The evolution of biological sequences, such as proteins or DNAs, is driven by the three basic edit operations: substitution, insertion, and deletion. Motivated by the recent progress of neural network models for biological tasks, we implement two neural network architectures that can treat such edit operations. The first proposal is the edit invariant neural networks, based on differentiable Needleman-Wunsch algorithms. The second is the use of deep CNNs with concatenations. Our analysis shows that CNNs can recognize star-free regular expressions, and that deeper CNNs can recognize more complex regular expressions including the insertion/deletion of characters. The experimental results for the protein secondary structure prediction task suggest the importance of insertion/deletion. The test accuracy on the widely-used CB513 dataset is 71.5%, which is 1.2-points better than the current best result on non-ensemble models.

Beyond local convolution networks, we explore how to harness various external human knowledge for endowing the networks with the capability of semantic global reasoning.

We propose a new type of generative model for high-dimensional data that learns a manifold geometry of the data, rather than density, and can generate points evenly along this manifold. This is in contrast to existing generative models that represent data density, and are strongly affected by noise and other artifacts of data collection. We demonstrate how this approach corrects sampling biases and artifacts, thus improves several downstream data analysis tasks, such as clustering and classification. Finally, we demonstrate that this approach is especially useful in biology where, despite the advent of single-cell technologies, rare subpopulations and gene-interaction relationships are affected by biased sampling. We show that SUGAR can generate hypothetical populations, and it is able to reveal intrinsic patterns and mutual-information relationships between genes on a single-cell RNA sequencing dataset of hematopoiesis.

We consider a multi-armed bandit game where N players compete for K arms for T turns. Each player has different expected rewards for the arms, and the instantaneous rewards are independent and identically distributed. Performance is measured using the expected sum of regrets, compared to the optimal assignment of arms to players. We assume that each player only knows her actions and the reward she received each turn. Players cannot observe the actions of other players, and no communication between players is possible. We present a distributed algorithm and prove that it achieves an expected sum of regrets of near-O\left(\log^{2}T\right). This is the first algorithm to achieve a poly-logarithmic regret in this fully distributed scenario. All other works have assumed that either all players have the same vector of expected rewards or that communication between players is possible.

Recurrent networks of spiking neurons (RSNNs) underlie the astounding computing and learning capabilities of the brain. But computing and learning capabilities of RSNN models have remained poor, at least in comparison with ANNs. We address two possible reasons for that. One is that RSNNs in the brain are not randomly connected or designed according to simple rules, and they do not start learning as a tabula rasa network. Rather, RSNNs in the brain were optimized for their tasks through evolution, development, and prior experience. Details of these optimization processes are largely unknown. But their functional contribution can be approximated through powerful optimization methods, such as backpropagation through time (BPTT). A second major mismatch between RSNNs in the brain and models is that the latter only show a small fraction of the dynamics of neurons and synapses in the brain. We include neurons in our RSNN model that reproduce one prominent dynamical process of biological neurons that takes place at the behaviourally relevant time scale of seconds: neuronal adaptation.

Gaussian processes provide a flexible framework for forecasting, removing noise, and interpreting long temporal datasets. State space modelling (Kalman filtering) enables these non-parametric models to be deployed on long datasets by reducing the complexity to linear in the number of data points. The complexity is still cubic in the state dimension m which is an impediment to practical application. In certain special cases (Gaussian likelihood, regular spacing) the GP posterior will reach a steady posterior state when the data are very long. We leverage this and formulate an inference scheme for GPs with general likelihoods, where inference is based on single-sweep EP (assumed density filtering). The infinite-horizon model tackles the cubic cost in the state dimensionality and reduces the cost in the state dimension m to O(m^2) per data point. The model is extended to online-learning of hyperparameters. We show examples for large finite-length modelling problems, and present how the method runs in real-time on a smartphone on a continuous data stream updated at 100 Hz.

Prior work has investigated variations of prediction markets that preserve participants' (differential) privacy, which formed the basis of useful mechanisms for purchasing data for machine learning objectives. Such markets required potentially unlimited financial subsidy, however, making them impractical. In this work, we design an adaptively-growing prediction market with a bounded financial subsidy, while achieving privacy, incentives to produce accurate predictions, and precision in the sense that market prices are not heavily impacted by the added privacy-preserving noise. We briefly discuss how our mechanism can extend to the data-purchasing setting, and its relationship to traditional learning algorithms.

Statistical leverage scores emerged as a fundamental tool for matrix sketching and column sampling with applications to low rank approximation, regression, random feature learning and quadrature. Yet, the very nature of this quantity is barely understood. Borrowing ideas from the orthogonal polynomial literature, we introduce the regularized Christoffel function associated to a positive definite kernel. This uncovers a variational formulation for leverage scores for kernel methods and allows to elucidate their relationships with the chosen kernel as well as population density. Our main result quantitatively describes a decreasing relation between leverage score and population density for a broad class of kernels on Euclidean spaces. Numerical simulations support our findings.

We consider the setting of prediction with expert advice; a learner makes predictions by aggregating those of a group of experts. Under this setting, and for the right choice of loss function and ``mixing'' algorithm, it is possible for the learner to achieve a constant regret regardless of the number of prediction rounds. For example, a constant regret can be achieved for \emph{mixable} losses using the \emph{aggregating algorithm}. The \emph{Generalized Aggregating Algorithm} (GAA) is a name for a family of algorithms parameterized by convex functions on simplices (entropies), which reduce to the aggregating algorithm when using the \emph{Shannon entropy} $\operatorname{S}$. For a given entropy $\Phi$, losses for which a constant regret is possible using the \textsc{GAA} are called $\Phi$-mixable. Which losses are $\Phi$-mixable was previously left as an open question. We fully characterize $\Phi$-mixability and answer other open questions posed by \cite{Reid2015}. We show that the Shannon entropy $\operatorname{S}$ is fundamental in nature when it comes to mixability; any $\Phi$-mixable loss is necessarily $\operatorname{S}$-mixable, and the lowest worst-case regret of the \textsc{GAA} is achieved using the Shannon entropy. Finally, by leveraging the connection between the \emph{mirror descent algorithm} and the update step of the GAA, we suggest a new \emph{adaptive} generalized aggregating algorithm and analyze its performance in terms of the regret bound.

In this paper we consider the case of generative models. In particular, we investigate generative adversarial networks (GANs) in the task of learning new categories in a sequential fashion. We first show that sequential fine tuning renders the network unable to properly generate images from previous categories (i.e.