraction of clinical rationale for treatment discontinuation in breast cancer"

overlap-code

Code for "Characterization of Overlap in Observational Studies" (AISTATS 2020)

eicu-code

Code shared by the research community for the eICU Collaborative Research Database

noise-estimation

Methods to estimate noise rates of classifiers

parkinsons-disease-progression-modeling

Code for Christina X Ji's MEng thesis: Modeling progression of Parkinson's disease https://dspace.mit.edu/handle/1721.1/124250

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