Group factor analysis (GFA) methods have been widely used to infer the common structure and the group-specific signals from multiple related datasets in various fields including systems biology and neuroimaging. To date, most available GFA models require Gibbs sampling or slice sampling to perform inference, which prevents the practical application of GFA to large-scale data. In this paper we present an efficient collapsed variational inference (CVI) algorithm for the nonparametric Bayesian group factor analysis (NGFA) model built upon an hierarchical beta Bernoulli process. Our CVI algorithm proceeds by marginalizing out the group-specific beta process parameters, and then approximating the true posterior in the collapsed space using mean field methods. Experimental results on both synthetic and real-world data demonstrate the effectiveness of our CVI algorithm for the NGFA compared with state-of-the-art GFA methods.

Machine Learning on graph-structured data is an important and omnipresent task for a vast variety of applications including anomaly detection and dynamic network analysis. In this paper, a deep generative model is introduced to capture continuous probability densities corresponding to the nodes of an arbitrary graph. In contrast to all learning formulations in the area of discriminative pattern recognition, we propose a scalable generative optimization/algorithm theoretically proved to capture distributions at the nodes of a graph. Our model is able to generate samples from the probability densities learned at each node. This probabilistic data generation model, i.e. convolutional graph auto-encoder (CGAE), is devised based on the localized first-order approximation of spectral graph convolutions, deep learning, and the variational Bayesian inference. We apply our CGAE to a new problem, the spatio-temporal probabilistic solar irradiance prediction. Multiple solar radiation measurement sites in a wide area in northern states of the US are modeled as an undirected graph. Using our proposed model, the distribution of future irradiance given historical radiation observations is estimated for every site/node. Numerical results on the National Solar Radiation Database show state-of-the-art performance for probabilistic radiation prediction on geographically distributed irradiance data in terms of reliability, sharpness, and continuous ranked probability score.

Simulation workflow is a top-level model for the design and control of simulation process. It connects multiple simulation components with time and interaction restrictions to form a complete simulation system. Before the construction and evaluation of the component models, the validation of upper-layer simulation workflow is of the most importance in a simulation system. However, the methods especially for validating simulation workflow is very limit. Many of the existing validation techniques are domain-dependent with cumbersome questionnaire design and expert scoring. Therefore, this paper present an empirical learning-based validation procedure to implement a semi-automated evaluation for simulation workflow. First, representative features of general simulation workflow and their relations with validation indices are proposed. The calculation process of workflow credibility based on Analytic Hierarchy Process (AHP) is then introduced. In order to make full use of the historical data and implement more efficient validation, four learning algorithms, including back propagation neural network (BPNN), extreme learning machine (ELM), evolving new-neuron (eNFN) and fast incremental gaussian mixture model (FIGMN), are introduced for constructing the empirical relation between the workflow credibility and its features. A case study on a landing-process simulation workflow is established to test the feasibility of the proposed procedure. The experimental results also provide some useful overview of the state-of-the-art learning algorithms on the credibility evaluation of simulation models.

Non-negative matrix factorization (NMF) is a knowledge discovery method that is used for many fields, besides, its variational inference and Gibbs sampling method are also well-known. However, the variational approximation accuracy is not yet clarified, since NMF is not statistically regular and the prior used in the variational Bayesian NMF (VBNMF) has zero or divergence points. In this paper, using algebraic geometrical methods, we theoretically analyze the difference of the negative log evidence/marginal likelihood (free energy) between VBNMF and Bayesian NMF, and give a lower bound of the approximation accuracy, asymptotically. The results quantitatively show how well the VBNMF algorithm can approximate Bayesian NMF.

Multi-target prediction (MTP) is concerned with the simultaneous prediction of multiple target variables of diverse type. Due to its enormous application potential, it has developed into an active and rapidly expanding research field that combines several subfields of machine learning, including multivariate regression, multi-label classification, multi-task learning, dyadic prediction, zero-shot learning, network inference, and matrix completion. In this paper, we present a unifying view on MTP problems and methods. First, we formally discuss commonalities and differences between existing MTP problems. To this end, we introduce a general framework that covers the above subfields as special cases. As a second contribution, we provide a structured overview of MTP methods. This is accomplished by identifying a number of key properties, which distinguish such methods and determine their suitability for different types of problems. Finally, we also discuss a few challenges for future research.

Risk scores are simple classification models that let users make quick risk predictions by adding and subtracting a few small numbers. These models are widely used in medicine and criminal justice, but are difficult to learn from data because they need to be calibrated, sparse, use small integer coefficients and obey application-specific constraints. In this paper, we present a new machine learning approach to learn risk scores. We formulate the risk score problem as a mixed integer nonlinear program, and present a new cutting plane algorithm for non-convex settings to efficiently recover its optimal solution. We improve our algorithm with specialized techniques to generate feasible solutions, narrow the optimality gap, and reduce data-related computation. Our approach can fit risk scores in a way that scales linearly in the number of samples, provides a certificate of optimality, and obeys real-world constraints without parameter tuning or post-processing. We illustrate the performance benefits of this approach through an extensive set of numerical experiments, where we compare risk scores built using our approach to those built using heuristic approaches. We also discuss the practical benefits of our approach through an application where we build a customized risk score for ICU seizure prediction in collaboration with the Massachusetts General Hospital.

Survival analysis is a hotspot in statistical research for modeling time-to-event information with data censorship handling, which has been widely used in many applications such as clinical research, information system and other fields with survivorship bias. Many works have been proposed for survival analysis ranging from traditional statistic methods to machine learning models. However, the existing methodologies either utilize counting-based statistics on the segmented data, or have a pre-assumption on the event probability distribution w.r.t. time. Moreover, few works consider sequential patterns within the feature space. In this paper, we propose a Deep Recurrent Survival Analysis model which combines deep learning for conditional probability prediction at fine-grained level of the data, and survival analysis for tackling the censorship. By capturing the time dependency through modeling the conditional probability of the event for each sample, our method predicts the likelihood of the true event occurrence and estimates the survival rate over time, i.e., the probability of the non-occurrence of the event, for the censored data. Meanwhile, without assuming any specific form of the event probability distribution, our model shows great advantages over the previous works on fitting various sophisticated data distributions. In the experiments on the three real-world tasks from different fields, our model significantly outperforms the state-of-the-art solutions under various metrics.

Spectral estimation (SE) aims to identify how the energy of a signal (e.g., a time series) is distributed across different frequencies. This can become particularly challenging when only partial and noisy observations are available, where current methods fail to handle uncertainty appropriately. In this context, we propose a joint probabilistic model for signals, observations and spectra, where SE is addressed as an inference problem. Assuming a Gaussian process prior over the signal, we apply Bayes' rule to find the analytic posterior distribution of the spectrum given a set of observations. Besides its expressiveness and natural account of spectral uncertainty, the proposed model also provides a functional-form representation of the power spectral density, which can be optimised efficiently. Comparison with previous approaches is addressed theoretically, showing that the proposed method is an infinite-dimensional variant of the Lomb-Scargle approach, and also empirically through three experiments.

When searching for gene pathways leading to specific disease outcomes, additional information on gene characteristics is often available that may facilitate to differentiate genes related to the disease from irrelevant background when connections involving both types of genes are observed and their relationships to the disease are unknown. We propose method to single out irrelevant background genes with the help of auxiliary information through a logistic regression, and cluster relevant genes into cohesive groups using the adjacency matrix. Expectation-maximization algorithm is modified to maximize a joint pseudo-likelihood assuming latent indicators for relevance to the disease and latent group memberships as well as Poisson or multinomial distributed link numbers within and between groups. A robust version allowing arbitrary linkage patterns within the background is further derived. Asymptotic consistency of label assignments under the stochastic blockmodel is proven. Superior performance and robustness in finite samples are observed in simulation studies. The proposed robust method identifies previously missed gene sets underlying autism related neurological diseases using diverse data sources including de novo mutations, gene expressions and protein-protein interactions.

Predicting keywords performance, such as number of impressions, click-through rate (CTR), conversion rate (CVR), revenue per click (RPC), and cost per click (CPC), is critical for sponsored search in the online advertising industry. An interesting phenomenon is that, despite the size of the overall data, the data are very sparse at the individual unit level. To overcome the sparsity and leverage hierarchical information across the data structure, we propose a Dynamic Hierarchical Empirical Bayesian (DHEB) model that dynamically determines the hierarchy through a data-driven process and provides shrinkage-based estimations. Our method is also equipped with an efficient empirical approach to derive inferences through the hierarchy. We evaluate the proposed method in both simulated and real-world datasets and compare to several competitive models. The results favor the proposed method among all comparisons in terms of both accuracy and efficiency. In the end, we design a two-phase system to serve prediction in real time.