In this work, we study the problem of clustering survival data $-$ a challenging and so far under-explored task. We introduce a novel semi-supervised probabilistic approach to cluster survival data by leveraging recent advances in stochastic gradient variational inference. In contrast to previous work, our proposed method employs a deep generative model to uncover the underlying distribution of both the explanatory variables and censored survival times. We compare our model to the related work on clustering and mixture models for survival data in comprehensive experiments on a wide range of synthetic, semi-synthetic, and real-world datasets, including medical imaging data. Our method performs better at identifying clusters and is competitive at predicting survival times. Relying on novel generative assumptions, the proposed model offers a holistic perspective on clustering survival data and holds a promise of discovering subpopulations whose survival is regulated by different generative mechanisms.
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In recent years, large-scale Bayesian learning draws a great deal of attention. However, in big-data era, the amount of data we face is growing much faster than our ability to deal with it. Fortunately, it is observed that large-scale datasets usually own rich internal structure and is somewhat redundant. In this paper, we attempt to simplify the Bayesian posterior via exploiting this structure. Specifically, we restrict our interest to the so-called well-clustered datasets and construct an \emph{approximate posterior} according to the clustering information. Fortunately, the clustering structure can be efficiently obtained via a particular clustering algorithm. When constructing the approximate posterior, the data points in the same cluster are all replaced by the centroid of the cluster. As a result, the posterior can be significantly simplified. Theoretically, we show that under certain conditions the approximate posterior we construct is close (measured by KL divergence) to the exact posterior. Furthermore, thorough experiments are conducted to validate the fact that the constructed posterior is a good approximation to the true posterior and much easier to sample from.
Survival outcomes are common in comparative effectiveness studies and require unique handling because they are usually incompletely observed due to right-censoring. A "once for all" approach for causal inference with survival outcomes constructs pseudo-observations and allows standard methods such as propensity score weighting to proceed as if the outcomes are completely observed. For a general class of model-free causal estimands with survival outcomes on user-specified target populations, we develop corresponding propensity score weighting estimators based on the pseudo-observations and establish their asymptotic properties. In particular, utilizing the functional delta-method and the von Mises expansion, we derive a new closed-form variance of the weighting estimator that takes into account the uncertainty due to both pseudo-observation calculation and propensity score estimation. This allows valid and computationally efficient inference without resampling. We also prove the optimal efficiency property of the overlap weights within the class of balancing weights for survival outcomes. The proposed methods are applicable to both binary and multiple treatments. Extensive simulations are conducted to explore the operating characteristics of the proposed method versus other commonly used alternatives. We apply the proposed method to compare the causal effects of three popular treatment approaches for prostate cancer patients.
Semiconductor device models are essential to understand the charge transport in thin film transistors (TFTs). Using these TFT models to draw inference involves estimating parameters used to fit to the experimental data. These experimental data can involve extracted charge carrier mobility or measured current. Estimating these parameters help us draw inferences about device performance. Fitting a TFT model for a given experimental data using the model parameters relies on manual fine tuning of multiple parameters by human experts. Several of these parameters may have confounding effects on the experimental data, making their individual effect extraction a non-intuitive process during manual tuning. To avoid this convoluted process, we propose a new method for automating the model parameter extraction process resulting in an accurate model fitting. In this work, model choice based approximate Bayesian computation (aBc) is used for generating the posterior distribution of the estimated parameters using observed mobility at various gate voltage values. Furthermore, it is shown that the extracted parameters can be accurately predicted from the mobility curves using gradient boosted trees. This work also provides a comparative analysis of the proposed framework with fine-tuned neural networks wherein the proposed framework is shown to perform better.
Meta-analyses of survival studies aim to reveal the variation of an effect measure of interest over different studies and present a meaningful summary. They must address between study heterogeneity in several dimensions and eliminate spurious sources of variation. Forest plots of the usual (adjusted) hazard ratios are fraught with difficulties from this perspective since both the magnitude and interpretation of these hazard ratios depend on factors ancillary to the true study-specific exposure effect. These factors generally include the study duration, the censoring patterns within studies, the covariates adjusted for and their distribution over exposure groups. Ignoring these mentioned features and accepting implausible hidden assumptions may critically affect interpretation of the pooled effect measure. Risk differences or restricted mean effects over a common follow-up interval and balanced distribution of a covariate set are natural candidates for exposure evaluation and possible treatment choice. In this paper, we propose differently standardized survival curves over a fitting time horizon, targeting various estimands with their own transportability. With each type of standardization comes a given interpretation within studies and overall, under stated assumptions. These curves can in turn be summarized by standardized study-specific contrasts, including hazard ratios with more consistent meaning. We prefer forest plots of risk differences at well chosen time points. Our case study examines overall survival among anal squamous cell carcinoma patients, expressing the tumor marker $p16^{INK4a}$ or not, based on the individual patient data of six studies.
In large epidemiologic studies, self-reported outcomes are often used to record disease status more frequently than by gold standard diagnostic tests alone. While self-reported disease outcomes are easier to obtain than diagnostic test results, they are often prone to error. There has recently been interest in using error-prone, auxiliary outcomes to improve the efficiency of inference for discrete time-to-event analyses. We have developed a new augmented likelihood approach that incorporates auxiliary data into the analysis of gold standard time-to-event outcome, which can be considered when self-reported outcomes are available in addition to a gold standard endpoint. We conduct a numerical study to show how we can improve statistical efficiency by using the proposed method instead of standard approaches for interval-censored survival data that do not leverage auxiliary data. We also extended this method for the complex survey design setting so that it can be applied in our motivating data example. We apply this method to data from the Hispanic Community Health Study/Study of Latinos in order to assess the association between energy and protein intake and the risk of incident diabetes. In our application, we demonstrate how our method can be used in combination with regression calibration to additionally address the covariate measurement error in the self-reported diet.
We propose a novel approach to disentangle the generative factors of variation underlying a given set of observations. Our method builds upon the idea that the (unknown) low-dimensional manifold underlying the data space can be explicitly modeled as a product of submanifolds. This gives rise to a new definition of disentanglement, and to a novel weakly-supervised algorithm for recovering the unknown explanatory factors behind the data. At training time, our algorithm only requires pairs of non i.i.d. data samples whose elements share at least one, possibly multidimensional, generative factor of variation. We require no knowledge on the nature of these transformations, and do not make any limiting assumption on the properties of each subspace. Our approach is easy to implement, and can be successfully applied to different kinds of data (from images to 3D surfaces) undergoing arbitrary transformations. In addition to standard synthetic benchmarks, we showcase our method in challenging real-world applications, where we compare favorably with the state of the art.
Combining clustering and representation learning is one of the most promising approaches for unsupervised learning of deep neural networks. However, doing so naively leads to ill posed learning problems with degenerate solutions. In this paper, we propose a novel and principled learning formulation that addresses these issues. The method is obtained by maximizing the information between labels and input data indices. We show that this criterion extends standard cross-entropy minimization to an optimal transport problem, which we solve efficiently for millions of input images and thousands of labels using a fast variant of the Sinkhorn-Knopp algorithm. The resulting method is able to self-label visual data so as to train highly competitive image representations without manual labels. Compared to the best previous method in this class, namely DeepCluster, our formulation minimizes a single objective function for both representation learning and clustering; it also significantly outperforms DeepCluster in standard benchmarks and reaches state of the art for learning a ResNet-50 self-supervisedly.
Clustering is one of the most fundamental and wide-spread techniques in exploratory data analysis. Yet, the basic approach to clustering has not really changed: a practitioner hand-picks a task-specific clustering loss to optimize and fit the given data to reveal the underlying cluster structure. Some types of losses---such as k-means, or its non-linear version: kernelized k-means (centroid based), and DBSCAN (density based)---are popular choices due to their good empirical performance on a range of applications. Although every so often the clustering output using these standard losses fails to reveal the underlying structure, and the practitioner has to custom-design their own variation. In this work we take an intrinsically different approach to clustering: rather than fitting a dataset to a specific clustering loss, we train a recurrent model that learns how to cluster. The model uses as training pairs examples of datasets (as input) and its corresponding cluster identities (as output). By providing multiple types of training datasets as inputs, our model has the ability to generalize well on unseen datasets (new clustering tasks). Our experiments reveal that by training on simple synthetically generated datasets or on existing real datasets, we can achieve better clustering performance on unseen real-world datasets when compared with standard benchmark clustering techniques. Our meta clustering model works well even for small datasets where the usual deep learning models tend to perform worse.
The Visual Question Answering (VQA) task combines challenges for processing data with both Visual and Linguistic processing, to answer basic `common sense' questions about given images. Given an image and a question in natural language, the VQA system tries to find the correct answer to it using visual elements of the image and inference gathered from textual questions. In this survey, we cover and discuss the recent datasets released in the VQA domain dealing with various types of question-formats and enabling robustness of the machine-learning models. Next, we discuss about new deep learning models that have shown promising results over the VQA datasets. At the end, we present and discuss some of the results computed by us over the vanilla VQA models, Stacked Attention Network and the VQA Challenge 2017 winner model. We also provide the detailed analysis along with the challenges and future research directions.
Autoencoders provide a powerful framework for learning compressed representations by encoding all of the information needed to reconstruct a data point in a latent code. In some cases, autoencoders can "interpolate": By decoding the convex combination of the latent codes for two datapoints, the autoencoder can produce an output which semantically mixes characteristics from the datapoints. In this paper, we propose a regularization procedure which encourages interpolated outputs to appear more realistic by fooling a critic network which has been trained to recover the mixing coefficient from interpolated data. We then develop a simple benchmark task where we can quantitatively measure the extent to which various autoencoders can interpolate and show that our regularizer dramatically improves interpolation in this setting. We also demonstrate empirically that our regularizer produces latent codes which are more effective on downstream tasks, suggesting a possible link between interpolation abilities and learning useful representations.
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