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11 changes: 1 addition & 10 deletions docs/datasets.html
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Expand Down Expand Up @@ -127,4 +118,4 @@ <h1>Index</h1>
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115 changes: 110 additions & 5 deletions docs/dsm_api.html
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Expand Up @@ -218,6 +218,30 @@ <h2 id="returns">Returns</h2>
<dd>numpy array of the survival probabilites at each time in t.</dd>
</dl></div>
</dd>
<dt id="dsm.dsm_api.DeepSurvivalMachines.predict_pdf"><code class="name flex">
<span>def <span class="ident">predict_pdf</span></span>(<span>self, x, t, risk=1)</span>
</code></dt>
<dd>
<p class="inheritance">
<em>Inherited from:</em>
<code><a title="dsm.dsm_api.DSMBase" href="#dsm.dsm_api.DSMBase">DSMBase</a></code>.<code><a title="dsm.dsm_api.DSMBase.predict_pdf" href="#dsm.dsm_api.DSMBase.predict_pdf">predict_pdf</a></code>
</p>
<div class="desc"><p>Returns the estimated pdf at time <span><span class="MathJax_Preview"> t </span><script type="math/tex"> t </script></span>,
<span><span class="MathJax_Preview"> \widehat{\mathbb{P}}(T = t|X) </span><script type="math/tex"> \widehat{\mathbb{P}}(T = t|X) </script></span> for some input data <span><span class="MathJax_Preview"> x </span><script type="math/tex"> x </script></span>. </p>
<h2 id="parameters">Parameters</h2>
<dl>
<dt><strong><code>x</code></strong> :&ensp;<code>np.ndarray</code></dt>
<dd>A numpy array of the input features, <span><span class="MathJax_Preview"> x </span><script type="math/tex"> x </script></span>.</dd>
<dt><strong><code>t</code></strong> :&ensp;<code>list</code> or <code>float</code></dt>
<dd>a list or float of the times at which pdf is
to be computed</dd>
</dl>
<h2 id="returns">Returns</h2>
<dl>
<dt><code>np.array</code></dt>
<dd>numpy array of the estimated pdf at each time in t.</dd>
</dl></div>
</dd>
</dl>
</dd>
<dt id="dsm.dsm_api.DeepRecurrentSurvivalMachines"><code class="flex name class">
Expand All @@ -226,7 +250,12 @@ <h2 id="returns">Returns</h2>
</code></dt>
<dd>
<div class="desc"><p>The Deep Recurrent Survival Machines model to handle data with
time-dependent covariates.</p></div>
time-dependent covariates.</p>
<p>For full details on Deep Recurrent Survival Machines, refer to our paper [1].</p>
<h2 id="references">References</h2>
<p>[1] <a href="http://proceedings.mlr.press/v146/nagpal21a.html">
Deep Parametric Time-to-Event Regression with Time-Varying Covariates
AAAI Spring Symposium on Survival Prediction</a></p></div>
<div class="git-link-div"><a href="https://github.com/autonlab/DeepSurvivalMachines" class="git-link">Browse git</a></div>
<h3>Methods</h3>
<dl>
Expand Down Expand Up @@ -364,6 +393,30 @@ <h2 id="returns">Returns</h2>
<dd>numpy array of the survival probabilites at each time in t.</dd>
</dl></div>
</dd>
<dt id="dsm.dsm_api.DeepRecurrentSurvivalMachines.predict_pdf"><code class="name flex">
<span>def <span class="ident">predict_pdf</span></span>(<span>self, x, t, risk=1)</span>
</code></dt>
<dd>
<p class="inheritance">
<em>Inherited from:</em>
<code><a title="dsm.dsm_api.DSMBase" href="#dsm.dsm_api.DSMBase">DSMBase</a></code>.<code><a title="dsm.dsm_api.DSMBase.predict_pdf" href="#dsm.dsm_api.DSMBase.predict_pdf">predict_pdf</a></code>
</p>
<div class="desc"><p>Returns the estimated pdf at time <span><span class="MathJax_Preview"> t </span><script type="math/tex"> t </script></span>,
<span><span class="MathJax_Preview"> \widehat{\mathbb{P}}(T = t|X) </span><script type="math/tex"> \widehat{\mathbb{P}}(T = t|X) </script></span> for some input data <span><span class="MathJax_Preview"> x </span><script type="math/tex"> x </script></span>. </p>
<h2 id="parameters">Parameters</h2>
<dl>
<dt><strong><code>x</code></strong> :&ensp;<code>np.ndarray</code></dt>
<dd>A numpy array of the input features, <span><span class="MathJax_Preview"> x </span><script type="math/tex"> x </script></span>.</dd>
<dt><strong><code>t</code></strong> :&ensp;<code>list</code> or <code>float</code></dt>
<dd>a list or float of the times at which pdf is
to be computed</dd>
</dl>
<h2 id="returns">Returns</h2>
<dl>
<dt><code>np.array</code></dt>
<dd>numpy array of the estimated pdf at each time in t.</dd>
</dl></div>
</dd>
</dl>
</dd>
<dt id="dsm.dsm_api.DeepConvolutionalSurvivalMachines"><code class="flex name class">
Expand Down Expand Up @@ -510,6 +563,30 @@ <h2 id="returns">Returns</h2>
<dd>numpy array of the survival probabilites at each time in t.</dd>
</dl></div>
</dd>
<dt id="dsm.dsm_api.DeepConvolutionalSurvivalMachines.predict_pdf"><code class="name flex">
<span>def <span class="ident">predict_pdf</span></span>(<span>self, x, t, risk=1)</span>
</code></dt>
<dd>
<p class="inheritance">
<em>Inherited from:</em>
<code><a title="dsm.dsm_api.DSMBase" href="#dsm.dsm_api.DSMBase">DSMBase</a></code>.<code><a title="dsm.dsm_api.DSMBase.predict_pdf" href="#dsm.dsm_api.DSMBase.predict_pdf">predict_pdf</a></code>
</p>
<div class="desc"><p>Returns the estimated pdf at time <span><span class="MathJax_Preview"> t </span><script type="math/tex"> t </script></span>,
<span><span class="MathJax_Preview"> \widehat{\mathbb{P}}(T = t|X) </span><script type="math/tex"> \widehat{\mathbb{P}}(T = t|X) </script></span> for some input data <span><span class="MathJax_Preview"> x </span><script type="math/tex"> x </script></span>. </p>
<h2 id="parameters">Parameters</h2>
<dl>
<dt><strong><code>x</code></strong> :&ensp;<code>np.ndarray</code></dt>
<dd>A numpy array of the input features, <span><span class="MathJax_Preview"> x </span><script type="math/tex"> x </script></span>.</dd>
<dt><strong><code>t</code></strong> :&ensp;<code>list</code> or <code>float</code></dt>
<dd>a list or float of the times at which pdf is
to be computed</dd>
</dl>
<h2 id="returns">Returns</h2>
<dl>
<dt><code>np.array</code></dt>
<dd>numpy array of the estimated pdf at each time in t.</dd>
</dl></div>
</dd>
</dl>
</dd>
<dt id="dsm.dsm_api.DeepCNNRNNSurvivalMachines"><code class="flex name class">
Expand Down Expand Up @@ -656,6 +733,30 @@ <h2 id="returns">Returns</h2>
<dd>numpy array of the survival probabilites at each time in t.</dd>
</dl></div>
</dd>
<dt id="dsm.dsm_api.DeepCNNRNNSurvivalMachines.predict_pdf"><code class="name flex">
<span>def <span class="ident">predict_pdf</span></span>(<span>self, x, t, risk=1)</span>
</code></dt>
<dd>
<p class="inheritance">
<em>Inherited from:</em>
<code><a title="dsm.dsm_api.DeepRecurrentSurvivalMachines" href="#dsm.dsm_api.DeepRecurrentSurvivalMachines">DeepRecurrentSurvivalMachines</a></code>.<code><a title="dsm.dsm_api.DeepRecurrentSurvivalMachines.predict_pdf" href="#dsm.dsm_api.DeepRecurrentSurvivalMachines.predict_pdf">predict_pdf</a></code>
</p>
<div class="desc"><p>Returns the estimated pdf at time <span><span class="MathJax_Preview"> t </span><script type="math/tex"> t </script></span>,
<span><span class="MathJax_Preview"> \widehat{\mathbb{P}}(T = t|X) </span><script type="math/tex"> \widehat{\mathbb{P}}(T = t|X) </script></span> for some input data <span><span class="MathJax_Preview"> x </span><script type="math/tex"> x </script></span>. </p>
<h2 id="parameters">Parameters</h2>
<dl>
<dt><strong><code>x</code></strong> :&ensp;<code>np.ndarray</code></dt>
<dd>A numpy array of the input features, <span><span class="MathJax_Preview"> x </span><script type="math/tex"> x </script></span>.</dd>
<dt><strong><code>t</code></strong> :&ensp;<code>list</code> or <code>float</code></dt>
<dd>a list or float of the times at which pdf is
to be computed</dd>
</dl>
<h2 id="returns">Returns</h2>
<dl>
<dt><code>np.array</code></dt>
<dd>numpy array of the estimated pdf at each time in t.</dd>
</dl></div>
</dd>
</dl>
</dd>
</dl>
Expand All @@ -677,42 +778,46 @@ <h1>Index</h1>
<ul>
<li>
<h4><code><a title="dsm.dsm_api.DeepSurvivalMachines" href="#dsm.dsm_api.DeepSurvivalMachines">DeepSurvivalMachines</a></code></h4>
<ul class="">
<ul class="two-column">
<li><code><a title="dsm.dsm_api.DeepSurvivalMachines.fit" href="#dsm.dsm_api.DeepSurvivalMachines.fit">fit</a></code></li>
<li><code><a title="dsm.dsm_api.DeepSurvivalMachines.compute_nll" href="#dsm.dsm_api.DeepSurvivalMachines.compute_nll">compute_nll</a></code></li>
<li><code><a title="dsm.dsm_api.DeepSurvivalMachines.predict_mean" href="#dsm.dsm_api.DeepSurvivalMachines.predict_mean">predict_mean</a></code></li>
<li><code><a title="dsm.dsm_api.DeepSurvivalMachines.predict_risk" href="#dsm.dsm_api.DeepSurvivalMachines.predict_risk">predict_risk</a></code></li>
<li><code><a title="dsm.dsm_api.DeepSurvivalMachines.predict_survival" href="#dsm.dsm_api.DeepSurvivalMachines.predict_survival">predict_survival</a></code></li>
<li><code><a title="dsm.dsm_api.DeepSurvivalMachines.predict_pdf" href="#dsm.dsm_api.DeepSurvivalMachines.predict_pdf">predict_pdf</a></code></li>
</ul>
</li>
<li>
<h4><code><a title="dsm.dsm_api.DeepRecurrentSurvivalMachines" href="#dsm.dsm_api.DeepRecurrentSurvivalMachines">DeepRecurrentSurvivalMachines</a></code></h4>
<ul class="">
<ul class="two-column">
<li><code><a title="dsm.dsm_api.DeepRecurrentSurvivalMachines.fit" href="#dsm.dsm_api.DeepRecurrentSurvivalMachines.fit">fit</a></code></li>
<li><code><a title="dsm.dsm_api.DeepRecurrentSurvivalMachines.compute_nll" href="#dsm.dsm_api.DeepRecurrentSurvivalMachines.compute_nll">compute_nll</a></code></li>
<li><code><a title="dsm.dsm_api.DeepRecurrentSurvivalMachines.predict_mean" href="#dsm.dsm_api.DeepRecurrentSurvivalMachines.predict_mean">predict_mean</a></code></li>
<li><code><a title="dsm.dsm_api.DeepRecurrentSurvivalMachines.predict_risk" href="#dsm.dsm_api.DeepRecurrentSurvivalMachines.predict_risk">predict_risk</a></code></li>
<li><code><a title="dsm.dsm_api.DeepRecurrentSurvivalMachines.predict_survival" href="#dsm.dsm_api.DeepRecurrentSurvivalMachines.predict_survival">predict_survival</a></code></li>
<li><code><a title="dsm.dsm_api.DeepRecurrentSurvivalMachines.predict_pdf" href="#dsm.dsm_api.DeepRecurrentSurvivalMachines.predict_pdf">predict_pdf</a></code></li>
</ul>
</li>
<li>
<h4><code><a title="dsm.dsm_api.DeepConvolutionalSurvivalMachines" href="#dsm.dsm_api.DeepConvolutionalSurvivalMachines">DeepConvolutionalSurvivalMachines</a></code></h4>
<ul class="">
<ul class="two-column">
<li><code><a title="dsm.dsm_api.DeepConvolutionalSurvivalMachines.fit" href="#dsm.dsm_api.DeepConvolutionalSurvivalMachines.fit">fit</a></code></li>
<li><code><a title="dsm.dsm_api.DeepConvolutionalSurvivalMachines.compute_nll" href="#dsm.dsm_api.DeepConvolutionalSurvivalMachines.compute_nll">compute_nll</a></code></li>
<li><code><a title="dsm.dsm_api.DeepConvolutionalSurvivalMachines.predict_mean" href="#dsm.dsm_api.DeepConvolutionalSurvivalMachines.predict_mean">predict_mean</a></code></li>
<li><code><a title="dsm.dsm_api.DeepConvolutionalSurvivalMachines.predict_risk" href="#dsm.dsm_api.DeepConvolutionalSurvivalMachines.predict_risk">predict_risk</a></code></li>
<li><code><a title="dsm.dsm_api.DeepConvolutionalSurvivalMachines.predict_survival" href="#dsm.dsm_api.DeepConvolutionalSurvivalMachines.predict_survival">predict_survival</a></code></li>
<li><code><a title="dsm.dsm_api.DeepConvolutionalSurvivalMachines.predict_pdf" href="#dsm.dsm_api.DeepConvolutionalSurvivalMachines.predict_pdf">predict_pdf</a></code></li>
</ul>
</li>
<li>
<h4><code><a title="dsm.dsm_api.DeepCNNRNNSurvivalMachines" href="#dsm.dsm_api.DeepCNNRNNSurvivalMachines">DeepCNNRNNSurvivalMachines</a></code></h4>
<ul class="">
<ul class="two-column">
<li><code><a title="dsm.dsm_api.DeepCNNRNNSurvivalMachines.fit" href="#dsm.dsm_api.DeepCNNRNNSurvivalMachines.fit">fit</a></code></li>
<li><code><a title="dsm.dsm_api.DeepCNNRNNSurvivalMachines.compute_nll" href="#dsm.dsm_api.DeepCNNRNNSurvivalMachines.compute_nll">compute_nll</a></code></li>
<li><code><a title="dsm.dsm_api.DeepCNNRNNSurvivalMachines.predict_mean" href="#dsm.dsm_api.DeepCNNRNNSurvivalMachines.predict_mean">predict_mean</a></code></li>
<li><code><a title="dsm.dsm_api.DeepCNNRNNSurvivalMachines.predict_risk" href="#dsm.dsm_api.DeepCNNRNNSurvivalMachines.predict_risk">predict_risk</a></code></li>
<li><code><a title="dsm.dsm_api.DeepCNNRNNSurvivalMachines.predict_survival" href="#dsm.dsm_api.DeepCNNRNNSurvivalMachines.predict_survival">predict_survival</a></code></li>
<li><code><a title="dsm.dsm_api.DeepCNNRNNSurvivalMachines.predict_pdf" href="#dsm.dsm_api.DeepCNNRNNSurvivalMachines.predict_pdf">predict_pdf</a></code></li>
</ul>
</li>
</ul>
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7 changes: 3 additions & 4 deletions docs/dsm_torch.html
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Expand Up @@ -236,7 +236,7 @@ <h2 id="args">Args</h2>
</dd>
<dt id="dsm.dsm_torch.DeepConvolutionalSurvivalMachinesTorch"><code class="flex name class">
<span>class <span class="ident">DeepConvolutionalSurvivalMachinesTorch</span></span>
<span>(</span><span>inputdim, k, typ='ConvNet', hidden=None, dist='Weibull', temp=1000.0, discount=1.0, optimizer='Adam', risks=1)</span>
<span>(</span><span>inputdim, k, embedding=None, hidden=None, dist='Weibull', temp=1000.0, discount=1.0, optimizer='Adam', risks=1)</span>
</code></dt>
<dd>
<div class="desc"><p>A Torch implementation of Deep Convolutional Survival Machines model.</p>
Expand All @@ -258,11 +258,10 @@ <h2 id="parameters">Parameters</h2>
<dd>Dimensionality of the input features. A tuple (height, width).</dd>
<dt><strong><code>k</code></strong> :&ensp;<code>int</code></dt>
<dd>The number of underlying parametric distributions.</dd>
<dt><strong><code>embedding</code></strong> :&ensp;<code>torch.nn.Module</code></dt>
<dd>A torch CNN to obtain the representation of the input data.</dd>
<dt><strong><code>hidden</code></strong> :&ensp;<code>int</code></dt>
<dd>The number of neurons in each hidden layer.</dd>
<dt><strong><code>init</code></strong> :&ensp;<code>tuple</code></dt>
<dd>A tuple for initialization of the parameters for the underlying
distributions. (shape, scale).</dd>
<dt><strong><code>dist</code></strong> :&ensp;<code>str</code></dt>
<dd>Choice of the underlying survival distributions.
One of 'Weibull', 'LogNormal'.
Expand Down
54 changes: 29 additions & 25 deletions docs/index.html
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Expand Up @@ -100,37 +100,18 @@ <h2 id="example-usage">Example Usage</h2>
&gt;&gt;&gt; # estimate the predicted risks at the time
&gt;&gt;&gt; model.predict_risk(x, 10)
</code></pre>
<h2 id="installation">Installation</h2>
<pre><code class="language-console">foo@bar:~$ git clone https://github.com/autonlab/DeepSurvivalMachines.git
foo@bar:~$ cd DeepSurvivalMachines
foo@bar:~$ pip install -r requirements.txt
</code></pre>
<h2 id="examples">Examples</h2>
<ol>
<li><a href="https://nbviewer.jupyter.org/github/autonlab/DeepSurvivalMachines/blob/master/examples/DSM%20on%20SUPPORT%20Dataset.ipynb">Deep Survival Machines on the SUPPORT Dataset</a></li>
</ol>
<h2 id="references">References</h2>
<p>Please cite the following papers if you are using the <code><a title="dsm" href="#dsm">dsm</a></code> package.</p>
<p>[1] <a href="https://arxiv.org/abs/2003.01176">Deep Survival Machines:
Fully Parametric Survival Regression and
Representation Learning for Censored Data with Competing Risks.
IEEE Journal of Biomedical \&amp; Health Informatics (2021)</a></a></p>
Representation Learning for Censored Data with Competing Risks."
arXiv preprint arXiv:2003.01176 (2020)</a></a></p>
<pre><code> @article{nagpal2020deep,
title={Deep Survival Machines: Fully Parametric Survival Regression and\
Representation Learning for Censored Data with Competing Risks},
author={Nagpal, Chirag and Li, Xinyu and Dubrawski, Artur},
journal={IEEE Journal of Biomedical and Health Informatics},
year={2021}
}
</code></pre>
<p>[2] <a href="">Recurrent Deep Survival Machines:
Deep Parametric Time-to-Event Regression with Time-Varying Covariates.
AAAI Spring Symposium (2021)</a></a></p>
<pre><code> @article{nagpal2021rdsm,
title={Deep Parametric Time-to-Event Regression with Time-Varying Covariates},
author={Nagpal, Chirag and Jeanselme, Vincent and Dubrawski, Artur},
journal={AAAI Spring Symposium on Survival Analysis},
year={2021}
journal={arXiv preprint arXiv:2003.01176},
year={2020}
}
</code></pre>
<h2 id="compatibility">Compatibility</h2>
Expand Down Expand Up @@ -168,6 +149,30 @@ <h2 id="license">License</h2>
<section>
<h2 class="section-title" id="header-submodules">Sub-modules</h2>
<dl>
<dt><code class="name"><a title="dsm.contrib" href="contrib/index.html">dsm.contrib</a></code></dt>
<dd>
<div class="desc"><p><code><a title="dsm" href="#dsm">dsm</a></code> includes extended functionality for survival analysis as part
of <code><a title="dsm.contrib" href="contrib/index.html">dsm.contrib</a></code>.</p>
<h2 id="contributed-modules">Contributed Modules</h2>
<p>This submodule incorporates contributed survival analysis methods.</p>
<h2 id="deep-cox-mixtures">Deep Cox Mixtures</h2>
<p>The Cox Mixture involves the assumption that the survival function
of the individual to be a mixture of K Cox Models. Conditioned on each
subgroup Z=k; the PH assumptions are assumed to hold and the baseline
hazard rates is determined non-parametrically using an spline-interpolated
Breslow's estimator.</p>
<p>For full details on Deep Cox Mixture, refer to the paper [1].</p>
<h2 id="references">References</h2>
<p>[1] <a href="https://arxiv.org/abs/2101.06536">Deep Cox Mixtures
for Survival Regression. Machine Learning in Health Conference (2021)</a></p>
<pre><code> @article{nagpal2021dcm,
title={Deep Cox mixtures for survival regression},
author={Nagpal, Chirag and Yadlowsky, Steve and Rostamzadeh, Negar and Heller, Katherine},
journal={arXiv preprint arXiv:2101.06536},
year={2021}
}
</code></pre></div>
</dd>
<dt><code class="name"><a title="dsm.datasets" href="datasets.html">dsm.datasets</a></code></dt>
<dd>
<div class="desc"><p>Utility functions to load standard datasets to train and evaluate the
Expand Down Expand Up @@ -224,8 +229,6 @@ <h1>Index</h1>
<li><a href="#deep-recurrent-survival-machines">Deep Recurrent Survival Machines</a></li>
<li><a href="#deep-convolutional-survival-machines">Deep Convolutional Survival Machines</a></li>
<li><a href="#example-usage">Example Usage</a></li>
<li><a href="#installation">Installation</a></li>
<li><a href="#examples">Examples</a></li>
<li><a href="#references">References</a></li>
<li><a href="#compatibility">Compatibility</a></li>
<li><a href="#contributing">Contributing</a></li>
Expand All @@ -235,6 +238,7 @@ <h1>Index</h1>
<ul id="index">
<li><h3><a href="#header-submodules">Sub-modules</a></h3>
<ul>
<li><code><a title="dsm.contrib" href="contrib/index.html">dsm.contrib</a></code></li>
<li><code><a title="dsm.datasets" href="datasets.html">dsm.datasets</a></code></li>
<li><code><a title="dsm.dsm_api" href="dsm_api.html">dsm.dsm_api</a></code></li>
<li><code><a title="dsm.dsm_torch" href="dsm_torch.html">dsm.dsm_torch</a></code></li>
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