Theproblem of support union recovery is to recover the subset of covariates that are active in at least one of the regression problems.

We consider the problem of extracting smooth low-dimensional ``neural trajectories'' that summarize the activity recorded simultaneously from tens to hundreds of neurons on individual experimental trials. Beyond the benefit of visualizing the high-dimensional noisy spiking activity in a compact denoised form, such trajectories can offer insight into the dynamics of the neural circuitry underlying the recorded activity. Current methods for extracting neural trajectories involve a two-stage process: the data are first ``denoised'' by smoothing over time, then a static dimensionality reduction technique is applied. We first describe extensions of the two-stage methods that allow the degree of smoothing to be chosen in a principled way, and account for spiking variability that may vary both across neurons and across time. We then present a novel method for extracting neural trajectories, Gaussian-process factor analysis (GPFA), which unifies the smoothing and dimensionality reduction operations in a common probabilistic framework. We applied these methods to the activity of 61 neurons recorded simultaneously in macaque premotor and motor cortices during reach planning and execution. By adopting a goodness-of-fit metric that measures how well the activity of each neuron can be predicted by all other recorded neurons, we found that GPFA provided a better characterization of the population activity than the two-stage methods. From the extracted single-trial neural trajectories, we directly observed a convergence in neural state during motor planning, an effect suggestive of attractor dynamics that was shown indirectly by previous studies.

Regularized risk minimization often involves non-smooth optimization, either because of the loss function (e.g., hinge loss) or the regularizer (e.g., $\ell_1$-regularizer). Gradient descent methods, though highly scalable and easy to implement, are known to converge slowly on these problems. In this paper, we develop novel accelerated gradient methods for stochastic optimization while still preserving their computational simplicity and scalability. The proposed algorithm, called SAGE (Stochastic Accelerated GradiEnt), exhibits fast convergence rates on stochastic optimization with both convex and strongly convex objectives. Experimental results show that SAGE is faster than recent (sub)gradient methods including FOLOS, SMIDAS and SCD. Moreover, SAGE can also be extended for online learning, resulting in a simple but powerful algorithm.

We show how to model documents as bags of words using family of two-layer, undirected graphical models. Each member of the family has the same number of binary hidden units but a different number of ``softmax visible units. All of the softmax units in all of the models in the family share the same weights to the binary hidden units. We describe efficient inference and learning procedures for such a family. Each member of the family models the probability distribution of documents of a specific length as a product of topic-specific distributions rather than as a mixture and this gives much better generalization than Latent Dirichlet Allocation for modeling the log probabilities of held-out documents. The low-dimensional topic vectors learned by the undirected family are also much better than LDA topic vectors for retrieving documents that are similar to a query document. The learned topics are more general than those found by LDA because precision is achieved by intersecting many general topics rather than by selecting a single precise topic to generate each word.

We study the problem of domain transfer for a supervised classification task in mRNA splicing. We consider a number of recent domain transfer methods from machine learning, including some that are novel, and evaluate them on genomic sequence data from model organisms of varying evolutionary distance. We find that in cases where the organisms are not closely related, the use of domain adaptation methods can help improve classification performance.

We introduce the first temporal-difference learning algorithm that is stable with linear function approximation and off-policy training, for any finite Markov decision process, target policy, and exciting behavior policy, and whose complexity scales linearly in the number of parameters. We consider an i.i.d.\ policy-evaluation setting in which the data need not come from on-policy experience. The gradient temporal-difference (GTD) algorithm estimates the expected update vector of the TD(0) algorithm and performs stochastic gradient descent on its L_2 norm. Our analysis proves that its expected update is in the direction of the gradient, assuring convergence under the usual stochastic approximation conditions to the same least-squares solution as found by the LSTD, but without its quadratic computational complexity. GTD is online and incremental, and does not involve multiplying by products of likelihood ratios as in importance-sampling methods.

Resting state activity is brain activation that arises in the absence of any task, and is usually measured in awake subjects during prolonged fMRI scanning sessions where the only instruction given is to close the eyes and do nothing. It has been recognized in recent years that resting state activity is implicated in a wide variety of brain function. While certain networks of brain areas have different levels of activation at rest and during a task, there is nevertheless significant similarity between activations in the two cases. This suggests that recordings of resting state activity can be used as a source of unlabeled data to augment discriminative regression techniques in a semi-supervised setting. We evaluate this setting empirically yielding three main results: (i) regression tends to be improved by the use of Laplacian regularization even when no additional unlabeled data are available, (ii) resting state data may have a similar marginal distribution to that recorded during the execution of a visual processing task reinforcing the hypothesis that these conditions have similar types of activation, and (iii) this source of information can be broadly exploited to improve the robustness of empirical inference in fMRI studies, an inherently data poor domain.

Detecting underlying clusters from large-scale data plays a central role in machine learning research. In this paper, we attempt to tackle clustering problems for complex data of multiple distributions and large multi-scales. To this end, we develop an algorithm named Zeta $l$-links, or Zell which consists of two parts: Zeta merging with a similarity graph and an initial set of small clusters derived from local $l$-links of the graph. More specifically, we propose to structurize a cluster using cycles in the associated subgraph. A mathematical tool, Zeta function of a graph, is introduced for the integration of all cycles, leading to a structural descriptor of the cluster in determinantal form. The popularity character of the cluster is conceptualized as the global fusion of variations of the structural descriptor by means of the leave-one-out strategy in the cluster. Zeta merging proceeds, in the agglomerative fashion, according to the maximum incremental popularity among all pairwise clusters. Experiments on toy data, real imagery data, and real sensory data show the promising performance of Zell. The $98.1\%$ accuracy, in the sense of the normalized mutual information, is obtained on the FRGC face data of 16028 samples and 466 facial clusters. The MATLAB codes of Zell will be made publicly available for peer evaluation.

As the availability and importance of relational data--such as the friendships summarized ona social networking website--increases, it becomes increasingly important to have good models for such data. The kinds of latent structure that have been considered for use in predicting links in such networks have been relatively limited. In particular, the machine learning community has focused on latent class models, adapting Bayesian nonparametric methods to jointly infer how many latent classesthere are while learning which entities belong to each class. We pursue a similar approach with a richer kind of latent variable--latent features--using a Bayesian nonparametric approach to simultaneously infer the number of features at the same time we learn which entities have each feature. Our model combines these inferred features with known covariates in order to perform link prediction. We demonstrate that the greater expressiveness of this approach allows us to improve performanceon three datasets.

Extensive labeled data for image annotation systems, which learn to assign class labels to image regions, is difficult to obtain. We explore a hybrid model framework for utilizing partially labeled data that integrates a generative topic model for image appearance with discriminative label prediction. We propose three alternative formulations for imposing a spatial smoothness prior on the image labels. Tests of the new models and some baseline approaches on two real image datasets demonstrate the effectiveness of incorporating the latent structure.