Sontag Lab (@clinicalml)
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clinicalml

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Top repositories

1

cfrnet

Counterfactual Regression
Python
261
star
2

structuredinference

Structured Inference Networks for Nonlinear State Space Models
Jupyter Notebook
255
star
3

embeddings

Code for AMIA CRI 2016 paper "Learning Low-Dimensional Representations of Medical Concepts"
Python
233
star
4

TabLLM

Python
162
star
5

dmm

Deep Markov Models
Jupyter Notebook
127
star
6

deepDiagnosis

A torch package for learning diagnosis models from temporal patient data.
Lua
110
star
7

HealthKnowledgeGraph

Health knowledge graph for 157 diseases and 491 symptoms, learned from >270,000 patients' data
96
star
8

co-llm

Co-LLM: Learning to Decode Collaboratively with Multiple Language Models
Python
87
star
9

omop-learn

Python package for machine learning for healthcare using a OMOP common data model
Python
86
star
10

prancer

Platform enabling Rapid Annotation for Clinical Entity Recognition
JavaScript
48
star
11

gumbel-max-scm

Code for "Counterfactual Off-Policy Evaluation with Gumbel-Max Structural Causal Models" (ICML 2019)
Python
39
star
12

ML-tools

Miscellaneous tools for clinical ML
Python
30
star
13

human_ai_deferral

Human-AI Deferral Evaluation Benchmark (Learning to Defer) AISTATS23
Python
18
star
14

anchorExplorer

Python
17
star
15

trajectory-inspection

Code for "Trajectory Inspection: A Method for Iterative Clinician-Driven Design of Reinforcement Learning Studies"
Jupyter Notebook
16
star
16

cotrain-prompting

Code for co-training large language models (e.g. T0) with smaller ones (e.g. BERT) to boost few-shot performance
Python
15
star
17

ContextualAutocomplete_MLHC2020

Code for Contextual Autocomplete paper published in MLHC2020
Jupyter Notebook
13
star
18

realhumaneval

Jupyter Notebook
12
star
19

teaching-to-understand-ai

Code and webpages for our study on teaching humans to defer to an AI
Jupyter Notebook
11
star
20

dgm

Deep Generative Model (Torch)
Lua
11
star
21

learn-to-defer

Code for "Consistent Estimators for Learning to Defer to an Expert" (ICML 2020)
Jupyter Notebook
11
star
22

sc-foundation-eval

Code for evaluating single cell foundation models scBERT and scGPT
Jupyter Notebook
10
star
23

SparsityBoost

http://cs.nyu.edu/~dsontag/papers/BrennerSontag_uai13.pdf
Python
10
star
24

proxy-anchor-regression

Code for ICML 2021 paper "Regularizing towards Causal Invariance: Linear Models with Proxies" (ICML 2021)
Jupyter Notebook
10
star
25

onboarding_human_ai

Onboarding Humans to work with AI: Algorithms to find regions and describe them in natural language that show how humans should collaborate with AI (NeurIPS23)
Jupyter Notebook
10
star
26

vae_ssl

Scalable semi-supervised learning with deep variational autoencoders
Jupyter Notebook
9
star
27

amr-uti-stm

Code for "A decision algorithm to promote outpatient antimicrobial stewardship for uncomplicated urinary tract infection"
Python
8
star
28

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.
R
8
star
29

mimic-language-model

A conditional language model for MIMIC-III.
Python
8
star
30

ml_mmrf

Machine Learning with data from the Multiple Myeloma Research Foundation
Jupyter Notebook
7
star
31

overparam

Python
6
star
32

ckd_progression

Python
6
star
33

parametric-robustness-evaluation

Code for paper "Evaluating Robustness to Dataset Shift via Parametric Robustness Sets"
Python
5
star
34

active_learn_to_defer

Code for Sample Efficient Learning of Predictors that Complement Humans (ICML 2022)
Python
5
star
35

surprising-sepsis

Python
4
star
36

large-scale-temporal-shift-study

Code for Large-Scale Study of Temporal Shift in Health Insurance Claims. Christina X Ji, Ahmed M Alaa, David Sontag. CHIL, 2023. https://arxiv.org/abs/2305.05087
Python
4
star
37

amr-uti-kdd

Treatment Policy Learning in Multiobjective Settings with Fully Observed Outcomes (KDD 2020)
Python
4
star
38

theanomodels

A lightweight wrapper around theano for rapid-prototyping of models
Python
3
star
39

clinical-anchors

Python
3
star
40

finding-decision-heterogeneity-regions

Code for "Finding Regions of Heterogeneity in Decision-Making via Expected Conditional Covariance" at NeurIPS 2021
Jupyter Notebook
3
star
41

fully-observed-policy-learning

Code for "Treatment Policy Learning in Multiobjective Settings with Fully Observed Outcomes" (KDD 2020)
Jupyter Notebook
3
star
42

mimic_annotations

2
star
43

fw-inference

Barrier Frank-Wolfe for Marginal Inference
C++
2
star
44

oncology_rationale_extraction

Functionality from "Automated NLP extraction of clinical rationale for treatment discontinuation in breast cancer"
Python
2
star
45

overlap-code

Code for "Characterization of Overlap in Observational Studies" (AISTATS 2020)
Python
2
star
46

omop-variation

Tools to identify and evaluate heterogeneity in decision-making processes.
Python
2
star
47

clinicalml-scBERT-NMI

analysis code to reproduce results in NMI submission
Jupyter Notebook
1
star
48

rct-obs-extrapolation

Code for paper, "Falsification before Extrapolation in Causal Effect Estimation"
Jupyter Notebook
1
star