Multitask Gaussian process (MTGP) is powerful for joint learning of multiple tasks with complicated correlation patterns. However, due to the assembling of additive independent latent functions (LFs), all current MTGPs including the salient linear model of coregionalization (LMC) and convolution frameworks cannot effectively represent and learn the hierarchical latent interactions between its LFs. In this paper, we further investigate the interactions in LMC of MTGP and then propose a novel kernel representation of the hierarchical interactions, which ameliorates both the expressiveness and the interpretability of MTGP. Specifically, we express the interaction as a product of function interaction (FI) and coefficient interaction. The FI is modeled by using cross convolution of LFs. The coefficient interaction between the LMCs is described as a free-form coupling coregionalization term. We validate that considering the interactions can promote knowledge transferring in MTGP and compare our approach with some state-of-the-art MTGPs on both synthetic-and real-world datasets.

Radiology reports are of core importance for the communication between the radiologist and clinician. A computer-aided radiology report system can assist radiologists in this task and reduce variation between reports thus facilitating communication with the medical doctor or clinician. Producing a well structured, clear, and clinically well-focused radiology report is essential for high-quality patient diagnosis and care. Despite recent advances in deep learning for image caption generation, this task remains highly challenging in a medical setting. Research has mainly focused on the design of tailored machine learning methods for this task, while little attention has been devoted to the development of evaluation metrics to assess the quality of AI-generated documents. Conventional quality metrics for natural language processing methods like the popular BLEU score, provide little information about the quality of the diagnostic content of AI-generated radiology reports. In particular, because radiology reports often use standardized sentences, BLEU scores of generated reports can be high while they lack diagnostically important information. We investigate this problem and propose a new measure that quantifies the diagnostic content of AI-generated radiology reports. In addition, we exploit the standardization of reports by generating a sequence of sentences. That is, instead of using a dictionary of words, as current image captioning methods do, we use a dictionary of sentences. The assumption underlying this choice is that radiologists use a well-focused vocabulary of 'standard' sentences, which should suffice for composing most reports. As a by-product, a significant training speed-up is achieved compared to models trained on a dictionary of words. Overall, results of our investigation indicate that standard validation metrics for AI-generated documents are weakly correlated with the diagnostic content of the reports. Therefore, these measures should be not used as only validation metrics, and measures evaluating diagnostic content should be preferred in such a medical context.

Abstract Long-term forecasting involves predicting a horizon that is far ahead of the last observation. It is a problem of high practical relevance, for instance for companies in order to decide upon expensive long-term investments. Despite the recent progress and success of Gaussian processes (GPs) based on spectral mixture kernels, long-term forecasting remains a challenging problem for these kernels because they decay exponentially at large horizons. This is mainly due to their use of a mixture of Gaussians to model spectral densities. Characteristics of the signal important for long-term forecasting can be unravelled by investigating the distribution of the Fourier coefficients of (the training part of) the signal, which is non-smooth, heavy-tailed, sparse, and skewed. The heavy tail and skewness characteristics of such distributions in the spectral domain allow to capture long-range covariance of the signal in the time domain. Motivated by these observations, we propose to model spectral densities using a skewed Laplace spectral mixture (SLSM) due to the skewness of its peaks, sparsity, non-smoothness, and heavy tail characteristics. By applying the inverse Fourier Transform to this spectral density we obtain a new GP kernel for long-term forecasting. In addition, we adapt the lottery ticket method, originally developed to prune weights of a neural network, to GPs in order to automatically select the number of kernel components. Results of extensive experiments, including a multivariate time series, show the beneficial effect of the proposed SLSM kernel for long-term extrapolation and robustness to the choice of the number of mixture components.

Multioutput Gaussian processes (MOGPs) are an extension of Gaussian processes (GPs) for predicting multiple output variables (also called channels/tasks) simultaneously. In this article, we use the convolution theorem to design a new kernel for MOGPs by modeling cross-channel dependencies through cross convolution of time-and phase-delayed components in the spectral domain. The resulting kernel is called multioutput convolution spectral mixture (MOCSM) kernel. The results of extensive experiments on synthetic and real-life data sets demonstrate the advantages of the proposed kernel and its state-of-the-art performance. MOCSM enjoys the desirable property to reduce to the well-known spectral mixture (SM) kernel when a single channel is considered. A comparison with the recently introduced multioutput SM kernel reveals that this is not the case for the latter kernel, which contains quadratic terms that generate undesirable scale effects when the spectral densities of different channels are either very close or very far from each other in the frequency domain.

Multitask Gaussian processes (MTGPs) are a powerful approach for modeling dependencies between multiple related tasks or functions for joint regression. Current kernels for MTGPs cannot fully model nonlinear task correlations and other types of dependencies. In this article, we address this limitation. We focus on spectral mixture (SM) kernels and propose an enhancement of this type of kernels, called multitask generalized convolution SM (MT-GCSM) kernel. The MT-GCSM kernel can model nonlinear task correlations and dependence between components, including time and phase delay dependence. Each task in MT-GCSM has its GCSM kernel with its number of convolution structures, and dependencies between all components from different tasks are considered. Another constraint of current kernels for MTGPs is that components from different tasks are aligned. Here, we lift this constraint by using inner and outer full cross convolution between a base component and the reversed complex conjugate of another base component. Extensive experiments on two synthetic and three real-life data sets illustrate the difference between MT-GCSM and previous SM kernels as well as the practical effectiveness of MT-GCSM.

We consider unsupervised domain adaptation: given labelled examples from a source domain and unlabelled examples from a related target domain, the goal is to infer the labels of target examples.Under the assumption that features from pre-trained deep neural networks are transferable across related domains, domain adaptation reduces to aligning source and target domain at class prediction uncertainty level.We tackle this problem by introducing a method based on adversarial learning which forces the label uncertainty predictions on the target domain to be indistinguishable from those on the source domain.Pre-trained deep neural networks are used to generate deep features having high transferability across related domains.We perform an extensive experimental analysis of the proposed method over a wide set of publicly available pre-trained deep neural networks.Results of our experiments on domain adaptation tasks for image classification show that class prediction uncertainty alignment with features extracted from pre-trained deep neural networks provides an efficient, robust and effective method for domain adaptation.

Unsupervised domain adaptation (UDA) amounts to assigning class labels to the unlabeled instances of a dataset from a target domain, using labeled instances of a dataset from a related source domain. In this paper we propose to cast this problem in a game-theoretic setting as a non-cooperative game and introduce a fully automatized iterative algorithm for UDA based on graph transduction games (GTG). The main advantages of this approach are its principled foundation, guaranteed termination of the iterative algorithms to a Nash equilibrium (which corresponds to a consistent labeling condition) and soft labels quantifying uncertainty of the label assignment process. We also investigate the beneficial effect of using pseudo-labels from linear classifiers to initialize the iterative process. The performance of the resulting methods is assessed on publicly available object recognition benchmark datasets involving both shallow and deep features. Results of experiments demonstrate the suitability of the proposed game-theoretic approach for solving UDA tasks.

Abstract Gaussian processes (GPs) are an elegant Bayesian approach to model an unknown function. The choice of the kernel characterizes one’s assumption on how the unknown function autocovaries. It is a core aspect of a GP design, since the posterior distribution can significantly vary for different kernels. The spectral mixture (SM) kernel is derived by modelling a spectral density - the Fourier transform of a kernel - with a linear mixture of Gaussian components. As such, the SM kernel cannot model dependencies between components. In this paper we use cross convolution to model dependencies between components and derive a new kernel called Generalized Convolution Spectral Mixture (GCSM). Experimental analysis of GCSM on synthetic and real-life datasets indicates the benefit of modeling dependencies between components for reducing uncertainty and for improving performance in extrapolation tasks.

Local network community detection is the task of finding a single community of nodes concentrated around few given seed nodes in a localized way. Conductance is a popular objective function used in many algorithms for local community detection. This paper studies a continuous relaxation of conductance. We show that continuous optimization of this objective still leads to discrete communities. We investigate the relation of conductance with weighted kernel k-means for a single community, which leads to the introduction of a new objective function, $\sigma$-conductance. Conductance is obtained by setting $\sigma$ to $0$. Two algorithms, EMc and PGDc, are proposed to locally optimize $\sigma$-conductance and automatically tune the parameter $\sigma$. They are based on expectation maximization and projected gradient descent, respectively. We prove locality and give performance guarantees for EMc and PGDc for a class of dense and well separated communities centered around the seeds. Experiments are conducted on networks with ground-truth communities, comparing to state-of-the-art graph diffusion algorithms for conductance optimization. On large graphs, results indicate that EMc and PGDc stay localized and produce communities most similar to the ground, while graph diffusion algorithms generate large communities of lower quality. (Source code of the algorithms used in the paper is available online.)

MOTIVATION: The in silico prediction of potential interactions between drugs and target proteins is of core importance for the identification of new drugs or novel targets for existing drugs. However, only a tiny portion of all drug-target pairs in current datasets are experimentally validated interactions. This motivates the need for developing computational methods that predict true interaction pairs with high accuracy. RESULTS: We show that a simple machine learning method that uses the drug-target network as the only source of information is capable of predicting true interaction pairs with high accuracy. Specifically, we introduce interaction profiles of drugs (and of targets) in a network, which are binary vectors specifying the presence or absence of interaction with every target (drug) in that network. We define a kernel on these profiles, called the Gaussian Interaction Profile (GIP) kernel, and use a simple classifier, (kernel) Regularized Least Squares (RLS), for prediction drug-target interactions. We test comparatively the effectiveness of RLS with the GIP kernel on four drug-target interaction networks used in previous studies. The proposed algorithm achieves area under the precision-recall curve (AUPR) up to 92.7, significantly improving over results of state-of-the-art methods. Moreover, we show that using also kernels based on chemical and genomic information further increases accuracy, with a neat improvement on small datasets. These results substantiate the relevance of the network topology (in the form of interaction profiles) as source of information for predicting drug-target interactions. AVAILABILITY: Software and Supplementary Material are available at http://cs.ru.nl/~tvanlaarhoven/drugtarget2011/. CONTACT: [email protected]; [email protected]. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.