This paper presents an approach that predicts the effectiveness of HIV combination therapies by simultaneously addressing several problems affecting the available HIV clinical data sets: the different treatment backgrounds of the samples, the uneven representation of the levels of therapy experience, the missing treatment history information, the uneven therapy representation and the unbalanced therapy outcome representation. The computational validation on clinical data shows that, compared to the most commonly used approach that does not account for the issues mentioned above, our model has significantly higher predictive power. This is especially true for samples stemming from patients with longer treatment history and samples associated with rare therapies. Furthermore, our approach is at least as powerful for the remaining samples.

The group Lasso is an extension of the Lasso for feature selection on (predefined) non-overlapping groups of features. The non-overlapping group structure limits its applicability in practice. There have been several recent attempts to study a more general formulation, where groups of features are given, potentially with overlaps between the groups. The resulting optimization is, however, much more challenging to solve due to the group overlaps. In this paper, we consider the efficient optimization of the overlapping group Lasso penalized problem. We reveal several key properties of the proximal operator associated with the overlapping group Lasso, and compute the proximal operator by solving the smooth and convex dual problem, which allows the use of the gradient descent type of algorithms for the optimization. We have performed empirical evaluations using both synthetic and the breast cancer gene expression data set, which consists of 8,141 genes organized into (overlapping) gene sets. Experimental results show that the proposed algorithm is more efficient than existing state-of-the-art algorithms.

Unlike existing nonparametric Bayesian models, which rely solely on specially conceived priors to incorporate domain knowledge for discovering improved latent representations, we study nonparametric Bayesian inference with regularization on the desired posterior distributions. While priors can indirectly affect posterior distributions through Bayes' theorem, imposing posterior regularization is arguably more direct and in some cases can be much easier. We particularly focus on developing infinite latent support vector machines (iLSVM) and multi-task infinite latent support vector machines (MT-iLSVM), which explore the large-margin idea in combination with a nonparametric Bayesian model for discovering predictive latent features for classification and multi-task learning, respectively. We present efficient inference methods and report empirical studies on several benchmark datasets. Our results appear to demonstrate the merits inherited from both large-margin learning and Bayesian nonparametrics.

In this paper we present an algorithm to learn a multi-label classifier which attempts at directly optimising the F-score. The key novelty of our formulation is that we explicitly allow for assortative (submodular) pairwise label interactions, i.e., we can leverage the co-ocurrence of pairs of labels in order to improve the quality of prediction. Prediction in this model consists of minimising a particular submodular set function, what can be accomplished exactly and efficiently via graph-cuts. Learning however is substantially more involved and requires the solution of an intractable combinatorial optimisation problem. We present an approximate algorithm for this problem and prove that it is sound in the sense that it never predicts incorrect labels. We also present a nontrivial test of a sufficient condition for our algorithm to have found an optimal solution. We present experiments on benchmark multi-label datasets, which attest the value of our proposed technique. We also make available source code that enables the reproduction of our experiments.

High dimensional similarity search in large scale databases becomes an important challenge due to the advent of Internet. For such applications, specialized data structures are required to achieve computational efficiency. Traditional approaches relied on algorithmic constructions that are often data independent (such as Locality Sensitive Hashing) or weakly dependent (such as kd-trees, k-means trees). While supervised learning algorithms have been applied to related problems, those proposed in the literature mainly focused on learning hash codes optimized for compact embedding of the data rather than search efficiency. Consequently such an embedding has to be used with linear scan or another search algorithm. Hence learning to hash does not directly address the search efficiency issue. This paper considers a new framework that applies supervised learning to directly optimize a data structure that supports efficient large scale search. Our approach takes both search quality and computational cost into consideration. Specifically, we learn a boosted search forest that is optimized using pair-wise similarity labeled examples. The output of this search forest can be efficiently converted into an inverted indexing data structure, which can leverage modern text search infrastructure to achieve both scalability and efficiency. Experimental results show that our approach significantly outperforms the start-of-the-art learning to hash methods (such as spectral hashing), as well as state-of-the-art high dimensional search algorithms (such as LSH and k-means trees).

The object people perceive in an image can depend on its orientation relative to the scene it is in (its reference frame). For example, the images of the symbols $\times$ and $+$ differ by a 45 degree rotation. Although real scenes have multiple images and reference frames, psychologists have focused on scenes with only one reference frame. We propose an ideal observer model based on nonparametric Bayesian statistics for inferring the number of reference frames in a scene and their parameters. When an ambiguous image could be assigned to two conflicting reference frames, the model predicts two factors should influence the reference frame inferred for the image: The image should be more likely to share the reference frame of the closer object ({\em proximity}) and it should be more likely to share the reference frame containing the most objects ({\em alignment}). We confirm people use both cues using a novel methodology that allows for easy testing of human reference frame inference.

We consider the problem of assigning class labels to an unlabeled test data set, given several labeled training data sets drawn from similar distributions. This problem arises in several applications where data distributions fluctuate because of biological, technical, or other sources of variation. We develop a distribution-free, kernel-based approach to the problem. This approach involves identifying an appropriate reproducing kernel Hilbert space and optimizing a regularized empirical risk over the space. We present generalization error analysis, describe universal kernels, and establish universal consistency of the proposed methodology. Experimental results on flow cytometry data are presented.

An accurate model of patient survival time can help in the treatment and care of cancer patients. The common practice of providing survival time estimates based only on population averages for the site and stage of cancer ignores many important individual differences among patients. In this paper, we propose a local regression method for learning patient-specific survival time distribution based on patient attributes such as blood tests and clinical assessments. When tested on a cohort of more than 2000 cancer patients, our method gives survival time predictions that are much more accurate than popular survival analysis models such as the Cox and Aalen regression models. Our results also show that using patient-specific attributes can reduce the prediction error on survival time by as much as 20% when compared to using cancer site and stage only.

Topic models are learned via a statistical model of variation within document collections, but designed to extract meaningful semantic structure. Desirable traits include the ability to incorporate annotations or metadata associated with documents; the discovery of correlated patterns of topic usage; and the avoidance of parametric assumptions, such as manual specification of the number of topics. We propose a doubly correlated nonparametric topic (DCNT) model, the first model to simultaneously capture all three of these properties. The DCNT models metadata via a flexible, Gaussian regression on arbitrary input features; correlations via a scalable square-root covariance representation; and nonparametric selection from an unbounded series of potential topics via a stick-breaking construction. We validate the semantic structure and predictive performance of the DCNT using a corpus of NIPS documents annotated by various metadata.

Inexpensive RGB-D cameras that give an RGB image together with depth data have become widely available. In this paper, we use this data to build 3D point clouds of full indoor scenes such as an office and address the task of semantic labeling of these 3D point clouds. We propose a graphical model that captures various features and contextual relations, including the local visual appearance and shape cues, object co-occurence relationships and geometric relationships. With a large number of object classes and relations, the model’s parsimony becomes important and we address that by using multiple types of edge potentials. The model admits efficient approximate inference, and we train it using a maximum-margin learning approach. In our experiments over a total of 52 3D scenes of homes and offices (composed from about 550 views, having 2495 segments labeled with 27 object classes), we get a performance of 84.06% in labeling 17 object classes for offices, and 73.38% in labeling 17 object classes for home scenes. Finally, we applied these algorithms successfully on a mobile robot for the task of finding objects in large cluttered rooms.