Many methods for quantitative structure-activity relationships (QSARs) deliver point estimates only, without quantifying the uncertainty inherent in the prediction. One way to quantify the uncertainy of a QSAR prediction is to predict the conditional density of the activity given the structure instead of a point estimate. If a conditional density estimate is available, it is easy to derive prediction intervals of activities. In this paper, we experimentally evaluate and compare three methods for conditional density estimation for their suitability in QSAR modeling. In contrast to traditional methods for conditional density estimation, they are based on generic machine learning schemes, more specifically, class probability estimators. Our experiments show that a kernel estimator based on class probability estimates from a random forest classifier is highly competitive with Gaussian process regression, while taking only a fraction of the time for training. Therefore, generic machine-learning based methods for conditional density estimation may be a good and fast option for quantifying uncertainty in QSAR modeling.
We propose a method for nonparametric density estimation that exhibits robustness to contamination of the training sample. This method achieves robustness by combining a traditional kernel density estimator (KDE) with ideas from classical $M$-estimation. We interpret the KDE based on a radial, positive semi-definite kernel as a sample mean in the associated reproducing kernel Hilbert space. Since the sample mean is sensitive to outliers, we estimate it robustly via $M$-estimation, yielding a robust kernel density estimator (RKDE). An RKDE can be computed efficiently via a kernelized iteratively re-weighted least squares (IRWLS) algorithm. Necessary and sufficient conditions are given for kernelized IRWLS to converge to the global minimizer of the $M$-estimator objective function. The robustness of the RKDE is demonstrated with a representer theorem, the influence function, and experimental results for density estimation and anomaly detection.
While robust parameter estimation has been well studied in parametric density estimation, there has been little investigation into robust density estimation in the nonparametric setting. We present a robust version of the popular kernel density estimator (KDE). As with other estimators, a robust version of the KDE is useful since sample contamination is a common issue with datasets. What ``robustness'' means for a nonparametric density estimate is not straightforward and is a topic we explore in this paper. To construct a robust KDE we scale the traditional KDE and project it to its nearest weighted KDE in the $L^2$ norm. Because the squared $L^2$ norm penalizes point-wise errors superlinearly this causes the weighted KDE to allocate more weight to high density regions. We demonstrate the robustness of the SPKDE with numerical experiments and a consistency result which shows that asymptotically the SPKDE recovers the uncontaminated density under sufficient conditions on the contamination.
This paper introduces a probability density estimator based on Green's function identities. A density model is constructed under the sole assumption that the probability density is differentiable. The method is implemented as a binary likelihood estimator for classification purposes, so issues such as mis-modeling and overtraining are also discussed. The identity behind the density estimator can be interpreted as a real-valued, non-scalar kernel method which is able to reconstruct differentiable density functions.
We address the problem of estimating the difference between two probability densities. A naive approach is a two-step procedure of first estimating two densities separately and then computing their difference. However, such a two-step procedure does not necessarily work well because the first step is performed without regard to the second step and thus a small estimation error incurred in the first stage can cause a big error in the second stage. In this paper, we propose a single-shot procedure for directly estimating the density difference without separately estimating two densities. We derive a non-parametric finite-sample error bound for the proposed single-shot density-difference estimator and show that it achieves the optimal convergence rate. We then show how the proposed density-difference estimator can be utilized in L2-distance approximation. Finally, we experimentally demonstrate the usefulness of the proposed method in robust distribution comparison such as class-prior estimation and change-point detection.