Viral sequence classification is an important task in pathogen detection, epidemiological surveys and evolutionary studies. Statistical learning methods are widely used to classify and identify viral sequences in samples from environments. These methods face several challenges associated with the nature and properties of viral genomes such as recombination, mutation rate and diversity. Also, new generations of sequencing technologies rise other difficulties by generating massive amounts of fragmented sequences. While linear classifiers are often used to classify viruses, there is a lack of exploration of the accuracy space of existing models in the context of alignment free approaches. In this study, we present an exhaustive assessment procedure exploring the power of linear classifiers in genotyping and subtyping partial and complete genomes. It is applied to the Hepatitis C viruses (HCV). Several variables are considered in this investigation such as classifier types (generative and discriminative) and their hyper-parameters (smoothing value and penalty function), the classification task (genotyping and subtyping), the length of the tested sequences (partial and complete) and the length of k-mer words. Overall, several classifiers perform well given a set of precise combination of the experimental variables mentioned above. Finally, we provide the procedure and benchmark data to allow for more robust assessment of classification from virus genomes.

Existing multi-view learning methods based on kernel function either require the user to select and tune a single predefined kernel or have to compute and store many Gram matrices to perform multiple kernel learning. Apart from the huge consumption of manpower, computation and memory resources, most of these models seek point estimation of their parameters, and are prone to overfit-ting to small training data. This paper presents an adaptive kernel nonlinear max-margin multi-view learning model under the Bayesian framework. Specifically, we regularize the posterior of an efficient multi-view latent variable model by explicitly mapping the latent representations extracted from multiple data views to a random Fourier feature space where max-margin classification constraints are imposed. Assuming these random features are drawn from Dirichlet process Gaussian mixtures, we can adaptively learn shift-invariant kernels from data according to Bochners theorem. For inference, we employ the data augmentation idea for hinge loss, and design an efficient gradient-based MCMC sampler in the augmented space. Having no need to compute the Gram matrix, our algorithm scales linearly with the size of training set. Extensive experiments on real-world datasets demonstrate that our method has superior performance.

Here, we use the nomenclature derived from the meta-learning literature which is the most prevalent at time of writing. Let S {( x l,y l)} L l 1 be a support-set containing input-output pairs, with L equal to one (1-shot) or five (5-shot), and Q { (x m,y m)} M m 1be a query-set (sometimes referred to in the literature as a target-set), with M typically one order of magnitude greater than L. For ease of notation, the support and query sets are grouped in a task T {S, Q}, with the dataset D {T n} N n 1 defined as a collection of such tasks. Models are trained on random tasks sampled from D . Then, given a new task T {S, Q } sampled from a test set, the objective is to condition the model on the samples of the support S to estimate the membership of the samples in the query set Q . In the most common scenario, the inputs x D belong to the same distribution p(x) and are distributed across training, validation, and test sets such that their class membership is non-overlapping. Note that y can be a continuous value (regression) or a discrete one (classification), even though most of the previous work has focused on classification. We also consider the cross-domain scenario, where the inputs are sampled from different distributions at training and test time; this is more representative of real-world scenarios.

We develop a novel approximate Bayesian computation (ABC) framework, ABCDP, that obeys the notion of differential privacy (DP). Under our framework, simply performing ABC inference with a mild modification yields differentially private posterior samples. We theoretically analyze the interplay between the ABC similarity threshold $\epsilon_{abc}$ (for comparing the similarity between real and simulated data) and the resulting privacy level $\epsilon_{dp}$ of the posterior samples, in two types of frequently-used ABC algorithms. We apply ABCDP to simulated data as well as privacy-sensitive real data. The results suggest that tuning the similarity threshold $\epsilon_{abc}$ helps us obtain better privacy and accuracy trade-off.

As the availability and importance of temporal interaction data--such as email communication--increases, it becomes increasingly important to understand the underlying structure that underpins these interactions. Often these interactions form a multigraph, where we might have multiple interactions between two entities. Such multigraphs tend to be sparse yet structured, and their distribution often evolves over time. Existing statistical models with interpretable parameters can capture some, but not all, of these properties. We propose a dynamic nonparametric model for interaction multigraphs that combines the sparsity of edge-exchangeable multigraphs with dynamic clustering patterns that tend to reinforce recent behavioral patterns. We show that our method yields improved held-out likelihood over stationary variants, and impressive predictive performance against a range of state-of-the-art dynamic graph models.

Dynamical system models (including RNNs) often lack the ability to adapt the sequence generation or prediction to a given context, limiting their real-world application. In this paper we show that hierarchical multi-task dynamical systems (MTDSs) provide direct user control over sequence generation, via use of a latent code $\mathbf{z}$ that specifies the customization to the individual data sequence. This enables style transfer, interpolation and morphing within generated sequences. We show the MTDS can improve predictions via latent code interpolation, and avoid the long-term performance degradation of standard RNN approaches.

Predictive business process monitoring aims at providing predictions about running instances by analyzing logs of completed cases in a business process. Recently, a lot of research focuses on increasing productivity and efficiency in a business process by forecasting potential problems during its executions. However, most of the studies lack suggesting concrete actions to improve the process. They leave it up to the subjective judgment of a user. In this paper, we propose a novel method to connect the results from predictive business process monitoring to actual business process improvements. More in detail, we optimize the resource allocation in a non-clairvoyant online environment, where we have limited information required for scheduling, by exploiting the predictions. The proposed method integrates the offline prediction model construction that predicts the processing time and the next activity of an ongoing instance using Bayesian Neural Networks (BNNs) with the online resource allocation that is extended from the minimum cost and maximum flow algorithm. To validate the proposed method, we performed experiments using an artificial event log and a real-life event log from a global financial organization.

Hierarchical Reinforcement Learning (HRL) is a promising approach to solving long-horizon problems with sparse and delayed rewards. Many existing HRL algorithms either use pre-trained low-level skills that are unadaptable, or require domain-specific information to define low-level rewards. In this paper, we aim to adapt low-level skills to downstream tasks while maintaining the generality of reward design. We propose an HRL framework which sets auxiliary rewards for low-level skill training based on the advantage function of the high-level policy. This auxiliary reward enables efficient, simultaneous learning of the high-level policy and low-level skills without using task-specific knowledge. In addition, we also theoretically prove that optimizing low-level skills with this auxiliary reward will increase the task return for the joint policy. Experimental results show that our algorithm dramatically outperforms other state-of-the-art HRL methods in Mujoco domains. We also find both low-level and high-level policies trained by our algorithm transferable.

We propose a general method for distributed Bayesian model choice, where each worker has access only to non-overlapping subsets of the data. Our approach approximates the model evidence for the full data set through Monte Carlo sampling from the posterior on every subset generating a model evidence per subset. The model evidences per worker are then consistently combined using a novel approach which corrects for the splitting using summary statistics of the generated samples. This divide-and-conquer approach allows Bayesian model choice in the large data setting, exploiting all available information but limiting communication between workers. Our work thereby complements the work on consensus Monte Carlo (Scott et al., 2016) by explicitly enabling model choice. In addition, we show how the suggested approach can be extended to model choice within a reversible jump setting that explores multiple models within one run.

Multi-head attention mechanism is capable of learning various representations from sequential data while paying attention to different subsequences, e.g., word-pieces or syllables in a spoken word. From the subsequences, it retrieves richer information than a single-head attention which only summarizes the whole sequence into one context vector. However, a naive use of the multi-head attention does not guarantee such richness as the attention heads may have positional and representational redundancy. In this paper, we propose a regularization technique for multi-head attention mechanism in an end-to-end neural keyword spotting system. Augmenting regularization terms which penalize positional and contextual non-orthogonality between the attention heads encourages to output different representations from separate subsequences, which in turn enables leveraging structured information without explicit sequence models such as hidden Markov models. In addition, intra-head contextual non-orthogonality regularization encourages each attention head to have similar representations across keyword examples, which helps classification by reducing feature variability. The experimental results demonstrate that the proposed regularization technique significantly improves the keyword spotting performance for the keyword "Hey Snapdragon".