In this study we present a kernel based convolution model to characterize neural responses to natural sounds by decoding their time-varying acoustic features. The model allows to decode natural sounds from high-dimensional neural recordings, such as magnetoencephalography (MEG), that track timing and location of human cortical signalling noninvasively across multiple channels. We used the MEG responses recorded from subjects listening to acoustically different environmental sounds. By decoding the stimulus frequencies from the responses, our model was able to accurately distinguish between two different sounds that it had never encountered before with 70% accuracy. Convolution models typically decode frequencies that appear at a certain time point in the sound signal by using neural responses from that time point until a certain fixed duration of the response. Using our model, we evaluated several fixed durations (time-lags) of the neural responses and observed auditory MEG responses to be most sensitive to spectral content of the sounds at time-lags of 250 ms to 500 ms. The proposed model should be useful for determining what aspects of natural sounds are represented by high-dimensional neural responses and may reveal novel properties of neural signals.

With the wealth of high-throughput sequencing data generated by recent large-scale consortia, predictive gene expression modelling has become an important tool for integrative analysis of transcriptomic and epigenetic data. However, sequencing data-sets are characteristically large, and previously modelling frameworks are typically inefficient and unable to leverage multi-core or distributed processing architectures. In this study, we detail an efficient and parallelised MapReduce implementation of gene expression modelling. We leverage the computational efficiency of this framework to provide an integrative analysis of over fifty histone modification data-sets across a variety of cancerous and non-cancerous cell-lines. Our results demonstrate that the genome-wide relationships between histone modifications and mRNA transcription are lineage, tissue and karyotype-invariant, and that models trained on matched epigenetic/transcriptomic data from non-cancerous cell-lines are able to predict cancerous expression with equivalent genome-wide fidelity.

Given a similarity graph between items, correlation clustering (CC) groups similar items together and dissimilar ones apart. One of the most popular CC algorithms is KwikCluster: an algorithm that serially clusters neighborhoods of vertices, and obtains a 3-approximation ratio. Unfortunately, KwikCluster in practice requires a large number of clustering rounds, a potential bottleneck for large graphs. We present C4 and ClusterWild!, two algorithms for parallel correlation clustering that run in a polylogarithmic number of rounds and achieve nearly linear speedups, provably. C4 uses concurrency control to enforce serializability of a parallel clustering process, and guarantees a 3-approximation ratio. ClusterWild! is a coordination free algorithm that abandons consistency for the benefit of better scaling; this leads to a provably small loss in the 3-approximation ratio. We provide extensive experimental results for both algorithms, where we outperform the state of the art, both in terms of clustering accuracy and running time. We show that our algorithms can cluster billion-edge graphs in under 5 seconds on 32 cores, while achieving a 15x speedup.

Much of the focus in machine learning research is placed in creating new architectures and optimization methods, but the overall loss function is seldom questioned. This paper interprets machine learning from a multi-objective optimization perspective, showing the limitations of the default linear combination of loss functions over a data set and introducing the hypervolume indicator as an alternative. It is shown that the gradient of the hypervolume is defined by a self-adjusting weighted mean of the individual loss gradients, making it similar to the gradient of a weighted mean loss but without requiring the weights to be defined a priori. This enables an inner boosting-like behavior, where the current model is used to automatically place higher weights on samples with higher losses but without requiring the use of multiple models. Results on a denoising autoencoder show that the new formulation is able to achieve better mean loss than the direct optimization of the mean loss, providing evidence to the conjecture that self-adjusting the weights creates a smoother loss surface.

We consider the problem of learning a dictionary matrix from a number of observed signals, which are assumed to be generated via a linear model with a common underlying dictionary. In particular, we derive lower bounds on the minimum achievable worst case mean squared error (MSE), regardless of computational complexity of the dictionary learning (DL) schemes. By casting DL as a classical (or frequentist) estimation problem, the lower bounds on the worst case MSE are derived by following an established information-theoretic approach to minimax estimation. The main conceptual contribution of this paper is the adaption of the information-theoretic approach to minimax estimation for the DL problem in order to derive lower bounds on the worst case MSE of any DL scheme. We derive three different lower bounds applying to different generative models for the observed signals. The first bound applies to a wide range of models, it only requires the existence of a covariance matrix of the (unknown) underlying coefficient vector. By specializing this bound to the case of sparse coefficient distributions, and assuming the true dictionary satisfies the restricted isometry property, we obtain a lower bound on the worst case MSE of DL schemes in terms of a signal to noise ratio (SNR). The third bound applies to a more restrictive subclass of coefficient distributions by requiring the non-zero coefficients to be Gaussian. While, compared with the previous two bounds, the applicability of this final bound is the most limited it is the tightest of the three bounds in the low SNR regime.

Recent years have seen the development of methods for multiagent planning under uncertainty that scale to tens or even hundreds of agents. However, most of these methods either make restrictive assumptions on the problem domain, or provide approximate solutions without any guarantees on quality. Methods in the former category typically build on heuristic search using upper bounds on the value function. Unfortunately, no techniques exist to compute such upper bounds for problems with non-factored value functions. To allow for meaningful benchmarking through measurable quality guarantees on a very general class of problems, this paper introduces a family of influence-optimistic upper bounds for factored decentralized partially observable Markov decision processes (Dec-POMDPs) that do not have factored value functions. Intuitively, we derive bounds on very large multiagent planning problems by subdividing them in sub-problems, and at each of these sub-problems making optimistic assumptions with respect to the influence that will be exerted by the rest of the system. We numerically compare the different upper bounds and demonstrate how we can achieve a non-trivial guarantee that a heuristic solution for problems with hundreds of agents is close to optimal. Furthermore, we provide evidence that the upper bounds may improve the effectiveness of heuristic influence search, and discuss further potential applications to multiagent planning.

We describe two nonconventional algorithms for linear regression, called GAME and CLASH. The salient characteristics of these approaches is that they exploit the convex $\ell_1$-ball and non-convex $\ell_0$-sparsity constraints jointly in sparse recovery. To establish the theoretical approximation guarantees of GAME and CLASH, we cover an interesting range of topics from game theory, convex and combinatorial optimization. We illustrate that these approaches lead to improved theoretical guarantees and empirical performance beyond convex and non-convex solvers alone.

The supertree construction problem is about combining several phylogenetic trees with possibly conflicting information into a single tree that has all the leaves of the source trees as its leaves and the relationships between the leaves are as consistent with the source trees as possible. This leads to an optimization problem that is computationally challenging and typically heuristic methods, such as matrix representation with parsimony (MRP), are used. In this paper we consider the use of answer set programming to solve the supertree construction problem in terms of two alternative encodings. The first is based on an existing encoding of trees using substructures known as quartets, while the other novel encoding captures the relationships present in trees through direct projections. We use these encodings to compute a genus-level supertree for the family of cats (Felidae). Furthermore, we compare our results to recent supertrees obtained by the MRP method.

Compressive sensing (CS) exploits sparsity to recover sparse or compressible signals from dimensionality reducing, non-adaptive sensing mechanisms. Sparsity is also used to enhance interpretability in machine learning and statistics applications: While the ambient dimension is vast in modern data analysis problems, the relevant information therein typically resides in a much lower dimensional space. However, many solutions proposed nowadays do not leverage the true underlying structure. Recent results in CS extend the simple sparsity idea to more sophisticated {\em structured} sparsity models, which describe the interdependency between the nonzero components of a signal, allowing to increase the interpretability of the results and lead to better recovery performance. In order to better understand the impact of structured sparsity, in this chapter we analyze the connections between the discrete models and their convex relaxations, highlighting their relative advantages. We start with the general group sparse model and then elaborate on two important special cases: the dispersive and the hierarchical models. For each, we present the models in their discrete nature, discuss how to solve the ensuing discrete problems and then describe convex relaxations. We also consider more general structures as defined by set functions and present their convex proxies. Further, we discuss efficient optimization solutions for structured sparsity problems and illustrate structured sparsity in action via three applications.

Marginalising out uncertain quantities within the internal representations or parameters of neural networks is of central importance for a wide range of learning techniques, such as empirical, variational or full Bayesian methods. We set out to generalise fast dropout (Wang & Manning, 2013) to cover a wider variety of noise processes in neural networks. This leads to an efficient calculation of the marginal likelihood and predictive distribution which evades sampling and the consequential increase in training time due to highly variant gradient estimates. This allows us to approximate variational Bayes for the parameters of feed-forward neural networks. Inspired by the minimum description length principle, we also propose and experimentally verify the direct optimisation of the regularised predictive distribution. The methods yield results competitive with previous neural network based approaches and Gaussian processes on a wide range of regression tasks.