Skip to content

Commit

Permalink
Update Docs
Browse files Browse the repository at this point in the history
  • Loading branch information
chiragnagpal committed Jun 28, 2022
1 parent 78ef0dd commit 8526620
Show file tree
Hide file tree
Showing 23 changed files with 180 additions and 180 deletions.
10 changes: 5 additions & 5 deletions docs/datasets.html
Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@ <h1 class="title">Module <code>auton_survival.datasets</code></h1>
<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>
Expand All @@ -44,7 +44,7 @@ <h2 class="section-title" id="header-functions">Functions</h2>
</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="auton_survival.datasets.load_support"><code class="name flex">
<span>def <span class="ident">load_support</span></span>(<span>)</span>
Expand All @@ -59,14 +59,14 @@ <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/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="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/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="auton_survival.datasets.load_dataset"><code class="name flex">
<span>def <span class="ident">load_dataset</span></span>(<span>dataset='SUPPORT', **kwargs)</span>
Expand Down Expand Up @@ -114,7 +114,7 @@ <h2 id="returns">Returns</h2>
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>
Expand Down
16 changes: 8 additions & 8 deletions docs/estimators.html
Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,7 @@ <h1 class="title">Module <code>auton_survival.estimators</code></h1>
</header>
<section id="section-intro">
<p>Utilities to train survival regression models and estimate survival.</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>
Expand Down Expand Up @@ -73,7 +73,7 @@ <h2 id="references">References</h2>
<p>[4] Nagpal, C., Yadlowsky, S., Rostamzadeh, N., and Heller, K. (2021c).
Deep cox mixtures for survival regression.
In Machine Learning for Healthcare Conference, pages 674–708. PMLR</p></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>
<h3>Methods</h3>
<dl>
<dt id="auton_survival.estimators.SurvivalModel.fit"><code class="name flex">
Expand Down Expand Up @@ -110,7 +110,7 @@ <h2 id="returns">Returns</h2>
<dt><code>self</code></dt>
<dd>Trained instance of a survival model.</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>
<dt id="auton_survival.estimators.SurvivalModel.predict_survival"><code class="name flex">
<span>def <span class="ident">predict_survival</span></span>(<span>self, features, times)</span>
Expand All @@ -132,7 +132,7 @@ <h2 id="returns">Returns</h2>
<dd>&nbsp;</dd>
</dl>
<p>time point in times.</p></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="auton_survival.estimators.SurvivalModel.predict_risk"><code class="name flex">
<span>def <span class="ident">predict_risk</span></span>(<span>self, features, times)</span>
Expand All @@ -152,7 +152,7 @@ <h2 id="returns">Returns</h2>
<dt><code>np.array</code></dt>
<dd>numpy array of the outcome risks at each time point in times.</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>
</dd>
Expand All @@ -163,22 +163,22 @@ <h2 id="returns">Returns</h2>
<dd>
<div class="desc"><p>Universal interface to train multiple different counterfactual
survival models.</p></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>
<h3>Methods</h3>
<dl>
<dt id="auton_survival.estimators.CounterfactualSurvivalModel.predict_counterfactual_survival"><code class="name flex">
<span>def <span class="ident">predict_counterfactual_survival</span></span>(<span>self, features, times)</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="auton_survival.estimators.CounterfactualSurvivalModel.predict_counterfactual_risk"><code class="name flex">
<span>def <span class="ident">predict_counterfactual_risk</span></span>(<span>self, features, times)</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>
</dl>
</dd>
Expand Down
10 changes: 5 additions & 5 deletions docs/experiments.html
Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,7 @@ <h1 class="title">Module <code>auton_survival.experiments</code></h1>
</header>
<section id="section-intro">
<p>Utilities to perform cross-validation.</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>
Expand Down Expand Up @@ -87,7 +87,7 @@ <h2 id="references">References</h2>
[4] Nagpal, C., Yadlowsky, S., Rostamzadeh, N., and Heller, K. (2021c).
Deep cox mixtures for survival regression.
In Machine Learning for Healthcare Conference, pages 674–708. PMLR</p></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>
<h3>Methods</h3>
<dl>
<dt id="auton_survival.experiments.SurvivalRegressionCV.fit"><code class="name flex">
Expand Down Expand Up @@ -116,7 +116,7 @@ <h2 id="parameters">Parameters</h2>
</dl>
<h2 id="returns">Returns</h2>
<p>Trained survival regression model(s).</p></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>
</dd>
Expand Down Expand Up @@ -160,7 +160,7 @@ <h2 id="references">References</h2>
<p>[4] Nagpal, C., Yadlowsky, S., Rostamzadeh, N., and Heller, K. (2021c).
Deep cox mixtures for survival regression.
In Machine Learning for Healthcare Conference, pages 674–708. PMLR</p></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>
<h3>Methods</h3>
<dl>
<dt id="auton_survival.experiments.CounterfactualSurvivalRegressionCV.fit"><code class="name flex">
Expand Down Expand Up @@ -197,7 +197,7 @@ <h2 id="returns">Returns</h2>
<dt><code>auton_survival.estimators.CounterfactualSurvivalModel:</code></dt>
<dd>The trained counterfactual survival model.</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>
</dd>
Expand Down
6 changes: 3 additions & 3 deletions docs/index.html
Original file line number Diff line number Diff line change
Expand Up @@ -51,7 +51,7 @@ <h2 id="what-is-survival-analysis">What is Survival Analysis?</h2>
regression problems, Survival Analysis differs in two major ways:</p>
<ul>
<li>The Event distribution, <span><span class="MathJax_Preview"> T </span><script type="math/tex"> T </script></span> has positive support,
<span><span class="MathJax_Preview"> T in [0, \infty) </span><script type="math/tex"> T in [0, \infty) </script></span>.</li>
<span><span class="MathJax_Preview"> T \in [0, \infty) </span><script type="math/tex"> T \in [0, \infty) </script></span>.</li>
<li>There is presence of censoring (ie. a large number of instances of data are
lost to follow up.)</li>
</ul>
Expand Down Expand Up @@ -331,7 +331,7 @@ <h2 id="citing-and-references">Citing And References</h2>
}
</code></pre>
<p><strong>Additionally, <code>auton-survival</code> implements the following methodologies:</strong></p>
<p>[2] <a href="https://arxiv.org/abs/2202.11089">Counterfactual Phenotyping with Censored Time-to-Events (2022)</a></a></p>
<p>[2] <a href="https://arxiv.org/abs/2202.11089">Counterfactual Phenotyping with Censored Time-to-Events. ACM Conference on Knowledge Discovery and Data Mining (KDD) 2022</a></a></p>
<pre><code> @article{nagpal2022counterfactual,
title={Counterfactual Phenotyping with Censored Time-to-Events},
author={Nagpal, Chirag and Goswami, Mononito and Dufendach, Keith and Dubrawski, Artur},
Expand Down Expand Up @@ -410,7 +410,7 @@ <h2 id="license">License</h2>
<img align="right" height ="110px" src="https://www.cs.cmu.edu/~chiragn/auton_logo.png"> </p>
<p><br><br><br><br><br>
<br><br><br><br><br></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>
<h2 class="section-title" id="header-submodules">Sub-modules</h2>
Expand Down
8 changes: 4 additions & 4 deletions docs/metrics.html
Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@ <h1 class="title">Module <code>auton_survival.metrics</code></h1>
<section id="section-intro">
<p>Tools to compute metrics used to assess survival outcomes and survival
model performance.</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>
Expand Down Expand Up @@ -89,7 +89,7 @@ <h2 id="parameters">Parameters</h2>
</dl>
<h2 id="returns">Returns</h2>
<p>float or list: The metric value(s) for the specified metric.</p></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="auton_survival.metrics.survival_regression_metric"><code class="name flex">
<span>def <span class="ident">survival_regression_metric</span></span>(<span>metric, outcomes, predictions, times, outcomes_train=None)</span>
Expand Down Expand Up @@ -119,7 +119,7 @@ <h2 id="parameters">Parameters</h2>
</dl>
<h2 id="returns">Returns</h2>
<p>float: The metric value for the specified metric.</p></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="auton_survival.metrics.phenotype_purity"><code class="name flex">
<span>def <span class="ident">phenotype_purity</span></span>(<span>phenotypes_train, outcomes_train, phenotypes_test=None, outcomes_test=None, strategy='instantaneous', horizons=None, bootstrap=None)</span>
Expand Down Expand Up @@ -156,7 +156,7 @@ <h2 id="returns">Returns</h2>
<dd>Columns are metric values computed for each event horizon.
If bootstrapping, rows are bootstrap results.</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>
Expand Down
12 changes: 6 additions & 6 deletions docs/models/cmhe/cmhe_torch.html
Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,7 @@
<h1 class="title">Module <code>auton_survival.models.cmhe.cmhe_torch</code></h1>
</header>
<section id="section-intro">
<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>
Expand All @@ -51,7 +51,7 @@ <h2 class="section-title" id="header-classes">Classes</h2>
hazard rates is determined non-parametrically using an spline-interpolated
Breslow's estimator.</p>
<p>Initializes internal Module state, shared by both nn.Module and ScriptModule.</p></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>
<h3>Class variables</h3>
<dl>
<dt id="auton_survival.models.cmhe.cmhe_torch.DeepCMHETorch.dump_patches"><code class="name">var <span class="ident">dump_patches</span> : bool</code></dt>
Expand All @@ -70,7 +70,7 @@ <h3>Methods</h3>
</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>
</dl>
</dd>
Expand All @@ -85,7 +85,7 @@ <h3>Methods</h3>
class is all zeros. This allows direct application of pytorch.nn.LogSoftmax
and pytorch.nn.Softmax.</p>
<p>Initializes internal Module state, shared by both nn.Module and ScriptModule.</p></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>
<h3>Class variables</h3>
<dl>
<dt id="auton_survival.models.cmhe.cmhe_torch.IdentifiableLinear.dump_patches"><code class="name">var <span class="ident">dump_patches</span> : bool</code></dt>
Expand All @@ -102,7 +102,7 @@ <h3>Instance variables</h3>
<dt id="auton_survival.models.cmhe.cmhe_torch.IdentifiableLinear.weight"><code class="name">var <span class="ident">weight</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>
</dl>
<h3>Methods</h3>
Expand All @@ -112,7 +112,7 @@ <h3>Methods</h3>
</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>
</dl>
</dd>
Expand Down
Loading

0 comments on commit 8526620

Please sign in to comment.