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
89
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

teaching-to-understand-ai

Code and webpages for our study on teaching humans to defer to an AI
Jupyter Notebook
11
star
19

dgm

Deep Generative Model (Torch)
Lua
11
star
20

realhumaneval

Jupyter Notebook
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