Metadata-Version: 2.1
Name: temporai
Version: 0.0.0
Summary: TemporAI: ML-centric Toolkit for Medical Time Series
Home-page: https://www.vanderschaar-lab.com/
Author: Evgeny Saveliev
Author-email: e.s.saveliev@gmail.com
License: Apache-2.0 license
Project-URL: Documentation, https://pyscaffold.org/
Platform: any
Classifier: Development Status :: 4 - Beta
Classifier: Programming Language :: Python
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# <img src="docs/assets/TemporAI_Logo_Icon.png" height=25> TemporAI

> **⚠️ Status**: **Work in progress, please come back at a later date.** We are migrating from a [previous iteration of the project](https://github.com/vanderschaarlab/clairvoyance).

*TemporAI* is a Machine Learning-centric time-series library for medicine.  The tasks that are currently of focus in TemporAI are: time-series prediction, time-to-event (a.k.a. survival) analysis with time-series data, and counterfactual inference (i.e. \[individualized\] treatment effects).  The library also aims to provide the user with understanding of their data, model, and problem, through e.g. integration with interpretability methods.

Key concepts:

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## Installation

[PiPy](https://pypi.org/) release is coming soon, for now install directly from the repository as follows:

```
pip install git+https://github.com/vanderschaarlab/temporai.git
```

To view the list of dependencies, see [here](./setup.cfg#L50).



<!--
## Models

**Time Series Prediction (Forecasting)**

| Model &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; | Affiliation &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp; &nbsp; &nbsp; &nbsp; | Paper | Status &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; |
| ----- | ----------- | ----- | ------ |
| A version of LSTM | Classic method | [📄](https://ieeexplore.ieee.org/abstract/document/6795963) | ✔️ Available |
| A version of GRU | Classic method | [📄](https://arxiv.org/abs/1409.1259) | ✔️ Available |
| A version of Seq2Seq | Classic method | [📄](https://proceedings.neurips.cc/paper/2014/hash/a14ac55a4f27472c5d894ec1c3c743d2-Abstract.html) | ✔️ Available |
| [NeuralLaplace](https://github.com/samholt/NeuralLaplace) | [van der Schaar Lab] | [📄](https://proceedings.mlr.press/v162/holt22a.html) | 🔵 Planned |

**Time Series Imputation**

| Model &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; | Affiliation &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp; &nbsp; &nbsp; &nbsp; | Paper | Status &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; |
| ----- | ----------- | ----- | ------ |
| `{f,b}fill` & Mean | Classic method(s) | N/A | ✔️ Available |
| [HyperImpute](https://github.com/vanderschaarlab/HyperImpute) | [van der Schaar Lab] | [📄](https://proceedings.mlr.press/v162/jarrett22a/jarrett22a.pdf) | 🔵 Planned

**Temporal Treatment Effects**

| Model &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; | Affiliation &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp; &nbsp; &nbsp; &nbsp; | Paper | Status &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; |
| ----- | ----------- | ----- | ------ |
| [CRN](https://github.com/vanderschaarlab/mlforhealthlabpub/tree/main/alg/counterfactual_recurrent_network) | [van der Schaar Lab] | [📄](https://openreview.net/forum?id=BJg866NFvB) | ✔️ Available |
| [SyncTwin](https://github.com/vanderschaarlab/SyncTwin-NeurIPS-2021/) | [van der Schaar Lab] | [📄](https://proceedings.neurips.cc/paper/2021/hash/19485224d128528da1602ca47383f078-Abstract.html) | ➰ Experimental |
| [TE-CDE](https://github.com/vanderschaarlab/TE-CDE/) | [van der Schaar Lab] | [📄](https://proceedings.mlr.press/v162/seedat22b/seedat22b.pdf) | 🔵 Planned |

**Temporal Survival Analysis**

| Model &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; | Affiliation &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp; &nbsp; &nbsp; &nbsp; | Paper | Status &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; |
| ----- | ----------- | ----- | ------ |
| [Dynamic DeepHit Lite](https://github.com/chl8856/prostate_temporal) | [van der Schaar Lab] | [📄](https://www.nature.com/articles/s41746-022-00659-w) | ➰ Experimental |
| [Dynamic DeepHit](https://github.com/vanderschaarlab/mlforhealthlabpub/tree/main/alg/dynamic_deephit) | [van der Schaar Lab] | [📄](https://pubmed.ncbi.nlm.nih.gov/30951460/) | 🔵 Planned |

**Interpretability**

| Model &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; | Affiliation &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp; &nbsp; &nbsp; &nbsp; | Paper | Status &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; |
| ----- | ----------- | ----- | ------ |
| [DynaMask](https://github.com/vanderschaarlab/Dynamask) | [van der Schaar Lab] | [📄](https://proceedings.mlr.press/v139/crabbe21a.html) | 🔵 Planned |

**Temporal Clustering**

| Model &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; | Affiliation &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp; &nbsp; &nbsp; &nbsp; | Paper | Status &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; |
| ----- | ----------- | ----- | ------ |
| [AC-TPC](https://github.com/vanderschaarlab/mlforhealthlabpub/tree/main/alg/ac_tpc) | [van der Schaar Lab] | [📄](https://proceedings.mlr.press/v119/lee20h.html) | 🔵 Planned |

\* `✔️ Available` & `➰ Experimental` may include some items still to be migrated from the [previous iteration of the project](https://github.com/vanderschaarlab/clairvoyance2).
-->

## TemporAI Pipeline
The diagram below illustrates the structure of a *TemporAI* pipeline:

<img src="docs/assets/Pipeline.png" alt="pipeline diagram">

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See [User Guide][docs/user_guide] for tutorials/examples.
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## Documentation

📖 See the project documentation [here](https://temporai.readthedocs.io/en/latest/).
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  [van der Schaar Lab]:    https://www.vanderschaar-lab.com/
  [docs]:                  https://temporai.readthedocs.io/en/latest/
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  [docs/user_guide]:       https://temporai.readthedocs.io/en/latest/user_guide/index.html
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