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@chiragnagpal
chiragnagpal committed Mar 2, 2022
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4 changes: 4 additions & 0 deletions auton_survival/phenotyping.py
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Expand Up @@ -397,3 +397,7 @@ def fit_phenotype(self, features):

return self.fit(features).phenotype(features)

class CoxMixturePhenotyper:

def __init__(self):
raise NotImplementedError()
68 changes: 49 additions & 19 deletions docs/datasets.html
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Expand Up @@ -3,8 +3,8 @@
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1, minimum-scale=1" />
<meta name="generator" content="pdoc 0.9.1" />
<title>dsm.datasets API documentation</title>
<meta name="generator" content="pdoc 0.9.2" />
<title>auton_survival.datasets API documentation</title>
<meta name="description" content="Utility functions to load standard datasets to train and evaluate the
Deep Survival Machines models." />
<link rel="preload stylesheet" as="style" href="https://cdnjs.cloudflare.com/ajax/libs/10up-sanitize.css/11.0.1/sanitize.min.css" integrity="sha256-PK9q560IAAa6WVRRh76LtCaI8pjTJ2z11v0miyNNjrs=" crossorigin>
Expand All @@ -25,12 +25,14 @@
<main>
<article id="content">
<header>
<h1 class="title">Module <code>dsm.datasets</code></h1>
<h1 class="title">Module <code>auton_survival.datasets</code></h1>
</header>
<section id="section-intro">
<p>Utility functions to load standard datasets to train and evaluate the
Deep Survival Machines models.</p>
<div class="git-link-div"><a href="https://github.com/autonlab/DeepSurvivalMachines" class="git-link">Browse git</a></div>
<div class="git-link-div"><a href="https://github.com/autonlab/auton-survival" class="git-link">Browse git</a></div>
</section>
<section>
</section>
<section>
</section>
Expand All @@ -39,19 +41,41 @@ <h1 class="title">Module <code>dsm.datasets</code></h1>
<section>
<h2 class="section-title" id="header-functions">Functions</h2>
<dl>
<dt id="dsm.datasets.increase_censoring"><code class="name flex">
<dt id="auton_survival.datasets.increase_censoring"><code class="name flex">
<span>def <span class="ident">increase_censoring</span></span>(<span>e, t, p)</span>
</code></dt>
<dd>
<div class="desc"></div>
<div class="git-link-div"><a href="https://github.com/autonlab/DeepSurvivalMachines" class="git-link">Browse git</a></div>
<div class="git-link-div"><a href="https://github.com/autonlab/auton-survival" class="git-link">Browse git</a></div>
</dd>
<dt id="dsm.datasets.load_dataset"><code class="name flex">
<dt id="auton_survival.datasets.load_support"><code class="name flex">
<span>def <span class="ident">load_support</span></span>(<span>)</span>
</code></dt>
<dd>
<div class="desc"><p>Helper function to load and preprocess the SUPPORT dataset.
The SUPPORT Dataset comes from the Vanderbilt University study
to estimate survival for seriously ill hospitalized adults [1].
Please refer to <a href="http://biostat.mc.vanderbilt.edu/wiki/Main/SupportDesc.">http://biostat.mc.vanderbilt.edu/wiki/Main/SupportDesc.</a>
for the original datasource.</p>
<h2 id="references">References</h2>
<p>[1]: Knaus WA, Harrell FE, Lynn J et al. (1995): The SUPPORT prognostic
model: Objective estimates of survival for seriously ill hospitalized
adults. Annals of Internal Medicine 122:191-203.</p></div>
<div class="git-link-div"><a href="https://github.com/autonlab/auton-survival" class="git-link">Browse git</a></div>
</dd>
<dt id="auton_survival.datasets.load_synthetic_cf_phenotyping"><code class="name flex">
<span>def <span class="ident">load_synthetic_cf_phenotyping</span></span>(<span>)</span>
</code></dt>
<dd>
<div class="desc"></div>
<div class="git-link-div"><a href="https://github.com/autonlab/auton-survival" class="git-link">Browse git</a></div>
</dd>
<dt id="auton_survival.datasets.load_dataset"><code class="name flex">
<span>def <span class="ident">load_dataset</span></span>(<span>dataset='SUPPORT', **kwargs)</span>
</code></dt>
<dd>
<div class="desc"><p>Helper function to load datasets to test Survival Analysis models.</p>
<p>Currently implemented datasets include:</p>
<div class="desc"><p>Helper function to load datasets to test Survival Analysis models.
Currently implemented datasets include:</p>
<p><strong>SUPPORT</strong>: This dataset comes from the Vanderbilt University study
to estimate survival for seriously ill hospitalized adults [1].
(Refer to <a href="http://biostat.mc.vanderbilt.edu/wiki/Main/SupportDesc.">http://biostat.mc.vanderbilt.edu/wiki/Main/SupportDesc.</a>
Expand All @@ -63,6 +87,9 @@ <h2 class="section-title" id="header-functions">Functions</h2>
known, ongoing Framingham Heart study [3] for studying epidemiology for
hypertensive and arteriosclerotic cardiovascular disease. It is a popular
dataset for longitudinal survival analysis with time dependent covariates.</p>
<p><strong>SYNTHETIC</strong>: This is a non-linear censored dataset for counterfactual
time-to-event phenotyping. Introduced in [4], the dataset is generated
such that the treatment effect is heterogenous conditioned on the covariates.</p>
<h2 id="references">References</h2>
<p>[1]: Knaus WA, Harrell FE, Lynn J et al. (1995): The SUPPORT prognostic
model: Objective estimates of survival for seriously ill hospitalized
Expand All @@ -72,6 +99,8 @@ <h2 id="references">References</h2>
<p>[3] Dawber, Thomas R., Gilcin F. Meadors, and Felix E. Moore Jr.
"Epidemiological approaches to heart disease: the Framingham Study."
American Journal of Public Health and the Nations Health 41.3 (1951).</p>
<p>[4] Nagpal, C., Goswami M., Dufendach K., and Artur Dubrawski.
"Counterfactual phenotyping for censored Time-to-Events" (2022).</p>
<h2 id="parameters">Parameters</h2>
<dl>
<dt><strong><code>dataset</code></strong> :&ensp;<code>str</code></dt>
Expand All @@ -83,39 +112,40 @@ <h2 id="parameters">Parameters</h2>
<h2 id="returns">Returns</h2>
<dl>
<dt><strong><code>tuple</code></strong> :&ensp;<code>(np.ndarray, np.ndarray, np.ndarray)</code></dt>
<dd>A tuple of the form of (x, t, e) where x, t, e are the input covariates,
event times and the censoring indicators respectively.</dd>
<dd>A tuple of the form of <span><span class="MathJax_Preview"> (x, t, e) </span><script type="math/tex"> (x, t, e) </script></span> where <span><span class="MathJax_Preview"> x </span><script type="math/tex"> x </script></span>
are the input covariates, <span><span class="MathJax_Preview"> t </span><script type="math/tex"> t </script></span> the event times and
<span><span class="MathJax_Preview"> e </span><script type="math/tex"> e </script></span> the censoring indicators.</dd>
</dl></div>
<div class="git-link-div"><a href="https://github.com/autonlab/DeepSurvivalMachines" class="git-link">Browse git</a></div>
<div class="git-link-div"><a href="https://github.com/autonlab/auton-survival" class="git-link">Browse git</a></div>
</dd>
</dl>
</section>
<section>
</section>
</article>
<nav id="sidebar">
<img src="https://ndownloader.figshare.com/files/26367844">
<img src="https://ndownloader.figshare.com/files/34052981">
<h1>Index</h1>
<div class="toc">
<ul></ul>
</div>
<ul id="index">
<li><h3>Super-module</h3>
<ul>
<li><code><a title="dsm" href="index.html">dsm</a></code></li>
<li><code><a title="auton_survival" href="index.html">auton_survival</a></code></li>
</ul>
</li>
<li><h3><a href="#header-functions">Functions</a></h3>
<ul class="">
<li><code><a title="dsm.datasets.increase_censoring" href="#dsm.datasets.increase_censoring">increase_censoring</a></code></li>
<li><code><a title="dsm.datasets.load_dataset" href="#dsm.datasets.load_dataset">load_dataset</a></code></li>
<li><code><a title="auton_survival.datasets.increase_censoring" href="#auton_survival.datasets.increase_censoring">increase_censoring</a></code></li>
<li><code><a title="auton_survival.datasets.load_support" href="#auton_survival.datasets.load_support">load_support</a></code></li>
<li><code><a title="auton_survival.datasets.load_synthetic_cf_phenotyping" href="#auton_survival.datasets.load_synthetic_cf_phenotyping">load_synthetic_cf_phenotyping</a></code></li>
<li><code><a title="auton_survival.datasets.load_dataset" href="#auton_survival.datasets.load_dataset">load_dataset</a></code></li>
</ul>
</li>
</ul>
</nav>
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